From 875a595db5559111d9ba358e28f7a2ca164d8489 Mon Sep 17 00:00:00 2001 From: Brian Walsh Date: Fri, 13 May 2022 07:51:15 -0700 Subject: [PATCH] Fixtures setup --- tests/fixtures/anvil/README.md | 4 + .../protected/DocumentReference.ndjson | 9609 ++++ .../protected/Patient.ndjson | 3202 ++ .../protected/ResearchSubject.ndjson | 3202 ++ .../protected/Specimen.ndjson | 3202 ++ .../protected/Task.ndjson | 3202 ++ .../public/Organization.ndjson | 4 + .../public/Practitioner.ndjson | 1 + .../public/PractitionerRole.ndjson | 1 + .../public/ResearchStudy.ndjson | 1 + .../ResearchStudyObservationSummary.ndjson | 120 + .../anvil/output/gen3/_definitions.yaml | 252 + .../fixtures/anvil/output/gen3/_settings.yaml | 6 + tests/fixtures/anvil/output/gen3/_terms.yaml | 1938 + tests/fixtures/dbgap/README.md | 10 + .../fixtures/dbgap/examples/observation.json | 34237 +++++++++++++ .../dbgap/examples/research_study.json | 221 + .../examples/research_subject_patient.json | 39851 ++++++++++++++++ .../dbgap/output/gen3/_definitions.yaml | 252 + .../fixtures/dbgap/output/gen3/_settings.yaml | 6 + tests/fixtures/dbgap/output/gen3/_terms.yaml | 1938 + tests/fixtures/ncpi/README.md | 5 + .../CodeSystem-ConditionInheritanceMode.json | 151 + .../ncpi/examples/CodeSystem-hpo.json | 7611 +++ .../examples/CodeSystem-loinc-answers.json | 139 + .../ncpi/examples/CodeSystem-mondo.json | 55 + .../ncpi/examples/CodeSystem-ncit.json | 55 + .../examples/CodeSystem-ncpi-data-types.json | 53 + .../ncpi/examples/CodeSystem-ncpi.json | 89 + .../ncpi/examples/CodeSystem-omim.json | 2035 + .../ncpi/examples/CodeSystem-tbd-codes.json | 136 + .../ncpi/examples/CodeSystem-v3-hgvs.json | 320 + .../examples/Condition-disease-example-1.json | 89 + .../Condition-phenotype-example-1.json | 67 + .../DiagnosticReport-diagnostic-report-1.json | 37 + ...ence-drs-document-reference-example-1.json | 21 + ...research-document-reference-example-1.json | 34 + ...nGuide-NCPI-FHIR-Implementation-Guide.json | 1130 + .../Observation-anvil-summary-cmg.json | 75 + .../Observation-anvil-summary-phs000711.json | 128 + .../Observation-diagnostic-implication-1.json | 75 + ...rvation-family-relationship-example-1.json | 41 + ...rvation-family-relationship-example-2.json | 41 + ...rvation-family-relationship-example-3.json | 46 + ...rvation-family-relationship-example-4.json | 46 + .../Observation-variant-example-1.json | 215 + .../Organization-organization-example-1.json | 43 + .../examples/Patient-patient-example-1.json | 182 + .../examples/Patient-patient-example-2.json | 130 + .../examples/Patient-patient-example-3.json | 130 + .../Practitioner-practitioner-example-1.json | 42 + ...ionerRole-practitioner-role-example-1.json | 35 + .../ResearchStudy-research-study-cmg.json | 33 + ...esearchStudy-research-study-example-1.json | 13 + ...esearchStudy-research-study-phs000711.json | 38 + ...rchSubject-research-subject-example-1.json | 15 + ...rchSubject-research-subject-example-2.json | 15 + ...rchSubject-research-subject-example-3.json | 15 + .../examples/Specimen-specimen-example-1.json | 112 + .../examples/StructureDefinition-disease.json | 2004 + ...ructureDefinition-family-relationship.json | 3009 ++ ...ructureDefinition-ncpi-drs-attachment.json | 603 + ...efinition-ncpi-drs-document-reference.json | 2453 + ...tion-ncpi-research-document-reference.json | 2480 + ...tructureDefinition-ncpi-specimen-task.json | 2996 ++ .../StructureDefinition-phenotype.json | 2004 + .../StructureDefinition-supporting-info.json | 296 + .../ncpi/examples/Task-task-example-1.json | 30 + .../ncpi/examples/Task-task-example-2.json | 44 + .../ValueSet-condition-inheritance-vs.json | 54 + .../ncpi/examples/ValueSet-disease-codes.json | 51 + .../ncpi/examples/ValueSet-loinc-answers.json | 45 + .../ncpi/examples/ValueSet-ncpi-vs.json | 47 + .../examples/ValueSet-phenotype-codes.json | 45 + .../ncpi/examples/ValueSet-tbd-codes.json | 56 + .../ncpi/output/gen3/_definitions.yaml | 252 + .../fixtures/ncpi/output/gen3/_settings.yaml | 6 + tests/fixtures/ncpi/output/gen3/_terms.yaml | 1938 + tests/fixtures/synthea/.gitignore | 1 + .../synthea/filtered/Condition.ndjson | 370 + .../synthea/filtered/DiagnosticReport.ndjson | 1148 + .../synthea/filtered/DocumentReference.ndjson | 810 + .../synthea/filtered/Encounter.ndjson | 810 + .../synthea/filtered/HospitalInformation.json | 18053 +++++++ .../synthea/filtered/Immunization.ndjson | 227 + .../synthea/filtered/Observation.ndjson | 2549 + .../fixtures/synthea/filtered/Patient.ndjson | 15 + .../filtered/PractitionerInformation.json | 20474 ++++++++ .../synthea/filtered/Procedure.ndjson | 977 + .../synthea/output/gen3/_definitions.yaml | 252 + .../synthea/output/gen3/_settings.yaml | 6 + .../fixtures/synthea/output/gen3/_terms.yaml | 1938 + 92 files changed, 180799 insertions(+) create mode 100644 tests/fixtures/anvil/README.md create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/DocumentReference.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/Patient.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/ResearchSubject.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/Specimen.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/Task.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/public/Organization.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/public/Practitioner.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/public/PractitionerRole.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/public/ResearchStudy.ndjson create mode 100644 tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/public/ResearchStudyObservationSummary.ndjson create mode 100644 tests/fixtures/anvil/output/gen3/_definitions.yaml create mode 100644 tests/fixtures/anvil/output/gen3/_settings.yaml create mode 100644 tests/fixtures/anvil/output/gen3/_terms.yaml create mode 100644 tests/fixtures/dbgap/README.md create mode 100644 tests/fixtures/dbgap/examples/observation.json create mode 100644 tests/fixtures/dbgap/examples/research_study.json create mode 100644 tests/fixtures/dbgap/examples/research_subject_patient.json create mode 100644 tests/fixtures/dbgap/output/gen3/_definitions.yaml create mode 100644 tests/fixtures/dbgap/output/gen3/_settings.yaml create mode 100644 tests/fixtures/dbgap/output/gen3/_terms.yaml create mode 100644 tests/fixtures/ncpi/README.md create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-ConditionInheritanceMode.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-hpo.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-loinc-answers.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-mondo.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-ncit.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-ncpi-data-types.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-ncpi.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-omim.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-tbd-codes.json create mode 100644 tests/fixtures/ncpi/examples/CodeSystem-v3-hgvs.json create mode 100644 tests/fixtures/ncpi/examples/Condition-disease-example-1.json create mode 100644 tests/fixtures/ncpi/examples/Condition-phenotype-example-1.json create mode 100644 tests/fixtures/ncpi/examples/DiagnosticReport-diagnostic-report-1.json create mode 100644 tests/fixtures/ncpi/examples/DocumentReference-drs-document-reference-example-1.json create mode 100644 tests/fixtures/ncpi/examples/DocumentReference-research-document-reference-example-1.json create mode 100644 tests/fixtures/ncpi/examples/ImplementationGuide-NCPI-FHIR-Implementation-Guide.json create mode 100644 tests/fixtures/ncpi/examples/Observation-anvil-summary-cmg.json create mode 100644 tests/fixtures/ncpi/examples/Observation-anvil-summary-phs000711.json create mode 100644 tests/fixtures/ncpi/examples/Observation-diagnostic-implication-1.json create mode 100644 tests/fixtures/ncpi/examples/Observation-family-relationship-example-1.json create mode 100644 tests/fixtures/ncpi/examples/Observation-family-relationship-example-2.json create mode 100644 tests/fixtures/ncpi/examples/Observation-family-relationship-example-3.json create mode 100644 tests/fixtures/ncpi/examples/Observation-family-relationship-example-4.json create mode 100644 tests/fixtures/ncpi/examples/Observation-variant-example-1.json create mode 100644 tests/fixtures/ncpi/examples/Organization-organization-example-1.json create mode 100644 tests/fixtures/ncpi/examples/Patient-patient-example-1.json create mode 100644 tests/fixtures/ncpi/examples/Patient-patient-example-2.json create mode 100644 tests/fixtures/ncpi/examples/Patient-patient-example-3.json create mode 100644 tests/fixtures/ncpi/examples/Practitioner-practitioner-example-1.json create mode 100644 tests/fixtures/ncpi/examples/PractitionerRole-practitioner-role-example-1.json create mode 100644 tests/fixtures/ncpi/examples/ResearchStudy-research-study-cmg.json create mode 100644 tests/fixtures/ncpi/examples/ResearchStudy-research-study-example-1.json create mode 100644 tests/fixtures/ncpi/examples/ResearchStudy-research-study-phs000711.json create mode 100644 tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-1.json create mode 100644 tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-2.json create mode 100644 tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-3.json create mode 100644 tests/fixtures/ncpi/examples/Specimen-specimen-example-1.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-disease.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-family-relationship.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-attachment.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-document-reference.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-ncpi-research-document-reference.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-ncpi-specimen-task.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-phenotype.json create mode 100644 tests/fixtures/ncpi/examples/StructureDefinition-supporting-info.json create mode 100644 tests/fixtures/ncpi/examples/Task-task-example-1.json create mode 100644 tests/fixtures/ncpi/examples/Task-task-example-2.json create mode 100644 tests/fixtures/ncpi/examples/ValueSet-condition-inheritance-vs.json create mode 100644 tests/fixtures/ncpi/examples/ValueSet-disease-codes.json create mode 100644 tests/fixtures/ncpi/examples/ValueSet-loinc-answers.json create mode 100644 tests/fixtures/ncpi/examples/ValueSet-ncpi-vs.json create mode 100644 tests/fixtures/ncpi/examples/ValueSet-phenotype-codes.json create mode 100644 tests/fixtures/ncpi/examples/ValueSet-tbd-codes.json create mode 100644 tests/fixtures/ncpi/output/gen3/_definitions.yaml create mode 100644 tests/fixtures/ncpi/output/gen3/_settings.yaml create mode 100644 tests/fixtures/ncpi/output/gen3/_terms.yaml create mode 100644 tests/fixtures/synthea/.gitignore create mode 100644 tests/fixtures/synthea/filtered/Condition.ndjson create mode 100644 tests/fixtures/synthea/filtered/DiagnosticReport.ndjson create mode 100644 tests/fixtures/synthea/filtered/DocumentReference.ndjson create mode 100644 tests/fixtures/synthea/filtered/Encounter.ndjson create mode 100644 tests/fixtures/synthea/filtered/HospitalInformation.json create mode 100644 tests/fixtures/synthea/filtered/Immunization.ndjson create mode 100644 tests/fixtures/synthea/filtered/Observation.ndjson create mode 100644 tests/fixtures/synthea/filtered/Patient.ndjson create mode 100644 tests/fixtures/synthea/filtered/PractitionerInformation.json create mode 100644 tests/fixtures/synthea/filtered/Procedure.ndjson create mode 100644 tests/fixtures/synthea/output/gen3/_definitions.yaml create mode 100644 tests/fixtures/synthea/output/gen3/_settings.yaml create mode 100644 tests/fixtures/synthea/output/gen3/_terms.yaml diff --git a/tests/fixtures/anvil/README.md b/tests/fixtures/anvil/README.md new file mode 100644 index 0000000..cfaa8bd --- /dev/null +++ b/tests/fixtures/anvil/README.md @@ -0,0 +1,4 @@ +## AnVIL + +### Download anvil_etl output +gs:///fhir/public \ No newline at end of file diff --git a/tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/DocumentReference.ndjson b/tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/DocumentReference.ndjson new file mode 100644 index 0000000..fa70162 --- /dev/null +++ b/tests/fixtures/anvil/fhir/public/Public/1000G-high-coverage-2019/protected/DocumentReference.ndjson @@ -0,0 +1,9609 @@ +{"id":"c07e3b64-f677-5ef7-9bb0-8a2a188592c2","content":[{"attachment":{"url":"gs://fc-56ac46ea-efc4-4683-b6d5-6d95bed41c5e/CCDG_14151/Project_CCDG_14151_B01_GRM_WGS.gVCF.2020-02-12/Project_CCDG_14151_B01_GRM_WGS.gVCF.2020-02-12/Sample_HG00405/analysis/HG00405.haplotypeCalls.er.raw.vcf.gz"}}],"identifier":[{"system":"https://anvil.terra.bio/#workspaces/anvil-datastorage/1000G-high-coverage-2019","value":"participant/ERS4367795#participant/gVCF"}],"status":"current","subject":{"reference":"Patient/b0440a52-b26c-538c-b3f2-364d6f4e25bf"},"resourceType":"DocumentReference"} 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"display": "Primary Disease", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "StudyDesign", + "display": "Study Design", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig" + } + ] + }, + "valueString": "Parent-Offspring Trios" + }, + { + "code": { + "coding": [ + { + "code": "DataType", + "display": "Data Type", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig" + } + ] + }, + "valueString": "Whole Genome" + }, + { + "code": { + "coding": [ + { + "code": "ConsentCodes", + "display": "Consent Codes", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig" + } + ] + }, + "valueString": "NRES" + } + ], + "focus": [ + { + "reference": "ResearchStudy/1000G-high-coverage-2019" + } + ], + "status": "final", + "resourceType": "Observation" +} diff --git a/tests/fixtures/anvil/output/gen3/_definitions.yaml b/tests/fixtures/anvil/output/gen3/_definitions.yaml new file mode 100644 index 0000000..da80111 --- /dev/null +++ b/tests/fixtures/anvil/output/gen3/_definitions.yaml @@ -0,0 +1,252 @@ +id: _definitions + +UUID: + term: + $ref: "_terms.yaml#/UUID" + type: string + pattern: "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$" + +parent_uuids: + type: array + minItems: 1 + items: + $ref: "#/UUID" + uniqueItems: true + +foreign_key_project: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: true + #Can either use 'id' which are Gen3 IDs (UUID) or 'code' + #which is the user defined ID for project + properties: + id: + $ref: "#/UUID" + code: + type: string + +to_one_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key_project" + +to_many_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + - $ref: "#/foreign_key_project" + +foreign_key: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: True + #Can either use 'id' which are GDC IDs (UUID) or 'submitter_id' + #which are user defined IDs ("submitter IDs in the backend") + properties: + id: + $ref: "#/UUID" + submitter_id: + type: string + +to_one: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key" + +to_many: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + - $ref: "#/foreign_key" + +datetime: + oneOf: + - type: string + format: date-time + - type: 'null' + term: + $ref: "_terms.yaml#/datetime" + +file_name: + type: string + term: + $ref: "_terms.yaml#/file_name" + +file_size: + type: integer + term: + $ref: "_terms.yaml#/file_size" + +file_format: + type: string + term: + $ref: "_terms.yaml#/file_format" + +ga4gh_drs_uri: + type: string + term: + $ref: "_terms.yaml#/ga4gh_drs_uri" + +md5sum: + type: string + term: + $ref: "_terms.yaml#/md5sum" + pattern: "^[a-f0-9]{32}$" + +object_id: + type: string + description: "The GUID of the object in the index service." + +release_state: + description: "Release state of an entity." + default: unreleased + enum: + - unreleased + - released + - redacted + +data_bundle_state: + description: "State of a data bundle." + default: submitted + enum: + - submitted + - validated + - error + - released + - suppressed + - redacted + +data_file_error_type: + term: + $ref: "_terms.yaml#/data_file_error_type" + enum: + - file_size + - file_format + - md5sum + +state: + term: + $ref: "_terms.yaml#/state" + default: validated + downloadable: + - uploaded + - md5summed + - validating + - validated + - error + - invalid + - released + public: + - live + oneOf: + - enum: #This list covers legacy data + - uploading + - uploaded + - md5summing + - md5summed + - validating + - error + - invalid + - suppressed + - redacted + - live + - enum: #This list covers all future data 1/15/16 + - validated + - submitted + - released + +file_state: + term: + $ref: "_terms.yaml#/file_state" + default: registered + enum: + - registered + - uploading + - uploaded + - validating + - validated + - submitted + - processing + - processed + - released + - error + +qc_metrics_state: + term: + $ref: "_terms.yaml#/qc_metric_state" + enum: + - FAIL + - PASS + - WARN + +project_id: + type: string + term: + $ref: "_terms.yaml#/project_id" + +data_file_properties: + $ref: "#/ubiquitous_properties" + file_name: + $ref: "#/file_name" + file_size: + $ref: "#/file_size" + file_format: + $ref: "#/file_format" + md5sum: + $ref: "#/md5sum" + object_id: + $ref: "#/object_id" + file_state: + $ref: "#/file_state" + error_type: + $ref: "#/data_file_error_type" + ga4gh_drs_uri: + $ref: "#/ga4gh_drs_uri" + +workflow_properties: + $ref: "#/ubiquitous_properties" + workflow_link: + description: "Link to Github hash for the CWL workflow used." + type: string + workflow_version: + description: "Major version for a GDC workflow." + type: string + workflow_start_datetime: + $ref: "#/datetime" + workflow_end_datetime: + $ref: "#/datetime" + +ubiquitous_properties: + type: + type: string + id: + $ref: "#/UUID" + systemAlias: node_id + submitter_id: + type: + - string + description: > + A project-specific identifier for a node. This property is the calling card/nickname/alias for + a unit of submission. It can be used in place of the UUID for identifying or recalling a node. + state: + $ref: "#/state" + project_id: + $ref: "#/project_id" + created_datetime: + $ref: "#/datetime" + updated_datetime: + $ref: "#/datetime" diff --git a/tests/fixtures/anvil/output/gen3/_settings.yaml b/tests/fixtures/anvil/output/gen3/_settings.yaml new file mode 100644 index 0000000..d7e2171 --- /dev/null +++ b/tests/fixtures/anvil/output/gen3/_settings.yaml @@ -0,0 +1,6 @@ +# Global settings for the graph + +# Is the graph case centric, that we want +# to create a link between all children to case +# to expedite case filter on nodes +enable_case_cache: false diff --git a/tests/fixtures/anvil/output/gen3/_terms.yaml b/tests/fixtures/anvil/output/gen3/_terms.yaml new file mode 100644 index 0000000..6024d85 --- /dev/null +++ b/tests/fixtures/anvil/output/gen3/_terms.yaml @@ -0,0 +1,1938 @@ +id: _terms + + + +28s_16s_ribosomal_rna_ratio: + description: > + The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA. + termDef: + term: "28s/18s Ribosomal RNA Ratio" + source: null + cde_id: null + cde_version: null + term_url: null + + + + + +a260_a280_ratio: + description: > + Numeric value that represents the sample ratio of nucleic acid absorbance at 260 nm and 280 nm, + used to determine a measure of DNA purity. + termDef: + term: Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value + source: caDSR + cde_id: 5432595 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" + +age: + description: > + Age at last visit. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Age at last visit. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +family_onset: + description: > + Typical age of onset for the family. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Typical age of onset for the family. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +disease_omim_id: + description: > + The ID of the term from OMIM which represents a disease. (CMG) + termDef: + term: The ID of the term from OMIM which represents a disease. (CMG) + source: OMIM + cde_id: OMIM + cde_version: 1.0 + term_url: "https://www.ncbi.nlm.nih.gov/omim" + +phenotype_hpo_id: + description: > + The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + termDef: + term: The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + source: HPO + cde_id: HPO + cde_version: 1.0 + term_url: "https://hpo.jax.org/app/" + +adapter_name: # TOREVIEW + description: > + Name of the sequencing adapter. + +adapter_sequence: # TOREVIEW + description: > + Base sequence of the sequencing adapter. + +age_of_onset: + description: > + Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + termDef: + term: Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +age_at_event_days_gt89: + description: > + Indicate whether the 'Age at the time an event occurs expressed in the number of days since birth' is greater than 32872 days (89 years). + +age_at_diagnosis: + description: > + Age at the time of diagnosis expressed in number of days since birth. If the age at diagnosis is greater than 32872 days (89 years), then see 'age_at_diagnosis_gt89'. + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +age_at_diagnosis_gt89: + description: > + Indicate whether the age at the time of diagnosis expressed in number of days since birth is greater than 32872 days (89 years). + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +ajcc_clinical_m: + description: > + Extent of the distant metastasis for the cancer based on evidence obtained from clinical + assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage + source: caDSR + cde_id: 3440331 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0" + +ajcc_clinical_n: + description: > + Extent of the regional lymph node involvement for the cancer based on evidence obtained from + clinical assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage + source: caDSR + cde_id: 3440330 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0" + +ajcc_clinical_stage: + description: > + Stage group determined from clinical information on the tumor (T), regional node (N) and + metastases (M) and by grouping cases with similar prognosis for cancer. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Group Stage + source: caDSR + cde_id: 3440332 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0" + +ajcc_clinical_t: + description: > + Extent of the primary cancer based on evidence obtained from clinical assessment parameters + determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage + source: caDSR + cde_id: 3440328 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0" + +ajcc_pathologic_m: + description: > + Code to represent the defined absence or presence of distant spread or metastases (M) to + locations via vascular channels or lymphatics beyond the regional lymph nodes, using + criteria established by the American Joint Committee on Cancer (AJCC). + termDef: + term: American Joint Committee on Cancer Metastasis Stage Code + source: caDSR + cde_id: 3045439 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0" + +ajcc_pathologic_n: + description: > + The codes that represent the stage of cancer based on the nodes present (N stage) according + to criteria based on multiple editions of the AJCC's Cancer Staging Manual. + termDef: + term: Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203106 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0" + +ajcc_pathologic_stage: + description: > + The extent of a cancer, especially whether the disease has spread from the original site to + other parts of the body based on AJCC staging criteria. + termDef: + term: Neoplasm Disease Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203222 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0" + +ajcc_pathologic_t: + description: > + Code of pathological T (primary tumor) to define the size or contiguous extension of the + primary tumor (T), using staging criteria from the American Joint Committee on Cancer + (AJCC). + termDef: + term: American Joint Committee on Cancer Tumor Stage Code + source: caDSR + cde_id: 3045435 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0" + +alcohol_history: + description: > + A response to a question that asks whether the participant has consumed at least 12 drinks of + any kind of alcoholic beverage in their lifetime. + termDef: + term: Alcohol Lifetime History Indicator + source: caDSR + cde_id: 2201918 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0" + +drink_number: + description: > + Units of drink consumed during Drink Period (DRNKPRD). (GTEx) + +aliquot_quantity: + description: > + The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +aliquot_volume: + description: > + The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Volume + source: null + cde_id: null + cde_version: null + term_url: null + +amount: # TOREVIEW + description: > + Weight in grams or volume in mL. + +analyte_quantity: + description: > + The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +analyte_type: + description: > + Text term that represents the kind of molecular specimen analyte. + termDef: + term: Molecular Specimen Type Text Name + source: caDSR + cde_id: 2513915 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" + +analyte_type_id: + description: > + A single letter code used to identify a type of molecular analyte. + termDef: + term: Molecular Analyte Identification Code + source: caDSR + cde_id: 5432508 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0" + +analyte_volume: + description: > + The volume in microliters (ml) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Volume + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_b_symptoms: + description: > + Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical + record. + termDef: + term: Lymphoma B-Symptoms Medical Record Documented Indicator + source: caDSR + cde_id: 2902402 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0" + +ann_arbor_clinical_stage: + description: > + The classification of the clinically confirmed anatomic disease extent of lymphoma (Hodgkin's + and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Clinical Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_extranodal_involvement: + description: > + Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement + of an extranodal site. + termDef: + term: Lymphomatous Extranodal Site Involvement Indicator + source: caDSR + cde_id: 3364582 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0" + +ann_arbor_pathologic_stage: + description: > + The classification of the pathologically confirmed anatomic disease extent of lymphoma + (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Pathologic Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_tumor_stage: + description: > + The classification of the anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based + on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Tumor Stage + source: null + cde_id: null + cde_version: null + term_url: null + +base_caller_name: # TOREVIEW + description: > + Name of the base caller. + +base_caller_version: # TOREVIEW + description: > + Version of the base caller. + +biomarker_name: + description: > + The name of the biomarker being tested for this specimen and set of test results. + termDef: + term: Biomarker Name + source: caDSR + cde_id: 5473 + cde_version: 11.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31" + +biomarker_result: + description: > + Text term to define the results of genetic testing. + termDef: + term: Laboratory Procedure Genetic Abnormality Test Result Type + source: caDSR + cde_id: 3234680 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0" + +biomarker_test_method: + description: > + Text descriptor of a molecular analysis method used for an individual. + termDef: + term: Disease Detection Molecular Analysis Method Type + source: caDSR + cde_id: 3121575 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0" + +biospecimen_anatomic_site_id: + description: > + Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +biospecimen_anatomic_site_label: + description: > + Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +bmi: + description: > + Autocalculated field of BMI: general indicator of the body fat an individual is carrying based upon the ratio of weight to height. BMI = 703 * weight in pounds/height in inches squared. (GTEx) + termDef: + term: Body Mass Index (BMI) + source: caDSR + cde_id: 4973892 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" + +burkitt_lymphoma_clinical_variant: + description: > + Burkitt's lymphoma categorization based on clinical features that differ from other forms of the + same disease. + termDef: + term: Burkitt Lymphoma Clinical Variant Type + source: caDSR + cde_id: 3770421 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" + +cause_of_death: + description: > + Text term to identify the cause of death for a patient. + termDef: + term: Patient Death Reason + source: caDSR + cde_id: 2554674 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0" + +cea_level_preoperative: + description: > + Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. [Manually- + curated] + termDef: + term: Preoperative Carcinoembryonic Antigen Result Value + source: caDSR + cde_id: 2716510 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0" + +cigarettes_per_day: + description: > + The average number of cigarettes smoked per day. + termDef: + term: Smoking Use Average Number + source: caDSR + cde_id: 2001716 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0" + +circumferential_resection_margin: + description: > + A value in millimeters indicating the measured length between a malignant lesion of the + colon or rectum and the nearest radial (or circumferential) border of tissue removed during + cancer surgery. + termDef: + term: Colorectal Surgical Margin Circumferential Distance Measurement + source: caDSR + cde_id: 64202 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0" + +classification_of_tumor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +colon_polyps_history: + description: > + Yes/No indicator to describe if the subject had a previous history of colon polyps as noted + in the history/physical or previous endoscopic report (s). + termDef: + term: Colon Carcinoma Polyp Occurrence Indicator + source: caDSR + cde_id: 3107197 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0" + +composition: + description: > + Text term that represents the cellular composition of the sample. + termDef: + term: Biospecimen Cellular Composition Type + source: caDSR + cde_id: 5432591 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" + +concentration: + description: > + Numeric value that represents the concentration of an analyte or aliquot extracted from the + sample or sample portion, measured in milligrams per milliliter. + termDef: + term: Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value + source: caDSR + cde_id: 5432594 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" + +creation_datetime: + description: > + The datetime of portion creation encoded as seconds from epoch. + termDef: + term: Biospecimen Portion Creation Seconds Date/Time + source: caDSR + cde_id: 5432592 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0" + +current_weight: + description: > + Numeric value that represents the current weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Current Weight Milligram Value + source: caDSR + cde_id: 5432606 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" + +data_category: # TOREVIEW + description: > + Broad categorization of the contents of the data file. + +data_file_error_type: # TOREVIEW + description: > + Type of error for the data file object. + +data_format: # TOREVIEW + description: > + Format of the data files. + +data_type: # TOREVIEW + description: > + Specific content type of the data file. (CMG) + +datetime: + description: > + A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] + +days_to_birth: + description: > + Time interval from a person's date of birth to the date of initial pathologic diagnosis, + represented as a calculated negative number of days. + termDef: + term: Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0" + +days_to_collection: + description: > + Time interval from the date of biospecimen collection to the date of initial pathologic + diagnosis, represented as a calculated number of days. + termDef: + term: Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008340 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0" + +days_to_death: + description: > + Time interval from a person's date of death to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Death Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3165475 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0" + +days_to_hiv_diagnosis: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of human + immunodeficiency diagnosis, represented as a calculated number of days. + termDef: + term: Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value + source: caDSR + cde_id: 4618491 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0" + +days_to_last_follow_up: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_last_known_disease_status: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_new_event: + description: > + Time interval from the date of new tumor event including progression, recurrence and new + primary malignacies to the date of initial pathologic diagnosis, represented as a calculated + number of days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_recurrence: + description: > + Time interval from the date of new tumor event including progression, recurrence and new primary + malignancies to the date of initial pathologic diagnosis, represented as a calculated number of + days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_sample_procurement: + description: > + The number of days from the date the patient was diagnosed to the date of the procedure that + produced the sample. + +days_to_treatment: + description: > + Number of days from date of initial pathologic diagnosis that treatment began. + termDef: + term: Days to Treatment Start + source: null + cde_id: null + cde_version: null + term_url: null + +days_to_treatment_end: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of treatment end, + represented as a calculated number of days. + termDef: + term: Treatment End Subtract First Pathologic Diagnosis Day Calculation Value + source: caDSR + cde_id: 5102431 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0" + +days_to_treatment_start: + description: > + Time interval from the date of the initial pathologic diagnosis to the start of treatment, + represented as a calculated number of days. + termDef: + term: Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value + source: caDSR + cde_id: 5102411 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0" + +diagnosis_pathologically_confirmed: + description: > + The histologic description of tissue or cells confirmed by a pathology review of frozen or + formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used + to extract analyte(s). + termDef: + term: Post-Diagnostic Pathology Review Confirmation + source: null + cde_id: null + cde_version: null + term_url: null + +dlco_ref_predictive_percent: + description: > + The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide + detected in a patient's lungs. + termDef: + term: Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value + source: caDSR + cde_id: 2180255 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0" + +encoding: + description: > + Version of ASCII encoding of quality values found in the file. + termDef: + term: Encoding + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +estrogen_receptor_percent_positive_ihc: + description: > + Classification to represent ER Positive results expressed as a percentage value. + termDef: + term: ER Level Cell Percentage Category + source: caDSR + cde_id: 3128341 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0" + +estrogen_receptor_result_ihc: + description: > + Text term to represent the overall result of Estrogen Receptor (ER) testing. + termDef: + term: Breast Carcinoma Estrogen Receptor Status + source: caDSR + cde_id: 2957359 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0" + +ethnicity: + description: > + An individual's self-described social and cultural grouping, specifically whether an individual + describes themselves as Hispanic or Latino (HARMONIZED). The provided values are based on the categories + defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (CMG, GTEx) + termDef: + term: Ethnic Group Category Text + source: caDSR + cde_id: 2192217 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" + +experiment_name: # TOREVIEW + description: > + Submitter-defined name for the experiment. + +experimental_strategy: # TOREVIEW + description: > + The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri. + +fastq_name: # TOREVIEW + description: > + Names of FASTQs. + +fev1_ref_post_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second post-bronchodilator. + termDef: + term: Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302948 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0" + +fev1_ref_pre_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second pre-bronchodilator. + termDef: + term: Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302947 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" + +fev1_fvc_post_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) post-bronchodilator. + termDef: + term: Post Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302956 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0" + +fev1_fvc_pre_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) pre-bronchodilator. + termDef: + term: Pre Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302955 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0" + +figo_stage: + description: > + The extent of a cervical or endometrial cancer within the body, especially whether the + disease has spread from the original site to other parts of the body, as described by the + International Federation of Gynecology and Obstetrics (FIGO) stages. + termDef: + term: Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage + source: caDSR + cde_id: 3225684 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" + +file_format: + description: > + The format of the data file object. + +file_name: # TOREVIEW + description: > + The name (or part of a name) of a file (of any type). + +file_size: # TOREVIEW + description: > + The size of the data file (object) in bytes. + +file_state: # TOREVIEW + description: > + The current state of the data file object. + +flow_cell_barcode: # TOREVIEW + description: > + Flow Cell Barcode. + +freezing_method: + description: > + Text term that represents the method used for freezing the sample. + termDef: + term: Tissue Sample Freezing Method Type + source: caDSR + cde_id: 5432607 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" + +ga4gh_drs_uri: + description: > + DRS URI as defined by GA4GH DRS spec for pointers to file objects. + +sex: + description: > + Text designations that identify gender (HARMONIZED). Gender is described as the assemblage of properties that + distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification + of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] (CMG) + termDef: + term: Person Gender Text Type + source: caDSR + cde_id: 2200604 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" + +height: + description: > + The height of Donor in inches as reported by Donor, family/next of kin, or medical record abstraction. (GTEx) + termDef: + term: Patient Height Measurement + source: caDSR + cde_id: 649 + cde_version: 4.1 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" + +her2_erbb2_percent_positive_ihc: + description: > + Classification to represent the number of positive HER2/ERBB2 cells in a specimen or sample. + termDef: + term: HER2 ERBB Positive Finding Cell Percentage Category + source: caDSR + cde_id: 3086980 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0" + +her2_erbb2_result_fish: + description: > + the type of outcome for HER2 as determined by an in situ hybridization (ISH) assay. + termDef: + term: Laboratory Procedure HER2/neu in situ Hybridization Outcome Type + source: caDSR + cde_id: 2854089 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0" + +her2_erbb2_result_ihc: + description: > + Text term to signify the result of the medical procedure that involves testing a sample of + blood or tissue for HER2 by histochemical localization of immunoreactive substances using + labeled antibodies as reagents. + termDef: + term: Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status + source: caDSR + cde_id: 2957563 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0" + +hiv_positive: + description: > + Text term to signify whether a physician has diagnosed HIV infection in a patient. + termDef: + term: Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator + source: caDSR + cde_id: 4030799 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0" + +hpv_positive_type: + description: > + Text classification to represent the strain or type of human papillomavirus identified in an + individual. + termDef: + term: Human Papillomavirus Type + source: caDSR + cde_id: 2922649 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0" + +hpv_status: + description: > + The findings of the oncogenic HPV. + termDef: + term: Oncogenic Human Papillomavirus Result Type + source: caDSR + cde_id: 2230033 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" + +includes_spike_ins: # TOREVIEW + description: > + Spike-in included? + +initial_weight: + description: > + Numeric value that represents the initial weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Initial Weight Milligram Value + source: caDSR + cde_id: 5432605 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0" + +instrument_model: + description: > + Numeric value that represents the sample dimension that is greater than the shortest + dimension and less than the longest dimension, measured in millimeters. + termDef: + term: Tissue Sample Intermediate Dimension Millimeter Measurement + source: caDSR + cde_id: 5432604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" + +intermediate_dimension: # TOREVIEW + description: > + Intermediate dimension of the sample, in millimeters. + +is_ffpe: + description: > + Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in + paraffin (FFPE). + termDef: + term: Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator + source: caDSR + cde_id: 4170557 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" + +is_paired_end: # TOREVIEW + description: > + Are the reads paired end? + +is_proband: # TOREVIEW + description: > + Boolean value to determine if the case is the proband. + +last_known_disease_status: + description: > + Text term that describes the last known state or condition of an individual's neoplasm. + termDef: + term: Person Last Known Neoplasm Status + source: caDSR + cde_id: 5424231 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0" + +laterality: + description: > + For tumors in paired organs, designates the side on which the cancer originates. + termDef: + term: Primary Tumor Laterality + source: caDSR + cde_id: 827 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0" + +ldh_level_at_diagnosis: + description: > + The 2 decimal place numeric laboratory value measured, assigned or computed related to the + assessment of lactate dehydrogenase in a specimen. + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value + source: caDSR + cde_id: 2798766 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0" + +ldh_normal_range_upper: + description: > + The top value of the range of statistical characteristics that are supposed to represent + accepted standard, non-pathological pattern for lactate dehydrogenase (units not specified). + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value + source: caDSR + cde_id: 2597015 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" + +library_strategy: # TOREVIEW + description: > + Library strategy. + +library_selection: # TOREVIEW + description: > + Library Selection Method + +library_name: # TOREVIEW + description: > + Name of the library. + +library_preparation_kit_name: # TOREVIEW + description: > + Name of Library Preparation Kit + +library_preparation_kit_vendor: # TOREVIEW + description: > + Vendor of Library Preparation Kit + +library_preparation_kit_catalog_number: # TOREVIEW + description: > + Catalog of Library Preparation Kit + +library_preparation_kit_version: # TOREVIEW + description: > + Version of Library Preparation Kit + +library_strand: # TOREVIEW + description: > + Library stranded-ness. + +longest_dimension: + description: > + Numeric value that represents the longest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Longest Dimension Millimeter Measurement + source: caDSR + cde_id: 5432602 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0" + +lymph_nodes_positive: + description: > + The number of lymph nodes involved with disease as determined by pathologic examination. + termDef: + term: Lymph Node(s) Positive Number + source: caDSR + cde_id: 89 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0" + +lymphatic_invasion_present: + description: > + A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating + lymphatic involvement + termDef: + term: Lymphatic/Small vessel Invasion Ind + source: caDSR + cde_id: 64171 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" + +method_of_diagnosis: + description: > + The method used to initially the patient's diagnosis. + termDef: + term: Method of Diagnosis + source: null + cde_id: null + cde_version: null + term_url: null + +method_of_sample_procurement: + description: > + The method used to procure the sample used to extract analyte(s). + termDef: + term: Method of Sample Procurement + source: null + cde_id: null + cde_version: null + term_url: null + +md5sum: # TOREVIEW + description: > + The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital + fingerprint. + +microsatellite_instability_abnormal: + description: > + The yes/no indicator to signify the status of a tumor for microsatellite instability. + termDef: + term: Microsatellite Instability Occurrence Indicator + source: caDSR + cde_id: 3123142 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0" + +morphology: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000 used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The study of the structure of the cells and their + arrangement to constitute tissues and, finally, the association among these to form organs. In + pathology, the microscopic process of identifying normal and abnormal morphologic + characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A + system of numbered categories for representation of data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code + source: caDSR + cde_id: 3226275 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0" + +new_event_anatomic_site: + description: > + Text term to specify the anatomic location of the return of tumor after treatment. + termDef: + term: New Neoplasm Event Occurrence Anatomic Site + source: caDSR + cde_id: 3108271 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0" + +new_event_type: + description: > + Text term to identify a new tumor event. + termDef: + term: New Neoplasm Event Type + source: caDSR + cde_id: 3119721 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0" + +normal_tumor_genotype_snp_match: + description: > + Text term that represents whether or not the genotype of the normal tumor matches or if the data + is not available. + termDef: + term: Normal Tumor Genotype Match Indicator + source: caDSR + cde_id: 4588156 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0" + +number_proliferating_cells: + description: > + Numeric value that represents the count of proliferating cells determined during pathologic + review of the sample slide(s). + termDef: + term: Pathology Review Slide Proliferating Cell Count + source: caDSR + cde_id: 5432636 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0" + +oct_embedded: + description: > + Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound. + termDef: + term: Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator + source: caDSR + cde_id: 5432538 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" + +years_smoked: + description: > + Number of years the Donor smoked. (GTEx) + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +percent_eosinophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or + specimen. + termDef: + term: Specimen Eosinophilia Percentage Value + source: caDSR + cde_id: 2897700 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0" + +percent_gc_content: + description: > + The overall %GC of all bases in all sequences. + termDef: + term: "%GC" + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +percent_granulocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or + specimen. + termDef: + term: Specimen Granulocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897705 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0" + +percent_inflam_infiltration: + description: > + Numeric value to represent local response to cellular injury, marked by capillary dilatation, + edema and leukocyte infiltration; clinically, inflammation is manifest by reddness, heat, pain, + swelling and loss of function, with the need to heal damaged tissue. + termDef: + term: Specimen Inflammation Change Percentage Value + source: caDSR + cde_id: 2897695 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0" + +percent_lymphocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue + normal sample or specimen. + termDef: + term: Specimen Lymphocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897710 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0" + +percent_monocyte_infiltration: + description: > + Numeric value to represent the percentage of monocyte infiltration in a sample or specimen. + termDef: + term: Specimen Monocyte Infiltration Percentage Value + source: caDSR + cde_id: 5455535 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0" + +percent_necrosis: + description: > + Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen. + termDef: + term: Malignant Neoplasm Necrosis Percentage Value + source: caDSR + cde_id: 2841237 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0" + +percent_neutrophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value + source: caDSR + cde_id: 2841267 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0" + +percent_normal_cells: + description: > + Numeric value to represent the percentage of normal cell content in a malignant tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Normal Cell Percentage Value + source: caDSR + cde_id: 2841233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0" + +percent_stromal_cells: + description: > + Numeric value to represent the percentage of reactive cells that are present in a malignant + tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc. + termDef: + term: Malignant Neoplasm Stromal Cell Percentage Value + source: caDSR + cde_id: 2841241 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0" + +percent_tumor_cells: + description: > + Numeric value that represents the percentage of infiltration by granulocytes in a sample. + termDef: + term: Specimen Tumor Cell Percentage Value + source: caDSR + cde_id: 5432686 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0" + +percent_tumor_nuclei: + description: > + Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen. + termDef: + term: Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value + source: caDSR + cde_id: 2841225 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0" + +perineural_invasion_present: + description: > + a yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is + present. + termDef: + term: Tumor Perineural Invasion Ind + source: caDSR + cde_id: 64181 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" + +platform: # TOREVIEW + description: > + Name of the platform used to obtain data. + +portion_number: + description: > + Numeric value that represents the sequential number assigned to a portion of the sample. + termDef: + term: Biospecimen Portion Sequence Number + source: caDSR + cde_id: 5432711 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0" + +portion_weight: + description: > + Numeric value that represents the sample portion weight, measured in milligrams. + termDef: + term: Biospecimen Portion Weight Milligram Value + source: caDSR + cde_id: 5432593 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0" + +preservation_method: + description: > + Text term that represents the method used to preserve the sample. + termDef: + term: Tissue Sample Preservation Method Type + source: caDSR + cde_id: 5432521 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" + + +prior_malignancy: + description: > + Text term to describe the patient's history of prior cancer diagnosis and the spatial location + of any previous cancer occurrence. + termDef: + term: Prior Cancer Diagnosis Occurrence Description Text + source: caDSR + cde_id: 3382736 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0" + +prior_treatment: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +progesterone_receptor_percent_positive_ihc: + description: > + Classification to represent Progesterone Receptor Positive results expressed as a percentage + value. + termDef: + term: Progesterone Receptor Level Cell Percentage Category + source: caDSR + cde_id: 3128342 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0" + +progesterone_receptor_result_ihc: + description: > + Text term to represent the overall result of Progresterone Receptor (PR) testing. + termDef: + term: Breast Carcinoma Progesterone Receptor Status + source: caDSR + cde_id: 2957357 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0" + +progression_or_recurrence: + description: > + Yes/No/Unknown indicator to identify whether a patient has had a new tumor event + after initial treatment. + termDef: + term: New Neoplasm Event Post Initial Therapy Indicator + source: caDSR + cde_id: 3121376 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" + +project_id: # TOREVIEW + description: > + Unique ID for any specific defined piece of work that is undertaken or attempted to + meet a single requirement. + +qc_metric_state: + description: > + State classification given by FASTQC for the metric. Metric specific details about the states + are available on their website. + termDef: + term: QC Metric State + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" + +race: + description: > + An arbitrary classification of a taxonomic group that is a division of a species (HARMONIZED). It usually + arises as a consequence of geographical isolation within a species and is characterized by + shared heredity, physical attributes and behavior, and in the case of humans, by common history, + nationality, or geographic distribution. The provided values are based on the categories defined + by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (GTEx) + termDef: + term: Race Category Text + source: caDSR + cde_id: 2192199 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" + +read_length: # TOREVIEW + description: > + The length of the reads. + +read_group_name: # TOREVIEW + description: > + The name of the read group. + +relationship_age_at_diagnosis: + description: > + The age (in years) when the patient's relative was first diagnosed. + termDef: + term: Relative Diagnosis Age Value + source: caDSR + cde_id: 5300571 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0" + +relationship_to_proband: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relationship_type: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relative_with_cancer_history: + description: > + Indicator to signify whether or not an individual's biological relative has been diagnosed with + another type of cancer. + termDef: + term: Other Cancer Biological Relative History Indicator + source: caDSR + cde_id: 3901752 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0" + +residual_disease: + description: > + Text terms to describe the status of a tissue margin following surgical resection. + termDef: + term: Surgical Margin Resection Status + source: caDSR + cde_id: 2608702 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" + +RIN: + description: > + A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the + RNA sample including the presence or absence of degradation products. + termDef: + term: Biospecimen RNA Integrity Number Value + source: caDSR + cde_id: 5278775 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" + +sample_type: + description: > + Text term to describe the source of a biospecimen used for a laboratory test. + termDef: + term: Specimen Type Collection Biospecimen Type + source: caDSR + cde_id: 3111302 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" + +sample_type_id: # TOREVIEW + description: > + The accompanying sample type id for the sample type. + +section_location: # TOREVIEW + description: > + Tissue source of the slide. + +sequencing_center: # TOREVIEW + description: > + Name of the center that provided the sequence files. + +shortest_dimension: + description: > + Numeric value that represents the shortest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Short Dimension Millimeter Measurement + source: caDSR + cde_id: 5432603 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0" + +site_of_resection_or_biopsy: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000, used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The description of an anatomical region or of a body part. + Named locations of, or within, the body. A system of numbered categories for representation of + data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code + source: caDSR + cde_id: 3226281 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" + +size_selection_range: # TOREVIEW + description: > + Range of size selection. + +smoking_history: + description: > + Category describing current smoking status and smoking history as self-reported by a patient. + termDef: + term: Smoking History + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +smoking_intensity: + description: > + Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes + smoked per day x number of years smoked divided by 20 + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +source_center: # TOREVIEW + description: > + Name of the center that provided the item. + +spectrophotometer_method: + description: > + Name of the method used to determine the concentration of purified nucleic acid within a + solution. + termDef: + term: Purification Nucleic Acid Solution Concentration Determination Method Type + source: caDSR + cde_id: 3008378 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" + +spike_ins_fasta: # TOREVIEW + description: > + Name of the FASTA file that contains the spike-in sequences. + +spike_ins_concentration: # TOREVIEW + description: > + Spike in concentration. + +state: # TOREVIEW + description: > + The current state of the object. + +target_capture_kit_name: # TOREVIEW + description: > + Name of Target Capture Kit. + +target_capture_kit_vendor: # TOREVIEW + description: > + Vendor of Target Capture Kit. + +target_capture_kit_catalog_number: # TOREVIEW + description: > + Catalog of Target Capture Kit. + +target_capture_kit_version: # TOREVIEW + description: > + Version of Target Capture Kit. + +target_capture_kit_target_region: # TOREVIEW + description: > + Target Capture Kit BED file. + +therapeutic_agents: + description: > + Text identification of the individual agent(s) used as part of a prior treatment regimen. + termDef: + term: Prior Therapy Regimen Text + source: caDSR + cde_id: 2975232 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0" + +time_between_clamping_and_freezing: + description: > + Numeric representation of the elapsed time between the surgical clamping of blood supply and + freezing of the sample, measured in minutes. + termDef: + term: Tissue Sample Clamping and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432611 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0" + +time_between_excision_and_freezing: + description: > + Numeric representation of the elapsed time between the excision and freezing of the sample, + measured in minutes. + termDef: + term: Tissue Sample Excision and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432612 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0" + +tissue_or_organ_of_origin: + description: > + Text term that describes the anatomic site of the tumor or disease. + termDef: + term: Tumor Disease Anatomic Site + source: caDSR + cde_id: 3427536 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0" + +tissue_type: + description: > + Text term that represents a description of the kind of tissue collected with respect to disease + status or proximity to tumor tissue. + termDef: + term: Tissue Sample Description Type + source: caDSR + cde_id: 5432687 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" + +to_trim_adapter_sequence: # TOREVIEW + description: > + Does the user suggest adapter trimming? + +tobacco_smoking_onset_year: + description: > + The year in which the participant began smoking. + termDef: + term: Started Smoking Year + source: caDSR + cde_id: 2228604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0" + +tobacco_smoking_quit_year: + description: > + The year in which the participant quit smoking. + termDef: + term: Stopped Smoking Year + source: caDSR + cde_id: 2228610 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0" + +tobacco_smoking_status: + description: > + Category describing current smoking status and smoking history as self-reported by a + patient. + termDef: + term: Patient Smoking History Category + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +total_sequences: + description: > + A count of the total number of sequences processed. + termDef: + term: Total Sequences + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +treatment_anatomic_site: + description: > + The anatomic site or field targeted by a treatment regimen or single agent therapy. + termDef: + term: Treatment Anatomic Site + source: null + cde_id: null + cde_version: null + term_url: null + +treatment_intent_type: + description: > + Text term to identify the reason for the administration of a treatment regimen. [Manually-curated] + termDef: + term: Treatment Regimen Intent Type + source: caDSR + cde_id: 2793511 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0" + +treatment_or_therapy: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +treatment_outcome: + description: > + Text term that describes the patient¿s final outcome after the treatment was administered. + termDef: + term: Treatment Outcome Type + source: caDSR + cde_id: 5102383 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0" + +treatment_type: + description: > + Text term that describes the kind of treatment administered. + termDef: + term: Treatment Method Type + source: caDSR + cde_id: 5102381 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" + +tumor_grade: + description: > + Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation + and aggressiveness. + termDef: + term: Neoplasm Histologic Grade + source: caDSR + cde_id: 2785839 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" + +tumor_code: # TOREVIEW + description: > + Diagnostic tumor code of the tissue sample source. + +tumor_code_id: # TOREVIEW + description: > + BCR-defined id code for the tumor sample. + +tumor_descriptor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +tumor_stage: + description: > + The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether + lymph nodes contain cancer, and whether the cancer has spread from the original site to other + parts of the body. The accepted values for tumor_stage depend on the tumor site, type, and + accepted staging system. These items should accompany the tumor_stage value as associated + metadata. + termDef: + term: Tumor Stage + source: NCIt + cde_id: C16899 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" + +UUID: + description: > + A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to + be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be + different. Its relatively small size lends itself well to sorting, ordering, and hashing of all + sorts, storing in databases, simple allocation, and ease of programming in general. + termDef: + term: Universally Unique Identifier + source: NCIt + cde_id: C54100 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" + +vascular_invasion_present: + description: > + The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or + presence in a tumor specimen. + termDef: + term: Tumor Vascular Invasion Ind-3 + source: caDSR + cde_id: 64358 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0" + +vital_status: + description: > + The survival state of the person registered on the protocol. + termDef: + term: Patient Vital Status + source: caDSR + cde_id: 5 + cde_version: 5.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" + +weight: + description: > + The weight of the patient measured in lbs (HARMONIZED). + termDef: + term: Patient Weight Measurement + source: caDSR + cde_id: 651 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" + +well_number: + description: > + Numeric value that represents the the well location within a plate for the analyte or + aliquot from the sample. + termDef: + term: Biospecimen Analyte or Aliquot Plate Well Number + source: caDSR + cde_id: 5432613 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0" + +workflow_type: + description: > + Generic name for the workflow used to analyze a data set. + +year_of_birth: + description: > + Numeric value to represent the calendar year in which an individual was born. + termDef: + term: Year Birth Date Number + source: caDSR + cde_id: 2896954 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" + +year_of_diagnosis: + description: > + Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. + termDef: + term: Year of initial pathologic diagnosis + source: caDSR + cde_id: 2896960 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" + +year_of_death: + description: > + Numeric value to represent the year of the death of an individual. + termDef: + term: Year Death Number + source: caDSR + cde_id: 2897030 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" + +years_smoked: + description: > + Numeric value (or unknown) to represent the number of years a person has been smoking (HARMONIZED). If the number of years is greater than 89, see 'years_smoked_gt89'. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" + +years_smoked_gt89: + description: > + Indicate whether the numeric value to represent the number of years a person has been smoking (HARMONIZED) is greater than 89 years. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" diff --git a/tests/fixtures/dbgap/README.md b/tests/fixtures/dbgap/README.md new file mode 100644 index 0000000..f0b496d --- /dev/null +++ b/tests/fixtures/dbgap/README.md @@ -0,0 +1,10 @@ +## dbGap + +### research study +wget 'https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/ResearchStudy?_id=phs002409&_include=ResearchStudy:sponsor' -O research_study.json + +### subject and patient +wget 'https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/ResearchSubject?study=phs002409&_count=1000&_include=ResearchSubject:individual' -O research_subject_patient.json + +### observations +wget 'https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/Observation?_security=phs002409-1&_count=1000' -O observation.json diff --git a/tests/fixtures/dbgap/examples/observation.json b/tests/fixtures/dbgap/examples/observation.json new file mode 100644 index 0000000..a5e3d60 --- /dev/null +++ b/tests/fixtures/dbgap/examples/observation.json @@ -0,0 +1,34237 @@ +{ + "resourceType": "Bundle", + "id": "5718849f-5fde-4bc7-8e7d-dc64e685a0da", + "meta": { + "lastUpdated": "2022-05-10T14:21:59.338-04:00" + }, + "type": "searchset", + "total": 466, + "link": [ { + "relation": "self", + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/Observation?_count=1000&_security=phs002409-1" + } ], + "entry": [ { + "fullUrl": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/Observation/492015-3635242-0", + "resource": { + "resourceType": "Observation", + "id": "492015-3635242-0", + "meta": { + "versionId": "1", + "lastUpdated": "2022-05-10T12:48:29.547-04:00", + "source": "#OsRfve1DOdUjpELy", + "security": [ { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-SecurityStudyConsent", + "code": "phs002409-1", + "display": "General Research Use" + } ] + }, + "extension": [ { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-instantiatesUri", + "valueUri": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/EvidenceVariable/phv00492015" + } ], + "code": { + "coding": [ { + "extension": [ { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertingEntity", + "valueReference": { + "reference": "Organization/dbGaP" + } + }, { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertedRelationship", + "valueCoding": { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-AssertedRelationship", + "code": "exact", + "display": "Exact" + } + } ], + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-VariableAccession", + "code": "phv00492015.v1.p1", + "display": "subj_id" + } ] + }, + "subject": { + "reference": "Patient/3635242" + }, + "valueQuantity": { + "value": 10100443, + "unit": "Units were not extracted correctly in this release. We will extract them in the next release.", + "system": "http://unitsofmeasure.org" + } + }, + "search": { + "mode": "match" + } + }, { + "fullUrl": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/Observation/492015-3635512-0", + "resource": { + "resourceType": "Observation", + "id": "492015-3635512-0", + "meta": { + "versionId": "1", + "lastUpdated": "2022-05-10T12:48:31.152-04:00", + "source": "#E4otX8EhiKsXzl1D", + "security": [ { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-SecurityStudyConsent", + "code": "phs002409-1", + "display": "General Research Use" + } ] + }, + "extension": [ { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-instantiatesUri", + "valueUri": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/EvidenceVariable/phv00492015" + } ], + "code": { + "coding": [ { + "extension": [ { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertingEntity", + "valueReference": { + "reference": "Organization/dbGaP" + } + }, { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertedRelationship", + "valueCoding": { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-AssertedRelationship", + "code": "exact", + "display": "Exact" + } + } ], + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-VariableAccession", + "code": "phv00492015.v1.p1", + "display": "subj_id" + } ] + }, + "subject": { + "reference": "Patient/3635512" + }, + "valueQuantity": { + "value": 10101167, + "unit": "Units were not extracted correctly in this release. We will extract them in the next release.", + "system": "http://unitsofmeasure.org" + } + }, + "search": { + "mode": "match" + } + }, { + "fullUrl": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/Observation/492015-3635550-0", + "resource": { + "resourceType": "Observation", + "id": "492015-3635550-0", + "meta": { + "versionId": "1", + "lastUpdated": "2022-05-10T12:48:31.193-04:00", + "source": "#o5aCgR1x7KnKucoe", + "security": [ { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-SecurityStudyConsent", + "code": "phs002409-1", + "display": "General Research Use" + } ] + }, + "extension": [ { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-instantiatesUri", + "valueUri": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/EvidenceVariable/phv00492015" + } ], + "code": { + "coding": [ { + "extension": [ { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertingEntity", + "valueReference": { + "reference": "Organization/dbGaP" + } + }, { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertedRelationship", + "valueCoding": { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-AssertedRelationship", + "code": "exact", + "display": "Exact" + } + } ], + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-VariableAccession", + "code": "phv00492015.v1.p1", + "display": "subj_id" + } ] + }, + "subject": { + "reference": "Patient/3635550" + }, + "valueQuantity": { + "value": 10101258, + "unit": "Units were not extracted correctly in this release. We will extract them in the next release.", + "system": "http://unitsofmeasure.org" + } + }, + "search": { + "mode": "match" + } + }, { + "fullUrl": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/Observation/492015-3635642-0", + "resource": { + "resourceType": "Observation", + "id": "492015-3635642-0", + "meta": { + "versionId": "1", + "lastUpdated": "2022-05-10T12:48:32.276-04:00", + "source": "#zkIRZ9ZSSeYZHIfz", + "security": [ { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-SecurityStudyConsent", + "code": "phs002409-1", + "display": "General Research Use" + } ] + }, + "extension": [ { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-instantiatesUri", + "valueUri": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/EvidenceVariable/phv00492015" + } ], + "code": { + "coding": [ { + "extension": [ { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertingEntity", + "valueReference": { + "reference": "Organization/dbGaP" + } + }, { + "url": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/Coding-AssertedRelationship", + "valueCoding": { + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-AssertedRelationship", + "code": "exact", + "display": "Exact" + } + } ], + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-VariableAccession", + "code": "phv00492015.v1.p1", + "display": "subj_id" + } ] + }, + "subject": { + "reference": "Patient/3635642" + }, + "valueQuantity": { + "value": 10101541, + "unit": "Units were not extracted correctly in this release. 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Identifier
" + }, + "identifier": [ { + "id": "3635976", + "system": "https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-DbGaPSubjectIdentifier" + } ], + "gender": "unknown" + }, + "search": { + "mode": "include" + } + } ] +} \ No newline at end of file diff --git a/tests/fixtures/dbgap/output/gen3/_definitions.yaml b/tests/fixtures/dbgap/output/gen3/_definitions.yaml new file mode 100644 index 0000000..da80111 --- /dev/null +++ b/tests/fixtures/dbgap/output/gen3/_definitions.yaml @@ -0,0 +1,252 @@ +id: _definitions + +UUID: + term: + $ref: "_terms.yaml#/UUID" + type: string + pattern: "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$" + +parent_uuids: + type: array + minItems: 1 + items: + $ref: "#/UUID" + uniqueItems: true + +foreign_key_project: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: true + #Can either use 'id' which are Gen3 IDs (UUID) or 'code' + #which is the user defined ID for project + properties: + id: + $ref: "#/UUID" + code: + type: string + +to_one_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key_project" + +to_many_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + - $ref: "#/foreign_key_project" + +foreign_key: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: True + #Can either use 'id' which are GDC IDs (UUID) or 'submitter_id' + #which are user defined IDs ("submitter IDs in the backend") + properties: + id: + $ref: "#/UUID" + submitter_id: + type: string + +to_one: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key" + +to_many: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + - $ref: "#/foreign_key" + +datetime: + oneOf: + - type: string + format: date-time + - type: 'null' + term: + $ref: "_terms.yaml#/datetime" + +file_name: + type: string + term: + $ref: "_terms.yaml#/file_name" + +file_size: + type: integer + term: + $ref: "_terms.yaml#/file_size" + +file_format: + type: string + term: + $ref: "_terms.yaml#/file_format" + +ga4gh_drs_uri: + type: string + term: + $ref: "_terms.yaml#/ga4gh_drs_uri" + +md5sum: + type: string + term: + $ref: "_terms.yaml#/md5sum" + pattern: "^[a-f0-9]{32}$" + +object_id: + type: string + description: "The GUID of the object in the index service." + +release_state: + description: "Release state of an entity." + default: unreleased + enum: + - unreleased + - released + - redacted + +data_bundle_state: + description: "State of a data bundle." + default: submitted + enum: + - submitted + - validated + - error + - released + - suppressed + - redacted + +data_file_error_type: + term: + $ref: "_terms.yaml#/data_file_error_type" + enum: + - file_size + - file_format + - md5sum + +state: + term: + $ref: "_terms.yaml#/state" + default: validated + downloadable: + - uploaded + - md5summed + - validating + - validated + - error + - invalid + - released + public: + - live + oneOf: + - enum: #This list covers legacy data + - uploading + - uploaded + - md5summing + - md5summed + - validating + - error + - invalid + - suppressed + - redacted + - live + - enum: #This list covers all future data 1/15/16 + - validated + - submitted + - released + +file_state: + term: + $ref: "_terms.yaml#/file_state" + default: registered + enum: + - registered + - uploading + - uploaded + - validating + - validated + - submitted + - processing + - processed + - released + - error + +qc_metrics_state: + term: + $ref: "_terms.yaml#/qc_metric_state" + enum: + - FAIL + - PASS + - WARN + +project_id: + type: string + term: + $ref: "_terms.yaml#/project_id" + +data_file_properties: + $ref: "#/ubiquitous_properties" + file_name: + $ref: "#/file_name" + file_size: + $ref: "#/file_size" + file_format: + $ref: "#/file_format" + md5sum: + $ref: "#/md5sum" + object_id: + $ref: "#/object_id" + file_state: + $ref: "#/file_state" + error_type: + $ref: "#/data_file_error_type" + ga4gh_drs_uri: + $ref: "#/ga4gh_drs_uri" + +workflow_properties: + $ref: "#/ubiquitous_properties" + workflow_link: + description: "Link to Github hash for the CWL workflow used." + type: string + workflow_version: + description: "Major version for a GDC workflow." + type: string + workflow_start_datetime: + $ref: "#/datetime" + workflow_end_datetime: + $ref: "#/datetime" + +ubiquitous_properties: + type: + type: string + id: + $ref: "#/UUID" + systemAlias: node_id + submitter_id: + type: + - string + description: > + A project-specific identifier for a node. This property is the calling card/nickname/alias for + a unit of submission. It can be used in place of the UUID for identifying or recalling a node. + state: + $ref: "#/state" + project_id: + $ref: "#/project_id" + created_datetime: + $ref: "#/datetime" + updated_datetime: + $ref: "#/datetime" diff --git a/tests/fixtures/dbgap/output/gen3/_settings.yaml b/tests/fixtures/dbgap/output/gen3/_settings.yaml new file mode 100644 index 0000000..d7e2171 --- /dev/null +++ b/tests/fixtures/dbgap/output/gen3/_settings.yaml @@ -0,0 +1,6 @@ +# Global settings for the graph + +# Is the graph case centric, that we want +# to create a link between all children to case +# to expedite case filter on nodes +enable_case_cache: false diff --git a/tests/fixtures/dbgap/output/gen3/_terms.yaml b/tests/fixtures/dbgap/output/gen3/_terms.yaml new file mode 100644 index 0000000..6024d85 --- /dev/null +++ b/tests/fixtures/dbgap/output/gen3/_terms.yaml @@ -0,0 +1,1938 @@ +id: _terms + + + +28s_16s_ribosomal_rna_ratio: + description: > + The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA. + termDef: + term: "28s/18s Ribosomal RNA Ratio" + source: null + cde_id: null + cde_version: null + term_url: null + + + + + +a260_a280_ratio: + description: > + Numeric value that represents the sample ratio of nucleic acid absorbance at 260 nm and 280 nm, + used to determine a measure of DNA purity. + termDef: + term: Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value + source: caDSR + cde_id: 5432595 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" + +age: + description: > + Age at last visit. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Age at last visit. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +family_onset: + description: > + Typical age of onset for the family. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Typical age of onset for the family. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +disease_omim_id: + description: > + The ID of the term from OMIM which represents a disease. (CMG) + termDef: + term: The ID of the term from OMIM which represents a disease. (CMG) + source: OMIM + cde_id: OMIM + cde_version: 1.0 + term_url: "https://www.ncbi.nlm.nih.gov/omim" + +phenotype_hpo_id: + description: > + The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + termDef: + term: The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + source: HPO + cde_id: HPO + cde_version: 1.0 + term_url: "https://hpo.jax.org/app/" + +adapter_name: # TOREVIEW + description: > + Name of the sequencing adapter. + +adapter_sequence: # TOREVIEW + description: > + Base sequence of the sequencing adapter. + +age_of_onset: + description: > + Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + termDef: + term: Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +age_at_event_days_gt89: + description: > + Indicate whether the 'Age at the time an event occurs expressed in the number of days since birth' is greater than 32872 days (89 years). + +age_at_diagnosis: + description: > + Age at the time of diagnosis expressed in number of days since birth. If the age at diagnosis is greater than 32872 days (89 years), then see 'age_at_diagnosis_gt89'. + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +age_at_diagnosis_gt89: + description: > + Indicate whether the age at the time of diagnosis expressed in number of days since birth is greater than 32872 days (89 years). + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +ajcc_clinical_m: + description: > + Extent of the distant metastasis for the cancer based on evidence obtained from clinical + assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage + source: caDSR + cde_id: 3440331 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0" + +ajcc_clinical_n: + description: > + Extent of the regional lymph node involvement for the cancer based on evidence obtained from + clinical assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage + source: caDSR + cde_id: 3440330 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0" + +ajcc_clinical_stage: + description: > + Stage group determined from clinical information on the tumor (T), regional node (N) and + metastases (M) and by grouping cases with similar prognosis for cancer. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Group Stage + source: caDSR + cde_id: 3440332 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0" + +ajcc_clinical_t: + description: > + Extent of the primary cancer based on evidence obtained from clinical assessment parameters + determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage + source: caDSR + cde_id: 3440328 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0" + +ajcc_pathologic_m: + description: > + Code to represent the defined absence or presence of distant spread or metastases (M) to + locations via vascular channels or lymphatics beyond the regional lymph nodes, using + criteria established by the American Joint Committee on Cancer (AJCC). + termDef: + term: American Joint Committee on Cancer Metastasis Stage Code + source: caDSR + cde_id: 3045439 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0" + +ajcc_pathologic_n: + description: > + The codes that represent the stage of cancer based on the nodes present (N stage) according + to criteria based on multiple editions of the AJCC's Cancer Staging Manual. + termDef: + term: Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203106 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0" + +ajcc_pathologic_stage: + description: > + The extent of a cancer, especially whether the disease has spread from the original site to + other parts of the body based on AJCC staging criteria. + termDef: + term: Neoplasm Disease Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203222 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0" + +ajcc_pathologic_t: + description: > + Code of pathological T (primary tumor) to define the size or contiguous extension of the + primary tumor (T), using staging criteria from the American Joint Committee on Cancer + (AJCC). + termDef: + term: American Joint Committee on Cancer Tumor Stage Code + source: caDSR + cde_id: 3045435 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0" + +alcohol_history: + description: > + A response to a question that asks whether the participant has consumed at least 12 drinks of + any kind of alcoholic beverage in their lifetime. + termDef: + term: Alcohol Lifetime History Indicator + source: caDSR + cde_id: 2201918 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0" + +drink_number: + description: > + Units of drink consumed during Drink Period (DRNKPRD). (GTEx) + +aliquot_quantity: + description: > + The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +aliquot_volume: + description: > + The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Volume + source: null + cde_id: null + cde_version: null + term_url: null + +amount: # TOREVIEW + description: > + Weight in grams or volume in mL. + +analyte_quantity: + description: > + The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +analyte_type: + description: > + Text term that represents the kind of molecular specimen analyte. + termDef: + term: Molecular Specimen Type Text Name + source: caDSR + cde_id: 2513915 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" + +analyte_type_id: + description: > + A single letter code used to identify a type of molecular analyte. + termDef: + term: Molecular Analyte Identification Code + source: caDSR + cde_id: 5432508 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0" + +analyte_volume: + description: > + The volume in microliters (ml) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Volume + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_b_symptoms: + description: > + Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical + record. + termDef: + term: Lymphoma B-Symptoms Medical Record Documented Indicator + source: caDSR + cde_id: 2902402 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0" + +ann_arbor_clinical_stage: + description: > + The classification of the clinically confirmed anatomic disease extent of lymphoma (Hodgkin's + and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Clinical Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_extranodal_involvement: + description: > + Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement + of an extranodal site. + termDef: + term: Lymphomatous Extranodal Site Involvement Indicator + source: caDSR + cde_id: 3364582 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0" + +ann_arbor_pathologic_stage: + description: > + The classification of the pathologically confirmed anatomic disease extent of lymphoma + (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Pathologic Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_tumor_stage: + description: > + The classification of the anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based + on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Tumor Stage + source: null + cde_id: null + cde_version: null + term_url: null + +base_caller_name: # TOREVIEW + description: > + Name of the base caller. + +base_caller_version: # TOREVIEW + description: > + Version of the base caller. + +biomarker_name: + description: > + The name of the biomarker being tested for this specimen and set of test results. + termDef: + term: Biomarker Name + source: caDSR + cde_id: 5473 + cde_version: 11.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31" + +biomarker_result: + description: > + Text term to define the results of genetic testing. + termDef: + term: Laboratory Procedure Genetic Abnormality Test Result Type + source: caDSR + cde_id: 3234680 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0" + +biomarker_test_method: + description: > + Text descriptor of a molecular analysis method used for an individual. + termDef: + term: Disease Detection Molecular Analysis Method Type + source: caDSR + cde_id: 3121575 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0" + +biospecimen_anatomic_site_id: + description: > + Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +biospecimen_anatomic_site_label: + description: > + Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +bmi: + description: > + Autocalculated field of BMI: general indicator of the body fat an individual is carrying based upon the ratio of weight to height. BMI = 703 * weight in pounds/height in inches squared. (GTEx) + termDef: + term: Body Mass Index (BMI) + source: caDSR + cde_id: 4973892 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" + +burkitt_lymphoma_clinical_variant: + description: > + Burkitt's lymphoma categorization based on clinical features that differ from other forms of the + same disease. + termDef: + term: Burkitt Lymphoma Clinical Variant Type + source: caDSR + cde_id: 3770421 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" + +cause_of_death: + description: > + Text term to identify the cause of death for a patient. + termDef: + term: Patient Death Reason + source: caDSR + cde_id: 2554674 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0" + +cea_level_preoperative: + description: > + Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. [Manually- + curated] + termDef: + term: Preoperative Carcinoembryonic Antigen Result Value + source: caDSR + cde_id: 2716510 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0" + +cigarettes_per_day: + description: > + The average number of cigarettes smoked per day. + termDef: + term: Smoking Use Average Number + source: caDSR + cde_id: 2001716 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0" + +circumferential_resection_margin: + description: > + A value in millimeters indicating the measured length between a malignant lesion of the + colon or rectum and the nearest radial (or circumferential) border of tissue removed during + cancer surgery. + termDef: + term: Colorectal Surgical Margin Circumferential Distance Measurement + source: caDSR + cde_id: 64202 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0" + +classification_of_tumor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +colon_polyps_history: + description: > + Yes/No indicator to describe if the subject had a previous history of colon polyps as noted + in the history/physical or previous endoscopic report (s). + termDef: + term: Colon Carcinoma Polyp Occurrence Indicator + source: caDSR + cde_id: 3107197 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0" + +composition: + description: > + Text term that represents the cellular composition of the sample. + termDef: + term: Biospecimen Cellular Composition Type + source: caDSR + cde_id: 5432591 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" + +concentration: + description: > + Numeric value that represents the concentration of an analyte or aliquot extracted from the + sample or sample portion, measured in milligrams per milliliter. + termDef: + term: Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value + source: caDSR + cde_id: 5432594 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" + +creation_datetime: + description: > + The datetime of portion creation encoded as seconds from epoch. + termDef: + term: Biospecimen Portion Creation Seconds Date/Time + source: caDSR + cde_id: 5432592 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0" + +current_weight: + description: > + Numeric value that represents the current weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Current Weight Milligram Value + source: caDSR + cde_id: 5432606 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" + +data_category: # TOREVIEW + description: > + Broad categorization of the contents of the data file. + +data_file_error_type: # TOREVIEW + description: > + Type of error for the data file object. + +data_format: # TOREVIEW + description: > + Format of the data files. + +data_type: # TOREVIEW + description: > + Specific content type of the data file. (CMG) + +datetime: + description: > + A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] + +days_to_birth: + description: > + Time interval from a person's date of birth to the date of initial pathologic diagnosis, + represented as a calculated negative number of days. + termDef: + term: Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0" + +days_to_collection: + description: > + Time interval from the date of biospecimen collection to the date of initial pathologic + diagnosis, represented as a calculated number of days. + termDef: + term: Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008340 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0" + +days_to_death: + description: > + Time interval from a person's date of death to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Death Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3165475 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0" + +days_to_hiv_diagnosis: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of human + immunodeficiency diagnosis, represented as a calculated number of days. + termDef: + term: Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value + source: caDSR + cde_id: 4618491 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0" + +days_to_last_follow_up: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_last_known_disease_status: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_new_event: + description: > + Time interval from the date of new tumor event including progression, recurrence and new + primary malignacies to the date of initial pathologic diagnosis, represented as a calculated + number of days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_recurrence: + description: > + Time interval from the date of new tumor event including progression, recurrence and new primary + malignancies to the date of initial pathologic diagnosis, represented as a calculated number of + days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_sample_procurement: + description: > + The number of days from the date the patient was diagnosed to the date of the procedure that + produced the sample. + +days_to_treatment: + description: > + Number of days from date of initial pathologic diagnosis that treatment began. + termDef: + term: Days to Treatment Start + source: null + cde_id: null + cde_version: null + term_url: null + +days_to_treatment_end: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of treatment end, + represented as a calculated number of days. + termDef: + term: Treatment End Subtract First Pathologic Diagnosis Day Calculation Value + source: caDSR + cde_id: 5102431 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0" + +days_to_treatment_start: + description: > + Time interval from the date of the initial pathologic diagnosis to the start of treatment, + represented as a calculated number of days. + termDef: + term: Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value + source: caDSR + cde_id: 5102411 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0" + +diagnosis_pathologically_confirmed: + description: > + The histologic description of tissue or cells confirmed by a pathology review of frozen or + formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used + to extract analyte(s). + termDef: + term: Post-Diagnostic Pathology Review Confirmation + source: null + cde_id: null + cde_version: null + term_url: null + +dlco_ref_predictive_percent: + description: > + The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide + detected in a patient's lungs. + termDef: + term: Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value + source: caDSR + cde_id: 2180255 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0" + +encoding: + description: > + Version of ASCII encoding of quality values found in the file. + termDef: + term: Encoding + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +estrogen_receptor_percent_positive_ihc: + description: > + Classification to represent ER Positive results expressed as a percentage value. + termDef: + term: ER Level Cell Percentage Category + source: caDSR + cde_id: 3128341 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0" + +estrogen_receptor_result_ihc: + description: > + Text term to represent the overall result of Estrogen Receptor (ER) testing. + termDef: + term: Breast Carcinoma Estrogen Receptor Status + source: caDSR + cde_id: 2957359 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0" + +ethnicity: + description: > + An individual's self-described social and cultural grouping, specifically whether an individual + describes themselves as Hispanic or Latino (HARMONIZED). The provided values are based on the categories + defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (CMG, GTEx) + termDef: + term: Ethnic Group Category Text + source: caDSR + cde_id: 2192217 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" + +experiment_name: # TOREVIEW + description: > + Submitter-defined name for the experiment. + +experimental_strategy: # TOREVIEW + description: > + The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri. + +fastq_name: # TOREVIEW + description: > + Names of FASTQs. + +fev1_ref_post_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second post-bronchodilator. + termDef: + term: Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302948 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0" + +fev1_ref_pre_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second pre-bronchodilator. + termDef: + term: Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302947 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" + +fev1_fvc_post_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) post-bronchodilator. + termDef: + term: Post Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302956 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0" + +fev1_fvc_pre_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) pre-bronchodilator. + termDef: + term: Pre Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302955 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0" + +figo_stage: + description: > + The extent of a cervical or endometrial cancer within the body, especially whether the + disease has spread from the original site to other parts of the body, as described by the + International Federation of Gynecology and Obstetrics (FIGO) stages. + termDef: + term: Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage + source: caDSR + cde_id: 3225684 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" + +file_format: + description: > + The format of the data file object. + +file_name: # TOREVIEW + description: > + The name (or part of a name) of a file (of any type). + +file_size: # TOREVIEW + description: > + The size of the data file (object) in bytes. + +file_state: # TOREVIEW + description: > + The current state of the data file object. + +flow_cell_barcode: # TOREVIEW + description: > + Flow Cell Barcode. + +freezing_method: + description: > + Text term that represents the method used for freezing the sample. + termDef: + term: Tissue Sample Freezing Method Type + source: caDSR + cde_id: 5432607 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" + +ga4gh_drs_uri: + description: > + DRS URI as defined by GA4GH DRS spec for pointers to file objects. + +sex: + description: > + Text designations that identify gender (HARMONIZED). Gender is described as the assemblage of properties that + distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification + of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] (CMG) + termDef: + term: Person Gender Text Type + source: caDSR + cde_id: 2200604 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" + +height: + description: > + The height of Donor in inches as reported by Donor, family/next of kin, or medical record abstraction. (GTEx) + termDef: + term: Patient Height Measurement + source: caDSR + cde_id: 649 + cde_version: 4.1 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" + +her2_erbb2_percent_positive_ihc: + description: > + Classification to represent the number of positive HER2/ERBB2 cells in a specimen or sample. + termDef: + term: HER2 ERBB Positive Finding Cell Percentage Category + source: caDSR + cde_id: 3086980 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0" + +her2_erbb2_result_fish: + description: > + the type of outcome for HER2 as determined by an in situ hybridization (ISH) assay. + termDef: + term: Laboratory Procedure HER2/neu in situ Hybridization Outcome Type + source: caDSR + cde_id: 2854089 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0" + +her2_erbb2_result_ihc: + description: > + Text term to signify the result of the medical procedure that involves testing a sample of + blood or tissue for HER2 by histochemical localization of immunoreactive substances using + labeled antibodies as reagents. + termDef: + term: Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status + source: caDSR + cde_id: 2957563 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0" + +hiv_positive: + description: > + Text term to signify whether a physician has diagnosed HIV infection in a patient. + termDef: + term: Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator + source: caDSR + cde_id: 4030799 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0" + +hpv_positive_type: + description: > + Text classification to represent the strain or type of human papillomavirus identified in an + individual. + termDef: + term: Human Papillomavirus Type + source: caDSR + cde_id: 2922649 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0" + +hpv_status: + description: > + The findings of the oncogenic HPV. + termDef: + term: Oncogenic Human Papillomavirus Result Type + source: caDSR + cde_id: 2230033 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" + +includes_spike_ins: # TOREVIEW + description: > + Spike-in included? + +initial_weight: + description: > + Numeric value that represents the initial weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Initial Weight Milligram Value + source: caDSR + cde_id: 5432605 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0" + +instrument_model: + description: > + Numeric value that represents the sample dimension that is greater than the shortest + dimension and less than the longest dimension, measured in millimeters. + termDef: + term: Tissue Sample Intermediate Dimension Millimeter Measurement + source: caDSR + cde_id: 5432604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" + +intermediate_dimension: # TOREVIEW + description: > + Intermediate dimension of the sample, in millimeters. + +is_ffpe: + description: > + Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in + paraffin (FFPE). + termDef: + term: Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator + source: caDSR + cde_id: 4170557 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" + +is_paired_end: # TOREVIEW + description: > + Are the reads paired end? + +is_proband: # TOREVIEW + description: > + Boolean value to determine if the case is the proband. + +last_known_disease_status: + description: > + Text term that describes the last known state or condition of an individual's neoplasm. + termDef: + term: Person Last Known Neoplasm Status + source: caDSR + cde_id: 5424231 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0" + +laterality: + description: > + For tumors in paired organs, designates the side on which the cancer originates. + termDef: + term: Primary Tumor Laterality + source: caDSR + cde_id: 827 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0" + +ldh_level_at_diagnosis: + description: > + The 2 decimal place numeric laboratory value measured, assigned or computed related to the + assessment of lactate dehydrogenase in a specimen. + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value + source: caDSR + cde_id: 2798766 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0" + +ldh_normal_range_upper: + description: > + The top value of the range of statistical characteristics that are supposed to represent + accepted standard, non-pathological pattern for lactate dehydrogenase (units not specified). + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value + source: caDSR + cde_id: 2597015 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" + +library_strategy: # TOREVIEW + description: > + Library strategy. + +library_selection: # TOREVIEW + description: > + Library Selection Method + +library_name: # TOREVIEW + description: > + Name of the library. + +library_preparation_kit_name: # TOREVIEW + description: > + Name of Library Preparation Kit + +library_preparation_kit_vendor: # TOREVIEW + description: > + Vendor of Library Preparation Kit + +library_preparation_kit_catalog_number: # TOREVIEW + description: > + Catalog of Library Preparation Kit + +library_preparation_kit_version: # TOREVIEW + description: > + Version of Library Preparation Kit + +library_strand: # TOREVIEW + description: > + Library stranded-ness. + +longest_dimension: + description: > + Numeric value that represents the longest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Longest Dimension Millimeter Measurement + source: caDSR + cde_id: 5432602 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0" + +lymph_nodes_positive: + description: > + The number of lymph nodes involved with disease as determined by pathologic examination. + termDef: + term: Lymph Node(s) Positive Number + source: caDSR + cde_id: 89 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0" + +lymphatic_invasion_present: + description: > + A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating + lymphatic involvement + termDef: + term: Lymphatic/Small vessel Invasion Ind + source: caDSR + cde_id: 64171 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" + +method_of_diagnosis: + description: > + The method used to initially the patient's diagnosis. + termDef: + term: Method of Diagnosis + source: null + cde_id: null + cde_version: null + term_url: null + +method_of_sample_procurement: + description: > + The method used to procure the sample used to extract analyte(s). + termDef: + term: Method of Sample Procurement + source: null + cde_id: null + cde_version: null + term_url: null + +md5sum: # TOREVIEW + description: > + The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital + fingerprint. + +microsatellite_instability_abnormal: + description: > + The yes/no indicator to signify the status of a tumor for microsatellite instability. + termDef: + term: Microsatellite Instability Occurrence Indicator + source: caDSR + cde_id: 3123142 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0" + +morphology: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000 used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The study of the structure of the cells and their + arrangement to constitute tissues and, finally, the association among these to form organs. In + pathology, the microscopic process of identifying normal and abnormal morphologic + characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A + system of numbered categories for representation of data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code + source: caDSR + cde_id: 3226275 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0" + +new_event_anatomic_site: + description: > + Text term to specify the anatomic location of the return of tumor after treatment. + termDef: + term: New Neoplasm Event Occurrence Anatomic Site + source: caDSR + cde_id: 3108271 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0" + +new_event_type: + description: > + Text term to identify a new tumor event. + termDef: + term: New Neoplasm Event Type + source: caDSR + cde_id: 3119721 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0" + +normal_tumor_genotype_snp_match: + description: > + Text term that represents whether or not the genotype of the normal tumor matches or if the data + is not available. + termDef: + term: Normal Tumor Genotype Match Indicator + source: caDSR + cde_id: 4588156 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0" + +number_proliferating_cells: + description: > + Numeric value that represents the count of proliferating cells determined during pathologic + review of the sample slide(s). + termDef: + term: Pathology Review Slide Proliferating Cell Count + source: caDSR + cde_id: 5432636 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0" + +oct_embedded: + description: > + Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound. + termDef: + term: Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator + source: caDSR + cde_id: 5432538 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" + +years_smoked: + description: > + Number of years the Donor smoked. (GTEx) + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +percent_eosinophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or + specimen. + termDef: + term: Specimen Eosinophilia Percentage Value + source: caDSR + cde_id: 2897700 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0" + +percent_gc_content: + description: > + The overall %GC of all bases in all sequences. + termDef: + term: "%GC" + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +percent_granulocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or + specimen. + termDef: + term: Specimen Granulocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897705 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0" + +percent_inflam_infiltration: + description: > + Numeric value to represent local response to cellular injury, marked by capillary dilatation, + edema and leukocyte infiltration; clinically, inflammation is manifest by reddness, heat, pain, + swelling and loss of function, with the need to heal damaged tissue. + termDef: + term: Specimen Inflammation Change Percentage Value + source: caDSR + cde_id: 2897695 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0" + +percent_lymphocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue + normal sample or specimen. + termDef: + term: Specimen Lymphocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897710 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0" + +percent_monocyte_infiltration: + description: > + Numeric value to represent the percentage of monocyte infiltration in a sample or specimen. + termDef: + term: Specimen Monocyte Infiltration Percentage Value + source: caDSR + cde_id: 5455535 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0" + +percent_necrosis: + description: > + Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen. + termDef: + term: Malignant Neoplasm Necrosis Percentage Value + source: caDSR + cde_id: 2841237 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0" + +percent_neutrophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value + source: caDSR + cde_id: 2841267 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0" + +percent_normal_cells: + description: > + Numeric value to represent the percentage of normal cell content in a malignant tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Normal Cell Percentage Value + source: caDSR + cde_id: 2841233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0" + +percent_stromal_cells: + description: > + Numeric value to represent the percentage of reactive cells that are present in a malignant + tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc. + termDef: + term: Malignant Neoplasm Stromal Cell Percentage Value + source: caDSR + cde_id: 2841241 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0" + +percent_tumor_cells: + description: > + Numeric value that represents the percentage of infiltration by granulocytes in a sample. + termDef: + term: Specimen Tumor Cell Percentage Value + source: caDSR + cde_id: 5432686 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0" + +percent_tumor_nuclei: + description: > + Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen. + termDef: + term: Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value + source: caDSR + cde_id: 2841225 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0" + +perineural_invasion_present: + description: > + a yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is + present. + termDef: + term: Tumor Perineural Invasion Ind + source: caDSR + cde_id: 64181 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" + +platform: # TOREVIEW + description: > + Name of the platform used to obtain data. + +portion_number: + description: > + Numeric value that represents the sequential number assigned to a portion of the sample. + termDef: + term: Biospecimen Portion Sequence Number + source: caDSR + cde_id: 5432711 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0" + +portion_weight: + description: > + Numeric value that represents the sample portion weight, measured in milligrams. + termDef: + term: Biospecimen Portion Weight Milligram Value + source: caDSR + cde_id: 5432593 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0" + +preservation_method: + description: > + Text term that represents the method used to preserve the sample. + termDef: + term: Tissue Sample Preservation Method Type + source: caDSR + cde_id: 5432521 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" + + +prior_malignancy: + description: > + Text term to describe the patient's history of prior cancer diagnosis and the spatial location + of any previous cancer occurrence. + termDef: + term: Prior Cancer Diagnosis Occurrence Description Text + source: caDSR + cde_id: 3382736 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0" + +prior_treatment: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +progesterone_receptor_percent_positive_ihc: + description: > + Classification to represent Progesterone Receptor Positive results expressed as a percentage + value. + termDef: + term: Progesterone Receptor Level Cell Percentage Category + source: caDSR + cde_id: 3128342 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0" + +progesterone_receptor_result_ihc: + description: > + Text term to represent the overall result of Progresterone Receptor (PR) testing. + termDef: + term: Breast Carcinoma Progesterone Receptor Status + source: caDSR + cde_id: 2957357 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0" + +progression_or_recurrence: + description: > + Yes/No/Unknown indicator to identify whether a patient has had a new tumor event + after initial treatment. + termDef: + term: New Neoplasm Event Post Initial Therapy Indicator + source: caDSR + cde_id: 3121376 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" + +project_id: # TOREVIEW + description: > + Unique ID for any specific defined piece of work that is undertaken or attempted to + meet a single requirement. + +qc_metric_state: + description: > + State classification given by FASTQC for the metric. Metric specific details about the states + are available on their website. + termDef: + term: QC Metric State + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" + +race: + description: > + An arbitrary classification of a taxonomic group that is a division of a species (HARMONIZED). It usually + arises as a consequence of geographical isolation within a species and is characterized by + shared heredity, physical attributes and behavior, and in the case of humans, by common history, + nationality, or geographic distribution. The provided values are based on the categories defined + by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (GTEx) + termDef: + term: Race Category Text + source: caDSR + cde_id: 2192199 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" + +read_length: # TOREVIEW + description: > + The length of the reads. + +read_group_name: # TOREVIEW + description: > + The name of the read group. + +relationship_age_at_diagnosis: + description: > + The age (in years) when the patient's relative was first diagnosed. + termDef: + term: Relative Diagnosis Age Value + source: caDSR + cde_id: 5300571 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0" + +relationship_to_proband: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relationship_type: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relative_with_cancer_history: + description: > + Indicator to signify whether or not an individual's biological relative has been diagnosed with + another type of cancer. + termDef: + term: Other Cancer Biological Relative History Indicator + source: caDSR + cde_id: 3901752 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0" + +residual_disease: + description: > + Text terms to describe the status of a tissue margin following surgical resection. + termDef: + term: Surgical Margin Resection Status + source: caDSR + cde_id: 2608702 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" + +RIN: + description: > + A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the + RNA sample including the presence or absence of degradation products. + termDef: + term: Biospecimen RNA Integrity Number Value + source: caDSR + cde_id: 5278775 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" + +sample_type: + description: > + Text term to describe the source of a biospecimen used for a laboratory test. + termDef: + term: Specimen Type Collection Biospecimen Type + source: caDSR + cde_id: 3111302 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" + +sample_type_id: # TOREVIEW + description: > + The accompanying sample type id for the sample type. + +section_location: # TOREVIEW + description: > + Tissue source of the slide. + +sequencing_center: # TOREVIEW + description: > + Name of the center that provided the sequence files. + +shortest_dimension: + description: > + Numeric value that represents the shortest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Short Dimension Millimeter Measurement + source: caDSR + cde_id: 5432603 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0" + +site_of_resection_or_biopsy: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000, used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The description of an anatomical region or of a body part. + Named locations of, or within, the body. A system of numbered categories for representation of + data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code + source: caDSR + cde_id: 3226281 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" + +size_selection_range: # TOREVIEW + description: > + Range of size selection. + +smoking_history: + description: > + Category describing current smoking status and smoking history as self-reported by a patient. + termDef: + term: Smoking History + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +smoking_intensity: + description: > + Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes + smoked per day x number of years smoked divided by 20 + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +source_center: # TOREVIEW + description: > + Name of the center that provided the item. + +spectrophotometer_method: + description: > + Name of the method used to determine the concentration of purified nucleic acid within a + solution. + termDef: + term: Purification Nucleic Acid Solution Concentration Determination Method Type + source: caDSR + cde_id: 3008378 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" + +spike_ins_fasta: # TOREVIEW + description: > + Name of the FASTA file that contains the spike-in sequences. + +spike_ins_concentration: # TOREVIEW + description: > + Spike in concentration. + +state: # TOREVIEW + description: > + The current state of the object. + +target_capture_kit_name: # TOREVIEW + description: > + Name of Target Capture Kit. + +target_capture_kit_vendor: # TOREVIEW + description: > + Vendor of Target Capture Kit. + +target_capture_kit_catalog_number: # TOREVIEW + description: > + Catalog of Target Capture Kit. + +target_capture_kit_version: # TOREVIEW + description: > + Version of Target Capture Kit. + +target_capture_kit_target_region: # TOREVIEW + description: > + Target Capture Kit BED file. + +therapeutic_agents: + description: > + Text identification of the individual agent(s) used as part of a prior treatment regimen. + termDef: + term: Prior Therapy Regimen Text + source: caDSR + cde_id: 2975232 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0" + +time_between_clamping_and_freezing: + description: > + Numeric representation of the elapsed time between the surgical clamping of blood supply and + freezing of the sample, measured in minutes. + termDef: + term: Tissue Sample Clamping and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432611 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0" + +time_between_excision_and_freezing: + description: > + Numeric representation of the elapsed time between the excision and freezing of the sample, + measured in minutes. + termDef: + term: Tissue Sample Excision and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432612 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0" + +tissue_or_organ_of_origin: + description: > + Text term that describes the anatomic site of the tumor or disease. + termDef: + term: Tumor Disease Anatomic Site + source: caDSR + cde_id: 3427536 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0" + +tissue_type: + description: > + Text term that represents a description of the kind of tissue collected with respect to disease + status or proximity to tumor tissue. + termDef: + term: Tissue Sample Description Type + source: caDSR + cde_id: 5432687 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" + +to_trim_adapter_sequence: # TOREVIEW + description: > + Does the user suggest adapter trimming? + +tobacco_smoking_onset_year: + description: > + The year in which the participant began smoking. + termDef: + term: Started Smoking Year + source: caDSR + cde_id: 2228604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0" + +tobacco_smoking_quit_year: + description: > + The year in which the participant quit smoking. + termDef: + term: Stopped Smoking Year + source: caDSR + cde_id: 2228610 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0" + +tobacco_smoking_status: + description: > + Category describing current smoking status and smoking history as self-reported by a + patient. + termDef: + term: Patient Smoking History Category + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +total_sequences: + description: > + A count of the total number of sequences processed. + termDef: + term: Total Sequences + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +treatment_anatomic_site: + description: > + The anatomic site or field targeted by a treatment regimen or single agent therapy. + termDef: + term: Treatment Anatomic Site + source: null + cde_id: null + cde_version: null + term_url: null + +treatment_intent_type: + description: > + Text term to identify the reason for the administration of a treatment regimen. [Manually-curated] + termDef: + term: Treatment Regimen Intent Type + source: caDSR + cde_id: 2793511 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0" + +treatment_or_therapy: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +treatment_outcome: + description: > + Text term that describes the patient¿s final outcome after the treatment was administered. + termDef: + term: Treatment Outcome Type + source: caDSR + cde_id: 5102383 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0" + +treatment_type: + description: > + Text term that describes the kind of treatment administered. + termDef: + term: Treatment Method Type + source: caDSR + cde_id: 5102381 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" + +tumor_grade: + description: > + Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation + and aggressiveness. + termDef: + term: Neoplasm Histologic Grade + source: caDSR + cde_id: 2785839 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" + +tumor_code: # TOREVIEW + description: > + Diagnostic tumor code of the tissue sample source. + +tumor_code_id: # TOREVIEW + description: > + BCR-defined id code for the tumor sample. + +tumor_descriptor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +tumor_stage: + description: > + The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether + lymph nodes contain cancer, and whether the cancer has spread from the original site to other + parts of the body. The accepted values for tumor_stage depend on the tumor site, type, and + accepted staging system. These items should accompany the tumor_stage value as associated + metadata. + termDef: + term: Tumor Stage + source: NCIt + cde_id: C16899 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" + +UUID: + description: > + A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to + be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be + different. Its relatively small size lends itself well to sorting, ordering, and hashing of all + sorts, storing in databases, simple allocation, and ease of programming in general. + termDef: + term: Universally Unique Identifier + source: NCIt + cde_id: C54100 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" + +vascular_invasion_present: + description: > + The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or + presence in a tumor specimen. + termDef: + term: Tumor Vascular Invasion Ind-3 + source: caDSR + cde_id: 64358 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0" + +vital_status: + description: > + The survival state of the person registered on the protocol. + termDef: + term: Patient Vital Status + source: caDSR + cde_id: 5 + cde_version: 5.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" + +weight: + description: > + The weight of the patient measured in lbs (HARMONIZED). + termDef: + term: Patient Weight Measurement + source: caDSR + cde_id: 651 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" + +well_number: + description: > + Numeric value that represents the the well location within a plate for the analyte or + aliquot from the sample. + termDef: + term: Biospecimen Analyte or Aliquot Plate Well Number + source: caDSR + cde_id: 5432613 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0" + +workflow_type: + description: > + Generic name for the workflow used to analyze a data set. + +year_of_birth: + description: > + Numeric value to represent the calendar year in which an individual was born. + termDef: + term: Year Birth Date Number + source: caDSR + cde_id: 2896954 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" + +year_of_diagnosis: + description: > + Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. + termDef: + term: Year of initial pathologic diagnosis + source: caDSR + cde_id: 2896960 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" + +year_of_death: + description: > + Numeric value to represent the year of the death of an individual. + termDef: + term: Year Death Number + source: caDSR + cde_id: 2897030 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" + +years_smoked: + description: > + Numeric value (or unknown) to represent the number of years a person has been smoking (HARMONIZED). If the number of years is greater than 89, see 'years_smoked_gt89'. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" + +years_smoked_gt89: + description: > + Indicate whether the numeric value to represent the number of years a person has been smoking (HARMONIZED) is greater than 89 years. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" diff --git a/tests/fixtures/ncpi/README.md b/tests/fixtures/ncpi/README.md new file mode 100644 index 0000000..5e538f7 --- /dev/null +++ b/tests/fixtures/ncpi/README.md @@ -0,0 +1,5 @@ +## ncpi + +### copy from IG build +curl https://nih-ncpi.github.io/ncpi-fhir-ig/examples.json.zip --output {output_path}/examples.json.zip 2> /dev/null +unzip {output_path}/examples.json.zip -d {output_path}/examples diff --git a/tests/fixtures/ncpi/examples/CodeSystem-ConditionInheritanceMode.json b/tests/fixtures/ncpi/examples/CodeSystem-ConditionInheritanceMode.json new file mode 100644 index 0000000..dce46d9 --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-ConditionInheritanceMode.json @@ -0,0 +1,151 @@ +{ + "resourceType": "CodeSystem", + "id": "ConditionInheritanceMode", + "text": { + "status": "generated", + "div": "

This code system https://ncpi-fhir.github.io/ncpi-fhir-ig/CodeSystem/ConditionInheritanceMode defines the following codes:

CodeDisplay
GENO:0000143 Codominant inheritance
GENO:0000889 Unknown inheritance
GENO:0000892 Mitochondrial inheritance (primarily or exclusively heteroplasmic)
GENO:0000893 Mitochondrial inheritance (primarily or exclusively homoplasmic)
HP:0000006 Autosomal dominant inheritance
HP:0000007 Autosomal recessive inheritance
HP:0001417 X-linked inheritance
HP:0001419 X-linked inheritance (recessive)
HP:0001423 X-linked inheritance (dominant)
HP:0001426 Multifactorial inheritance
HP:0001427 Mitochondrial inheritance
HP:0001428 Somatic mutation
HP:0001450 Y-linked inheritance
HP:0001470 Autosomal dominant inheritance (sex-limited)
HP:0003743 Genetic anticipation
HP:0003745 Sporadic
HP:0010983 Oligogenic
HP:0012274 Autosomal dominant inheritance (with paternal imprinting)
HP:0012275 Autosomal dominant inheritance (with maternal imprinting)
HP:0025352 Autosomal dominant inheritance (primarily or exclusively de novo)
HP:0031362 Autosomal recessive inheritance (sex-limited)
SEPIO-CG:97020 Semidominant inheritance
SEPIO-CG:97021 X-linked inheritance (primarily recessive with milder female expression)
SEPIO-CG:97022 Autosomal dominant inheritance (with genetic anticipation)
SEPIO-CG:97023 Autosomal recessive inheritance (with genetic anticipation)
" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/CodeSystem/ConditionInheritanceMode", + "version": "0.1.0", + "name": "ConditionInheritanceMode", + "title": "Condition Inheritance Pattern", + "status": "active", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "A set of terms that describe the transmission pattern of a condition in a pedigree.", + "jurisdiction": [ + { + "coding": [ + { + "system": "http://unstats.un.org/unsd/methods/m49/m49.htm", + "code": "001" + } + ] + } + ], + "content": "complete", + "count": 25, + "concept": [ + { + "code": "GENO:0000143", + "display": "Codominant inheritance" + }, + { + "code": "GENO:0000889", + "display": "Unknown inheritance" + }, + { + "code": "GENO:0000892", + "display": "Mitochondrial inheritance (primarily or exclusively heteroplasmic)" + }, + { + "code": "GENO:0000893", + "display": "Mitochondrial inheritance (primarily or exclusively homoplasmic)" + }, + { + "code": "HP:0000006", + "display": "Autosomal dominant inheritance" + }, + { + "code": "HP:0000007", + "display": "Autosomal recessive inheritance" + }, + { + "code": "HP:0001417", + "display": "X-linked inheritance" + }, + { + "code": "HP:0001419", + "display": "X-linked inheritance (recessive)" + }, + { + "code": "HP:0001423", + "display": "X-linked inheritance (dominant)" + }, + { + "code": "HP:0001426", + "display": "Multifactorial inheritance" + }, + { + "code": "HP:0001427", + "display": "Mitochondrial inheritance" + }, + { + "code": "HP:0001428", + "display": "Somatic mutation" + }, + { + "code": "HP:0001450", + "display": "Y-linked inheritance" + }, + { + "code": "HP:0001470", + "display": "Autosomal dominant inheritance (sex-limited)" + }, + { + "code": "HP:0003743", + "display": "Genetic anticipation" + }, + { + "code": "HP:0003745", + "display": "Sporadic" + }, + { + "code": "HP:0010983", + "display": "Oligogenic" + }, + { + "code": "HP:0012274", + "display": "Autosomal dominant inheritance (with paternal imprinting)" + }, + { + "code": "HP:0012275", + "display": "Autosomal dominant inheritance (with maternal imprinting)" + }, + { + "code": "HP:0025352", + "display": "Autosomal dominant inheritance (primarily or exclusively de novo)" + }, + { + "code": "HP:0031362", + "display": "Autosomal recessive inheritance (sex-limited)" + }, + { + "code": "SEPIO-CG:97020", + "display": "Semidominant inheritance" + }, + { + "code": "SEPIO-CG:97021", + "display": "X-linked inheritance (primarily recessive with milder female expression)" + }, + { + "code": "SEPIO-CG:97022", + "display": "Autosomal dominant inheritance (with genetic anticipation)" + }, + { + "code": "SEPIO-CG:97023", + "display": "Autosomal recessive inheritance (with genetic anticipation)" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-hpo.json b/tests/fixtures/ncpi/examples/CodeSystem-hpo.json new file mode 100644 index 0000000..e24c936 --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-hpo.json @@ -0,0 +1,7611 @@ +{ + "resourceType": "CodeSystem", + "id": "hpo", + "text": { + "status": "generated", + "div": "

Properties

CodeTypeDescription
parentcodeParent codes.
importedbooleanIndicates if the concept is imported from another code system.
rootbooleanIndicates if this concept is a root concept (i.e. Thing is equivalent or a direct parent)
deprecatedbooleanIndicates if this concept is deprecated.

Filters

CodeDescriptionoperatorValue
root= True or false.
deprecated= True or false.
imported= True or false

This code system http://purl.obolibrary.org/obo/hp.owl defines the following codes:

CodeDisplay
HP:0000365 Hearing impairment
HP:0002564 obsolete Malformation of the heart and great vessels
HP:0001028 Hemangioma
HP:0000476 Cystic hygroma
HP:0000568 Microphthalmia
HP:0000518 Cataract
HP:0000612 Iris coloboma
HP:0000567 Chorioretinal coloboma
HP:0000316 Hypertelorism
HP:0000482 Microcornea
HP:0000588 Optic nerve coloboma
HP:0004426 Abnormality of the cheek
HP:0009125 Lipodystrophy
HP:0002023 Anal atresia
HP:0003468 Abnormal vertebral morphology
HP:0000545 Myopia
HP:0000122 Unilateral renal agenesis
HP:0002143 Abnormality of the spinal cord
HP:0003508 Proportionate short stature
HP:0000271 Abnormality of the face
HP:0000637 Long palpebral fissure
HP:0000492 Abnormal eyelid morphology
HP:0000389 Chronic otitis media
HP:0000400 Macrotia
HP:0000405 Conductive hearing impairment
HP:0012712 Mild hearing impairment
HP:0005280 Depressed nasal bridge
HP:0000431 Wide nasal bridge
HP:0000319 Smooth philtrum
HP:0000175 Cleft palate
HP:0001611 Nasal speech
HP:0002099 Asthma
HP:0001397 Hepatic steatosis
HP:0001081 Cholelithiasis
HP:0002650 Scoliosis
HP:0001212 Prominent fingertip pads
HP:0001328 Specific learning disability
HP:0000824 Growth hormone deficiency
HP:0002607 Bowel incontinence
HP:0100731 Transverse facial cleft
HP:0000528 Anophthalmia
HP:0000601 Hypotelorism
HP:0000369 Low-set ears
HP:0001274 Agenesis of corpus callosum
HP:0002084 Encephalocele
HP:0007033 Cerebellar dysplasia
HP:0100336 Bilateral cleft lip
HP:0100337 Bilateral cleft palate
HP:0001511 Intrauterine growth retardation
HP:0011451 Congenital microcephaly
HP:0000324 Facial asymmetry
HP:0000581 Blepharophimosis
HP:0000508 Ptosis
HP:0008551 Microtia
HP:0001631 Atrial septal defect
HP:0000085 Horseshoe kidney
HP:0011927 Short digit
HP:0001156 Brachydactyly
HP:0002066 Gait ataxia
HP:0001250 Seizure
HP:0001263 Global developmental delay
HP:0001562 Oligohydramnios
HP:0001195 Single umbilical artery
HP:0006349 Agenesis of permanent teeth
HP:0000668 Hypodontia
HP:0000677 Oligodontia
HP:0001252 Muscular hypotonia
HP:0003429 CNS hypomyelination
HP:0010864 Intellectual disability, severe
HP:0004325 Decreased body weight
HP:0000666 Horizontal nystagmus
HP:0000218 High palate
HP:0010809 Broad uvula
HP:0000767 Pectus excavatum
HP:0003691 Scapular winging
HP:0002616 Aortic root aneurysm
HP:0001601 Laryngomalacia
HP:0002021 Pyloric stenosis
HP:0001388 Joint laxity
HP:0001187 Hyperextensibility of the finger joints
HP:0000741 Apathy
HP:0000817 Poor eye contact
HP:0000821 Hypothyroidism
HP:0000002 Abnormality of body height
HP:0000079 Abnormality of the urinary system
HP:0000164 Abnormality of the dentition
HP:0000364 Hearing abnormality
HP:0000366 Abnormality of the nose
HP:0000464 Abnormality of the neck
HP:0000707 Abnormality of the nervous system
HP:0000708 Behavioral abnormality
HP:0000769 Abnormality of the breast
HP:0000772 Abnormality of the ribs
HP:0000775 Abnormality of the diaphragm
HP:0000889 Abnormality of the clavicle
HP:0000925 Abnormality of the vertebral column
HP:0001080 Biliary tract abnormality
HP:0001392 Abnormality of the liver
HP:0001438 Abnormal abdomen morphology
HP:0001608 Abnormality of the voice
HP:0001627 Abnormal heart morphology
HP:0001732 Abnormality of the pancreas
HP:0001739 Abnormality of the nasopharynx
HP:0001743 Abnormality of the spleen
HP:0001760 Abnormal foot morphology
HP:0001871 Abnormality of blood and blood-forming tissues
HP:0002031 Abnormal esophagus morphology
HP:0002244 Abnormality of the small intestine
HP:0002246 Abnormality of the duodenum
HP:0002250 Abnormal large intestine morphology
HP:0002644 Abnormality of pelvic girdle bone morphology
HP:0002664 Neoplasm
HP:0002715 Abnormality of the immune system
HP:0002814 Abnormality of the lower limb
HP:0002817 Abnormality of the upper limb
HP:0005483 Abnormal epiglottis morphology
HP:0008777 Abnormal vocal cord morphology
HP:0011844 Abnormal appendicular skeleton morphology
HP:0012732 Anorectal anomaly
HP:0001508 Failure to thrive
HP:0002902 Hyponatremia
HP:0012236 Elevated sweat chloride
HP:0000347 Micrognathia
HP:0000926 Platyspondyly
HP:0001371 Flexion contracture
HP:0001875 Neutropenia
HP:0001888 Lymphopenia
HP:0002857 Genu valgum
HP:0002986 Radial bowing
HP:0003015 Flared metaphysis
HP:0003025 Metaphyseal irregularity
HP:0003097 Short femur
HP:0003300 Ovoid vertebral bodies
HP:0003307 Hyperlordosis
HP:0004209 Clinodactyly of the 5th finger
HP:0004322 Short stature
HP:0005792 Short humerus
HP:0006248 Limited wrist movement
HP:0000944 Abnormality of the metaphysis
HP:0011921 Exudative pleural effusion
HP:0003043 Abnormality of the shoulder
HP:0000290 Abnormality of the forehead
HP:0005288 Abnormality of the nares
HP:0000234 Abnormality of the head
HP:0004323 Abnormality of body weight
HP:0000483 Astigmatism
HP:0011003 High myopia
HP:0000470 Short neck
HP:0030044 Flexion contracture of digit
HP:0100871 Abnormality of the palm
HP:0004334 Dermal atrophy
HP:0001845 Overlapping toe
HP:0000496 Abnormality of eye movement
HP:0001780 Abnormality of toe
HP:0001626 Abnormality of the cardiovascular system
HP:0002086 Abnormality of the respiratory system
HP:0000818 Abnormality of the endocrine system
HP:0012372 Abnormal eye morphology
HP:0009473 Joint contracture of the hand
HP:0003199 Decreased muscle mass
HP:0003202 Skeletal muscle atrophy
HP:0003551 Difficulty climbing stairs
HP:0002355 Difficulty walking
HP:0003546 Exercise intolerance
HP:0003325 Limb-girdle muscle weakness
HP:0003701 Proximal muscle weakness
HP:0003547 Shoulder girdle muscle weakness
HP:0007340 Lower limb muscle weakness
HP:0002168 Scanning speech
HP:0001265 Hyporeflexia
HP:0001284 Areflexia
HP:0003477 Peripheral axonal neuropathy
HP:0000924 Abnormality of the skeletal system
HP:0001291 Abnormal cranial nerve morphology
HP:0003687 Centrally nucleated skeletal muscle fibers
HP:0001324 Muscle weakness
HP:0002515 Waddling gait
HP:0100280 Crohn's disease
HP:0002631 obsolete Dilatation of ascending aorta
HP:0100026 Arteriovenous malformation
HP:0002637 Cerebral ischemia
HP:0002619 Varicose veins
HP:0001159 Syndactyly
HP:0002069 Bilateral tonic-clonic seizure
HP:0000977 Soft skin
HP:0010648 Dermal translucency
HP:0000978 Bruising susceptibility
HP:0001956 Truncal obesity
HP:0000189 Narrow palate
HP:0000678 Dental crowding
HP:0002870 Obstructive sleep apnea
HP:0001763 Pes planus
HP:0000782 Abnormality of the scapula
HP:0001600 Abnormality of the larynx
HP:0002088 Abnormal lung morphology
HP:0011407 Proportionate tall stature
HP:0000541 Retinal detachment
HP:0001373 Joint dislocation
HP:0000938 Osteopenia
HP:0002942 Thoracic kyphosis
HP:0001840 Metatarsus adductus
HP:0001844 Abnormality of the hallux
HP:0001765 Hammertoe
HP:0000606 Abnormality of the periorbital region
HP:0002757 Recurrent fractures
HP:0000647 Sclerocornea
HP:0001166 Arachnodactyly
HP:0005490 Postnatal macrocephaly
HP:0011363 Abnormality of hair growth rate
HP:0000276 Long face
HP:0000275 Narrow face
HP:0000337 Broad forehead
HP:0002267 Exaggerated startle response
HP:0002187 Intellectual disability, profound
HP:0000728 Impaired ability to form peer relationships
HP:0000733 Stereotypy
HP:0000739 Anxiety
HP:0000929 Abnormal skull morphology
HP:0001965 Abnormal scalp morphology
HP:0100538 Abnormality of the supraorbital ridges
HP:0000309 Abnormality of the midface
HP:0000277 Abnormality of the mandible
HP:0000765 Abnormality of the thorax
HP:0100008 Schwannoma
HP:0030038 Enchondroma
HP:0100777 Exostoses
HP:0011663 Right ventricular cardiomyopathy
HP:0011675 Arrhythmia
HP:0001962 Palpitations
HP:0001279 Syncope
HP:0004756 Ventricular tachycardia
HP:0000252 Microcephaly
HP:0000303 Mandibular prognathia
HP:0000664 Synophrys
HP:0001609 Hoarse voice
HP:0002558 Supernumerary nipple
HP:0001634 Mitral valve prolapse
HP:0000028 Cryptorchidism
HP:0000973 Cutis laxa
HP:0001518 Small for gestational age
HP:0000527 Long eyelashes
HP:0002808 Kyphosis
HP:0000248 Brachycephaly
HP:0000505 Visual impairment
HP:0000512 Abnormal electroretinogram
HP:0000517 Abnormality of the lens
HP:0000529 Progressive visual loss
HP:0000586 Shallow orbits
HP:0000603 Central scotoma
HP:0000939 Osteoporosis
HP:0001377 Limited elbow extension
HP:0001387 Joint stiffness
HP:0001822 Hallux valgus
HP:0002657 Spondylometaphyseal dysplasia
HP:0003026 Short long bone
HP:0006462 Generalized bone demineralization
HP:0008873 Disproportionate short-limb short stature
HP:0008905 Rhizomelia
HP:0008922 Childhood-onset short-trunk short stature
HP:0200020 Corneal erosion
HP:0001172 Abnormal thumb morphology
HP:0002286 Fair hair
HP:0010719 Abnormality of hair texture
HP:0010720 Abnormal hair pattern
HP:0001635 Congestive heart failure
HP:0001644 Dilated cardiomyopathy
HP:0001663 Ventricular fibrillation
HP:0011712 Right bundle branch block
HP:0000272 Malar flattening
HP:0000286 Epicanthus
HP:0000322 Short philtrum
HP:0000463 Anteverted nares
HP:0000494 Downslanted palpebral fissures
HP:0000543 Optic disc pallor
HP:0000699 Diastema
HP:0000773 Short ribs
HP:0000887 Cupped ribs
HP:0000946 Hypoplastic ilia
HP:0000954 Single transverse palmar crease
HP:0001182 Tapered finger
HP:0001537 Umbilical hernia
HP:0002007 Frontal bossing
HP:0002980 Femoral bowing
HP:0002982 Tibial bowing
HP:0003021 Metaphyseal cupping
HP:0005011 Mesomelic arm shortening
HP:0008803 obsolete Narrow sacroiliac notch
HP:0009117 Aplasia/Hypoplasia of the maxilla
HP:0011220 Prominent forehead
HP:0012801 Narrow jaw
HP:0000243 Trigonocephaly
HP:0000358 Posteriorly rotated ears
HP:0000411 Protruding ear
HP:0000646 Amblyopia
HP:0002812 Coxa vara
HP:0002970 Genu varum
HP:0012775 Stellate iris
HP:0000278 Retrognathia
HP:0009796 Branchial cyst
HP:0002474 Expressive language delay
HP:0007018 Attention deficit hyperactivity disorder
HP:0003198 Myopathy
HP:0003324 Generalized muscle weakness
HP:0003552 Muscle stiffness
HP:0003554 Type 2 muscle fiber atrophy
HP:0003557 Increased variability in muscle fiber diameter
HP:0009025 Increased connective tissue
HP:0003635 Loss of subcutaneous adipose tissue in limbs
HP:0002597 Abnormality of the vasculature
HP:0001649 Tachycardia
HP:0001638 Cardiomyopathy
HP:0001654 Abnormal heart valve morphology
HP:0001671 Abnormal cardiac septum morphology
HP:0000103 Polyuria
HP:0000114 Proximal tubulopathy
HP:0001878 Hemolytic anemia
HP:0001931 Hypochromic anemia
HP:0001935 Microcytic anemia
HP:0001959 Polydipsia
HP:0001994 Renal Fanconi syndrome
HP:0002134 Abnormality of the basal ganglia
HP:0002188 Delayed CNS myelination
HP:0002908 Conjugated hyperbilirubinemia
HP:0003774 Stage 5 chronic kidney disease
HP:0010700 obsolete Total cataract
HP:0000193 Bifid uvula
HP:0000219 Thin upper lip vermilion
HP:0000426 Prominent nasal bridge
HP:0000452 Choanal stenosis
HP:0000490 Deeply set eye
HP:0000540 Hypermetropia
HP:0000579 Nasolacrimal duct obstruction
HP:0000684 Delayed eruption of teeth
HP:0000960 Sacral dimple
HP:0000998 Hypertrichosis
HP:0001643 Patent ductus arteriosus
HP:0010813 Abnormal number of hair whorls
HP:0012384 Rhinitis
HP:0012745 Short palpebral fissure
HP:0000359 Abnormality of the inner ear
HP:0000429 Abnormality of the nasal alae
HP:0000436 Abnormality of the nasal tip
HP:0000499 Abnormal eyelash morphology
HP:0000534 Abnormal eyebrow morphology
HP:0000951 Abnormality of the skin
HP:0001000 Abnormality of skin pigmentation
HP:0001597 Abnormality of the nail
HP:0006483 Abnormal number of teeth
HP:0009929 Abnormality of the columella
HP:0011119 Abnormality of the nasal dorsum
HP:0012808 Abnormal nasal base
HP:0100490 Camptodactyly of finger
HP:0000964 Eczema
HP:0004442 Sagittal craniosynostosis
HP:0000414 Bulbous nose
HP:0003180 Flat acetabular roof
HP:0000422 Abnormality of the nasal bridge
HP:0000614 Abnormal nasolacrimal system morphology
HP:0001167 Abnormality of finger
HP:0001595 Abnormal hair morphology
HP:0012373 Abnormal eye physiology
HP:0001655 Patent foramen ovale
HP:0001647 Bicuspid aortic valve
HP:0000574 Thick eyebrow
HP:0001169 Broad palm
HP:0006471 Fixed elbow flexion
HP:0008689 Bilateral cryptorchidism
HP:0011304 Broad thumb
HP:0005110 Atrial fibrillation
HP:0001633 Abnormal mitral valve morphology
HP:0001641 Abnormal pulmonary valve morphology
HP:0001702 Abnormal tricuspid valve morphology
HP:0000012 Urinary urgency
HP:0000020 Urinary incontinence
HP:0000131 Uterine leiomyoma
HP:0000132 Menorrhagia
HP:0000138 Ovarian cyst
HP:0000853 Goiter
HP:0000953 Hyperpigmentation of the skin
HP:0001061 Acne
HP:0002315 Headache
HP:0004324 Increased body weight
HP:0000069 Abnormality of the ureter
HP:0000077 Abnormality of the kidney
HP:0000759 Abnormal peripheral nervous system morphology
HP:0008069 Neoplasm of the skin
HP:0011276 Vascular skin abnormality
HP:0000705 Amelogenesis imperfecta
HP:0001256 Intellectual disability, mild
HP:0000325 Triangular face
HP:0000160 Narrow mouth
HP:0009487 Ulnar deviation of the hand
HP:0001249 Intellectual disability
HP:0008064 Ichthyosis
HP:0000311 Round face
HP:0001653 Mitral regurgitation
HP:0001771 Achilles tendon contracture
HP:0012032 Lipoma
HP:0012368 Flat face
HP:0030053 Stiff skin
HP:0011124 Abnormality of epidermal morphology
HP:0011097 Epileptic spasm
HP:0000407 Sensorineural hearing impairment
HP:0000331 Short chin
HP:0000340 Sloping forehead
HP:0000486 Strabismus
HP:0000713 Agitation
HP:0000802 Impotence
HP:0001272 Cerebellar atrophy
HP:0001276 Hypertonia
HP:0001321 Cerebellar hypoplasia
HP:0001322 obsolete Brain very small
HP:0002061 Lower limb spasticity
HP:0002529 Neuronal loss in central nervous system
HP:0002540 Inability to walk
HP:0005484 Postnatal microcephaly
HP:0012850 Small intestinal dysmotility
HP:0000504 Abnormality of vision
HP:0002118 Abnormality of the cerebral ventricles
HP:0002363 Abnormality of brainstem morphology
HP:0010651 Abnormal meningeal morphology
HP:0100024 Conspicuously happy disposition
HP:0002538 Abnormality of the cerebral cortex
HP:0000054 Micropenis
HP:0000215 Thick upper lip vermilion
HP:0000293 Full cheeks
HP:0000349 Widow's peak
HP:0000444 Convex nasal ridge
HP:0000506 Telecanthus
HP:0000592 Blue sclerae
HP:0000691 Microdontia
HP:0000698 Conical tooth
HP:0002000 Short columella
HP:0002097 Emphysema
HP:0002209 Sparse scalp hair
HP:0002816 Genu recurvatum
HP:0005116 Arterial tortuosity
HP:0007957 Corneal opacity
HP:0008070 Sparse hair
HP:0009623 Proximal placement of thumb
HP:0010055 Broad hallux
HP:0011318 Bicoronal synostosis
HP:0011968 Feeding difficulties
HP:0200067 Recurrent spontaneous abortion
HP:0011819 Submucous cleft soft palate
HP:0000268 Dolichocephaly
HP:0003302 Spondylolisthesis
HP:0000582 Upslanted palpebral fissure
HP:0000952 Jaundice
HP:0001298 Encephalopathy
HP:0001396 Cholestasis
HP:0002059 Cerebral atrophy
HP:0002171 Gliosis
HP:0002240 Hepatomegaly
HP:0002353 EEG abnormality
HP:0002446 Astrocytosis
HP:0003287 Abnormality of mitochondrial metabolism
HP:0011449 Knee clonus
HP:0012852 Hepatic bridging fibrosis
HP:0100626 Chronic hepatic failure
HP:0000385 Small earlobe
HP:0009748 Large earlobe
HP:0000157 Abnormality of the tongue
HP:0000172 Abnormality of the uvula
HP:0000174 Abnormal palate morphology
HP:0000306 Abnormality of the chin
HP:0004408 Abnormality of the sense of smell
HP:0009912 Abnormality of the tragus
HP:0000537 Epicanthus inversus
HP:0000565 Esotropia
HP:0000752 Hyperactivity
HP:0003186 Inverted nipples
HP:0012503 Abnormality of the pituitary gland
HP:0100710 Impulsivity
HP:0000357 Abnormal location of ears
HP:0000820 Abnormality of the thyroid gland
HP:0000828 Abnormality of the parathyroid gland
HP:0000834 Abnormality of the adrenal glands
HP:0012093 Abnormality of endocrine pancreas physiology
HP:0000269 Prominent occiput
HP:0000535 Sparse and thin eyebrow
HP:0000639 Nystagmus
HP:0000718 Aggressive behavior
HP:0000957 Cafe-au-lait spot
HP:0000256 Macrocephaly
HP:0000750 Delayed speech and language development
HP:0000963 Thin skin
HP:0001260 Dysarthria
HP:0002194 Delayed gross motor development
HP:0003196 Short nose
HP:0001155 Abnormality of the hand
HP:0100022 Abnormality of movement
HP:0010862 Delayed fine motor development
HP:0000343 Long philtrum
HP:0000717 Autism
HP:0001883 Talipes
HP:0002553 Highly arched eyebrow
HP:0007488 Diffuse skin atrophy
HP:0000822 Hypertension
HP:0001278 Orthostatic hypotension
HP:0001944 Dehydration
HP:0001945 Fever
HP:0002019 Constipation
HP:0002020 Gastroesophageal reflux
HP:0002027 Abdominal pain
HP:0002718 Recurrent bacterial infections
HP:0002841 Recurrent fungal infections
HP:0004395 Malnutrition
HP:0009830 Peripheral neuropathy
HP:0000126 Hydronephrosis
HP:0000519 Developmental cataract
HP:0000648 Optic atrophy
HP:0001053 Hypopigmented skin patches
HP:0001087 Developmental glaucoma
HP:0002119 Ventriculomegaly
HP:0002280 Enlarged cisterna magna
HP:0003298 Spina bifida occulta
HP:0004467 Preauricular pit
HP:0008511 Central posterior corneal opacity
HP:0010780 Hyperacusis
HP:0030048 Colpocephaly
HP:0100335 Non-midline cleft lip
HP:0000525 Abnormality iris morphology
HP:0002719 Recurrent infections
HP:0000153 Abnormality of the mouth
HP:0001903 Anemia
HP:0002094 Dyspnea
HP:0002206 Pulmonary fibrosis
HP:0002789 Tachypnea
HP:0002793 Abnormal pattern of respiration
HP:0003565 Elevated erythrocyte sedimentation rate
HP:0006517 Intraalveolar phospholipid accumulation
HP:0006530 Interstitial pulmonary abnormality
HP:0100759 Clubbing of fingers
HP:0002103 Abnormal pleura morphology
HP:0001596 Alopecia
HP:0001882 Leukopenia
HP:0002013 Vomiting
HP:0002028 Chronic diarrhea
HP:0002573 Hematochezia
HP:0002960 Autoimmunity
HP:0005387 Combined immunodeficiency
HP:0011109 Chronic sinusitis
HP:0004429 Recurrent viral infections
HP:0000280 Coarse facial features
HP:0000294 Low anterior hairline
HP:0000577 Exotropia
HP:0001873 Thrombocytopenia
HP:0002011 Morphological central nervous system abnormality
HP:0006610 Wide intermamillary distance
HP:0011231 Prominent eyelashes
HP:0012718 Morphological abnormality of the gastrointestinal tract
HP:0002024 Malabsorption
HP:0001394 Cirrhosis
HP:0001414 Microvesicular hepatic steatosis
HP:0001403 Macrovesicular hepatic steatosis
HP:0001410 Decreased liver function
HP:0001409 Portal hypertension
HP:0001744 Splenomegaly
HP:0003394 Muscle spasm
HP:0003750 Increased muscle fatiguability
HP:0002123 Generalized myoclonic seizure
HP:0002219 Facial hypertrichosis
HP:0000831 Insulin-resistant diabetes mellitus
HP:0001891 Iron deficiency anemia
HP:0001264 Spastic diplegia
HP:0002313 Spastic paraparesis
HP:0001347 Hyperreflexia
HP:0002460 Distal muscle weakness
HP:0000763 Sensory neuropathy
HP:0001268 Mental deterioration
HP:0002169 Clonus
HP:0001332 Dystonia
HP:0100716 Self-injurious behavior
HP:0000602 Ophthalmoplegia
HP:0001251 Ataxia
HP:0000776 Congenital diaphragmatic hernia
HP:0000410 Mixed hearing impairment
HP:0000510 Rod-cone dystrophy
HP:0004437 Cranial hyperostosis
HP:0011001 Increased bone mineral density
HP:0000956 Acanthosis nigricans
HP:0000958 Dry skin
HP:0000580 Pigmentary retinopathy
HP:0000649 Abnormality of visual evoked potentials
HP:0000657 Oculomotor apraxia
HP:0000479 Abnormal retinal morphology
HP:0001317 Abnormal cerebellum morphology
HP:0001533 Slender build
HP:0001629 Ventricular septal defect
HP:0000703 Dentinogenesis imperfecta
HP:0000914 Shield chest
HP:0001500 Broad finger
HP:0003086 Acromesomelia
HP:0003416 Spinal canal stenosis
HP:0002815 Abnormality of the knee
HP:0002992 Abnormality of tibia morphology
HP:0001639 Hypertrophic cardiomyopathy
HP:0003236 Elevated serum creatine kinase
HP:0001369 Arthritis
HP:0003560 Muscular dystrophy
HP:0003974 Absent radius
HP:0002818 Abnormality of the radius
HP:0001561 Polyhydramnios
HP:0002299 Brittle hair
HP:0002208 Coarse hair
HP:0002213 Fine hair
HP:0000522 Alacrima
HP:0100704 Cerebral visual impairment
HP:0012713 Moderate hearing impairment
HP:0002307 Drooling
HP:0002714 Downturned corners of mouth
HP:0000191 Accessory oral frenulum
HP:0000158 Macroglossia
HP:0012020 Right aortic arch
HP:0002104 Apnea
HP:0000598 Abnormality of the ear
HP:0007874 Almond-shaped palpebral fissure
HP:0010804 Tented upper lip vermilion
HP:0000885 Broad ribs
HP:0000768 Pectus carinatum
HP:0001680 Coarctation of aorta
HP:0000687 Widely spaced teeth
HP:0000047 Hypospadias
HP:0001943 Hypoglycemia
HP:0012369 Abnormality of malar bones
HP:0009900 Unilateral deafness
HP:0000023 Inguinal hernia
HP:0000074 Ureteropelvic junction obstruction
HP:0001800 Hypoplastic toenails
HP:0001804 Hypoplastic fingernail
HP:0002949 Fused cervical vertebrae
HP:0008050 Abnormality of the palpebral fissures
HP:0008577 Underfolded helix
HP:0008589 Hypoplastic helices
HP:0010863 Receptive language delay
HP:0002282 Gray matter heterotopia
HP:0002085 Occipital encephalocele
HP:0001057 Aplasia cutis congenita
HP:0000211 Trismus
HP:0008422 Vertebral wedging
HP:0003170 Abnormality of the acetabulum
HP:0003272 Abnormality of the hip bone
HP:0003028 Abnormality of the ankles
HP:0003301 Irregular vertebral endplates
HP:0010508 Metatarsus valgus
HP:0009811 Abnormality of the elbow
HP:0000736 Short attention span
HP:0002912 Methylmalonic acidemia
HP:0001941 Acidosis
HP:0001992 Organic aciduria
HP:0009027 Foot dorsiflexor weakness
HP:0002063 Rigidity
HP:0000384 Preauricular skin tag
HP:0200046 Cat cry
HP:0001357 Plagiocephaly
HP:0000670 Carious teeth
HP:0011090 Fused teeth
HP:0012810 Wide nasal base
HP:0010296 Ankyloglossia
HP:0001636 Tetralogy of Fallot
HP:0001305 Dandy-Walker malformation
HP:0000238 Hydrocephalus
HP:0005469 Flat occiput
HP:0000270 Delayed cranial suture closure
HP:0000239 Large fontanelles
HP:0010537 Wide cranial sutures
HP:0002217 Slow-growing hair
HP:0000587 Abnormality of the optic nerve
HP:0005989 Redundant neck skin
HP:0010775 Vascular ring
HP:0002779 Tracheomalacia
HP:0002827 Hip dislocation
HP:0001302 Pachygyria
HP:0007362 Aplasia/Hypoplasia of the brainstem
HP:0001558 Decreased fetal movement
HP:0010878 Fetal cystic hygroma
HP:0011398 Central hypotonia
HP:0002071 Abnormality of extrapyramidal motor function
HP:0000826 Precocious puberty
HP:0000014 Abnormality of the bladder
HP:0005037 Proximal radio-ulnar synostosis
HP:0100543 Cognitive impairment
HP:0000481 Abnormal cornea morphology
HP:0000076 Vesicoureteral reflux
HP:0000297 Facial hypotonia
HP:0000391 Thickened helices
HP:0001162 Postaxial hand polydactyly
HP:0001385 Hip dysplasia
HP:0002342 Intellectual disability, moderate
HP:0003191 Cleft ala nasi
HP:0009765 Low hanging columella
HP:0010297 Bifid tongue
HP:0011330 Metopic synostosis
HP:0012804 Corneal ulceration
HP:0010485 Hyperextensibility at elbow
HP:0000609 Optic nerve hypoplasia
HP:0001176 Large hands
HP:0004233 Advanced ossification of carpal bones
HP:0100842 Septo-optic dysplasia
HP:0002034 Abnormality of the rectum
HP:0002283 Global brain atrophy
HP:0003115 Abnormal EKG
HP:0002577 Abnormal stomach morphology
HP:0002539 Cortical dysplasia
HP:0006818 4-layered lissencephaly
HP:0000593 Abnormal anterior chamber morphology
HP:0000179 Thick lower lip vermilion
HP:0002002 Deep philtrum
HP:0009931 Enlarged naris
HP:0002948 Vertebral fusion
HP:0002937 Hemivertebrae
HP:0002308 Arnold-Chiari malformation
HP:0011320 Unilambdoid synostosis
HP:0002781 Upper airway obstruction
HP:0001363 Craniosynostosis
HP:0000204 Cleft upper lip
HP:0001738 Exocrine pancreatic insufficiency
HP:0002823 Abnormality of femur morphology
HP:0000823 Delayed puberty
HP:0100279 Ulcerative colitis
HP:0003834 Shoulder dislocation
HP:0001065 Striae distensae
HP:0000448 Prominent nose
HP:0000554 Uveitis
HP:0001006 obsolete Hypotrichosis
HP:0000501 Glaucoma
HP:0000262 Turricephaly
HP:0000729 Autistic behavior
HP:0010800 Absent cupid's bow
HP:0010808 Protruding tongue
HP:0009927 Aplasia of the nose
HP:0100539 Periorbital edema
HP:0000629 Periorbital fullness
HP:0000178 Abnormality of lower lip
HP:0000168 Abnormality of the gingiva
HP:0001022 Albinism
HP:0000177 Abnormality of upper lip
HP:0001337 Tremor
HP:0002135 Basal ganglia calcification
HP:0002352 Leukoencephalopathy
HP:0002514 Cerebral calcification
HP:0010576 Intracranial cystic lesion
HP:0001622 Premature birth
HP:0002415 Leukodystrophy
HP:0001320 Cerebellar vermis hypoplasia
HP:0001773 Short foot
HP:0002750 Delayed skeletal maturation
HP:0004415 Pulmonary artery stenosis
HP:0012741 Unilateral cryptorchidism
HP:0000036 Abnormality of the penis
HP:0002408 Cerebral arteriovenous malformation
HP:0007457 Prominent veins on trunk
HP:0000378 Cupped ear
HP:0000396 Overfolded helix
HP:0000035 Abnormal testis morphology
HP:0009895 Abnormality of the crus of the helix
HP:0000034 Hydrocele testis
HP:0000722 Obsessive-compulsive behavior
HP:0000845 Growth hormone excess
HP:0100829 Galactorrhea
HP:0001578 Increased circulating cortisol level
HP:0000786 Primary amenorrhea
HP:0001701 Pericarditis
HP:0002076 Migraine
HP:0004755 Supraventricular tachycardia
HP:0010522 Dyslexia
HP:0004313 Decreased circulating antibody level
HP:0000011 Neurogenic bladder
HP:0000641 Dysmetric saccades
HP:0007772 Impaired smooth pursuit
HP:0001583 Rotary nystagmus
HP:0010544 Vertical nystagmus
HP:0012735 Cough
HP:0002075 Dysdiadochokinesis
HP:0007256 Abnormal pyramidal sign
HP:0001257 Spasticity
HP:0002321 Vertigo
HP:0002384 Focal impaired awareness seizure
HP:0011376 Morphological abnormality of the vestibule of the inner ear
HP:0002326 Transient ischemic attack
HP:0005584 Renal cell carcinoma
HP:0003124 Hypercholesterolemia
HP:0003002 Breast carcinoma
HP:0004953 obsolete Dilatation of abdominal aorta
HP:0004944 Dilatation of the cerebral artery
HP:0000100 Nephrotic syndrome
HP:0002783 Recurrent lower respiratory tract infections
HP:0003470 Paralysis
HP:0006597 Diaphragmatic paralysis
HP:0008151 Prolonged prothrombin time
HP:0010628 Facial palsy
HP:0011892 Low levels of vitamin K
HP:0001075 Atrophic scars
HP:0001816 Thin nail
HP:0002216 Premature graying of hair
HP:0003401 Paresthesia
HP:0100134 Abnormality of the axillary hair
HP:0100797 Toenail dysplasia
HP:0010461 Abnormality of the male genitalia
HP:0000044 Hypogonadotropic hypogonadism
HP:0100568 Neoplasm of the endocrine system
HP:0001646 Abnormal aortic valve morphology
HP:0000813 Bicornuate uterus
HP:0004380 Aortic valve calcification
HP:0001650 Aortic valve stenosis
HP:0000073 Ureteral duplication
HP:0100651 Type I diabetes mellitus
HP:0000819 Diabetes mellitus
HP:0000573 Retinal hemorrhage
HP:0005264 Abnormality of the gallbladder
HP:0000475 Broad neck
HP:0000089 Renal hypoplasia
HP:0000921 Missing ribs
HP:0001789 Hydrops fetalis
HP:0002089 Pulmonary hypoplasia
HP:0003422 Vertebral segmentation defect
HP:0002323 Anencephaly
HP:0000341 Narrow forehead
HP:0002869 Flared iliac wings
HP:0003100 Slender long bone
HP:0003275 Narrow pelvis bone
HP:0009891 Underdeveloped supraorbital ridges
HP:0011039 Abnormality of the helix
HP:0008572 External ear malformation
HP:0009738 Abnormality of the antihelix
HP:0011328 Abnormality of fontanelles
HP:0012155 Decreased corneal sensation
HP:0004602 Cervical C2/C3 vertebral fusion
HP:0002997 Abnormality of the ulna
HP:0009777 Absent thumb
HP:0002893 Pituitary adenoma
HP:0040278 Prolactinoma
HP:0001555 Asymmetry of the thorax
HP:0000902 Rib fusion
HP:0002164 Nail dysplasia
HP:0011314 Abnormality of long bone morphology
HP:0002867 Abnormality of the ilium
HP:0000774 Narrow chest
HP:0006482 Abnormality of dental morphology
HP:0004383 Hypoplastic left heart
HP:0002015 Dysphagia
HP:0500093 Food allergy
HP:0001519 Disproportionate tall stature
HP:0003179 Protrusio acetabuli
HP:0007385 Aplasia cutis congenita of scalp
HP:0000716 Depressivity
HP:0012583 Unilateral renal hypoplasia
HP:0000618 Blindness
HP:0001004 Lymphedema
HP:0002652 Skeletal dysplasia
HP:0012520 Perivascular spaces
HP:0005293 Venous insufficiency
HP:0012432 Chronic fatigue
HP:0002578 Gastroparesis
HP:0001658 Myocardial infarction
HP:0001802 Absent toenail
HP:0001821 Broad nail
HP:0000807 Glandular hypospadias
HP:0100582 Nasal polyposis
HP:0002653 Bone pain
HP:0001073 Cigarette-paper scars
HP:0031913 Rhombencephalosynapsis
HP:0002617 Dilatation
HP:0005107 Abnormal sacrum morphology
HP:0002025 Anal stenosis
HP:0009099 Median cleft palate
HP:0003212 Increased circulating IgE level
HP:0001319 Neonatal hypotonia
HP:0002659 Increased susceptibility to fractures
HP:0025246 Trichilemmal cyst
HP:0002107 Pneumothorax
HP:0000107 Renal cyst
HP:0001025 Urticaria
HP:0002204 Pulmonary embolism
HP:0001058 Poor wound healing
HP:0003010 Prolonged bleeding time
HP:0100502 Vitamin B12 deficiency
HP:0100510 Low levels of vitamin C
HP:0030976 Abnormal factor VIII activity
HP:0100789 Torus palatinus
HP:0000108 Renal corticomedullary cysts
HP:0000072 Hydroureter
HP:0000019 Urinary hesitancy
HP:0100771 Hypoperistalsis
HP:0000021 Megacystis
HP:0004388 Microcolon
HP:0005247 Hypoplasia of the abdominal wall musculature
HP:0004794 Malrotation of small bowel
HP:0000045 Abnormality of the scrotum
HP:0002236 Frontal upsweep of hair
HP:0000212 Gingival overgrowth
HP:0001808 Fragile nails
HP:0000225 Gingival bleeding
HP:0006009 Broad phalanx
HP:0001837 Broad toe
HP:0001946 Ketosis
HP:0002490 Increased CSF lactate
HP:0002922 Increased CSF protein
HP:0003128 Lactic acidosis
HP:0003111 Abnormal blood ion concentration
HP:0032234 Increased circulating creatine kinase MM isoform
HP:0003348 Hyperalaninemia
HP:0008347 Decreased activity of mitochondrial complex IV
HP:0000326 Abnormality of the maxilla
HP:0010758 Abnormality of the premaxilla
HP:0005681 Juvenile rheumatoid arthritis
HP:0000514 Slow saccadic eye movements
HP:0002788 Recurrent upper respiratory tract infections
HP:0003396 Syringomyelia
HP:0003011 Abnormality of the musculature
HP:0002098 Respiratory distress
HP:0002018 Nausea
HP:0002014 Diarrhea
HP:0025168 Left ventricular diastolic dysfunction
HP:0001679 Abnormal aortic morphology
HP:0000159 Abnormal lip morphology
HP:0011338 Abnormality of mouth shape
HP:0000478 Abnormality of the eye
HP:0000154 Wide mouth
HP:0001513 Obesity
HP:0002475 Myelomeningocele
HP:0003765 Psoriasiform dermatitis
HP:0010289 Cleft of alveolar ridge of maxilla
HP:0003908 Corner fracture of metaphysis
HP:0002190 Choroid plexus cyst
HP:0004370 Abnormality of temperature regulation
HP:0011611 Interrupted aortic arch
HP:0000737 Irritability
HP:0001344 Absent speech
HP:0002376 Developmental regression
HP:0002140 Ischemic stroke
HP:0001287 Meningitis
HP:0002721 Immunodeficiency
HP:0000041 Chordee
HP:0012854 Midshaft hypospadias
HP:0000808 Penoscrotal hypospadias
HP:0000048 Bifid scrotum
HP:0001047 Atopic dermatitis
HP:0001621 Weak voice
HP:0002372 Normal interictal EEG
HP:0012803 Anisometropia
HP:0011386 Narrow internal auditory canal
HP:0012714 Severe hearing impairment
HP:0006485 Agenesis of incisor
HP:0000787 Nephrolithiasis
HP:0011332 Hemifacial hypoplasia
HP:0001909 Leukemia
HP:0004808 Acute myeloid leukemia
HP:0006495 Aplasia/Hypoplasia of the ulna
HP:0001180 Hand oligodactyly
HP:0002991 Abnormality of fibula morphology
HP:0001849 Foot oligodactyly
HP:0006507 Aplasia/hypoplasia of the humerus
HP:0005613 Aplasia/hypoplasia of the femur
HP:0006492 Aplasia/Hypoplasia of the fibula
HP:0000098 Tall stature
HP:0003311 Hypoplasia of the odontoid process
HP:0005752 Flattened moderately deformed vertebrae
HP:0030039 Fused thoracic vertebrae
HP:0003304 Spondylolysis
HP:0001659 Aortic regurgitation
HP:0002984 Hypoplasia of the radius
HP:0009944 Partial duplication of thumb phalanx
HP:0005819 Short middle phalanx of finger
HP:0002110 Bronchiectasis
HP:0001677 Coronary artery atherosclerosis
HP:0001737 Pancreatic cysts
HP:0005113 Aortic arch aneurysm
HP:0003022 Hypoplasia of the ulna
HP:0002205 Recurrent respiratory infections
HP:0001669 Transposition of the great arteries
HP:0001716 Wolff-Parkinson-White syndrome
HP:0002758 Osteoarthritis
HP:0002037 Inflammation of the large intestine
HP:0009892 Anotia
HP:0011331 Hemifacial atrophy
HP:0009118 Aplasia/Hypoplasia of the mandible
HP:0009940 Asymmetry of the mandible
HP:0000682 Abnormality of dental enamel
HP:0009908 Anterior creases of earlobe
HP:0001541 Ascites
HP:0006687 Aortic tortuosity
HP:0010535 Sleep apnea
HP:0100633 Esophagitis
HP:0002105 Hemoptysis
HP:0002613 Biliary cirrhosis
HP:0004469 Chronic bronchitis
HP:0002720 Decreased circulating IgA level
HP:0002904 Hyperbilirubinemia
HP:0003237 Increased circulating IgG level
HP:0003262 Smooth muscle antibody positivity
HP:0011227 Elevated C-reactive protein level
HP:0001852 Sandal gap
HP:0004381 Supravalvular aortic stenosis
HP:0100700 Abnormal arachnoid mater morphology
HP:0002624 Abnormal venous morphology
HP:0002289 Alopecia universalis
HP:0009588 Vestibular Schwannoma
HP:0001648 Cor pulmonale
HP:0002091 Restrictive ventilatory defect
HP:0002092 Pulmonary arterial hypertension
HP:0002113 Pulmonary infiltrates
HP:0003138 Increased blood urea nitrogen
HP:0003259 Elevated serum creatinine
HP:0005180 Tricuspid regurgitation
HP:0012585 Renal atrophy
HP:0005133 Right ventricular dilatation
HP:0005575 Hemolytic-uremic syndrome
HP:0001697 Abnormal pericardium morphology
HP:0012486 Myelitis
HP:0002385 Paraparesis
HP:0006706 Cystic liver disease
HP:0010880 Increased nuchal translucency
HP:0000457 Depressed nasal ridge
HP:0002263 Exaggerated cupid's bow
HP:0002500 Abnormality of the cerebral white matter
HP:0002835 Aspiration
HP:0000600 Abnormality of the pharynx
HP:0004327 Abnormal vitreous humor morphology
HP:0004378 Abnormality of the anus
HP:0012374 obsolete Abnormal globe morphology
HP:0100768 Choriocarcinoma
HP:0030991 Sclerosing cholangitis
HP:0006510 Chronic pulmonary obstruction
HP:0000710 Hyperorality
HP:0001270 Motor delay
HP:0001548 Overgrowth
HP:0002311 Incoordination
HP:0006288 Advanced eruption of teeth
HP:0006323 Premature loss of primary teeth
HP:0009890 High anterior hairline
HP:0100034 Motor tics
HP:0100035 Phonic tics
HP:0000348 High forehead
HP:0001520 Large for gestational age
HP:0001239 Wrist flexion contracture
HP:0007359 Focal-onset seizure
HP:0000430 Underdeveloped nasal alae
HP:0007400 Irregular hyperpigmentation
HP:0100495 Mastocytosis
HP:0012378 Fatigue
HP:0002046 Heat intolerance
HP:0003270 Abdominal distention
HP:0002180 Neurodegeneration
HP:0003493 Antinuclear antibody positivity
HP:0030057 Autoimmune antibody positivity
HP:0006802 Abnormal anterior horn cell morphology
HP:0000064 Hypoplastic labia minora
HP:0000338 Hypomimic face
HP:0001642 Pulmonic stenosis
HP:0011344 Severe global developmental delay
HP:0200007 Abnormal size of the palpebral fissures
HP:0004464 Postauricular pit
HP:0000130 Abnormality of the uterus
HP:0000137 Abnormality of the ovary
HP:0000142 Abnormal vagina morphology
HP:0000370 Abnormality of the middle ear
HP:0011787 Central hypothyroidism
HP:0000274 Small face
HP:0000446 Narrow nasal bridge
HP:0000622 Blurred vision
HP:0001245 Small thenar eminence
HP:0009601 Aplasia/Hypoplasia of the thumb
HP:0011343 Moderate global developmental delay
HP:0000419 Abnormality of the nasal septum
HP:0000502 Abnormal conjunctiva morphology
HP:0000591 Abnormal sclera morphology
HP:0000615 Abnormal pupil morphology
HP:0001163 Abnormality of the metacarpal bones
HP:0001832 Abnormal metatarsal morphology
HP:0001850 Abnormality of the tarsal bones
HP:0010490 Abnormality of the palmar creases
HP:0010881 Abnormality of the umbilical cord
HP:0009113 Diaphragmatic weakness
HP:0011664 Left ventricular noncompaction cardiomyopathy
HP:0100240 Synostosis of joints
HP:0001838 Rocker bottom foot
HP:0003717 Minimal subcutaneous fat
HP:0001339 Lissencephaly
HP:0001591 Bell-shaped thorax
HP:0002655 Spondyloepiphyseal dysplasia
HP:0002983 Micromelia
HP:0003016 Metaphyseal widening
HP:0009826 Limb undergrowth
HP:0004488 Macrocephaly at birth
HP:0001695 Cardiac arrest
HP:0001712 Left ventricular hypertrophy
HP:0100775 Dural ectasia
HP:0000846 Adrenal insufficiency
HP:0002925 Increased thyroid-stimulating hormone level
HP:0100646 Thyroiditis
HP:0000836 Hyperthyroidism
HP:0004414 Abnormality of the pulmonary artery
HP:0000465 Webbed neck
HP:0000723 Restrictive behavior
HP:0002253 Colonic diverticula
HP:0001310 Dysmetria
HP:0000093 Proteinuria
HP:0002907 Microscopic hematuria
HP:0003073 Hypoalbuminemia
HP:0004315 Decreased circulating IgG level
HP:0000795 Abnormality of the urethra
HP:0001015 Prominent superficial veins
HP:0004691 2-3 toe syndactyly
HP:0005328 Progeroid facial appearance
HP:0005487 Prominent metopic ridge
HP:0007552 Abnormal subcutaneous fat tissue distribution
HP:0100678 Premature skin wrinkling
HP:0031137 Storage in hepatocytes
HP:0002521 Hypsarrhythmia
HP:0005390 Recurrent opportunistic infections
HP:0002716 Lymphadenopathy
HP:0005379 obsolete Severe T lymphocytopenia
HP:0004432 Agammaglobulinemia
HP:0006695 Atrioventricular canal defect
HP:0001733 Pancreatitis
HP:0002350 Cerebellar cyst
HP:0012110 Hypoplasia of the pons
HP:0001948 Alkalosis
HP:0003113 Hypochloremia
HP:0003155 Elevated alkaline phosphatase
HP:0003542 Increased serum pyruvate
HP:0000421 Epistaxis
HP:0200136 Oral-pharyngeal dysphagia
HP:0000805 Enuresis
HP:0005616 Accelerated skeletal maturation
HP:0002459 obsolete Dysautonomia
HP:0007302 Bipolar affective disorder
HP:0100602 Preeclampsia
HP:0100508 Abnormality of vitamin metabolism
HP:0001140 Limbal dermoid
HP:0000143 Rectovaginal fistula
HP:0001746 Asplenia
HP:0012715 Profound hearing impairment
HP:0001748 Polysplenia
HP:0003072 Hypercalcemia
HP:0002905 Hyperphosphatemia
HP:0002901 Hypocalcemia
HP:0001367 Abnormal joint morphology
HP:0010562 Keloids
HP:0004430 Severe combined immunodeficiency
HP:0000003 Multicystic kidney dysplasia
HP:0010980 Hyperlipoproteinemia
HP:0002155 Hypertriglyceridemia
HP:0000520 Proptosis
HP:0000180 Lobulated tongue
HP:0005486 Small fontanelle
HP:0000891 Cervical ribs
HP:0002557 Hypoplastic nipples
HP:0009112 Aplasia of the left hemidiaphragm
HP:0001719 Double outlet right ventricle
HP:0001682 Subvalvular aortic stenosis
HP:0001667 Right ventricular hypertrophy
HP:0002101 Abnormal lung lobation
HP:0002202 Pleural effusion
HP:0002566 Intestinal malrotation
HP:0004510 Pancreatic islet-cell hyperplasia
HP:0001747 Accessory spleen
HP:0002181 Cerebral edema
HP:0000967 Petechiae
HP:0009702 Carpal synostosis
HP:0000927 Abnormality of skeletal maturation
HP:0004348 Abnormality of bone mineral density
HP:0003019 Abnormality of the wrist
HP:0003063 Abnormality of the humerus
HP:0001059 Pterygium
HP:0001528 Hemihypertrophy
HP:0011228 Horizontal eyebrow
HP:0000766 Abnormality of the sternum
HP:0001254 Lethargy
HP:0002360 Sleep disturbance
HP:0001063 Acrocyanosis
HP:0001769 Broad foot
HP:0010280 Stomatitis
HP:0001288 Gait disturbance
HP:0008330 Reduced von Willebrand factor activity
HP:0001954 Recurrent fever
HP:0004311 Abnormal macrophage morphology
HP:0012539 Non-Hodgkin lymphoma
HP:0002074 Increased neuronal autofluorescent lipopigment
HP:0002973 Abnormality of the forearm
HP:0003203 Impaired oxidative burst
HP:0003027 Mesomelia
HP:0002754 Osteomyelitis
HP:0004431 Complement deficiency
HP:0001258 Spastic paraplegia
HP:0012811 Wide nasal ridge
HP:0011832 Narrow nasal tip
HP:0000288 Abnormality of the philtrum
HP:0002357 Dysphasia
HP:0000871 Panhypopituitarism
HP:0000233 Thin vermilion border
HP:0003281 Increased serum ferritin
HP:0010752 Cleft mandible
HP:0000437 Depressed nasal tip
HP:0000453 Choanal atresia
HP:0000863 Central diabetes insipidus
HP:0000058 Abnormality of the labia
HP:0007418 Alopecia totalis
HP:0100765 Abnormality of the tonsils
HP:0100747 Macrodactyly of toe
HP:0002109 obsolete Abnormality of the bronchi
HP:0011950 Bronchiolitis
HP:0002850 Decreased circulating total IgM
HP:0001395 Hepatic fibrosis
HP:0010701 Abnormal immunoglobulin level
HP:0009928 Thick nasal alae
HP:0010807 Open bite
HP:0002126 Polymicrogyria
HP:0002900 Hypokalemia
HP:0000155 Oral ulcer
HP:0000135 Hypogonadism
HP:0100783 Breast aplasia
HP:0000336 Prominent supraorbital ridges
HP:0010557 Overlapping fingers
HP:0005100 Premature birth following premature rupture of fetal membranes
HP:0002594 Pancreatic hypoplasia
HP:0010109 Short hallux
HP:0002334 Abnormality of the cerebellar vermis
HP:0003326 Myalgia
HP:0001645 Sudden cardiac death
HP:0001612 Weak cry
HP:0001618 Dysphonia
HP:0001336 Myoclonus
HP:0001283 Bulbar palsy
HP:0002080 Intention tremor
HP:0002174 Postural tremor
HP:0002064 Spastic gait
HP:0009800 Maternal diabetes
HP:0001662 Bradycardia
HP:0006595 Scapulohumeral synostosis
HP:0005815 Supernumerary ribs
HP:0000307 Pointed chin
HP:0012371 Hyperplasia of midface
HP:0002643 Neonatal respiratory distress
HP:0002093 Respiratory insufficiency
HP:0010310 Chylothorax
HP:0006376 Limited elbow flexion
HP:0006467 Limited shoulder movement
HP:0010505 Limitation of movement at ankles
HP:0010501 Limitation of knee mobility
HP:0009896 Abnormality of the antitragus
HP:0004404 Abnormal nipple morphology
HP:0011957 Abnormal pectoral muscle morphology
HP:0000777 Abnormality of the thymus
HP:0000418 Narrow nasal ridge
HP:0001572 Macrodontia
HP:0002967 Cubitus valgus
HP:0000988 Skin rash
HP:0009733 Glioma
HP:0012452 Restless legs
HP:0100031 Neoplasm of the thyroid gland
HP:0030127 Endometriosis
HP:0000123 Nephritis
HP:0001974 Leukocytosis
HP:0010976 B lymphocytopenia
HP:0000010 Recurrent urinary tract infections
HP:0100807 Long fingers
HP:0000653 Sparse eyelashes
HP:0000171 Microglossia
HP:0002575 Tracheoesophageal fistula
HP:0009933 Narrow naris
HP:0000883 Thin ribs
HP:0000121 Nephrocalcinosis
HP:0001349 Facial diplegia
HP:0012037 Pectoralis amyotrophy
HP:0100560 Upper limb asymmetry
HP:0005684 Distal arthrogryposis
HP:0010722 Asymmetry of the ears
HP:0009380 Aplasia of the fingers
HP:0001657 Prolonged QT interval
HP:0002040 Esophageal varix
HP:0000613 Photophobia
HP:0000561 Absent eyelashes
HP:0002223 Absent eyebrow
HP:0002591 Polyphagia
HP:0002373 Febrile seizure (within the age range of 3 months to 6 years)
HP:0002419 Molar tooth sign on MRI
HP:0001010 Hypopigmentation of the skin
HP:0005772 Aplasia/Hypoplasia of the tibia
HP:0002211 White forelock
HP:0007126 Proximal amyotrophy
HP:0003798 Nemaline bodies
HP:0006533 Bronchodysplasia
HP:0003391 Gowers sign
HP:0000771 Gynecomastia
HP:0100785 Insomnia
HP:0010529 Echolalia
HP:0000363 Abnormality of earlobe
HP:0002612 Congenital hepatic fibrosis
HP:0006721 Acute lymphoblastic leukemia
HP:0001958 Nonketotic hypoglycemia
HP:0003457 EMG abnormality
HP:0010636 Schizencephaly
HP:0005266 Intestinal polyp
HP:0200063 Colorectal polyposis
HP:0001762 Talipes equinovarus
HP:0000056 Abnormality of the clitoris
HP:0008655 Aplasia/Hypoplasia of the fallopian tube
HP:0002072 Chorea
HP:0008734 Decreased testicular size
HP:0002136 Broad-based gait
HP:0010958 Bilateral renal agenesis
HP:0002510 Spastic tetraplegia
HP:0003234 Decreased plasma carnitine
HP:0000720 Mood swings
HP:0012638 Abnormal nervous system physiology
HP:0002803 Congenital contracture
HP:0000152 Abnormality of head or neck
HP:0004377 Hematological neoplasm
HP:0100006 Neoplasm of the central nervous system
HP:0012759 Neurodevelopmental abnormality
HP:0011805 Abnormal skeletal muscle morphology
HP:0003634 Amyoplasia
HP:0001507 Growth abnormality
HP:0001939 Abnormality of metabolism/homeostasis
HP:0011013 Abnormal circulating carbohydrate concentration
HP:0410008 Abnormality of the peripheral nervous system
HP:0200134 Epileptic encephalopathy
HP:0001881 Abnormal leukocyte morphology
HP:0005549 obsolete Congenital neutropenia
HP:0004439 Craniofacial dysostosis
HP:0012443 Abnormality of brain morphology
HP:0000202 Oral cleft
HP:0011842 Abnormality of skeletal morphology
HP:0003808 Abnormal muscle tone
HP:0001574 Abnormality of the integument
HP:0030056 Uncombable hair
HP:0003549 Abnormality of connective tissue
HP:0030875 Abnormality of pulmonary circulation
HP:0000118 Phenotypic abnormality
HP:0012469 Infantile spasms
HP:0032894 Seizure precipitated by febrile infection
HP:0100661 Trigeminal neuralgia
HP:0012207 Reduced sperm motility
HP:0000798 Oligospermia
HP:0012864 Abnormal sperm morphology
HP:0008232 Elevated circulating follicle stimulating hormone level
HP:0040306 Decreased male libido
HP:0012208 Immotile sperm
HP:0000027 Azoospermia
HP:0000870 Increased circulating prolactin concentration
HP:0008187 Absence of secondary sex characteristics
HP:0010469 Absent testis
HP:0011969 Elevated circulating luteinizing hormone level
HP:0040171 Decreased serum testosterone level
HP:0003251 Male infertility
HP:0009804 Reduced number of teeth
HP:0000548 Cone/cone-rod dystrophy
HP:0000546 Retinal degeneration
HP:0008002 Abnormality of macular pigmentation
HP:0000608 Macular degeneration
HP:0030611 Retinal pigment epithelial loss on macular OCT
HP:0001135 Chorioretinal dystrophy
HP:0030468 Abnormal multifocal electroretinogram
HP:00030532 Visual acuity test abnormality
HP:0007401 Macular atrophy
HP:0030466 Abnormal full-field electroretinogram
HP:007737 Bone spicule pigmentation of the retina
HP:0011342 Mild global developmental delay
HP:0030610 Photoreceptor outer segment loss on macular OCT
HP:0007722 Retinal pigment epithelial atrophy
HP:0030493 Abnormality of foveal pigmentation
HP:0007843 Attenuation of retinal blood vessels
HP:0007754 Macular dystrophy
HP:0011509 Macular hyperpigmentation
HP:0008527 Congenital sensorineural hearing impairment
HP:0200070 Peripheral retinal atrophy
HP:0007793 Granular macular appearance
HP:0007987 Progressive visual field defects
HP:0100817 Renovascular hypertension
HP:0007868 obsolete Age-related macular degeneration
HP:0030527 Very severe constriction of peripheral visual field
HP:0030551 Visual acuity light perception with projection
HP:0011505 Cystoid macular edema
HP:0010442 Polydactyly
HP:0007642 Congenital stationary night blindness
HP:0009073 Progressive proximal muscle weakness
HP:0003741 Congenital muscular dystrophy
HP:0100299 Muscle fiber inclusion bodies
HP:0003540 Impaired platelet aggregation
HP:0010489 Absent palmar crease
HP:0009824 Upper limb undergrowth
HP:0002395 Lower limb hyperreflexia
HP:0001138 Optic neuropathy
HP:0007103 Hypointensity of cerebral white matter on MRI
HP:0003458 EMG: myopathic abnormalities
HP:0002987 Elbow flexion contracture
HP:0006466 Ankle flexion contracture
HP:0008458 Progressive congenital scoliosis
HP:0000473 Torticollis
HP:0011800 Midface retrusion
HP:0000597 Ophthalmoparesis
HP:0005853 Congenital foot contraction deformities
HP:0007002 Motor axonal neuropathy
HP:0003327 Axial muscle weakness
HP:0003306 Spinal rigidity
HP:0002068 Neuromuscular dysphagia
HP:0001002 obsolete Decreased subcutaneous fat
HP:0002880 obsolete Respiratory difficulties
HP:0006829 Severe muscular hypotonia
HP:0011448 Ankle clonus
HP:0003487 Babinski sign
HP:0002378 Hand tremor
HP:0002747 Respiratory insufficiency due to muscle weakness
HP:0002579 Gastrointestinal dysmotility
HP:0001041 Facial erythema
HP:0040180 Hyperkeratosis pilaris
HP:0001382 Joint hypermobility
HP:0003722 Neck flexor weakness
HP:0003323 Progressive muscle weakness
HP:0002380 Fasciculations
HP:0012785 Flexion contracture of finger
HP:0007936 Restrictive external ophthalmoplegia
HP:0030319 Weakness of facial musculature
HP:0008936 Muscular hypotonia of the trunk
HP:0030230 Central core regions in muscle fibers
HP:0011471 Gastrostomy tube feeding in infancy
HP:0001290 Generalized hypotonia
HP:0002421 Poor head control
HP:0010301 Spinal dysraphism
HP:0004303 Abnormal muscle fiber morphology
HP:0009046 Difficulty running
HP:0003715 Myofibrillar myopathy
HP:0000467 Neck muscle weakness
HP:0001999 Abnormal facial shape
HP:0002751 Kyphoscoliosis
HP:0030223 Perseveration
HP:0002344 Progressive neurologic deterioration
HP:0002522 Areflexia of lower limbs
HP:0003805 Rimmed vacuoles
HP:0005781 Contractures of the large joints
HP:0040083 Toe walking
HP:0003749 Pelvic girdle muscle weakness
HP:0012444 Brain atrophy
HP:0003738 Exercise-induced myalgia
HP:0003756 Skeletal myopathy
HP:0002492 Morphological abnormality of the corticospinal tract
HP:0100302 Muscle fiber tubuloreticular inclusions
HP:0006817 Aplasia/Hypoplasia of the cerebellar vermis
HP:0003473 Fatigable weakness
HP:0002077 Migraine with aura
HP:0100559 Lower limb asymmetry
HP:0002079 Hypoplasia of the corpus callosum
HP:0002804 Arthrogryposis multiplex congenita
HP:0011623 Muscular ventricular septal defect
HP:0002191 Progressive spasticity
HP:0003390 Sensory axonal neuropathy
HP:0006986 Upper limb spasticity
HP:0002464 Spastic dysarthria
HP:0001308 Tongue fasciculations
HP:0007010 Poor fine motor coordination
HP:0003737 Mitochondrial myopathy
HP:0008012 obsolete Congenital myopia
HP:0008872 Feeding difficulties in infancy
HP:0005750 Contractures of the joints of the lower limbs
HP:0009067 Progressive spinal muscular atrophy
HP:0001623 Breech presentation
HP:0001374 Congenital hip dislocation
HP:0002359 Frequent falls
HP:0003803 Type 1 muscle fiber predominance
HP:0011410 Caesarian section
HP:0008947 Infantile muscular hypotonia
HP:0100501 Recurrent bronchiolitis
HP:0003789 Minicore myopathy
HP:0000544 External ophthalmoplegia
HP:0001605 Vocal cord paralysis
HP:0003712 Skeletal muscle hypertrophy
HP:0012507 Weakness of orbicularis oculi muscle
HP:0009816 Lower limb undergrowth
HP:0008935 Generalized neonatal hypotonia
HP:0003484 Upper limb muscle weakness
HP:0008331 Elevated creatine kinase after exercise
HP:0001315 Reduced tendon reflexes
HP:0012473 Tongue atrophy
HP:0003273 Hip contracture
HP:0006380 Knee flexion contracture
HP:0003752 Episodic flaccid weakness
HP:0100298 Motheaten muscle fibers
HP:0003693 Distal amyotrophy
HP:0002167 Neurological speech impairment
HP:0003388 Easy fatigability
HP:0001348 Brisk reflexes
HP:0003445 EMG: neuropathic changes
HP:0009063 Progressive distal muscle weakness
HP:0003720 Generalized muscle hypertrophy
HP:0002493 Upper motor neuron dysfunction
HP:0012448 Delayed myelination
HP:0001338 Partial agenesis of the corpus callosum
HP:0006879 Pontocerebellar atrophy
HP:0200101 Decreased/absent ankle reflexes
HP:0009020 Exercise-induced muscle fatigue
HP:0002067 Bradykinesia
HP:0012751 Abnormal basal ganglia MRI signal intensity
HP:0003355 Aminoaciduria
HP:0012450 Chronic constipation
HP:0011834 Moyamoya phenomenon
HP:0001297 Stroke
HP:0200049 Upper limb hypertonia
HP:0008981 Calf muscle hypertrophy
HP:0006785 Limb-girdle muscular dystrophy
HP:0006957 Loss of ability to walk
HP:0030098 Reduced muscle dystrophin expression
HP:0030115 Reduced muscle fiber dysferlin
HP:0002058 Myopathic facies
HP:0007858 Chorioretinal lacunae
HP:0006657 Hypoplasia of first ribs
HP:0007165 Periventricular heterotopia
HP:0009779 3-4 toe syndactyly
HP:0010665 Bilateral coxa valga
HP:0007598 Bilateral single transverse palmar creases
HP:0006101 Finger syndactyly
HP:0010511 Long toe
HP:0002370 Poor coordination
HP:0000480 Retinal coloboma
HP:0001770 Toe syndactyly
HP:0010851 EEG with burst suppression
HP:0002791 Hypoventilation
HP:0040075 Hypopituitarism
HP:0012506 Small pituitary gland
HP:0000538 Pseudopapilledema
HP:0012717 Severe conductive hearing impairment
HP:0001370 Rheumatoid arthritis
HP:0000016 Urinary retention
HP:0012537 Food intolerance
HP:0011297 Abnormal digit morphology
HP:0001273 Abnormal corpus callosum morphology
HP:0030148 Heart murmur
HP:0045018 Partial duplication of eyebrows
HP:0008998 Pectoralis hypoplasia
HP:0001707 Abnormal right ventricle morphology
HP:0001540 Diastasis recti
HP:0100693 Iridodonesis
HP:0002265 Large fleshy ears
HP:0001132 Lens subluxation
HP:0004927 Pulmonary artery dilatation
HP:0005619 Thoracolumbar kyphosis
HP:0008619 Bilateral sensorineural hearing impairment
HP:0001045 Vitiligo
HP:0009124 Abnormal adipose tissue morphology
HP:0002979 Bowing of the legs
HP:0000455 Broad nasal tip
HP:0001007 Hirsutism
HP:0010314 Premature thelarche
HP:0000075 Renal duplication
HP:0000368 Low-set, posteriorly rotated ears
HP:0001052 Nevus flammeus
HP:0200048 Cyanotic episode
HP:0001902 Giant platelets
HP:0030043 Hip subluxation
HP:0002938 Lumbar hyperlordosis
HP:0030084 Clinodactyly
HP:0005560 Imbalanced hemoglobin synthesis
HP:0001539 Omphalocele
HP:0009778 Short thumb
HP:0002277 Horner syndrome
HP:0011701 Multifocal atrial tachycardia
HP:0005274 Prominent nasal tip
HP:0001262 Excessive daytime somnolence
HP:0001285 Spastic tetraparesis
HP:0012171 Stereotypical hand wringing
HP:0002518 Abnormality of the periventricular white matter
HP:0005692 Joint hyperflexibility
HP:0007440 Generalized hyperpigmentation
HP:0001805 Onychogryposis
HP:0011945 Bronchiolitis obliterans organizing pneumonia
HP:0003763 Bruxism
HP:0010500 Hyperextensibility of the knee
HP:0040115 Abnormality of the Eustachian tube
HP:0008751 Laryngeal cleft
HP:0000403 Recurrent otitis media
HP:0001787 Abnormal delivery
HP:0002571 Achalasia
HP:0002615 Hypotension
HP:0003550 Predominantly lower limb lymphedema
HP:0030363 Primary Caesarian section
HP:0001727 Thromboembolic stroke
HP:0100603 Toxemia of pregnancy
HP:0010836 Abnormal circulating copper concentration
HP:0000356 Abnormality of the outer ear
HP:0002197 Generalized-onset seizure
HP:0011436 Abnormal maternal serum screening
HP:0003517 Birth length greater than 97th percentile
HP:0003561 Birth length less than 3rd percentile
HP:0012188 Hyperemesis gravidarum
HP:0010519 Increased fetal movement
HP:0030244 Maternal fever in pregnancy
HP:0008071 Maternal hypertension
HP:0100622 Maternal seizure
HP:0011438 Maternal teratogenic exposure
HP:0001998 Neonatal hypoglycemia
HP:0040187 Neonatal sepsis
HP:0002033 Poor suck
HP:0006579 Prolonged neonatal jaundice
HP:0001724 obsolete Aortic dilatation
HP:0010621 Cutaneous syndactyly of toes
HP:0001880 Eosinophilia
HP:0000162 Glossoptosis
HP:0100578 Lipoatrophy
HP:0002562 Low-set nipples
HP:0012893 Neck muscle hypertrophy
HP:0001027 Soft, doughy skin
HP:0100738 Abnormal eating behavior
HP:0007328 Impaired pain sensation
HP:0002878 Respiratory failure
HP:0001776 Bilateral talipes equinovarus
HP:0001360 Holoprosencephaly
HP:0001973 Autoimmune thrombocytopenia
HP:0100749 Chest pain
HP:0012531 Pain
HP:0007585 Skin fragility with non-scarring blistering
HP:0002108 Spontaneous pneumothorax
HP:0006562 Viral hepatitis
HP:0012647 Abnormal inflammatory response
HP:0012088 Abnormal urinary odor
HP:0011458 Abdominal symptom
HP:0002829 Arthralgia
HP:0010783 Erythema
HP:0010307 Stridor
HP:0001269 Hemiparesis
HP:0006532 Recurrent pneumonia
HP:0002580 Volvulus
HP:0012387 Bronchitis
HP:0001266 Choreoathetosis
HP:0001531 Failure to thrive in infancy
HP:0011470 Nasogastric tube feeding in infancy
HP:0001361 Nystagmus-induced head nodding
HP:0001997 Gout
HP:0000965 Cutis marmorata
HP:0010316 Ebstein anomaly of the tricuspid valve
HP:0010543 Opsoclonus
HP:0007704 Paroxysmal involuntary eye movements
HP:0030364 Secondary Caesarian section
HP:0007738 Uncontrolled eye movements
HP:0030366 Delivery by Odon device
HP:0011411 Forceps delivery
HP:0030369 Induced vaginal delivery
HP:0005268 Spontaneous abortion
HP:0030365 Vaginal birth after Caesarian
HP:0011412 Ventouse delivery
HP:0002572 Episodic vomiting
HP:0030350 Erythematous papule
HP:0001386 Joint swelling
HP:0000147 Polycystic ovaries
HP:0012412 Premature adrenarche
HP:0004411 Deviated nasal septum
HP:0040183 Encopresis
HP:0100507 Reduced blood folate concentration
HP:0007011 Fourth cranial nerve palsy
HP:0000375 Abnormal cochlea morphology
HP:0009911 Abnormal temporal bone morphology
HP:0000081 Duplicated collecting system
HP:0006894 Hypoplastic olfactory lobes
HP:0011380 Morphological abnormality of the semicircular canal
HP:0000110 Renal dysplasia
HP:0030025 Auricular pit
HP:0010044 Short 4th metacarpal
HP:0010047 Short 5th metacarpal
HP:0000201 Pierre-Robin sequence
HP:0100837 Atrophodermia vermiculata
HP:0002673 Coxa valga
HP:0001476 Delayed closure of the anterior fontanelle
HP:0011069 Increased number of teeth
HP:0009879 Simplified gyral pattern
HP:0006315 Single median maxillary incisor
HP:0001194 Abnormalities of placenta or umbilical cord
HP:0100767 Abnormal placenta morphology
HP:0006543 Cardiorespiratory arrest
HP:0003074 Hyperglycemia
HP:0000842 Hyperinsulinemia
HP:0011951 Aspiration pneumonia
HP:0006528 Chronic lung disease
HP:0002383 Encephalitis
HP:0000388 Otitis media
HP:0002530 Axial dystonia
HP:0002780 Bronchomalacia
HP:0008755 Laryngotracheomalacia
HP:0000308 Microretrognathia
HP:0002786 Tracheobronchomalacia
HP:0012389 Appendicular hypotonia
HP:0011323 Cleft of chin
HP:0000417 Slender nose
HP:0001863 Toe clinodactyly
HP:0008386 Aplasia/Hypoplasia of the nails
HP:0006989 Dysplastic corpus callosum
HP:0100954 Open operculum
HP:0004482 Relative macrocephaly
HP:3000033 Abnormal nasopharyngeal adenoid morphology
HP:0009062 Infantile axial hypotonia
HP:0002189 obsolete Excessive daytime sleepiness
HP:0002141 Gait imbalance
HP:0012734 Ketotic hypoglycemia
HP:0005968 Temperature instability
HP:0012538 Gluten intolerance
HP:0000979 Purpura
HP:0001988 Recurrent hypoglycemia
HP:0001488 Bilateral ptosis
HP:0011229 Broad eyebrow
HP:0004440 Coronal craniosynostosis
HP:0004453 Overfolding of the superior helices
HP:0012547 Abnormal involuntary eye movements
HP:0100814 Blue nevus
HP:0010751 Dimple chin
HP:0007087 obsolete Involuntary jerking movements
HP:0012498 Nuchal cord
HP:0002472 Small cerebral cortex
HP:0100307 Cerebellar hemisphere hypoplasia
HP:0002151 Increased serum lactate
HP:0001698 Pericardial effusion
HP:0006903 Congenital peripheral neuropathy
HP:0006895 Lower limb hypertonia
HP:0002744 Bilateral cleft lip and palate
HP:0010664 Fusion of the left and right thalami
HP:0000327 Hypoplasia of the maxilla
HP:0000474 Thickened nuchal skin fold
HP:0000105 Enlarged kidney
HP:0000113 Polycystic kidney dysplasia
HP:0000104 Renal agenesis
HP:0001362 Calvarial skull defect
HP:0008245 Pituitary hypothyroidism
HP:0001552 Barrel-shaped chest
HP:0006297 Hypoplasia of dental enamel
HP:0100023 Recurrent hand flapping
HP:0005518 Increased mean corpuscular volume
HP:0012418 Hypoxemia
HP:0100259 Postaxial polydactyly
HP:0010814 Abnormal position of hair whorl
HP:0003764 Nevus
HP:0000445 Wide nose
HP:0010677 Enuresis nocturna
HP:0001510 Growth delay
HP:0012428 Prominent calcaneus
HP:0012471 Thick vermilion border
HP:0007110 Central hypoventilation
HP:0010614 Fibroma
HP:0001034 Hypermelanotic macule
HP:0011365 Patchy hypopigmentation of hair
HP:0001920 Renal artery stenosis
HP:0002828 Multiple joint contractures
HP:0002144 Tethered cord
HP:0010964 Abnormal circulating long-chain fatty-acid concentration
HP:0010536 Central sleep apnea
HP:0011262 Crimped helix
HP:0040079 Irregular dentition
HP:0011481 Abnormal lacrimal duct morphology
HP:0000220 Velopharyngeal insufficiency
HP:0002153 Hyperkalemia
HP:0002148 Hypophosphatemia
HP:0012621 Persistent cloaca
HP:0000867 Secondary hyperparathyroidism
HP:0003762 Uterus didelphys
HP:0100512 Low levels of vitamin D
HP:0012156 Hemophagocytosis
HP:0008209 Premature ovarian insufficiency
HP:0004349 Reduced bone mineral density
HP:0001924 Sideroblastic anemia
HP:0011703 Sinus tachycardia
HP:0010609 Skin tags
HP:0002725 Systemic lupus erythematosus
HP:0003193 Allergic rhinitis
HP:0006896 Hypnopompic hallucinations
HP:0002524 Cataplexy
HP:0005227 Adenomatous colonic polyposis
HP:0012173 Orthostatic tachycardia
HP:0001271 Polyneuropathy
HP:0009120 Aplasia/Hypoplasia involving the sinuses
HP:0000625 Eyelid coloboma
HP:0009754 Fibrous syngnathia
HP:0012478 Temporomandibular joint ankylosis
HP:0001233 2-3 finger syndactyly
HP:0000811 Abnormal external genitalia
HP:0005120 Abnormal cardiac atrium morphology
HP:0008388 Abnormal toenail morphology
HP:0011467 Absent gallbladder
HP:0010760 Absent toe
HP:0001545 Anteriorly placed anus
HP:0001640 Cardiomegaly
HP:0002990 Fibular aplasia
HP:0004443 Lambdoidal craniosynostosis
HP:0008569 Microtia, second degree
HP:0006277 Pancreatic hyperplasia
HP:0010445 Primum atrial septal defect
HP:0011640 Single coronary artery origin
HP:0011608 Type II truncus arteriosus
HP:0011327 Posterior plagiocephaly
HP:0007655 Eversion of lateral third of lower eyelids
HP:0010747 Medial flaring of the eyebrow
HP:0005957 Breathing dysregulation
HP:0000992 Cutaneous photosensitivity
HP:0011995 Atrial septal dilatation
HP:0000377 Abnormality of the pinna
HP:0011266 Microtia, first degree
HP:0012650 Perisylvian polymicrogyria
HP:0004970 Ascending tubular aorta aneurysm
HP:0008348 Decreased circulating IgG2 level
HP:0012115 Hepatitis
HP:0006979 Sleep-wake cycle disturbance
HP:0008587 Mild neurosensory hearing impairment
HP:0006097 3-4 finger syndactyly
HP:0005263 Gastritis
HP:0200043 Verrucae
HP:0009600 Flexion contracture of thumb
HP:0010818 Generalized tonic seizure
HP:0002599 Head titubation
HP:0002090 Pneumonia
HP:0030423 Splenic cyst
HP:0030187 Titubation
HP:0002375 Hypokinesia
HP:0007166 Paroxysmal dyskinesia
HP:0003077 Hyperlipidemia
HP:0000017 Nocturia
HP:0100555 Asymmetric growth
HP:0011847 Giant cell tumor of bone
HP:0000112 Nephropathy
HP:0000246 Sinusitis
HP:0001012 Multiple lipomas
HP:0000851 Congenital hypothyroidism
HP:0002345 Action tremor
HP:0002677 Small foramen magnum
HP:0011947 Respiratory tract infection
HP:0012151 Hemothorax
HP:0005988 Congenital muscular torticollis
HP:0002329 Drowsiness
HP:0012395 Seasonal allergy
HP:0011679 Tetralogy of Fallot with pulmonary stenosis
HP:0001864 Clinodactyly of the 5th toe
HP:0006934 Congenital nystagmus
HP:0100355 Contractures of the distal interphalangeal joint of the 5th toe
HP:0007894 Hypopigmentation of the fundus
HP:0012377 Hemianopia
HP:0002354 Memory impairment
HP:0000872 Hashimoto thyroiditis
HP:0002519 Hypnagogic hallucinations
HP:0010647 Abnormal elasticity of skin
HP:0002592 Gastric ulcer
HP:0004938 Tortuous cerebral arteries
HP:0004948 Vascular tortuosity
HP:0002516 Increased intracranial pressure
HP:0006460 Increased laxity of ankles
HP:0002317 Unsteady gait
HP:0000182 Movement abnormality of the tongue
HP:0009887 Abnormality of hair pigmentation
HP:0005824 Clinodactyly of the 2nd toe
HP:0002212 Curly hair
HP:0009803 Short phalanx of finger
HP:0000572 Visual loss
HP:0005216 Impaired mastication
HP:0000619 Impaired convergence
HP:0002403 Positive Romberg sign
HP:0008744 Abnormal aryepiglottic fold morphology
HP:0002374 Diminished movement
HP:0008277 Abnormal blood zinc concentration
HP:0012781 Mid-frequency hearing loss
HP:0100758 Gangrene
HP:0003256 Abnormality of the coagulation cascade
HP:0004387 Enterocolitis
HP:0011029 Internal hemorrhage
HP:0011649 Patent ductus arteriosus after premature birth
HP:0012050 Anasarca
HP:0001683 Ectopia cordis
HP:0011682 Perimembranous ventricular septal defect
HP:0010624 Aplastic/hypoplastic toenail
HP:0002705 High, narrow palate
HP:0011340 Incomplete cleft of the upper lip
HP:0011613 Interrupted aortic arch type B
HP:0006167 Prominent proximal interphalangeal joints
HP:0002918 Hypermagnesemia
HP:0011937 Hypoplastic fifth toenail
HP:0001067 Neurofibromas
HP:0011403 Abnormal umbilical cord blood vessels
HP:0003316 Butterfly vertebrae
HP:0002247 Duodenal atresia
HP:0008439 Lumbar hemivertebrae
HP:0011599 Mesocardia
HP:0008467 Thoracic hemivertebrae
HP:0004626 Lumbar scoliosis
HP:0006808 Cerebral hypomyelination
HP:0002926 Abnormality of thyroid physiology
HP:0007970 Congenital ptosis
" + }, + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "0.1.0", + "name": "HPO", + "title": "Human Phenotype Ontology", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Please see license of HPO at http://www.human-phenotype-ontology.org", + "valueSet": "http://fhir.ncpi-project-forge.io/ValueSet/phenotype-codes", + "hierarchyMeaning": "is-a", + "compositional": false, + "versionNeeded": false, + "content": "complete", + "count": 1880, + "filter": [ + { + "code": "root", + "operator": [ + "=" + ], + "value": "True or false." + }, + { + "code": "deprecated", + "operator": [ + "=" + ], + "value": "True or false." + }, + { + "code": "imported", + "operator": [ + "=" + ], + "value": "True or false" + } + ], + "property": [ + { + "code": "parent", + "description": "Parent codes.", + "type": "code" + }, + { + "code": "imported", + "description": "Indicates if the concept is imported from another code system.", + "type": "boolean" + }, + { + "code": "root", + "description": "Indicates if this concept is a root concept (i.e. Thing is equivalent or a direct parent)", + "type": "boolean" + }, + { + "code": "deprecated", + "description": "Indicates if this concept is deprecated.", + "type": "boolean" + } + ], + "concept": [ + { + "code": "HP:0000365", + "display": "Hearing impairment" + }, + { + "code": "HP:0002564", + "display": "obsolete Malformation of the heart and great vessels" + }, + { + "code": "HP:0001028", + "display": "Hemangioma" + }, + { + "code": "HP:0000476", + "display": "Cystic hygroma" + }, + { + "code": "HP:0000568", + "display": "Microphthalmia" + }, + { + "code": "HP:0000518", + "display": "Cataract" + }, + { + "code": "HP:0000612", + "display": "Iris coloboma" + }, + { + "code": "HP:0000567", + "display": "Chorioretinal coloboma" + }, + { + "code": "HP:0000316", + "display": "Hypertelorism" + }, + { + "code": "HP:0000482", + "display": "Microcornea" + }, + { + "code": "HP:0000588", + "display": "Optic nerve coloboma" + }, + { + "code": "HP:0004426", + "display": "Abnormality of the cheek" + }, + { + "code": "HP:0009125", + "display": "Lipodystrophy" + }, + { + "code": "HP:0002023", + "display": "Anal atresia" + }, + { + "code": "HP:0003468", + "display": "Abnormal vertebral morphology" + }, + { + "code": "HP:0000545", + "display": "Myopia" + }, + { + "code": "HP:0000122", + "display": "Unilateral renal agenesis" + }, + { + "code": "HP:0002143", + "display": "Abnormality of the spinal cord" + }, + { + "code": "HP:0003508", + "display": "Proportionate short stature" + }, + { + "code": "HP:0000271", + "display": "Abnormality of the face" + }, + { + "code": "HP:0000637", + "display": "Long palpebral fissure" + }, + { + "code": "HP:0000492", + "display": "Abnormal eyelid morphology" + }, + { + "code": "HP:0000389", + "display": "Chronic otitis media" + }, + { + "code": "HP:0000400", + "display": "Macrotia" + }, + { + "code": "HP:0000405", + "display": "Conductive hearing impairment" + }, + { + "code": "HP:0012712", + "display": "Mild hearing impairment" + }, + { + "code": "HP:0005280", + "display": "Depressed nasal bridge" + }, + { + "code": "HP:0000431", + "display": "Wide nasal bridge" + }, + { + "code": "HP:0000319", + "display": "Smooth philtrum" + }, + { + "code": "HP:0000175", + "display": "Cleft palate" + }, + { + "code": "HP:0001611", + "display": "Nasal speech" + }, + { + "code": "HP:0002099", + "display": "Asthma" + }, + { + "code": "HP:0001397", + "display": "Hepatic steatosis" + }, + { + "code": "HP:0001081", + "display": "Cholelithiasis" + }, + { + "code": "HP:0002650", + "display": "Scoliosis" + }, + { + "code": "HP:0001212", + "display": "Prominent fingertip pads" + }, + { + "code": "HP:0001328", + "display": "Specific learning disability" + }, + { + "code": "HP:0000824", + "display": "Growth hormone deficiency" + }, + { + "code": "HP:0002607", + "display": "Bowel incontinence" + }, + { + "code": "HP:0100731", + "display": "Transverse facial cleft" + }, + { + "code": "HP:0000528", + "display": "Anophthalmia" + }, + { + "code": "HP:0000601", + "display": "Hypotelorism" + }, + { + "code": "HP:0000369", + "display": "Low-set ears" + }, + { + "code": "HP:0001274", + "display": "Agenesis of corpus callosum" + }, + { + "code": "HP:0002084", + "display": "Encephalocele" + }, + { + "code": "HP:0007033", + "display": "Cerebellar dysplasia" + }, + { + "code": "HP:0100336", + "display": "Bilateral cleft lip" + }, + { + "code": "HP:0100337", + "display": "Bilateral cleft palate" + }, + { + "code": "HP:0001511", + "display": "Intrauterine growth retardation" + }, + { + "code": "HP:0011451", + "display": "Congenital microcephaly" + }, + { + "code": "HP:0000324", + "display": "Facial asymmetry" + }, + { + "code": "HP:0000581", + "display": "Blepharophimosis" + }, + { + "code": "HP:0000508", + "display": "Ptosis" + }, + { + "code": "HP:0008551", + "display": "Microtia" + }, + { + "code": "HP:0001631", + "display": "Atrial septal defect" + }, + { + "code": "HP:0000085", + "display": "Horseshoe kidney" + }, + { + "code": "HP:0011927", + "display": "Short digit" + }, + { + "code": "HP:0001156", + "display": "Brachydactyly" + }, + { + "code": "HP:0002066", + "display": "Gait ataxia" + }, + { + "code": "HP:0001250", + "display": "Seizure" + }, + { + "code": "HP:0001263", + "display": "Global developmental delay" + }, + { + "code": "HP:0001562", + "display": "Oligohydramnios" + }, + { + "code": "HP:0001195", + "display": "Single umbilical artery" + }, + { + "code": "HP:0006349", + "display": "Agenesis of permanent teeth" + }, + { + "code": "HP:0000668", + "display": "Hypodontia" + }, + { + "code": "HP:0000677", + "display": "Oligodontia" + }, + { + "code": "HP:0001252", + "display": "Muscular hypotonia" + }, + { + "code": "HP:0003429", + "display": "CNS hypomyelination" + }, + { + "code": "HP:0010864", + "display": "Intellectual disability, severe" + }, + { + "code": "HP:0004325", + "display": "Decreased body weight" + }, + { + "code": "HP:0000666", + "display": "Horizontal nystagmus" + }, + { + "code": "HP:0000218", + "display": "High palate" + }, + { + "code": "HP:0010809", + "display": "Broad uvula" + }, + { + "code": "HP:0000767", + "display": "Pectus excavatum" + }, + { + "code": "HP:0003691", + "display": "Scapular winging" + }, + { + "code": "HP:0002616", + "display": "Aortic root aneurysm" + }, + { + "code": "HP:0001601", + "display": "Laryngomalacia" + }, + { + "code": "HP:0002021", + "display": "Pyloric stenosis" + }, + { + "code": "HP:0001388", + "display": "Joint laxity" + }, + { + "code": "HP:0001187", + "display": "Hyperextensibility of the finger joints" + }, + { + "code": "HP:0000741", + "display": "Apathy" + }, + { + "code": "HP:0000817", + "display": "Poor eye contact" + }, + { + "code": "HP:0000821", + "display": "Hypothyroidism" + }, + { + "code": "HP:0000002", + "display": "Abnormality of body height" + }, + { + "code": "HP:0000079", + "display": "Abnormality of the urinary system" + }, + { + "code": "HP:0000164", + "display": "Abnormality of the dentition" + }, + { + "code": "HP:0000364", + "display": "Hearing abnormality" + }, + { + "code": "HP:0000366", + "display": "Abnormality of the nose" + }, + { + "code": "HP:0000464", + "display": "Abnormality of the neck" + }, + { + "code": "HP:0000707", + "display": "Abnormality of the nervous system" + }, + { + "code": "HP:0000708", + "display": "Behavioral abnormality" + }, + { + "code": "HP:0000769", + "display": "Abnormality of the breast" + }, + { + "code": "HP:0000772", + "display": "Abnormality of the ribs" + }, + { + "code": "HP:0000775", + "display": "Abnormality of the diaphragm" + }, + { + "code": "HP:0000889", + "display": "Abnormality of the clavicle" + }, + { + "code": "HP:0000925", + "display": "Abnormality of the vertebral column" + }, + { + "code": "HP:0001080", + "display": "Biliary tract abnormality" + }, + { + "code": "HP:0001392", + "display": "Abnormality of the liver" + }, + { + "code": "HP:0001438", + "display": "Abnormal abdomen morphology" + }, + { + "code": "HP:0001608", + "display": "Abnormality of the voice" + }, + { + "code": "HP:0001627", + "display": "Abnormal heart morphology" + }, + { + "code": "HP:0001732", + "display": "Abnormality of the pancreas" + }, + { + "code": "HP:0001739", + "display": "Abnormality of the nasopharynx" + }, + { + "code": "HP:0001743", + "display": "Abnormality of the spleen" + }, + { + "code": "HP:0001760", + "display": "Abnormal foot morphology" + }, + { + "code": "HP:0001871", + "display": "Abnormality of blood and blood-forming tissues" + }, + { + "code": "HP:0002031", + "display": "Abnormal esophagus morphology" + }, + { + "code": "HP:0002244", + "display": "Abnormality of the small intestine" + }, + { + "code": "HP:0002246", + "display": "Abnormality of the duodenum" + }, + { + "code": "HP:0002250", + "display": "Abnormal large intestine morphology" + }, + { + "code": "HP:0002644", + "display": "Abnormality of pelvic girdle bone morphology" + }, + { + "code": "HP:0002664", + "display": "Neoplasm" + }, + { + "code": "HP:0002715", + "display": "Abnormality of the immune system" + }, + { + "code": "HP:0002814", + "display": "Abnormality of the 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"HP:0002986", + "display": "Radial bowing" + }, + { + "code": "HP:0003015", + "display": "Flared metaphysis" + }, + { + "code": "HP:0003025", + "display": "Metaphyseal irregularity" + }, + { + "code": "HP:0003097", + "display": "Short femur" + }, + { + "code": "HP:0003300", + "display": "Ovoid vertebral bodies" + }, + { + "code": "HP:0003307", + "display": "Hyperlordosis" + }, + { + "code": "HP:0004209", + "display": "Clinodactyly of the 5th finger" + }, + { + "code": "HP:0004322", + "display": "Short stature" + }, + { + "code": "HP:0005792", + "display": "Short humerus" + }, + { + "code": "HP:0006248", + "display": "Limited wrist movement" + }, + { + "code": "HP:0000944", + "display": "Abnormality of the metaphysis" + }, + { + "code": "HP:0011921", + "display": "Exudative pleural effusion" + }, + { + "code": "HP:0003043", + "display": "Abnormality of the shoulder" + }, + { + "code": "HP:0000290", + "display": "Abnormality of the forehead" + }, + { + "code": "HP:0005288", + "display": "Abnormality of the nares" + }, + { + "code": "HP:0000234", + "display": "Abnormality of the head" + }, + { + "code": "HP:0004323", + "display": "Abnormality of body weight" + }, + { + "code": "HP:0000483", + "display": "Astigmatism" + }, + { + "code": "HP:0011003", + "display": "High myopia" + }, + { + "code": "HP:0000470", + "display": "Short neck" + }, + { + "code": "HP:0030044", + "display": "Flexion contracture of digit" + }, + { + "code": "HP:0100871", + "display": "Abnormality of the palm" + }, + { + "code": "HP:0004334", + "display": "Dermal atrophy" + }, + { + "code": "HP:0001845", + "display": "Overlapping toe" + }, + { + "code": "HP:0000496", + "display": "Abnormality of eye movement" + }, + { + "code": "HP:0001780", + "display": "Abnormality of toe" + }, + { + "code": "HP:0001626", + "display": "Abnormality of the cardiovascular system" + }, + { + "code": "HP:0002086", + "display": "Abnormality of the respiratory system" + }, + { + "code": "HP:0000818", + "display": "Abnormality of the endocrine system" + }, + { + "code": "HP:0012372", + "display": "Abnormal eye morphology" + }, + { + "code": "HP:0009473", + "display": "Joint contracture of the hand" + }, + { + "code": "HP:0003199", + "display": "Decreased muscle mass" + }, + { + "code": "HP:0003202", + "display": "Skeletal muscle atrophy" + }, + { + "code": "HP:0003551", + "display": "Difficulty climbing stairs" + }, + { + "code": "HP:0002355", + "display": "Difficulty walking" + }, + { + "code": "HP:0003546", + "display": "Exercise intolerance" + }, + { + "code": "HP:0003325", + "display": "Limb-girdle muscle weakness" + }, + { + "code": "HP:0003701", + "display": "Proximal muscle weakness" + }, + { + "code": "HP:0003547", + "display": "Shoulder girdle muscle weakness" + }, + { + "code": "HP:0007340", + "display": "Lower limb muscle weakness" + }, + { + "code": "HP:0002168", + "display": "Scanning speech" + }, + { + "code": "HP:0001265", + "display": "Hyporeflexia" + }, + { + "code": "HP:0001284", + "display": "Areflexia" + }, + { + "code": "HP:0003477", + "display": "Peripheral axonal neuropathy" + }, + { + "code": "HP:0000924", + "display": "Abnormality of the skeletal system" + }, + { + "code": "HP:0001291", + "display": "Abnormal cranial nerve morphology" + }, + { + "code": "HP:0003687", + "display": "Centrally nucleated skeletal muscle fibers" + }, + { + "code": "HP:0001324", + "display": "Muscle weakness" + }, + { + "code": "HP:0002515", + "display": "Waddling gait" + }, + { + "code": "HP:0100280", + "display": "Crohn's disease" + }, + { + "code": "HP:0002631", + "display": "obsolete Dilatation of ascending aorta" + }, + { + "code": "HP:0100026", + "display": "Arteriovenous malformation" + }, + { + "code": "HP:0002637", + "display": "Cerebral ischemia" + }, + { + "code": "HP:0002619", + "display": "Varicose veins" + }, + { + "code": "HP:0001159", + "display": "Syndactyly" + }, + { + "code": "HP:0002069", + "display": "Bilateral tonic-clonic seizure" + }, + { + "code": "HP:0000977", + "display": "Soft skin" + }, + { + "code": "HP:0010648", + "display": "Dermal translucency" + }, + { + "code": "HP:0000978", + "display": "Bruising susceptibility" + }, + { + "code": "HP:0001956", + "display": "Truncal obesity" + }, + { + "code": "HP:0000189", + "display": "Narrow palate" + }, + { + "code": "HP:0000678", + "display": "Dental crowding" + }, + { + "code": "HP:0002870", + "display": "Obstructive sleep apnea" + }, + { + "code": "HP:0001763", + "display": "Pes planus" + }, + { + "code": "HP:0000782", + "display": "Abnormality of the scapula" + }, + { + "code": "HP:0001600", + "display": "Abnormality of the larynx" + }, + { + "code": "HP:0002088", + "display": "Abnormal lung morphology" + }, + { + "code": "HP:0011407", + "display": "Proportionate tall stature" + }, + { + "code": "HP:0000541", + "display": "Retinal detachment" + }, + { + "code": "HP:0001373", + "display": "Joint dislocation" + }, + { + "code": "HP:0000938", + "display": "Osteopenia" + }, + { + "code": "HP:0002942", + "display": "Thoracic kyphosis" + }, + { + "code": "HP:0001840", + "display": "Metatarsus adductus" + }, + { + "code": "HP:0001844", + "display": "Abnormality of the hallux" + }, + { + "code": "HP:0001765", + "display": "Hammertoe" + }, + { + "code": "HP:0000606", + "display": "Abnormality of the periorbital region" + }, + { + "code": "HP:0002757", + "display": "Recurrent fractures" + }, + { + "code": "HP:0000647", + "display": "Sclerocornea" + }, + { + "code": "HP:0001166", + "display": "Arachnodactyly" + }, + { + "code": "HP:0005490", + "display": "Postnatal macrocephaly" + }, + { + "code": "HP:0011363", + "display": "Abnormality of hair growth rate" + }, + { + "code": "HP:0000276", + "display": "Long face" + }, + { + "code": "HP:0000275", + "display": "Narrow face" + }, + { + "code": "HP:0000337", + "display": "Broad forehead" + }, + { + "code": "HP:0002267", + "display": "Exaggerated startle response" + }, + { + "code": "HP:0002187", + "display": "Intellectual disability, profound" + }, + { + "code": "HP:0000728", + "display": "Impaired ability to form peer relationships" + }, + { + "code": "HP:0000733", + "display": "Stereotypy" + }, + { + "code": "HP:0000739", + "display": "Anxiety" + }, + { + "code": "HP:0000929", + "display": "Abnormal skull morphology" + }, + { + "code": "HP:0001965", + "display": "Abnormal scalp morphology" + }, + { + "code": "HP:0100538", + "display": "Abnormality of the supraorbital ridges" + }, + { + "code": "HP:0000309", + "display": "Abnormality of the midface" + }, + { + "code": "HP:0000277", + "display": "Abnormality of the mandible" + }, + { + "code": "HP:0000765", + "display": "Abnormality of the thorax" + }, + { + "code": "HP:0100008", + "display": "Schwannoma" + }, + { + "code": "HP:0030038", + "display": "Enchondroma" + }, + { + "code": "HP:0100777", + "display": "Exostoses" + }, + { + "code": "HP:0011663", + "display": "Right ventricular cardiomyopathy" + }, + { + "code": "HP:0011675", + "display": "Arrhythmia" + }, + { + "code": "HP:0001962", + "display": "Palpitations" + }, + { + "code": "HP:0001279", + "display": "Syncope" + }, + { + "code": "HP:0004756", + "display": "Ventricular tachycardia" + }, + { + "code": "HP:0000252", + "display": "Microcephaly" + }, + { + "code": "HP:0000303", + "display": "Mandibular prognathia" + }, + { + "code": "HP:0000664", + "display": "Synophrys" + }, + { + "code": "HP:0001609", + "display": "Hoarse voice" + }, + { + "code": "HP:0002558", + "display": "Supernumerary nipple" + }, + { + "code": "HP:0001634", + "display": "Mitral valve prolapse" + }, + { + "code": "HP:0000028", + "display": "Cryptorchidism" + }, + { + "code": "HP:0000973", + "display": "Cutis laxa" + }, + { + "code": "HP:0001518", + "display": "Small for gestational age" + }, + { + "code": "HP:0000527", + "display": "Long eyelashes" + }, + { + "code": "HP:0002808", + "display": "Kyphosis" + }, + { + "code": "HP:0000248", + "display": "Brachycephaly" + }, + { + "code": "HP:0000505", + "display": "Visual impairment" + }, + { + "code": "HP:0000512", + "display": "Abnormal electroretinogram" + }, + { + "code": "HP:0000517", + "display": "Abnormality of the lens" + }, + { + "code": "HP:0000529", + "display": "Progressive visual loss" + }, + { + "code": "HP:0000586", + "display": "Shallow orbits" + }, + { + "code": "HP:0000603", + "display": "Central scotoma" + }, + { + "code": "HP:0000939", + "display": "Osteoporosis" + }, + { + "code": "HP:0001377", + "display": "Limited elbow extension" + }, + { + "code": "HP:0001387", + "display": "Joint stiffness" + }, + { + "code": "HP:0001822", + "display": "Hallux valgus" + }, + { + "code": "HP:0002657", + "display": "Spondylometaphyseal dysplasia" + }, + { + "code": "HP:0003026", + "display": "Short long bone" + }, + { + "code": "HP:0006462", + "display": "Generalized bone demineralization" + }, + { + "code": "HP:0008873", + "display": "Disproportionate short-limb short stature" + }, + { + "code": "HP:0008905", + "display": "Rhizomelia" + }, + { + "code": "HP:0008922", + "display": "Childhood-onset short-trunk short stature" + }, + { + "code": "HP:0200020", + "display": "Corneal erosion" + }, + { + "code": "HP:0001172", + "display": "Abnormal thumb morphology" + }, + { + "code": "HP:0002286", + "display": "Fair hair" + }, + { + "code": "HP:0010719", + "display": "Abnormality of hair texture" + }, + { + "code": "HP:0010720", + "display": "Abnormal hair pattern" + }, + { + "code": "HP:0001635", + "display": "Congestive heart failure" + }, + { + "code": "HP:0001644", + "display": "Dilated cardiomyopathy" + }, + { + "code": "HP:0001663", + "display": "Ventricular fibrillation" + }, + { + "code": "HP:0011712", + "display": "Right bundle branch block" + }, + { + "code": "HP:0000272", + "display": "Malar flattening" + }, + { + "code": "HP:0000286", + "display": "Epicanthus" + }, + { + "code": "HP:0000322", + "display": "Short philtrum" + }, + { + "code": "HP:0000463", + "display": "Anteverted nares" + }, + { + "code": "HP:0000494", + "display": "Downslanted palpebral fissures" + }, + { + "code": "HP:0000543", + "display": "Optic disc pallor" + }, + { + "code": "HP:0000699", + "display": "Diastema" + }, + { + "code": "HP:0000773", + "display": "Short ribs" + }, + { + "code": "HP:0000887", + "display": "Cupped ribs" + }, + { + "code": "HP:0000946", + "display": "Hypoplastic ilia" + }, + { + "code": "HP:0000954", + "display": "Single transverse palmar crease" + }, + { + "code": "HP:0001182", + "display": "Tapered finger" + }, + { + "code": "HP:0001537", + "display": "Umbilical hernia" + }, + { + "code": "HP:0002007", + "display": "Frontal bossing" + }, + { + "code": "HP:0002980", + "display": "Femoral bowing" + }, + { + "code": "HP:0002982", + "display": "Tibial bowing" + }, + { + "code": "HP:0003021", + "display": "Metaphyseal cupping" + }, + { + "code": "HP:0005011", + "display": "Mesomelic arm shortening" + }, + { + "code": "HP:0008803", + "display": "obsolete Narrow sacroiliac notch" + }, + { + "code": "HP:0009117", + "display": "Aplasia/Hypoplasia of the maxilla" + }, + { + "code": "HP:0011220", + "display": "Prominent forehead" + }, + { + "code": "HP:0012801", + "display": "Narrow jaw" + }, + { + "code": "HP:0000243", + "display": "Trigonocephaly" + }, + { + "code": "HP:0000358", + "display": "Posteriorly rotated ears" + }, + { + "code": "HP:0000411", + "display": "Protruding ear" + }, + { + "code": "HP:0000646", + "display": "Amblyopia" + }, + { + "code": "HP:0002812", + "display": "Coxa vara" + }, + { + "code": "HP:0002970", + "display": "Genu varum" + }, + { + "code": "HP:0012775", + "display": "Stellate iris" + }, + { + "code": "HP:0000278", + "display": "Retrognathia" + }, + { + "code": "HP:0009796", + "display": "Branchial cyst" + }, + { + "code": "HP:0002474", + "display": "Expressive language delay" + }, + { + "code": "HP:0007018", + "display": "Attention deficit hyperactivity disorder" + }, + { + "code": "HP:0003198", + "display": "Myopathy" + }, + { + "code": "HP:0003324", + "display": "Generalized muscle weakness" + }, + { + "code": "HP:0003552", + "display": "Muscle stiffness" + }, + { + "code": "HP:0003554", + "display": "Type 2 muscle fiber atrophy" + }, + { + "code": "HP:0003557", + "display": "Increased variability in muscle fiber diameter" + }, + { + "code": "HP:0009025", + "display": "Increased connective tissue" + }, + { + "code": "HP:0003635", + "display": "Loss of subcutaneous adipose tissue in limbs" + }, + { + "code": "HP:0002597", + "display": "Abnormality of the vasculature" + }, + { + "code": "HP:0001649", + "display": "Tachycardia" + }, + { + "code": "HP:0001638", + "display": "Cardiomyopathy" + }, + { + "code": "HP:0001654", + "display": "Abnormal heart valve morphology" + }, + { + "code": "HP:0001671", + "display": "Abnormal cardiac septum morphology" + }, + { + "code": "HP:0000103", + "display": "Polyuria" + }, + { + "code": "HP:0000114", + "display": "Proximal tubulopathy" + }, + { + "code": "HP:0001878", 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}, + { + "code": "HP:0011097", + "display": "Epileptic spasm" + }, + { + "code": "HP:0000407", + "display": "Sensorineural hearing impairment" + }, + { + "code": "HP:0000331", + "display": "Short chin" + }, + { + "code": "HP:0000340", + "display": "Sloping forehead" + }, + { + "code": "HP:0000486", + "display": "Strabismus" + }, + { + "code": "HP:0000713", + "display": "Agitation" + }, + { + "code": "HP:0000802", + "display": "Impotence" + }, + { + "code": "HP:0001272", + "display": "Cerebellar atrophy" + }, + { + "code": "HP:0001276", + "display": "Hypertonia" + }, + { + "code": "HP:0001321", + "display": "Cerebellar hypoplasia" + }, + { + "code": "HP:0001322", + "display": "obsolete Brain very small" + }, + { + "code": "HP:0002061", + "display": "Lower limb spasticity" + }, + { + "code": "HP:0002529", + "display": "Neuronal loss in central nervous system" + }, + { + "code": "HP:0002540", + "display": "Inability to walk" + }, + { + "code": "HP:0005484", + "display": "Postnatal 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"display": "Gastroesophageal reflux" + }, + { + "code": "HP:0002027", + "display": "Abdominal pain" + }, + { + "code": "HP:0002718", + "display": "Recurrent bacterial infections" + }, + { + "code": "HP:0002841", + "display": "Recurrent fungal infections" + }, + { + "code": "HP:0004395", + "display": "Malnutrition" + }, + { + "code": "HP:0009830", + "display": "Peripheral neuropathy" + }, + { + "code": "HP:0000126", + "display": "Hydronephrosis" + }, + { + "code": "HP:0000519", + "display": "Developmental cataract" + }, + { + "code": "HP:0000648", + "display": "Optic atrophy" + }, + { + "code": "HP:0001053", + "display": "Hypopigmented skin patches" + }, + { + "code": "HP:0001087", + "display": "Developmental glaucoma" + }, + { + "code": "HP:0002119", + "display": "Ventriculomegaly" + }, + { + "code": "HP:0002280", + "display": "Enlarged cisterna magna" + }, + { + "code": "HP:0003298", + "display": "Spina bifida occulta" + }, + { + "code": "HP:0004467", + "display": "Preauricular pit" + 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"display": "Ventricular septal defect" + }, + { + "code": "HP:0000703", + "display": "Dentinogenesis imperfecta" + }, + { + "code": "HP:0000914", + "display": "Shield chest" + }, + { + "code": "HP:0001500", + "display": "Broad finger" + }, + { + "code": "HP:0003086", + "display": "Acromesomelia" + }, + { + "code": "HP:0003416", + "display": "Spinal canal stenosis" + }, + { + "code": "HP:0002815", + "display": "Abnormality of the knee" + }, + { + "code": "HP:0002992", + "display": "Abnormality of tibia morphology" + }, + { + "code": "HP:0001639", + "display": "Hypertrophic cardiomyopathy" + }, + { + "code": "HP:0003236", + "display": "Elevated serum creatine kinase" + }, + { + "code": "HP:0001369", + "display": "Arthritis" + }, + { + "code": "HP:0003560", + "display": "Muscular dystrophy" + }, + { + "code": "HP:0003974", + "display": "Absent radius" + }, + { + "code": "HP:0002818", + "display": "Abnormality of the radius" + }, + { + "code": "HP:0001561", + "display": "Polyhydramnios" + }, + { + "code": "HP:0002299", + "display": "Brittle hair" + }, + { + "code": "HP:0002208", + "display": "Coarse hair" + }, + { + "code": "HP:0002213", + "display": "Fine hair" + }, + { + "code": "HP:0000522", + "display": "Alacrima" + }, + { + "code": "HP:0100704", + "display": "Cerebral visual impairment" + }, + { + "code": "HP:0012713", + "display": "Moderate hearing impairment" + }, + { + "code": "HP:0002307", + "display": "Drooling" + }, + { + "code": "HP:0002714", + "display": "Downturned corners of mouth" + }, + { + "code": "HP:0000191", + "display": "Accessory oral frenulum" + }, + { + "code": "HP:0000158", + "display": "Macroglossia" + }, + { + "code": "HP:0012020", + "display": "Right aortic arch" + }, + { + "code": "HP:0002104", + "display": "Apnea" + }, + { + "code": "HP:0000598", + "display": "Abnormality of the ear" + }, + { + "code": "HP:0007874", + "display": "Almond-shaped palpebral fissure" + }, + { + "code": "HP:0010804", + "display": "Tented upper lip vermilion" + }, + { + "code": "HP:0000885", + "display": "Broad ribs" + }, + { + "code": "HP:0000768", + "display": "Pectus carinatum" + }, + { + "code": "HP:0001680", + "display": "Coarctation of aorta" + }, + { + "code": "HP:0000687", + "display": "Widely spaced teeth" + }, + { + "code": "HP:0000047", + "display": "Hypospadias" + }, + { + "code": "HP:0001943", + "display": "Hypoglycemia" + }, + { + "code": "HP:0012369", + "display": "Abnormality of malar bones" + }, + { + "code": "HP:0009900", + "display": "Unilateral deafness" + }, + { + "code": "HP:0000023", + "display": "Inguinal hernia" + }, + { + "code": "HP:0000074", + "display": "Ureteropelvic junction obstruction" + }, + { + "code": "HP:0001800", + "display": "Hypoplastic toenails" + }, + { + "code": "HP:0001804", + "display": "Hypoplastic fingernail" + }, + { + "code": "HP:0002949", + "display": "Fused cervical vertebrae" + }, + { + "code": "HP:0008050", + "display": "Abnormality of the palpebral fissures" + }, + { + "code": "HP:0008577", + "display": "Underfolded helix" + }, + { + "code": "HP:0008589", + "display": "Hypoplastic helices" + }, + { + "code": "HP:0010863", + "display": "Receptive language delay" + }, + { + "code": "HP:0002282", + "display": "Gray matter heterotopia" + }, + { + "code": "HP:0002085", + "display": "Occipital encephalocele" + }, + { + "code": "HP:0001057", + "display": "Aplasia cutis congenita" + }, + { + "code": "HP:0000211", + "display": "Trismus" + }, + { + "code": "HP:0008422", + "display": "Vertebral wedging" + }, + { + "code": "HP:0003170", + "display": "Abnormality of the acetabulum" + }, + { + "code": "HP:0003272", + "display": "Abnormality of the hip bone" + }, + { + "code": "HP:0003028", + "display": "Abnormality of the ankles" + }, + { + "code": "HP:0003301", + "display": "Irregular vertebral endplates" + }, + { + "code": "HP:0010508", + "display": "Metatarsus valgus" + }, + { + "code": "HP:0009811", + "display": "Abnormality of the elbow" + }, + { + "code": "HP:0000736", + "display": "Short attention span" + }, + { + "code": "HP:0002912", + "display": "Methylmalonic acidemia" + }, + { + "code": "HP:0001941", + "display": "Acidosis" + }, + { + "code": "HP:0001992", + "display": "Organic aciduria" + }, + { + "code": "HP:0009027", + "display": "Foot dorsiflexor weakness" + }, + { + "code": "HP:0002063", + "display": "Rigidity" + }, + { + "code": "HP:0000384", + "display": "Preauricular skin tag" + }, + { + "code": "HP:0200046", + "display": "Cat cry" + }, + { + "code": "HP:0001357", + "display": "Plagiocephaly" + }, + { + "code": "HP:0000670", + "display": "Carious teeth" + }, + { + "code": "HP:0011090", + "display": "Fused teeth" + }, + { + "code": "HP:0012810", + "display": "Wide nasal base" + }, + { + "code": "HP:0010296", + "display": "Ankyloglossia" + }, + { + "code": "HP:0001636", + "display": "Tetralogy of Fallot" + }, + { + "code": "HP:0001305", + "display": "Dandy-Walker malformation" + }, + { + "code": "HP:0000238", + "display": "Hydrocephalus" + }, + { + "code": "HP:0005469", + "display": "Flat occiput" + }, + { + "code": "HP:0000270", + "display": "Delayed cranial suture closure" + }, + { + "code": "HP:0000239", + "display": "Large fontanelles" + }, + { + "code": "HP:0010537", + "display": "Wide cranial sutures" + }, + { + "code": "HP:0002217", + "display": "Slow-growing hair" + }, + { + "code": "HP:0000587", + "display": "Abnormality of the optic nerve" + }, + { + "code": "HP:0005989", + "display": "Redundant neck skin" + }, + { + "code": "HP:0010775", + "display": "Vascular ring" + }, + { + "code": "HP:0002779", + "display": "Tracheomalacia" + }, + { + "code": "HP:0002827", + "display": "Hip dislocation" + }, + { + "code": "HP:0001302", + "display": "Pachygyria" + }, + { + "code": "HP:0007362", + "display": "Aplasia/Hypoplasia of the brainstem" + }, + { + "code": "HP:0001558", + "display": "Decreased fetal movement" + }, + { + "code": "HP:0010878", + "display": "Fetal cystic hygroma" + }, + { + "code": "HP:0011398", + "display": "Central hypotonia" + }, + { + "code": "HP:0002071", + "display": "Abnormality of extrapyramidal motor function" + }, + { + "code": "HP:0000826", + "display": "Precocious puberty" + }, + { + "code": "HP:0000014", + "display": "Abnormality of the bladder" + }, + { + "code": "HP:0005037", + "display": "Proximal radio-ulnar synostosis" + }, + { + "code": "HP:0100543", + "display": "Cognitive impairment" + }, + { + "code": "HP:0000481", + "display": "Abnormal cornea morphology" + }, + { + "code": "HP:0000076", + "display": "Vesicoureteral reflux" + }, + { + "code": "HP:0000297", + "display": "Facial hypotonia" + }, + { + "code": "HP:0000391", + "display": "Thickened helices" + }, + { + "code": "HP:0001162", + "display": "Postaxial hand polydactyly" + }, + { + "code": "HP:0001385", + "display": "Hip dysplasia" + }, + { + "code": "HP:0002342", + "display": "Intellectual disability, moderate" + }, + { + "code": "HP:0003191", + "display": "Cleft ala nasi" + }, + { + "code": "HP:0009765", + "display": "Low hanging columella" + }, + { + "code": "HP:0010297", + "display": "Bifid tongue" + }, + { + "code": "HP:0011330", + "display": "Metopic synostosis" + }, + { + "code": "HP:0012804", + "display": "Corneal ulceration" + }, + { + "code": "HP:0010485", + "display": "Hyperextensibility at elbow" + }, + { + "code": "HP:0000609", + "display": "Optic nerve hypoplasia" + }, + { + "code": "HP:0001176", + "display": "Large hands" + }, + { + "code": "HP:0004233", + "display": "Advanced ossification of carpal bones" + }, + { + "code": "HP:0100842", + "display": "Septo-optic dysplasia" + }, + { + "code": "HP:0002034", + "display": "Abnormality of the rectum" + }, + { + "code": "HP:0002283", + "display": "Global brain atrophy" + }, + { + "code": "HP:0003115", + "display": "Abnormal EKG" + }, + { + "code": "HP:0002577", + "display": "Abnormal stomach morphology" + }, + { + "code": "HP:0002539", + "display": "Cortical dysplasia" + }, + { + "code": "HP:0006818", + "display": "4-layered lissencephaly" + }, + { + "code": "HP:0000593", + "display": "Abnormal anterior chamber morphology" + }, + { + "code": "HP:0000179", + "display": "Thick lower lip vermilion" + }, + { + "code": "HP:0002002", + "display": "Deep philtrum" + }, + { + "code": "HP:0009931", + "display": "Enlarged naris" + }, + { + "code": "HP:0002948", + "display": "Vertebral fusion" + }, + { + "code": "HP:0002937", + "display": "Hemivertebrae" + }, + { + "code": "HP:0002308", + "display": "Arnold-Chiari malformation" + }, + { + "code": "HP:0011320", + "display": "Unilambdoid synostosis" + }, + { + "code": "HP:0002781", + "display": "Upper airway obstruction" + }, + { + "code": "HP:0001363", + "display": "Craniosynostosis" + }, + { + "code": "HP:0000204", + "display": "Cleft upper lip" + }, + { + "code": "HP:0001738", + "display": "Exocrine pancreatic insufficiency" + }, + { + "code": "HP:0002823", + "display": "Abnormality of femur morphology" + }, + { + "code": "HP:0000823", + "display": "Delayed puberty" + }, + { + "code": "HP:0100279", + "display": "Ulcerative colitis" + }, + { + "code": "HP:0003834", + "display": "Shoulder dislocation" + }, + { + "code": "HP:0001065", + "display": "Striae distensae" + }, + { + "code": "HP:0000448", + "display": "Prominent nose" + }, + { + "code": "HP:0000554", + "display": "Uveitis" + }, + { + "code": "HP:0001006", + "display": "obsolete Hypotrichosis" + }, + { + "code": "HP:0000501", + "display": "Glaucoma" + }, + { + "code": "HP:0000262", + "display": "Turricephaly" + }, + { + "code": "HP:0000729", + "display": "Autistic behavior" + }, + { + "code": "HP:0010800", + "display": "Absent cupid's bow" + }, + { + "code": "HP:0010808", + "display": "Protruding tongue" + }, + { + "code": "HP:0009927", + "display": "Aplasia of the nose" + }, + { + "code": "HP:0100539", + "display": "Periorbital edema" + }, + { + "code": "HP:0000629", + "display": "Periorbital fullness" + }, + { + "code": "HP:0000178", + "display": "Abnormality 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"HP:0012741", + "display": "Unilateral cryptorchidism" + }, + { + "code": "HP:0000036", + "display": "Abnormality of the penis" + }, + { + "code": "HP:0002408", + "display": "Cerebral arteriovenous malformation" + }, + { + "code": "HP:0007457", + "display": "Prominent veins on trunk" + }, + { + "code": "HP:0000378", + "display": "Cupped ear" + }, + { + "code": "HP:0000396", + "display": "Overfolded helix" + }, + { + "code": "HP:0000035", + "display": "Abnormal testis morphology" + }, + { + "code": "HP:0009895", + "display": "Abnormality of the crus of the helix" + }, + { + "code": "HP:0000034", + "display": "Hydrocele testis" + }, + { + "code": "HP:0000722", + "display": "Obsessive-compulsive behavior" + }, + { + "code": "HP:0000845", + "display": "Growth hormone excess" + }, + { + "code": "HP:0100829", + "display": "Galactorrhea" + }, + { + "code": "HP:0001578", + "display": "Increased circulating cortisol level" + }, + { + "code": "HP:0000786", + "display": "Primary amenorrhea" + }, 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"HP:0010628", + "display": "Facial palsy" + }, + { + "code": "HP:0011892", + "display": "Low levels of vitamin K" + }, + { + "code": "HP:0001075", + "display": "Atrophic scars" + }, + { + "code": "HP:0001816", + "display": "Thin nail" + }, + { + "code": "HP:0002216", + "display": "Premature graying of hair" + }, + { + "code": "HP:0003401", + "display": "Paresthesia" + }, + { + "code": "HP:0100134", + "display": "Abnormality of the axillary hair" + }, + { + "code": "HP:0100797", + "display": "Toenail dysplasia" + }, + { + "code": "HP:0010461", + "display": "Abnormality of the male genitalia" + }, + { + "code": "HP:0000044", + "display": "Hypogonadotropic hypogonadism" + }, + { + "code": "HP:0100568", + "display": "Neoplasm of the endocrine system" + }, + { + "code": "HP:0001646", + "display": "Abnormal aortic valve morphology" + }, + { + "code": "HP:0000813", + "display": "Bicornuate uterus" + }, + { + "code": "HP:0004380", + "display": "Aortic valve calcification" + }, + { + "code": 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+ "code": "HP:0003100", + "display": "Slender long bone" + }, + { + "code": "HP:0003275", + "display": "Narrow pelvis bone" + }, + { + "code": "HP:0009891", + "display": "Underdeveloped supraorbital ridges" + }, + { + "code": "HP:0011039", + "display": "Abnormality of the helix" + }, + { + "code": "HP:0008572", + "display": "External ear malformation" + }, + { + "code": "HP:0009738", + "display": "Abnormality of the antihelix" + }, + { + "code": "HP:0011328", + "display": "Abnormality of fontanelles" + }, + { + "code": "HP:0012155", + "display": "Decreased corneal sensation" + }, + { + "code": "HP:0004602", + "display": "Cervical C2/C3 vertebral fusion" + }, + { + "code": "HP:0002997", + "display": "Abnormality of the ulna" + }, + { + "code": "HP:0009777", + "display": "Absent thumb" + }, + { + "code": "HP:0002893", + "display": "Pituitary adenoma" + }, + { + "code": "HP:0040278", + "display": "Prolactinoma" + }, + { + "code": "HP:0001555", + "display": "Asymmetry of the thorax" + }, + { + "code": "HP:0000902", + "display": "Rib fusion" + }, + { + "code": "HP:0002164", + "display": "Nail dysplasia" + }, + { + "code": "HP:0011314", + "display": "Abnormality of long bone morphology" + }, + { + "code": "HP:0002867", + "display": "Abnormality of the ilium" + }, + { + "code": "HP:0000774", + "display": "Narrow chest" + }, + { + "code": "HP:0006482", + "display": "Abnormality of dental morphology" + }, + { + "code": "HP:0004383", + "display": "Hypoplastic left heart" + }, + { + "code": "HP:0002015", + "display": "Dysphagia" + }, + { + "code": "HP:0500093", + "display": "Food allergy" + }, + { + "code": "HP:0001519", + "display": "Disproportionate tall stature" + }, + { + "code": "HP:0003179", + "display": "Protrusio acetabuli" + }, + { + "code": "HP:0007385", + "display": "Aplasia cutis congenita of scalp" + }, + { + "code": "HP:0000716", + "display": "Depressivity" + }, + { + "code": "HP:0012583", + "display": "Unilateral renal hypoplasia" + }, + { + "code": "HP:0000618", 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}, + { + "code": "HP:0005107", + "display": "Abnormal sacrum morphology" + }, + { + "code": "HP:0002025", + "display": "Anal stenosis" + }, + { + "code": "HP:0009099", + "display": "Median cleft palate" + }, + { + "code": "HP:0003212", + "display": "Increased circulating IgE level" + }, + { + "code": "HP:0001319", + "display": "Neonatal hypotonia" + }, + { + "code": "HP:0002659", + "display": "Increased susceptibility to fractures" + }, + { + "code": "HP:0025246", + "display": "Trichilemmal cyst" + }, + { + "code": "HP:0002107", + "display": "Pneumothorax" + }, + { + "code": "HP:0000107", + "display": "Renal cyst" + }, + { + "code": "HP:0001025", + "display": "Urticaria" + }, + { + "code": "HP:0002204", + "display": "Pulmonary embolism" + }, + { + "code": "HP:0001058", + "display": "Poor wound healing" + }, + { + "code": "HP:0003010", + "display": "Prolonged bleeding time" + }, + { + "code": "HP:0100502", + "display": "Vitamin B12 deficiency" + }, + { + "code": "HP:0100510", + "display": "Low levels of vitamin C" + }, + { + "code": "HP:0030976", + "display": "Abnormal factor VIII activity" + }, + { + "code": "HP:0100789", + "display": "Torus palatinus" + }, + { + "code": "HP:0000108", + "display": "Renal corticomedullary cysts" + }, + { + "code": "HP:0000072", + "display": "Hydroureter" + }, + { + "code": "HP:0000019", + "display": "Urinary hesitancy" + }, + { + "code": "HP:0100771", + "display": "Hypoperistalsis" + }, + { + "code": "HP:0000021", + "display": "Megacystis" + }, + { + "code": "HP:0004388", + "display": "Microcolon" + }, + { + "code": "HP:0005247", + "display": "Hypoplasia of the abdominal wall musculature" + }, + { + "code": "HP:0004794", + "display": "Malrotation of small bowel" + }, + { + "code": "HP:0000045", + "display": "Abnormality of the scrotum" + }, + { + "code": "HP:0002236", + "display": "Frontal upsweep of hair" + }, + { + "code": "HP:0000212", + "display": "Gingival overgrowth" + }, + { + "code": "HP:0001808", + "display": "Fragile nails" + }, + { + "code": "HP:0000225", + "display": "Gingival bleeding" + }, + { + "code": "HP:0006009", + "display": "Broad phalanx" + }, + { + "code": "HP:0001837", + "display": "Broad toe" + }, + { + "code": "HP:0001946", + "display": "Ketosis" + }, + { + "code": "HP:0002490", + "display": "Increased CSF lactate" + }, + { + "code": "HP:0002922", + "display": "Increased CSF protein" + }, + { + "code": "HP:0003128", + "display": "Lactic acidosis" + }, + { + "code": "HP:0003111", + "display": "Abnormal blood ion concentration" + }, + { + "code": "HP:0032234", + "display": "Increased circulating creatine kinase MM isoform" + }, + { + "code": "HP:0003348", + "display": "Hyperalaninemia" + }, + { + "code": "HP:0008347", + "display": "Decreased activity of mitochondrial complex IV" + }, + { + "code": "HP:0000326", + "display": "Abnormality of the maxilla" + }, + { + "code": "HP:0010758", + "display": "Abnormality of the premaxilla" + }, + { + "code": "HP:0005681", + "display": "Juvenile rheumatoid arthritis" + }, + { + "code": "HP:0000514", + "display": "Slow saccadic eye movements" + }, + { + "code": "HP:0002788", + "display": "Recurrent upper respiratory tract infections" + }, + { + "code": "HP:0003396", + "display": "Syringomyelia" + }, + { + "code": "HP:0003011", + "display": "Abnormality of the musculature" + }, + { + "code": "HP:0002098", + "display": "Respiratory distress" + }, + { + "code": "HP:0002018", + "display": "Nausea" + }, + { + "code": "HP:0002014", + "display": "Diarrhea" + }, + { + "code": "HP:0025168", + "display": "Left ventricular diastolic dysfunction" + }, + { + "code": "HP:0001679", + "display": "Abnormal aortic morphology" + }, + { + "code": "HP:0000159", + "display": "Abnormal lip morphology" + }, + { + "code": "HP:0011338", + "display": "Abnormality of mouth shape" + }, + { + "code": "HP:0000478", + "display": "Abnormality of the eye" + }, + { + "code": "HP:0000154", + "display": "Wide mouth" + }, + { + "code": "HP:0001513", + "display": "Obesity" + }, + { + "code": "HP:0002475", + "display": "Myelomeningocele" + }, + { + "code": "HP:0003765", + "display": "Psoriasiform dermatitis" + }, + { + "code": "HP:0010289", + "display": "Cleft of alveolar ridge of maxilla" + }, + { + "code": "HP:0003908", + "display": "Corner fracture of metaphysis" + }, + { + "code": "HP:0002190", + "display": "Choroid plexus cyst" + }, + { + "code": "HP:0004370", + "display": "Abnormality of temperature regulation" + }, + { + "code": "HP:0011611", + "display": "Interrupted aortic arch" + }, + { + "code": "HP:0000737", + "display": "Irritability" + }, + { + "code": "HP:0001344", + "display": "Absent speech" + }, + { + "code": "HP:0002376", + "display": "Developmental regression" + }, + { + "code": "HP:0002140", + "display": "Ischemic stroke" + }, + { + "code": "HP:0001287", + "display": "Meningitis" + }, + { + "code": "HP:0002721", + "display": "Immunodeficiency" + }, + { + "code": "HP:0000041", + "display": "Chordee" + }, + { + "code": "HP:0012854", + "display": "Midshaft hypospadias" + }, + { + "code": "HP:0000808", + "display": "Penoscrotal hypospadias" + }, + { + "code": "HP:0000048", + "display": "Bifid scrotum" + }, + { + "code": "HP:0001047", + "display": "Atopic dermatitis" + }, + { + "code": "HP:0001621", + "display": "Weak voice" + }, + { + "code": "HP:0002372", + "display": "Normal interictal EEG" + }, + { + "code": "HP:0012803", + "display": "Anisometropia" + }, + { + "code": "HP:0011386", + "display": "Narrow internal auditory canal" + }, + { + "code": "HP:0012714", + "display": "Severe hearing impairment" + }, + { + "code": "HP:0006485", + "display": "Agenesis of incisor" + }, + { + "code": "HP:0000787", + "display": "Nephrolithiasis" + }, + { + "code": "HP:0011332", + "display": "Hemifacial hypoplasia" + }, + { + "code": "HP:0001909", + "display": "Leukemia" + }, + { + "code": "HP:0004808", + "display": "Acute myeloid leukemia" + }, + { + "code": "HP:0006495", + "display": "Aplasia/Hypoplasia of 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"HP:0009944", + "display": "Partial duplication of thumb phalanx" + }, + { + "code": "HP:0005819", + "display": "Short middle phalanx of finger" + }, + { + "code": "HP:0002110", + "display": "Bronchiectasis" + }, + { + "code": "HP:0001677", + "display": "Coronary artery atherosclerosis" + }, + { + "code": "HP:0001737", + "display": "Pancreatic cysts" + }, + { + "code": "HP:0005113", + "display": "Aortic arch aneurysm" + }, + { + "code": "HP:0003022", + "display": "Hypoplasia of the ulna" + }, + { + "code": "HP:0002205", + "display": "Recurrent respiratory infections" + }, + { + "code": "HP:0001669", + "display": "Transposition of the great arteries" + }, + { + "code": "HP:0001716", + "display": "Wolff-Parkinson-White syndrome" + }, + { + "code": "HP:0002758", + "display": "Osteoarthritis" + }, + { + "code": "HP:0002037", + "display": "Inflammation of the large intestine" + }, + { + "code": "HP:0009892", + "display": "Anotia" + }, + { + "code": "HP:0011331", + "display": "Hemifacial 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"display": "Broad foot" + }, + { + "code": "HP:0010280", + "display": "Stomatitis" + }, + { + "code": "HP:0001288", + "display": "Gait disturbance" + }, + { + "code": "HP:0008330", + "display": "Reduced von Willebrand factor activity" + }, + { + "code": "HP:0001954", + "display": "Recurrent fever" + }, + { + "code": "HP:0004311", + "display": "Abnormal macrophage morphology" + }, + { + "code": "HP:0012539", + "display": "Non-Hodgkin lymphoma" + }, + { + "code": "HP:0002074", + "display": "Increased neuronal autofluorescent lipopigment" + }, + { + "code": "HP:0002973", + "display": "Abnormality of the forearm" + }, + { + "code": "HP:0003203", + "display": "Impaired oxidative burst" + }, + { + "code": "HP:0003027", + "display": "Mesomelia" + }, + { + "code": "HP:0002754", + "display": "Osteomyelitis" + }, + { + "code": "HP:0004431", + "display": "Complement deficiency" + }, + { + "code": "HP:0001258", + "display": "Spastic paraplegia" + }, + { + "code": "HP:0012811", + "display": "Wide 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"display": "Abnormality of the thymus" + }, + { + "code": "HP:0000418", + "display": "Narrow nasal ridge" + }, + { + "code": "HP:0001572", + "display": "Macrodontia" + }, + { + "code": "HP:0002967", + "display": "Cubitus valgus" + }, + { + "code": "HP:0000988", + "display": "Skin rash" + }, + { + "code": "HP:0009733", + "display": "Glioma" + }, + { + "code": "HP:0012452", + "display": "Restless legs" + }, + { + "code": "HP:0100031", + "display": "Neoplasm of the thyroid gland" + }, + { + "code": "HP:0030127", + "display": "Endometriosis" + }, + { + "code": "HP:0000123", + "display": "Nephritis" + }, + { + "code": "HP:0001974", + "display": "Leukocytosis" + }, + { + "code": "HP:0010976", + "display": "B lymphocytopenia" + }, + { + "code": "HP:0000010", + "display": "Recurrent urinary tract infections" + }, + { + "code": "HP:0100807", + "display": "Long fingers" + }, + { + "code": "HP:0000653", + "display": "Sparse eyelashes" + }, + { + "code": "HP:0000171", + "display": "Microglossia" + }, + { + "code": "HP:0002575", + "display": "Tracheoesophageal fistula" + }, + { + "code": "HP:0009933", + "display": "Narrow naris" + }, + { + "code": "HP:0000883", + "display": "Thin ribs" + }, + { + "code": "HP:0000121", + "display": "Nephrocalcinosis" + }, + { + "code": "HP:0001349", + "display": "Facial diplegia" + }, + { + "code": "HP:0012037", + "display": "Pectoralis amyotrophy" + }, + { + "code": "HP:0100560", + "display": "Upper limb asymmetry" + }, + { + "code": "HP:0005684", + "display": "Distal arthrogryposis" + }, + { + "code": "HP:0010722", + "display": "Asymmetry of the ears" + }, + { + "code": "HP:0009380", + "display": "Aplasia of the fingers" + }, + { + "code": "HP:0001657", + "display": "Prolonged QT interval" + }, + { + "code": "HP:0002040", + "display": "Esophageal varix" + }, + { + "code": "HP:0000613", + "display": "Photophobia" + }, + { + "code": "HP:0000561", + "display": "Absent eyelashes" + }, + { + "code": "HP:0002223", + "display": "Absent eyebrow" + }, + { + "code": "HP:0002591", + "display": "Polyphagia" + }, + { + "code": "HP:0002373", + "display": "Febrile seizure (within the age range of 3 months to 6 years)" + }, + { + "code": "HP:0002419", + "display": "Molar tooth sign on MRI" + }, + { + "code": "HP:0001010", + "display": "Hypopigmentation of the skin" + }, + { + "code": "HP:0005772", + "display": "Aplasia/Hypoplasia of the tibia" + }, + { + "code": "HP:0002211", + "display": "White forelock" + }, + { + "code": "HP:0007126", + "display": "Proximal amyotrophy" + }, + { + "code": "HP:0003798", + "display": "Nemaline bodies" + }, + { + "code": "HP:0006533", + "display": "Bronchodysplasia" + }, + { + "code": "HP:0003391", + "display": "Gowers sign" + }, + { + "code": "HP:0000771", + "display": "Gynecomastia" + }, + { + "code": "HP:0100785", + "display": "Insomnia" + }, + { + "code": "HP:0010529", + "display": "Echolalia" + }, + { + "code": "HP:0000363", + "display": "Abnormality of earlobe" + }, + { + "code": "HP:0002612", + "display": "Congenital hepatic fibrosis" + }, + { + "code": "HP:0006721", + "display": "Acute lymphoblastic leukemia" + }, + { + "code": "HP:0001958", + "display": "Nonketotic hypoglycemia" + }, + { + "code": "HP:0003457", + "display": "EMG abnormality" + }, + { + "code": "HP:0010636", + "display": "Schizencephaly" + }, + { + "code": "HP:0005266", + "display": "Intestinal polyp" + }, + { + "code": "HP:0200063", + "display": "Colorectal polyposis" + }, + { + "code": "HP:0001762", + "display": "Talipes equinovarus" + }, + { + "code": "HP:0000056", + "display": "Abnormality of the clitoris" + }, + { + "code": "HP:0008655", + "display": "Aplasia/Hypoplasia of the fallopian tube" + }, + { + "code": "HP:0002072", + "display": "Chorea" + }, + { + "code": "HP:0008734", + "display": "Decreased testicular size" + }, + { + "code": "HP:0002136", + "display": "Broad-based gait" + }, + { + "code": "HP:0010958", + "display": "Bilateral renal agenesis" + }, + { + "code": "HP:0002510", + "display": 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{ + "code": "HP:0010469", + "display": "Absent testis" + }, + { + "code": "HP:0011969", + "display": "Elevated circulating luteinizing hormone level" + }, + { + "code": "HP:0040171", + "display": "Decreased serum testosterone level" + }, + { + "code": "HP:0003251", + "display": "Male infertility" + }, + { + "code": "HP:0009804", + "display": "Reduced number of teeth" + }, + { + "code": "HP:0000548", + "display": "Cone/cone-rod dystrophy" + }, + { + "code": "HP:0000546", + "display": "Retinal degeneration" + }, + { + "code": "HP:0008002", + "display": "Abnormality of macular pigmentation" + }, + { + "code": "HP:0000608", + "display": "Macular degeneration" + }, + { + "code": "HP:0030611", + "display": "Retinal pigment epithelial loss on macular OCT" + }, + { + "code": "HP:0001135", + "display": "Chorioretinal dystrophy" + }, + { + "code": "HP:0030468", + "display": "Abnormal multifocal electroretinogram" + }, + { + "code": "HP:00030532", + "display": "Visual acuity test abnormality" + 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"code": "HP:0007002", + "display": "Motor axonal neuropathy" + }, + { + "code": "HP:0003327", + "display": "Axial muscle weakness" + }, + { + "code": "HP:0003306", + "display": "Spinal rigidity" + }, + { + "code": "HP:0002068", + "display": "Neuromuscular dysphagia" + }, + { + "code": "HP:0001002", + "display": "obsolete Decreased subcutaneous fat" + }, + { + "code": "HP:0002880", + "display": "obsolete Respiratory difficulties" + }, + { + "code": "HP:0006829", + "display": "Severe muscular hypotonia" + }, + { + "code": "HP:0011448", + "display": "Ankle clonus" + }, + { + "code": "HP:0003487", + "display": "Babinski sign" + }, + { + "code": "HP:0002378", + "display": "Hand tremor" + }, + { + "code": "HP:0002747", + "display": "Respiratory insufficiency due to muscle weakness" + }, + { + "code": "HP:0002579", + "display": "Gastrointestinal dysmotility" + }, + { + "code": "HP:0001041", + "display": "Facial erythema" + }, + { + "code": "HP:0040180", + "display": "Hyperkeratosis pilaris" + 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"Exercise-induced myalgia" + }, + { + "code": "HP:0003756", + "display": "Skeletal myopathy" + }, + { + "code": "HP:0002492", + "display": "Morphological abnormality of the corticospinal tract" + }, + { + "code": "HP:0100302", + "display": "Muscle fiber tubuloreticular inclusions" + }, + { + "code": "HP:0006817", + "display": "Aplasia/Hypoplasia of the cerebellar vermis" + }, + { + "code": "HP:0003473", + "display": "Fatigable weakness" + }, + { + "code": "HP:0002077", + "display": "Migraine with aura" + }, + { + "code": "HP:0100559", + "display": "Lower limb asymmetry" + }, + { + "code": "HP:0002079", + "display": "Hypoplasia of the corpus callosum" + }, + { + "code": "HP:0002804", + "display": "Arthrogryposis multiplex congenita" + }, + { + "code": "HP:0011623", + "display": "Muscular ventricular septal defect" + }, + { + "code": "HP:0002191", + "display": "Progressive spasticity" + }, + { + "code": "HP:0003390", + "display": "Sensory axonal neuropathy" + }, + { + "code": 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"display": "Caesarian section" + }, + { + "code": "HP:0008947", + "display": "Infantile muscular hypotonia" + }, + { + "code": "HP:0100501", + "display": "Recurrent bronchiolitis" + }, + { + "code": "HP:0003789", + "display": "Minicore myopathy" + }, + { + "code": "HP:0000544", + "display": "External ophthalmoplegia" + }, + { + "code": "HP:0001605", + "display": "Vocal cord paralysis" + }, + { + "code": "HP:0003712", + "display": "Skeletal muscle hypertrophy" + }, + { + "code": "HP:0012507", + "display": "Weakness of orbicularis oculi muscle" + }, + { + "code": "HP:0009816", + "display": "Lower limb undergrowth" + }, + { + "code": "HP:0008935", + "display": "Generalized neonatal hypotonia" + }, + { + "code": "HP:0003484", + "display": "Upper limb muscle weakness" + }, + { + "code": "HP:0008331", + "display": "Elevated creatine kinase after exercise" + }, + { + "code": "HP:0001315", + "display": "Reduced tendon reflexes" + }, + { + "code": "HP:0012473", + "display": "Tongue atrophy" + }, + { + "code": "HP:0003273", + "display": "Hip contracture" + }, + { + "code": "HP:0006380", + "display": "Knee flexion contracture" + }, + { + "code": "HP:0003752", + "display": "Episodic flaccid weakness" + }, + { + "code": "HP:0100298", + "display": "Motheaten muscle fibers" + }, + { + "code": "HP:0003693", + "display": "Distal amyotrophy" + }, + { + "code": "HP:0002167", + "display": "Neurological speech impairment" + }, + { + "code": "HP:0003388", + "display": "Easy fatigability" + }, + { + "code": "HP:0001348", + "display": "Brisk reflexes" + }, + { + "code": "HP:0003445", + "display": "EMG: neuropathic changes" + }, + { + "code": "HP:0009063", + "display": "Progressive distal muscle weakness" + }, + { + "code": "HP:0003720", + "display": "Generalized muscle hypertrophy" + }, + { + "code": "HP:0002493", + "display": "Upper motor neuron dysfunction" + }, + { + "code": "HP:0012448", + "display": "Delayed myelination" + }, + { + "code": "HP:0001338", + "display": "Partial agenesis 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"display": "Reduced muscle dystrophin expression" + }, + { + "code": "HP:0030115", + "display": "Reduced muscle fiber dysferlin" + }, + { + "code": "HP:0002058", + "display": "Myopathic facies" + }, + { + "code": "HP:0007858", + "display": "Chorioretinal lacunae" + }, + { + "code": "HP:0006657", + "display": "Hypoplasia of first ribs" + }, + { + "code": "HP:0007165", + "display": "Periventricular heterotopia" + }, + { + "code": "HP:0009779", + "display": "3-4 toe syndactyly" + }, + { + "code": "HP:0010665", + "display": "Bilateral coxa valga" + }, + { + "code": "HP:0007598", + "display": "Bilateral single transverse palmar creases" + }, + { + "code": "HP:0006101", + "display": "Finger syndactyly" + }, + { + "code": "HP:0010511", + "display": "Long toe" + }, + { + "code": "HP:0002370", + "display": "Poor coordination" + }, + { + "code": "HP:0000480", + "display": "Retinal coloboma" + }, + { + "code": "HP:0001770", + "display": "Toe syndactyly" + }, + { + "code": "HP:0010851", + "display": "EEG with burst suppression" + }, + { + "code": "HP:0002791", + "display": "Hypoventilation" + }, + { + "code": "HP:0040075", + "display": "Hypopituitarism" + }, + { + "code": "HP:0012506", + "display": "Small pituitary gland" + }, + { + "code": "HP:0000538", + "display": "Pseudopapilledema" + }, + { + "code": "HP:0012717", + "display": "Severe conductive hearing impairment" + }, + { + "code": "HP:0001370", + "display": "Rheumatoid arthritis" + }, + { + "code": "HP:0000016", + "display": "Urinary retention" + }, + { + "code": "HP:0012537", + "display": "Food intolerance" + }, + { + "code": "HP:0011297", + "display": "Abnormal digit morphology" + }, + { + "code": "HP:0001273", + "display": "Abnormal corpus callosum morphology" + }, + { + "code": "HP:0030148", + "display": "Heart murmur" + }, + { + "code": "HP:0045018", + "display": "Partial duplication of eyebrows" + }, + { + "code": "HP:0008998", + "display": "Pectoralis hypoplasia" + }, + { + "code": "HP:0001707", + "display": "Abnormal right ventricle morphology" + }, + { + "code": "HP:0001540", + "display": "Diastasis recti" + }, + { + "code": "HP:0100693", + "display": "Iridodonesis" + }, + { + "code": "HP:0002265", + "display": "Large fleshy ears" + }, + { + "code": "HP:0001132", + "display": "Lens subluxation" + }, + { + "code": "HP:0004927", + "display": "Pulmonary artery dilatation" + }, + { + "code": "HP:0005619", + "display": "Thoracolumbar kyphosis" + }, + { + "code": "HP:0008619", + "display": "Bilateral sensorineural hearing impairment" + }, + { + "code": "HP:0001045", + "display": "Vitiligo" + }, + { + "code": "HP:0009124", + "display": "Abnormal adipose tissue morphology" + }, + { + "code": "HP:0002979", + "display": "Bowing of the legs" + }, + { + "code": "HP:0000455", + "display": "Broad nasal tip" + }, + { + "code": "HP:0001007", + "display": "Hirsutism" + }, + { + "code": "HP:0010314", + "display": "Premature thelarche" + }, + { + "code": "HP:0000075", + "display": "Renal 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"code": "HP:0012412", + "display": "Premature adrenarche" + }, + { + "code": "HP:0004411", + "display": "Deviated nasal septum" + }, + { + "code": "HP:0040183", + "display": "Encopresis" + }, + { + "code": "HP:0100507", + "display": "Reduced blood folate concentration" + }, + { + "code": "HP:0007011", + "display": "Fourth cranial nerve palsy" + }, + { + "code": "HP:0000375", + "display": "Abnormal cochlea morphology" + }, + { + "code": "HP:0009911", + "display": "Abnormal temporal bone morphology" + }, + { + "code": "HP:0000081", + "display": "Duplicated collecting system" + }, + { + "code": "HP:0006894", + "display": "Hypoplastic olfactory lobes" + }, + { + "code": "HP:0011380", + "display": "Morphological abnormality of the semicircular canal" + }, + { + "code": "HP:0000110", + "display": "Renal dysplasia" + }, + { + "code": "HP:0030025", + "display": "Auricular pit" + }, + { + "code": "HP:0010044", + "display": "Short 4th metacarpal" + }, + { + "code": "HP:0010047", + "display": 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"code": "HP:0012547", + "display": "Abnormal involuntary eye movements" + }, + { + "code": "HP:0100814", + "display": "Blue nevus" + }, + { + "code": "HP:0010751", + "display": "Dimple chin" + }, + { + "code": "HP:0007087", + "display": "obsolete Involuntary jerking movements" + }, + { + "code": "HP:0012498", + "display": "Nuchal cord" + }, + { + "code": "HP:0002472", + "display": "Small cerebral cortex" + }, + { + "code": "HP:0100307", + "display": "Cerebellar hemisphere hypoplasia" + }, + { + "code": "HP:0002151", + "display": "Increased serum lactate" + }, + { + "code": "HP:0001698", + "display": "Pericardial effusion" + }, + { + "code": "HP:0006903", + "display": "Congenital peripheral neuropathy" + }, + { + "code": "HP:0006895", + "display": "Lower limb hypertonia" + }, + { + "code": "HP:0002744", + "display": "Bilateral cleft lip and palate" + }, + { + "code": "HP:0010664", + "display": "Fusion of the left and right thalami" + }, + { + "code": "HP:0000327", + "display": "Hypoplasia of the maxilla" + }, + { + "code": "HP:0000474", + "display": "Thickened nuchal skin fold" + }, + { + "code": "HP:0000105", + "display": "Enlarged kidney" + }, + { + "code": "HP:0000113", + "display": "Polycystic kidney dysplasia" + }, + { + "code": "HP:0000104", + "display": "Renal agenesis" + }, + { + "code": "HP:0001362", + "display": "Calvarial skull defect" + }, + { + "code": "HP:0008245", + "display": "Pituitary hypothyroidism" + }, + { + "code": "HP:0001552", + "display": "Barrel-shaped chest" + }, + { + "code": "HP:0006297", + "display": "Hypoplasia of dental enamel" + }, + { + "code": "HP:0100023", + "display": "Recurrent hand flapping" + }, + { + "code": "HP:0005518", + "display": "Increased mean corpuscular volume" + }, + { + "code": "HP:0012418", + "display": "Hypoxemia" + }, + { + "code": "HP:0100259", + "display": "Postaxial polydactyly" + }, + { + "code": "HP:0010814", + "display": "Abnormal position of hair whorl" + }, + { + "code": "HP:0003764", + "display": "Nevus" + }, + { + "code": "HP:0000445", + "display": "Wide nose" + }, + { + "code": "HP:0010677", + "display": "Enuresis nocturna" + }, + { + "code": "HP:0001510", + "display": "Growth delay" + }, + { + "code": "HP:0012428", + "display": "Prominent calcaneus" + }, + { + "code": "HP:0012471", + "display": "Thick vermilion border" + }, + { + "code": "HP:0007110", + "display": "Central hypoventilation" + }, + { + "code": "HP:0010614", + "display": "Fibroma" + }, + { + "code": "HP:0001034", + "display": "Hypermelanotic macule" + }, + { + "code": "HP:0011365", + "display": "Patchy hypopigmentation of hair" + }, + { + "code": "HP:0001920", + "display": "Renal artery stenosis" + }, + { + "code": "HP:0002828", + "display": "Multiple joint contractures" + }, + { + "code": "HP:0002144", + "display": "Tethered cord" + }, + { + "code": "HP:0010964", + "display": "Abnormal circulating long-chain fatty-acid concentration" + }, + { + "code": "HP:0010536", + "display": "Central sleep apnea" + }, + { + "code": "HP:0011262", + "display": "Crimped helix" + }, + { + "code": "HP:0040079", + "display": "Irregular dentition" + }, + { + "code": "HP:0011481", + "display": "Abnormal lacrimal duct morphology" + }, + { + "code": "HP:0000220", + "display": "Velopharyngeal insufficiency" + }, + { + "code": "HP:0002153", + "display": "Hyperkalemia" + }, + { + "code": "HP:0002148", + "display": "Hypophosphatemia" + }, + { + "code": "HP:0012621", + "display": "Persistent cloaca" + }, + { + "code": "HP:0000867", + "display": "Secondary hyperparathyroidism" + }, + { + "code": "HP:0003762", + "display": "Uterus didelphys" + }, + { + "code": "HP:0100512", + "display": "Low levels of vitamin D" + }, + { + "code": "HP:0012156", + "display": "Hemophagocytosis" + }, + { + "code": "HP:0008209", + "display": "Premature ovarian insufficiency" + }, + { + "code": "HP:0004349", + "display": "Reduced bone mineral density" + }, + { + "code": "HP:0001924", + "display": "Sideroblastic anemia" + }, + { + "code": "HP:0011703", + "display": "Sinus tachycardia" + }, + { + "code": "HP:0010609", + "display": "Skin tags" + }, + { + "code": "HP:0002725", + "display": "Systemic lupus erythematosus" + }, + { + "code": "HP:0003193", + "display": "Allergic rhinitis" + }, + { + "code": "HP:0006896", + "display": "Hypnopompic hallucinations" + }, + { + "code": "HP:0002524", + "display": "Cataplexy" + }, + { + "code": "HP:0005227", + "display": "Adenomatous colonic polyposis" + }, + { + "code": "HP:0012173", + "display": "Orthostatic tachycardia" + }, + { + "code": "HP:0001271", + "display": "Polyneuropathy" + }, + { + "code": "HP:0009120", + "display": "Aplasia/Hypoplasia involving the sinuses" + }, + { + "code": "HP:0000625", + "display": "Eyelid coloboma" + }, + { + "code": "HP:0009754", + "display": "Fibrous syngnathia" + }, + { + "code": "HP:0012478", + "display": "Temporomandibular joint ankylosis" + }, + { + "code": "HP:0001233", + "display": "2-3 finger syndactyly" + }, + { + "code": "HP:0000811", + "display": "Abnormal external genitalia" + }, + { + "code": "HP:0005120", + "display": "Abnormal cardiac atrium morphology" + }, + { + "code": "HP:0008388", + "display": "Abnormal toenail morphology" + }, + { + "code": "HP:0011467", + "display": "Absent gallbladder" + }, + { + "code": "HP:0010760", + "display": "Absent toe" + }, + { + "code": "HP:0001545", + "display": "Anteriorly placed anus" + }, + { + "code": "HP:0001640", + "display": "Cardiomegaly" + }, + { + "code": "HP:0002990", + "display": "Fibular aplasia" + }, + { + "code": "HP:0004443", + "display": "Lambdoidal craniosynostosis" + }, + { + "code": "HP:0008569", + "display": "Microtia, second degree" + }, + { + "code": "HP:0006277", + "display": "Pancreatic hyperplasia" + }, + { + "code": "HP:0010445", + "display": "Primum atrial septal defect" + }, + { + "code": "HP:0011640", + "display": "Single coronary artery origin" + }, + { + "code": "HP:0011608", + "display": "Type II truncus arteriosus" + }, + { + "code": "HP:0011327", + "display": "Posterior plagiocephaly" + }, + { + "code": "HP:0007655", + "display": "Eversion of lateral third of lower eyelids" + }, + { + "code": "HP:0010747", + "display": "Medial flaring of the eyebrow" + }, + { + "code": "HP:0005957", + "display": "Breathing dysregulation" + }, + { + "code": "HP:0000992", + "display": "Cutaneous photosensitivity" + }, + { + "code": "HP:0011995", + "display": "Atrial septal dilatation" + }, + { + "code": "HP:0000377", + "display": "Abnormality of the pinna" + }, + { + "code": "HP:0011266", + "display": "Microtia, first degree" + }, + { + "code": "HP:0012650", + "display": "Perisylvian polymicrogyria" + }, + { + "code": "HP:0004970", + "display": "Ascending tubular aorta aneurysm" + }, + { + "code": "HP:0008348", + "display": "Decreased circulating IgG2 level" + }, + { + "code": "HP:0012115", + "display": "Hepatitis" + }, + { + "code": "HP:0006979", + "display": "Sleep-wake cycle disturbance" + }, + { + "code": "HP:0008587", + "display": "Mild neurosensory hearing impairment" + }, + { + "code": "HP:0006097", + "display": "3-4 finger syndactyly" + }, + { + "code": "HP:0005263", + "display": "Gastritis" + }, + { + "code": "HP:0200043", + "display": "Verrucae" + }, + { + "code": "HP:0009600", + "display": "Flexion contracture of thumb" + }, + { + "code": "HP:0010818", + "display": "Generalized tonic seizure" + }, + { + "code": "HP:0002599", + "display": "Head titubation" + }, + { + "code": "HP:0002090", + "display": "Pneumonia" + }, + { + "code": "HP:0030423", + "display": "Splenic cyst" + }, + { + "code": "HP:0030187", + "display": "Titubation" + }, + { + "code": "HP:0002375", + "display": "Hypokinesia" + }, + { + "code": "HP:0007166", + "display": "Paroxysmal dyskinesia" + }, + { + "code": "HP:0003077", + "display": "Hyperlipidemia" + }, + { + "code": "HP:0000017", + "display": "Nocturia" + }, + { + "code": "HP:0100555", + "display": "Asymmetric growth" + }, + { + "code": "HP:0011847", + "display": "Giant cell tumor of bone" + }, + { + "code": "HP:0000112", + "display": "Nephropathy" + }, + { + "code": "HP:0000246", + "display": "Sinusitis" + }, + { + "code": "HP:0001012", + "display": "Multiple lipomas" + }, + { + "code": "HP:0000851", + "display": "Congenital hypothyroidism" + }, + { + "code": "HP:0002345", + "display": "Action tremor" + }, + { + "code": "HP:0002677", + "display": "Small foramen magnum" + }, + { + "code": "HP:0011947", + "display": "Respiratory tract infection" + }, + { + "code": "HP:0012151", + "display": "Hemothorax" + }, + { + "code": "HP:0005988", + "display": "Congenital muscular torticollis" + }, + { + "code": "HP:0002329", + "display": "Drowsiness" + }, + { + "code": "HP:0012395", + "display": "Seasonal allergy" + }, + { + "code": "HP:0011679", + "display": "Tetralogy of Fallot with pulmonary stenosis" + }, + { + "code": "HP:0001864", + "display": "Clinodactyly of the 5th toe" + }, + { + "code": "HP:0006934", + "display": "Congenital nystagmus" + }, + { + "code": "HP:0100355", + "display": "Contractures of the distal interphalangeal joint of the 5th toe" + }, + { + "code": "HP:0007894", + "display": "Hypopigmentation of the fundus" + }, + { + "code": "HP:0012377", + "display": "Hemianopia" + }, + { + "code": "HP:0002354", + "display": "Memory impairment" + }, + { + "code": "HP:0000872", + "display": "Hashimoto thyroiditis" + }, + { + "code": "HP:0002519", + "display": "Hypnagogic hallucinations" + }, + { + "code": "HP:0010647", + "display": "Abnormal elasticity of skin" + }, + { + "code": "HP:0002592", + "display": "Gastric ulcer" + }, + { + "code": "HP:0004938", + "display": "Tortuous cerebral arteries" + }, + { + "code": "HP:0004948", + "display": "Vascular tortuosity" + }, + { + "code": "HP:0002516", + "display": "Increased intracranial pressure" + }, + { + "code": "HP:0006460", + "display": "Increased laxity of ankles" + }, + { + "code": "HP:0002317", + "display": "Unsteady gait" + }, + { + "code": "HP:0000182", + "display": "Movement abnormality of the tongue" + }, + { + "code": "HP:0009887", + "display": "Abnormality of hair pigmentation" + }, + { + "code": "HP:0005824", + "display": "Clinodactyly of the 2nd toe" + }, + { + "code": "HP:0002212", + "display": "Curly hair" + }, + { + "code": "HP:0009803", + "display": "Short phalanx of finger" + }, + { + "code": "HP:0000572", + "display": "Visual loss" + }, + { + "code": "HP:0005216", + "display": "Impaired mastication" + }, + { + "code": "HP:0000619", + "display": "Impaired convergence" + }, + { + "code": "HP:0002403", + "display": "Positive Romberg sign" + }, + { + "code": "HP:0008744", + "display": "Abnormal aryepiglottic fold morphology" + }, + { + "code": "HP:0002374", + "display": "Diminished movement" + }, + { + "code": "HP:0008277", + "display": "Abnormal blood zinc concentration" + }, + { + "code": "HP:0012781", + "display": "Mid-frequency hearing loss" + }, + { + "code": "HP:0100758", + "display": "Gangrene" + }, + { + "code": "HP:0003256", + "display": "Abnormality of the coagulation cascade" + }, + { + "code": "HP:0004387", + "display": "Enterocolitis" + }, + { + "code": "HP:0011029", + "display": "Internal hemorrhage" + }, + { + "code": "HP:0011649", + "display": "Patent ductus arteriosus after premature birth" + }, + { + "code": "HP:0012050", + "display": "Anasarca" + }, + { + "code": "HP:0001683", + "display": "Ectopia cordis" + }, + { + "code": "HP:0011682", + "display": "Perimembranous ventricular septal defect" + }, + { + "code": "HP:0010624", + "display": "Aplastic/hypoplastic toenail" + }, + { + "code": "HP:0002705", + "display": "High, narrow palate" + }, + { + "code": "HP:0011340", + "display": "Incomplete cleft of the upper lip" + }, + { + "code": "HP:0011613", + "display": "Interrupted aortic arch type B" + }, + { + "code": "HP:0006167", + "display": "Prominent proximal interphalangeal joints" + }, + { + "code": "HP:0002918", + "display": "Hypermagnesemia" + }, + { + "code": "HP:0011937", + "display": "Hypoplastic fifth toenail" + }, + { + "code": "HP:0001067", + "display": "Neurofibromas" + }, + { + "code": "HP:0011403", + "display": "Abnormal umbilical cord blood vessels" + }, + { + "code": "HP:0003316", + "display": "Butterfly vertebrae" + }, + { + "code": "HP:0002247", + "display": "Duodenal atresia" + }, + { + "code": "HP:0008439", + "display": "Lumbar hemivertebrae" + }, + { + "code": "HP:0011599", + "display": "Mesocardia" + }, + { + "code": "HP:0008467", + "display": "Thoracic hemivertebrae" + }, + { + "code": "HP:0004626", + "display": "Lumbar scoliosis" + }, + { + "code": "HP:0006808", + "display": "Cerebral hypomyelination" + }, + { + "code": "HP:0002926", + "display": "Abnormality of thyroid physiology" + }, + { + "code": "HP:0007970", + "display": "Congenital ptosis" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-loinc-answers.json b/tests/fixtures/ncpi/examples/CodeSystem-loinc-answers.json new file mode 100644 index 0000000..a6628ae --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-loinc-answers.json @@ -0,0 +1,139 @@ +{ + "resourceType": "CodeSystem", + "id": "loinc-answers", + "text": { + "status": "generated", + "div": "

This code system ncpi:loinc-answers defines the following codes:

CodeDisplay
LA21254-0 Chromosome 1
LA21255-7 Chromosome 2
LA21256-5 Chromosome 3
LA21257-3 Chromosome 4
LA21258-1 Chromosome 5
LA21259-9 Chromosome 6
LA21260-7 Chromosome 7
LA21261-5 Chromosome 8
LA21262-3 Chromosome 9
LA21263-1 Chromosome 10
LA21264-9 Chromosome 11
LA21265-6 Chromosome 12
LA21266-4 Chromosome 13
LA21267-2 Chromosome 14
LA21268-0 Chromosome 15
LA21269-8 Chromosome 16
LA21270-6 Chromosome 17
LA21271-4 Chromosome 18
LA21272-2 Chromosome 19
LA21273-0 Chromosome 20
LA21274-8 Chromosome 21
LA21275-5 Chromosome 22
LA21276-3 Chromosome X
LA21277-1 Chromosome Y
" + }, + "url": "ncpi:loinc-answers", + "version": "0.1.0", + "name": "LoincAnswers", + "title": "LOINC Answers", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "LOINC ANSWERS used by NCPI resources", + "caseSensitive": true, + "content": "complete", + "count": 24, + "concept": [ + { + "code": "LA21254-0", + "display": "Chromosome 1" + }, + { + "code": "LA21255-7", + "display": "Chromosome 2" + }, + { + "code": "LA21256-5", + "display": "Chromosome 3" + }, + { + "code": "LA21257-3", + "display": "Chromosome 4" + }, + { + "code": "LA21258-1", + "display": "Chromosome 5" + }, + { + "code": "LA21259-9", + "display": "Chromosome 6" + }, + { + "code": "LA21260-7", + "display": "Chromosome 7" + }, + { + "code": "LA21261-5", + "display": "Chromosome 8" + }, + { + "code": "LA21262-3", + "display": "Chromosome 9" + }, + { + "code": "LA21263-1", + "display": "Chromosome 10" + }, + { + "code": "LA21264-9", + "display": "Chromosome 11" + }, + { + "code": "LA21265-6", + "display": "Chromosome 12" + }, + { + "code": "LA21266-4", + "display": "Chromosome 13" + }, + { + "code": "LA21267-2", + "display": "Chromosome 14" + }, + { + "code": "LA21268-0", + "display": "Chromosome 15" + }, + { + "code": "LA21269-8", + "display": "Chromosome 16" + }, + { + "code": "LA21270-6", + "display": "Chromosome 17" + }, + { + "code": "LA21271-4", + "display": "Chromosome 18" + }, + { + "code": "LA21272-2", + "display": "Chromosome 19" + }, + { + "code": "LA21273-0", + "display": "Chromosome 20" + }, + { + "code": "LA21274-8", + "display": "Chromosome 21" + }, + { + "code": "LA21275-5", + "display": "Chromosome 22" + }, + { + "code": "LA21276-3", + "display": "Chromosome X" + }, + { + "code": "LA21277-1", + "display": "Chromosome Y" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-mondo.json b/tests/fixtures/ncpi/examples/CodeSystem-mondo.json new file mode 100644 index 0000000..f32b47c --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-mondo.json @@ -0,0 +1,55 @@ +{ + "resourceType": "CodeSystem", + "id": "mondo", + "text": { + "status": "generated", + "div": "

This code system http://purl.obolibrary.org/obo/mondo.owl defines many codes, of which the following are a subset:

CodeDisplay
MONDO:0005072 neuroblastoma
MONDO:0002749 extracranial neuroblastoma
MONDO:0008542 tetralogy of fallot
" + }, + "url": "http://purl.obolibrary.org/obo/mondo.owl", + "version": "0.1.0", + "name": "Mondo", + "title": "Mondo Disease Ontology", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. The name Mondo comes from the latin word 'mundus' and means 'for the world.'", + "caseSensitive": true, + "content": "fragment", + "count": 3, + "concept": [ + { + "code": "MONDO:0005072", + "display": "neuroblastoma" + }, + { + "code": "MONDO:0002749", + "display": "extracranial neuroblastoma" + }, + { + "code": "MONDO:0008542", + "display": "tetralogy of fallot" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-ncit.json b/tests/fixtures/ncpi/examples/CodeSystem-ncit.json new file mode 100644 index 0000000..651eb18 --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-ncit.json @@ -0,0 +1,55 @@ +{ + "resourceType": "CodeSystem", + "id": "ncit", + "text": { + "status": "generated", + "div": "

This code system http://purl.obolibrary.org/obo/ncit.owl defines many codes, of which the following are a subset:

CodeDisplay
C3270 Neuroblastoma
C5437 Extracranial Neuroblastoma
C84505 Tetralogy of Fallot
" + }, + "url": "http://purl.obolibrary.org/obo/ncit.owl", + "version": "0.1.0", + "name": "NCIt", + "title": "NCI Thesaurus", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.", + "caseSensitive": true, + "content": "fragment", + "count": 3, + "concept": [ + { + "code": "C3270", + "display": "Neuroblastoma" + }, + { + "code": "C5437", + "display": "Extracranial Neuroblastoma" + }, + { + "code": "C84505", + "display": "Tetralogy of Fallot" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-ncpi-data-types.json b/tests/fixtures/ncpi/examples/CodeSystem-ncpi-data-types.json new file mode 100644 index 0000000..4387a65 --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-ncpi-data-types.json @@ -0,0 +1,53 @@ +{ + "resourceType": "CodeSystem", + "id": "ncpi-data-types", + "text": { + "status": "generated", + "div": "

This code system https://nih-ncpi.github.io/ncpi-fhir-ig/datatypes defines many codes, of which the following are a subset:

CodeDisplay
Exome Exome Sequence Data
WholeGenome Whole Genome Sequence Data
GWAS Genome-Wide Association Studies
" + }, + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig/datatypes", + "version": "0.1.0", + "name": "NcpiDataTypes", + "title": "Data Types for NCPI Research", + "status": "active", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Data Types for NCPI Research", + "content": "fragment", + "concept": [ + { + "code": "Exome", + "display": "Exome Sequence Data" + }, + { + "code": "WholeGenome", + "display": "Whole Genome Sequence Data" + }, + { + "code": "GWAS", + "display": "Genome-Wide Association Studies" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-ncpi.json b/tests/fixtures/ncpi/examples/CodeSystem-ncpi.json new file mode 100644 index 0000000..cc27a6c --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-ncpi.json @@ -0,0 +1,89 @@ +{ + "resourceType": "CodeSystem", + "id": "ncpi", + "text": { + "status": "generated", + "div": "

This code system https://nih-ncpi.github.io/ncpi-fhir-ig defines many codes, of which the following are a subset:

CodeDisplay
Consortium Study Consortium
StudyCohort Study Cohort
Summary Summary Data
CohortCount Number of Cohorts
SampleCount Number of Samples
Participant Number of Participants
StorageSize Size on Disk
ConsentCodes Consent Codes
TerraWorkspace Terra Workspace Name
PrimaryDisease Primary Disease
AccessType Access Type
StudyDesign Study Design
" + }, + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "version": "0.1.0", + "name": "Ncpi", + "title": "NCPI FHIR Codes", + "status": "active", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Codes that would apply to NCPI projects", + "content": "fragment", + "concept": [ + { + "code": "Consortium", + "display": "Study Consortium" + }, + { + "code": "StudyCohort", + "display": "Study Cohort" + }, + { + "code": "Summary", + "display": "Summary Data" + }, + { + "code": "CohortCount", + "display": "Number of Cohorts" + }, + { + "code": "SampleCount", + "display": "Number of Samples" + }, + { + "code": "Participant", + "display": "Number of Participants" + }, + { + "code": "StorageSize", + "display": "Size on Disk" + }, + { + "code": "ConsentCodes", + "display": "Consent Codes" + }, + { + "code": "TerraWorkspace", + "display": "Terra Workspace Name" + }, + { + "code": "PrimaryDisease", + "display": "Primary Disease" + }, + { + "code": "AccessType", + "display": "Access Type" + }, + { + "code": "StudyDesign", + "display": "Study Design" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-omim.json b/tests/fixtures/ncpi/examples/CodeSystem-omim.json new file mode 100644 index 0000000..f167545 --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-omim.json @@ -0,0 +1,2035 @@ +{ + "resourceType": "CodeSystem", + "id": "omim", + "text": { + "status": "generated", + "div": "

This code system https://omim.org/ defines many codes, of which the following are a subset:

CodeDisplay
OMIM:613801 Retinitis pigmentosa-40
OMIM:213300 Joubert syndrome 1
OMIM:615780 Retinitis pigmentosa 69
OMIM:613826 Leber congenital amaurosis 6
OMIM:310200 Duchenne muscular dystrophy
OMIM:617194 Lethal congenital contracture syndrome 11
OMIM:105400 AMYOTROPHIC LATERAL SCLEROSIS 1; ALS1
OMIM:108120 ARTHROGRYPOSIS, DISTAL, TYPE 1A; DA1A
OMIM:114300 ARTHROGRYPOSIS, DISTAL, TYPE 3; DA3
OMIM:115195 CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 2; CMH2
OMIM:115196 CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 3; CMH3
OMIM:115197 CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 4; CMH4
OMIM:115200 CARDIOMYOPATHY, DILATED, 1A; CMD1A
OMIM:117000 CENTRAL CORE DISEASE OF MUSCLE; CCD
OMIM:117360 SPINOCEREBELLAR ATAXIA 29; SCA29
OMIM:119530 OROFACIAL CLEFT 1; OFC1
OMIM:122470 CORNELIA DE LANGE SYNDROME 1; CDLS1
OMIM:130600 ELLIPTOCYTOSIS 2; EL2
OMIM:135900 COFFIN-SIRIS SYNDROME 1; CSS1
OMIM:136140 FLOATING-HARBOR SYNDROME; FLHS
OMIM:137920 RENAL CYSTS AND DIABETES SYNDROME; RCAD
OMIM:139090 GRAY PLATELET SYNDROME; GPS
OMIM:139210 MYHRE SYNDROME; MYHRS
OMIM:143095 SPONDYLOEPIPHYSEAL DYSPLASIA WITH CONGENITAL JOINT DISLOCATIONS; SEDCJD
OMIM:143465 ATTENTION DEFICIT-HYPERACTIVITY DISORDER; ADHD
OMIM:147891 ISCHIOCOXOPODOPATELLAR SYNDROME WITH OR WITHOUT PULMONARY ARTERIAL HYPERTENSION; ICPPS
OMIM:147920 KABUKI SYNDROME 1; KABUK1
OMIM:148050 KBG SYNDROME; KBGS
OMIM:149400 HYPEREKPLEXIA 1; HKPX1
OMIM:152950 MICROCEPHALY WITH OR WITHOUT CHORIORETINOPATHY, LYMPHEDEMA, OR MENTAL RETARDATION; MCLMR
OMIM:153670 BERNARD-SOULIER SYNDROME, TYPE A2, AUTOSOMAL DOMINANT; BSSA2
OMIM:154400 ACROFACIAL DYSOSTOSIS 1, NAGER TYPE; AFD1
OMIM:154700 MARFAN SYNDROME; MFS
OMIM:155310 VISCERAL MYOPATHY; VSCM
OMIM:158590 NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE IIA; HMN2A
OMIM:158810 BETHLEM MYOPATHY 1; BTHLM1
OMIM:159550 ATAXIA-PANCYTOPENIA SYNDROME; ATXPC
OMIM:160150 MYOPATHY, CENTRONUCLEAR, 1; CNM1
OMIM:160500 MYOPATHY, DISTAL, 1; MPD1
OMIM:160800 MYOTONIA CONGENITA, AUTOSOMAL DOMINANT
OMIM:160900 MYOTONIC DYSTROPHY 1; DM1
OMIM:161800 NEMALINE MYOPATHY 3; NEM3
OMIM:163950 NOONAN SYNDROME 1; NS1
OMIM:178110 CONTRACTURES, PTERYGIA, AND SPONDYLOCARPOTARSAL FUSION SYNDROME 1A; CPSFS1A
OMIM:178500 PULMONARY FIBROSIS, IDIOPATHIC; IPF
OMIM:180100 RETINITIS PIGMENTOSA 1; RP1
OMIM:180849 RUBINSTEIN-TAYBI SYNDROME 1; RSTS1
OMIM:181430 SCAPULOPERONEAL MYOPATHY, MYH7-RELATED; SPMM
OMIM:182601 SPASTIC PARAPLEGIA 4, AUTOSOMAL DOMINANT; SPG4
OMIM:188000 THROMBOCYTOPENIA 2; THC2
OMIM:191480 UNCOMBABLE HAIR SYNDROME 1; UHS1
OMIM:203800 ALSTROM SYNDROME; ALMS
OMIM:204200 CEROID LIPOFUSCINOSIS, NEURONAL, 3; CLN3
OMIM:204500 CEROID LIPOFUSCINOSIS, NEURONAL, 2; CLN2
OMIM:205100 AMYOTROPHIC LATERAL SCLEROSIS 2, JUVENILE; ALS2
OMIM:206900 MICROPHTHALMIA, SYNDROMIC 3; MCOPS3
OMIM:208900 ATAXIA-TELANGIECTASIA; AT
OMIM:209850 AUTISM
OMIM:209900 BARDET-BIEDL SYNDROME 1; BBS1
OMIM:210000 BEHR SYNDROME; BEHRS
OMIM:210720 MICROCEPHALIC OSTEODYSPLASTIC PRIMORDIAL DWARFISM, TYPE II; MOPD2
OMIM:210900 BLOOM SYNDROME; BLM
OMIM:212065 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ia; CDG1A
OMIM:212066 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIa; CDG2A
OMIM:214500 CHEDIAK-HIGASHI SYNDROME; CHS
OMIM:214800 CHARGE SYNDROME
OMIM:215500 CHOROIDAL DYSTROPHY, CENTRAL AREOLAR, 1; CACD1
OMIM:216400 COCKAYNE SYNDROME A; CSA
OMIM:216550 COHEN SYNDROME; COH1
OMIM:217080 JALILI SYNDROME
OMIM:217980 CORPUS CALLOSUM, AGENESIS OF, WITH FACIAL ANOMALIES AND ROBIN SEQUENCE
OMIM:218340 TEMTAMY SYNDROME; TEMTYS
OMIM:219200 CUTIS LAXA, AUTOSOMAL RECESSIVE, TYPE IIA; ARCL2A
OMIM:224050 CEREBELLAR ATAXIA, MENTAL RETARDATION, AND DYSEQUILIBRIUM SYNDROME 1; CAMRQ1
OMIM:224690 MEIER-GORLIN SYNDROME 1; MGORS1
OMIM:225753 PONTOCEREBELLAR HYPOPLASIA, TYPE 4; PCH4
OMIM:225790 PROLIFERATIVE VASCULOPATHY AND HYDRANENCEPHALY-HYDROCEPHALY SYNDROME; PVHH
OMIM:227650 FANCONI ANEMIA, COMPLEMENTATION GROUP A; FANCA
OMIM:229600 FRUCTOSE INTOLERANCE, HEREDITARY; HFI
OMIM:230000 FUCOSIDOSIS
OMIM:230500 GM1-GANGLIOSIDOSIS, TYPE I
OMIM:232300 GLYCOGEN STORAGE DISEASE II; GSD2
OMIM:232600 GLYCOGEN STORAGE DISEASE V; GSD5
OMIM:234200 NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 1; NBIA1
OMIM:234500 HARTNUP DISORDER; HND
OMIM:236000 LYMPHOMA, HODGKIN, CLASSIC; CHL
OMIM:236600 HYDROCEPHALUS, CONGENITAL, 1; HYC1
OMIM:236792 L-2-HYDROXYGLUTARIC ACIDURIA; L2HGA
OMIM:243310 BARAITSER-WINTER SYNDROME 1; BRWS1
OMIM:244450 KAUFMAN OCULOCEREBROFACIAL SYNDROME; KOS
OMIM:245200 KRABBE DISEASE
OMIM:245359 missing
OMIM:248200 STARGARDT DISEASE 1; STGD1
OMIM:248700 MARDEN-WALKER SYNDROME; MWKS
OMIM:249000 MECKEL SYNDROME, TYPE 1; MKS1
OMIM:249900 METACHROMATIC LEUKODYSTROPHY DUE TO SAPOSIN B DEFICIENCY
OMIM:250100 METACHROMATIC LEUKODYSTROPHY; MLD
OMIM:250620 3-HYDROXYISOBUTYRYL-CoA HYDROLASE DEFICIENCY; HIBCHD
OMIM:251200 MICROCEPHALY 1, PRIMARY, AUTOSOMAL RECESSIVE; MCPH1
OMIM:251260 NIJMEGEN BREAKAGE SYNDROME; NBS
OMIM:251280 DIENCEPHALIC-MESENCEPHALIC JUNCTION DYSPLASIA SYNDROME 1; DMJDS1
OMIM:251290 PSEUDO-TORCH SYNDROME 1; PTORCH1
OMIM:251300 GALLOWAY-MOWAT SYNDROME 1; GAMOS1
OMIM:252010 MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 1; MC1DN1
OMIM:252160 MOLYBDENUM COFACTOR DEFICIENCY, COMPLEMENTATION GROUP B; MOCODB
OMIM:252920 MUCOPOLYSACCHARIDOSIS, TYPE IIIB; MPS3B
OMIM:253250 MULIBREY NANISM
OMIM:253600 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 1; LGMDR1
OMIM:253601 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 2; LGMDR2
OMIM:253700 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 5; LGMDR5
OMIM:254090 ULLRICH CONGENITAL MUSCULAR DYSTROPHY 1; UCMD1
OMIM:254110 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 8; LGMDR8
OMIM:254300 MYASTHENIC SYNDROME, CONGENITAL, 10; CMS10
OMIM:254780 MYOCLONIC EPILEPSY OF LAFORA
OMIM:254940 CAREY-FINEMAN-ZITER SYNDROME; CFZS
OMIM:255310 MYOPATHY, CONGENITAL, WITH FIBER-TYPE DISPROPORTION; CFTD
OMIM:255320 MINICORE MYOPATHY WITH EXTERNAL OPHTHALMOPLEGIA
OMIM:255800 SCHWARTZ-JAMPEL SYNDROME, TYPE 1; SJS1
OMIM:256000 LEIGH SYNDROME; LS
OMIM:256300 NEPHROTIC SYNDROME, TYPE 1; NPHS1
OMIM:256600 NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 2A; NBIA2A
OMIM:256700 NEUROBLASTOMA, SUSCEPTIBILITY TO, 1; NBLST1
OMIM:256730 CEROID LIPOFUSCINOSIS, NEURONAL, 1; CLN1
OMIM:256731 CEROID LIPOFUSCINOSIS, NEURONAL, 5; CLN5
OMIM:256800 INSENSITIVITY TO PAIN, CONGENITAL, WITH ANHIDROSIS; CIPA
OMIM:256850 GIANT AXONAL NEUROPATHY 1, AUTOSOMAL RECESSIVE; GAN1
OMIM:257220 NIEMANN-PICK DISEASE, TYPE C1; NPC1
OMIM:257320 LISSENCEPHALY 2; LIS2
OMIM:260400 SHWACHMAN-DIAMOND SYNDROME 1; SDS1
OMIM:260565 PEHO SYNDROME; PEHO
OMIM:261630 HYPERPHENYLALANINEMIA, BH4-DEFICIENT, C; HPABH4C
OMIM:262500 LARON SYNDROME
OMIM:263200 POLYCYSTIC KIDNEY DISEASE 4 WITH OR WITHOUT POLYCYSTIC LIVER DISEASE; PKD4
OMIM:265000 MULTIPLE PTERYGIUM SYNDROME, ESCOBAR VARIANT; EVMPS
OMIM:266100 EPILEPSY, PYRIDOXINE-DEPENDENT; EPD
OMIM:266265 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIc; CDG2C
OMIM:266500 REFSUM DISEASE, CLASSIC
OMIM:266510 PEROXISOME BIOGENESIS DISORDER 3B; PBD3B
OMIM:268800 SANDHOFF DISEASE
OMIM:270200 SJOGREN-LARSSON SYNDROME; SLS
OMIM:270800 SPASTIC PARAPLEGIA 5A, AUTOSOMAL RECESSIVE; SPG5A
OMIM:271900 CANAVAN DISEASE
OMIM:272800 TAY-SACHS DISEASE; TSD
OMIM:273300 TESTICULAR GERM CELL TUMOR; TGCT
OMIM:274000 THROMBOCYTOPENIA-ABSENT RADIUS SYNDROME; TAR
OMIM:276901 USHER SYNDROME, TYPE IIA; USH2A
OMIM:277470 PONTOCEREBELLAR HYPOPLASIA, TYPE 2A; PCH2A
OMIM:300029 RETINITIS PIGMENTOSA 3; RP3
OMIM:300067 LISSENCEPHALY, X-LINKED, 1; LISX1
OMIM:300088 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 9; DEE9
OMIM:300100 ADRENOLEUKODYSTROPHY; ALD
OMIM:300376 MUSCULAR DYSTROPHY, BECKER TYPE; BMD
OMIM:300387 MENTAL RETARDATION, X-LINKED 63; MRX63
OMIM:300476 CONE-ROD DYSTROPHY, X-LINKED, 3; CORDX3
OMIM:300486 MENTAL RETARDATION, X-LINKED, WITH CEREBELLAR HYPOPLASIA AND DISTINCTIVE FACIAL APPEARANCE
OMIM:300495 AUTISM, SUSCEPTIBILITY TO, X-LINKED 2; AUTSX2
OMIM:300523 ALLAN-HERNDON-DUDLEY SYNDROME; AHDS
OMIM:300534 MENTAL RETARDATION, X-LINKED, SYNDROMIC, CLAES-JENSEN TYPE; MRXSCJ
OMIM:300695 SCAPULOPERONEAL MYOPATHY, X-LINKED DOMINANT; SPM
OMIM:300749 MENTAL RETARDATION AND MICROCEPHALY WITH PONTINE AND CEREBELLAR HYPOPLASIA; MICPCH
OMIM:300804 JOUBERT SYNDROME 10; JBTS10
OMIM:300881 MOVED TO 615777
OMIM:300882 CORNELIA DE LANGE SYNDROME 5; CDLS5
OMIM:300894 NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 5; NBIA5
OMIM:300908 ANEMIA, NONSPHEROCYTIC HEMOLYTIC, DUE TO G6PD DEFICIENCY
OMIM:300957 MENTAL RETARDATION, X-LINKED 12; MRX12
OMIM:300958 INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, SNIJDERS BLOK TYPE; MRXSSB
OMIM:300966 MENTAL RETARDATION, X-LINKED, SYNDROMIC 33; MRXS33
OMIM:300968 MENTAL RETARDATION, X-LINKED 99, SYNDROMIC, FEMALE-RESTRICTED; MRXS99F
OMIM:300983 MENTAL RETARDATION, X-LINKED 104; MRX104
OMIM:300986 MENTAL RETARDATION, X-LINKED, SYNDROMIC, BAIN TYPE; MRXSB
OMIM:301050 ALPORT SYNDROME 1, X-LINKED; ATS1
OMIM:301310 ANEMIA, SIDEROBLASTIC, AND SPINOCEREBELLAR ATAXIA; ASAT
OMIM:304340 PETTIGREW SYNDROME; PGS
OMIM:305100 ECTODERMAL DYSPLASIA 1, HYPOHIDROTIC, X-LINKED; XHED
OMIM:308350 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 1; DEE1
OMIM:309500 RENPENNING SYNDROME 1; RENS1
OMIM:309541 METHYLMALONIC ACIDEMIA AND HOMOCYSTEINEMIA, cblX TYPE
OMIM:309580 MENTAL RETARDATION-HYPOTONIC FACIES SYNDROME, X-LINKED, 1; MRXHF1
OMIM:310468 NEPHROLITHIASIS, X-LINKED RECESSIVE, WITH RENAL FAILURE; XRN
OMIM:311070 CHARCOT-MARIE-TOOTH DISEASE, X-LINKED RECESSIVE, 5; CMTX5
OMIM:313850 THORACOABDOMINAL SYNDROME; THAS
OMIM:314580 WIEACKER-WOLFF SYNDROME; WRWF
OMIM:600059 RETINITIS PIGMENTOSA 13; RP13
OMIM:600105 RETINITIS PIGMENTOSA 12; RP12
OMIM:600118 WARBURG MICRO SYNDROME 1; WARBM1
OMIM:600132 RETINITIS PIGMENTOSA 14; RP14
OMIM:600138 RETINITIS PIGMENTOSA 11; RP11
OMIM:600143 CEROID LIPOFUSCINOSIS, NEURONAL, 8; CLN8
OMIM:600334 TIBIAL MUSCULAR DYSTROPHY, TARDIVE; TMD
OMIM:600373 CODAS SYNDROME
OMIM:600618 ETS VARIANT GENE 6; ETV6
OMIM:600995 NEPHROTIC SYNDROME, TYPE 2; NPHS2
OMIM:601088 AYME-GRIPP SYNDROME; AYGRP
OMIM:601414 RETINITIS PIGMENTOSA 18; RP18
OMIM:601419 MYOPATHY, MYOFIBRILLAR, 1; MFM1
OMIM:601680 ARTHROGRYPOSIS, DISTAL, TYPE 2B1; DA2B1
OMIM:601718 RETINITIS PIGMENTOSA 19; RP19
OMIM:601780 CEROID LIPOFUSCINOSIS, NEURONAL, 6; CLN6
OMIM:601815 PHOSPHOGLYCERATE DEHYDROGENASE DEFICIENCY; PHGDHD
OMIM:601954 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 7; LGMDR7
OMIM:602482 AXENFELD-RIEGER SYNDROME, TYPE 3; RIEG3
OMIM:602579 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ib; CDG1B
OMIM:602772 RETINITIS PIGMENTOSA 25; RP25
OMIM:603511 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL DOMINANT 1; LGMDD1
OMIM:603896 LEUKOENCEPHALOPATHY WITH VANISHING WHITE MATTER; VWM
OMIM:604004 MEGALENCEPHALIC LEUKOENCEPHALOPATHY WITH SUBCORTICAL CYSTS 1; MLC1
OMIM:604116 CONE-ROD DYSTROPHY 3; CORD3
OMIM:604273 MITOCHONDRIAL COMPLEX V (ATP SYNTHASE) DEFICIENCY, NUCLEAR TYPE 1; MC5DN1
OMIM:604286 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 4; LGMDR4
OMIM:604317 MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH OR WITHOUT CORTICAL MALFORMATIONS; MCPH2
OMIM:604360 SPASTIC PARAPLEGIA 11, AUTOSOMAL RECESSIVE; SPG11
OMIM:604387 NEPHRONOPHTHISIS 3; NPHP3
OMIM:604537 LEBER CONGENITAL AMAUROSIS 5; LCA5
OMIM:604592 T CELL IMMUNE REGULATOR 1; TCIRG1
OMIM:605130 WIEDEMANN-STEINER SYNDROME; WDSTS
OMIM:605355 NEMALINE MYOPATHY 5; NEM5
OMIM:605407 SEGAWA SYNDROME, AUTOSOMAL RECESSIVE
OMIM:605637 MYOPATHY, PROXIMAL, WITH OPHTHALMOPLEGIA; MYPOP
OMIM:605670 LATE-ONSET RETINAL DEGENERATION; LORD
OMIM:605820 NONAKA MYOPATHY; NM
OMIM:605899 GLYCINE ENCEPHALOPATHY; GCE
OMIM:606068 RETINITIS PIGMENTOSA 28; RP28
OMIM:606170 GENITOPATELLAR SYNDROME; GTPTS
OMIM:606232 PHELAN-MCDERMID SYNDROME; PHMDS
OMIM:606777 GLUT1 DEFICIENCY SYNDROME 1; GLUT1DS1
OMIM:606854 POLYMICROGYRIA, BILATERAL FRONTOPARIETAL; BFPP
OMIM:606966 NEPHRONOPHTHISIS 4; NPHP4
OMIM:606996 SENIOR-LOKEN SYNDROME 4; SLSN4
OMIM:607015 HURLER-SCHEIE SYNDROME
OMIM:607155 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 5; MDDGC5
OMIM:607196 MICROCEPHALY, AMISH TYPE; MCPHA
OMIM:607225 SPASTIC PARALYSIS, INFANTILE-ONSET ASCENDING; IAHSP
OMIM:607426 COENZYME Q10 DEFICIENCY, PRIMARY, 1; COQ10D1
OMIM:607432 LISSENCEPHALY 1; LIS1
OMIM:607483 THIAMINE METABOLISM DYSFUNCTION SYNDROME 2 (BIOTIN- OR THIAMINE-RESPONSIVE TYPE); THMD2
OMIM:607595 MOVED TO 175780
OMIM:607596 PONTOCEREBELLAR HYPOPLASIA, TYPE 1A; PCH1A
OMIM:607855 MUSCULAR DYSTROPHY, CONGENITAL MEROSIN-DEFICIENT, 1A; MDC1A
OMIM:608027 PONTOCEREBELLAR HYPOPLASIA, TYPE 3; PCH3
OMIM:608091 JOUBERT SYNDROME 2; JBTS2
OMIM:608099 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 3; LGMDR3
OMIM:608133 RETINITIS PIGMENTOSA 7; RP7
OMIM:608358 MYOPATHY, MYOSIN STORAGE, AUTOSOMAL DOMINANT; MSMA
OMIM:608380 RETINITIS PIGMENTOSA 26; RP26
OMIM:608393 MICROCEPHALY 6, PRIMARY, AUTOSOMAL RECESSIVE; MCPH6
OMIM:608415 PROLONGED ELECTRORETINAL RESPONSE SUPPRESSION; PERRS
OMIM:608423 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL DOMINANT 2; LGMDD2
OMIM:608540 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ik; CDG1K
OMIM:608629 JOUBERT SYNDROME 3; JBTS3
OMIM:608643 AROMATIC L-AMINO ACID DECARBOXYLASE DEFICIENCY
OMIM:608716 MICROCEPHALY 5, PRIMARY, AUTOSOMAL RECESSIVE; MCPH5
OMIM:608804 LEUKODYSTROPHY, HYPOMYELINATING, 2; HLD2
OMIM:608807 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 10; LGMDR10
OMIM:609033 POSTERIOR COLUMN ATAXIA WITH RETINITIS PIGMENTOSA; AXPC1
OMIM:609056 SALT AND PEPPER DEVELOPMENTAL REGRESSION SYNDROME; SPDRS
OMIM:609195 SPASTIC PARAPLEGIA 26, AUTOSOMAL RECESSIVE; SPG26
OMIM:609200 MYOPATHY, MYOFIBRILLAR, 3; MFM3
OMIM:609260 CHARCOT-MARIE-TOOTH DISEASE, AXONAL, AUTOSOMAL DOMINANT, TYPE 2A2A; CMT2A2A
OMIM:609270 SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 7; SCAR7
OMIM:609304 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 3; DEE3
OMIM:609524 MYOPATHY, MYOFIBRILLAR, 5; MFM5
OMIM:609560 MITOCHONDRIAL DNA DEPLETION SYNDROME 2 (MYOPATHIC TYPE); MTDPS2
OMIM:609923 RETINITIS PIGMENTOSA 31; RP31
OMIM:610019 CATARACT 18; CTRCT18
OMIM:610031 CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 7; CDCBM7
OMIM:610127 CEROID LIPOFUSCINOSIS, NEURONAL, 10; CLN10
OMIM:610181 AICARDI-GOUTIERES SYNDROME 2; AGS2
OMIM:610188 JOUBERT SYNDROME 5; JBTS5
OMIM:610217 NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 2B; NBIA2B
OMIM:610329 AICARDI-GOUTIERES SYNDROME 3; AGS3
OMIM:610333 AICARDI-GOUTIERES SYNDROME 4; AGS4
OMIM:610359 RETINITIS PIGMENTOSA 33; RP33
OMIM:610443 KOOLEN-DE VRIES SYNDROME; KDVS
OMIM:610444 NIGHT BLINDNESS, CONGENITAL STATIONARY, AUTOSOMAL DOMINANT 3; CSNBAD3
OMIM:610489 PIGMENTED NODULAR ADRENOCORTICAL DISEASE, PRIMARY, 1; PPNAD1
OMIM:610532 LEUKODYSTROPHY, HYPOMYELINATING, 5; HLD5
OMIM:610688 JOUBERT SYNDROME 6; JBTS6
OMIM:610725 NEPHROTIC SYNDROME, TYPE 3; NPHS3
OMIM:610951 CEROID LIPOFUSCINOSIS, NEURONAL, 7; CLN7
OMIM:611091 MENTAL RETARDATION, AUTOSOMAL RECESSIVE 5; MRT5
OMIM:611302 SPASTIC ATAXIA 2, AUTOSOMAL RECESSIVE; SPAX2
OMIM:611307 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 12; LGMDR12
OMIM:611560 JOUBERT SYNDROME 7; JBTS7
OMIM:611603 LISSENCEPHALY 3; LIS3
OMIM:611705 SALIH MYOPATHY; SALMY
OMIM:611721 COMBINED SAPOSIN DEFICIENCY
OMIM:611726 EPILEPSY, PROGRESSIVE MYOCLONIC, 3, WITH OR WITHOUT INTRACELLULAR INCLUSIONS; EPM3
OMIM:611755 LEBER CONGENITAL AMAUROSIS 10; LCA10
OMIM:612015 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE In; CDG1N
OMIM:612095 RETINITIS PIGMENTOSA 41; RP41
OMIM:612126 GLUT1 DEFICIENCY SYNDROME 2; GLUT1DS2
OMIM:612285 JOUBERT SYNDROME 9; JBTS9
OMIM:612337 MENTAL RETARDATION, AUTOSOMAL DOMINANT 22; MRD22
OMIM:612370 HYPOGONADOTROPIC HYPOGONADISM 5 WITH OR WITHOUT ANOSMIA; HH5
OMIM:612438 LEUKODYSTROPHY, HYPOMYELINATING, 6; HLD6
OMIM:612528 DIAMOND-BLACKFAN ANEMIA 5; DBA5
OMIM:612621 MENTAL RETARDATION, AUTOSOMAL DOMINANT 5; MRD5
OMIM:612712 LEBER CONGENITAL AMAUROSIS 13; LCA13
OMIM:612716 DYSTONIA, DOPA-RESPONSIVE, DUE TO SEPIAPTERIN REDUCTASE DEFICIENCY
OMIM:612780 SEIZURES, SENSORINEURAL DEAFNESS, ATAXIA, MENTAL RETARDATION, AND ELECTROLYTE IMBALANCE; SESAMES
OMIM:612936 SPASTIC PARAPLEGIA 50, AUTOSOMAL RECESSIVE; SPG50
OMIM:612943 RETINITIS PIGMENTOSA 42; RP42
OMIM:612951 LEUKOENCEPHALOPATHY, CYSTIC, WITHOUT MEGALENCEPHALY
OMIM:613065 LEUKEMIA, ACUTE LYMPHOBLASTIC; ALL
OMIM:613091 SHORT-RIB THORACIC DYSPLASIA 3 WITH OR WITHOUT POLYDACTYLY; SRTD3
OMIM:613155 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL IMPAIRMENT), TYPE B, 1; MDDGB1
OMIM:613156 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 2; MDDGB2
OMIM:613158 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 2; MDDGC2
OMIM:613192 MENTAL RETARDATION, AUTOSOMAL RECESSIVE 13; MRT13
OMIM:613205 MUSCULAR DYSTROPHY, CONGENITAL, LMNA-RELATED
OMIM:613216 NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1C; CSNB1C
OMIM:613217 DIARRHEA 5, WITH TUFTING ENTEROPATHY, CONGENITAL; DIAR5
OMIM:613402 MICROCEPHALY, SEIZURES, AND DEVELOPMENTAL DELAY; MCSZ
OMIM:613428 RETINITIS PIGMENTOSA 54; RP54
OMIM:613454 RETT SYNDROME, CONGENITAL VARIANT
OMIM:613550 NEPHRONOPHTHISIS 11; NPHP11
OMIM:613561 MYOPATHY, LACTIC ACIDOSIS, AND SIDEROBLASTIC ANEMIA 2; MLASA2
OMIM:613587 OCCULT MACULAR DYSTROPHY; OCMD
OMIM:613612 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIi; CDG2I
OMIM:613660 CONE-ROD DYSTROPHY 15; CORD15
OMIM:613668 MICROCEPHALY, POSTNATAL PROGRESSIVE, WITH SEIZURES AND BRAIN ATROPHY
OMIM:613680 BEAULIEU-BOYCOTT-INNES SYNDROME; BBIS
OMIM:613684 RUBINSTEIN-TAYBI SYNDROME 2; RSTS2
OMIM:613690 CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 7; CMH7
OMIM:613706 NOONAN SYNDROME 7; NS7
OMIM:613722 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 12; DEE12
OMIM:613731 RETINITIS PIGMENTOSA 4; RP4
OMIM:613744 SPASTIC PARAPLEGIA 51, AUTOSOMAL RECESSIVE; SPG51
OMIM:613750 RETINITIS PIGMENTOSA 27; RP27
OMIM:613756 RETINITIS PIGMENTOSA 49; RP49
OMIM:613767 RETINITIS PIGMENTOSA 45; RP45
OMIM:613794 RETINITIS PIGMENTOSA 20; RP20
OMIM:613809 RETINITIS PIGMENTOSA 39; RP39
OMIM:613810 RETINITIS PIGMENTOSA 43; RP43
OMIM:613811 PONTOCEREBELLAR HYPOPLASIA, TYPE 2D; PCH2D
OMIM:613820 NEPHRONOPHTHISIS 12; NPHP12
OMIM:613835 LEBER CONGENITAL AMAUROSIS 8; LCA8
OMIM:613861 RETINITIS PIGMENTOSA 59; RP59
OMIM:613862 RETINITIS PIGMENTOSA 38; RP38
OMIM:614034 HEME OXYGENASE 1 DEFICIENCY; HMOX1D
OMIM:614065 MYOPATHY, DISTAL, 4; MPD4
OMIM:614173 JOUBERT SYNDROME 13; JBTS13
OMIM:614180 RETINITIS PIGMENTOSA 61; RP61
OMIM:614181 RETINITIS PIGMENTOSA 62; RP62
OMIM:614199 NEPHROTIC SYNDROME, TYPE 5, WITH OR WITHOUT OCULAR ABNORMALITIES; NPHS5
OMIM:614202 RAFIQ SYNDROME; RAFQS
OMIM:614225 WARBURG MICRO SYNDROME 2; WARBM2
OMIM:614254 NEURODEVELOPMENTAL DISORDER WITH OR WITHOUT HYPERKINETIC MOVEMENTS AND SEIZURES, AUTOSOMAL DOMINANT; NDHMSD
OMIM:614255 NESCAV SYNDROME; NESCAVS
OMIM:614299 MULTIPLE MITOCHONDRIAL DYSFUNCTIONS SYNDROME 2 WITH HYPERGLYCINEMIA; MMDS2
OMIM:614381 LEUKODYSTROPHY, HYPOMYELINATING, 8, WITH OR WITHOUT OLIGODONTIA AND/OR HYPOGONADOTROPIC HYPOGONADISM; HLD8
OMIM:614424 JOUBERT SYNDROME 14; JBTS14
OMIM:614500 CONE-ROD DYSTROPHY 16; CORD16
OMIM:614557 EHLERS-DANLOS SYNDROME, KYPHOSCOLIOTIC TYPE, 2; EDSKSCL2
OMIM:614607 COFFIN-SIRIS SYNDROME 2; CSS2
OMIM:614615 JOUBERT SYNDROME 17; JBTS17
OMIM:614669 AURICULOCONDYLAR SYNDROME 2; ARCND2
OMIM:614678 PONTOCEREBELLAR HYPOPLASIA, TYPE 1B; PCH1B
OMIM:614744 FACIAL PARESIS, HEREDITARY CONGENITAL, 3; HCFP3
OMIM:614753 SOTOS SYNDROME 2; SOTOS2
OMIM:614831 SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 13; SCAR13
OMIM:614833 MICROCEPHALY, SHORT STATURE, AND POLYMICROGYRIA WITH OR WITHOUT SEIZURES; MSSP
OMIM:614876 PEROXISOME BIOGENESIS DISORDER 8A (ZELLWEGER); PBD8A
OMIM:614877 PEROXISOME BIOGENESIS DISORDER 8B; PBD8B
OMIM:614932 COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 13; COXPD13
OMIM:614945 DEAFNESS, AUTOSOMAL RECESSIVE 18B; DFNB18B
OMIM:615030 SPASTIC PARAPLEGIA 56, AUTOSOMAL RECESSIVE; SPG56
OMIM:615031 SPASTIC PARAPLEGIA 49, AUTOSOMAL RECESSIVE; SPG49
OMIM:615065 ARTHROGRYPOSIS, DISTAL, TYPE 5D; DA5D
OMIM:615071 ALAZAMI SYNDROME; ALAZS
OMIM:615095 MICROCEPHALY 10, PRIMARY, AUTOSOMAL RECESSIVE; MCPH10
OMIM:615181 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 11; MDDGA11
OMIM:615190 DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE 5; DKCB5
OMIM:615191 LISSENCEPHALY 5; LIS5
OMIM:615268 CEREBELLAR ATAXIA, MENTAL RETARDATION, AND DYSEQUILIBRIUM SYNDROME 4; CAMRQ4
OMIM:615286 MENTAL RETARDATION, AUTOSOMAL RECESSIVE 36; MRT36
OMIM:615352 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 14; MDDGC14
OMIM:615411 CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 3; CDCBM3
OMIM:615412 CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 4; CDCBM4
OMIM:615419 HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 1; IHPRF1
OMIM:615471 MITOCHONDRIAL DNA DEPLETION SYNDROME 13 (ENCEPHALOMYOPATHIC TYPE); MTDPS13
OMIM:615476 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 18; DEE18
OMIM:615485 BAINBRIDGE-ROPERS SYNDROME; BRPS
OMIM:615502 MENTAL RETARDATION, AUTOSOMAL DOMINANT 21; MRD21
OMIM:615546 VAN MALDERGEM SYNDROME 2; VMLDS2
OMIM:615574 ASPARAGINE SYNTHETASE DEFICIENCY; ASNSD
OMIM:615681 SPASTIC PARAPLEGIA 62, AUTOSOMAL RECESSIVE; SPG62
OMIM:615715 BONE MARROW FAILURE SYNDROME 2; BMFS2
OMIM:615716 HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 4; HPMRS4
OMIM:615760 MICROCEPHALY, PROGRESSIVE, WITH SEIZURES AND CEREBRAL AND CEREBELLAR ATROPHY; MSCCA
OMIM:615763 CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 5; CDCBM5
OMIM:615809 PONTOCEREBELLAR HYPOPLASIA, TYPE 9; PCH9
OMIM:615829 XIA-GIBBS SYNDROME; XIGIS
OMIM:615834 MENTAL RETARDATION, AUTOSOMAL DOMINANT 26; MRD26
OMIM:615846 AICARDI-GOUTIERES SYNDROME 7; AGS7
OMIM:615866 COFFIN-SIRIS SYNDROME 9; CSS9
OMIM:615909 DIAMOND-BLACKFAN ANEMIA 13; DBA13
OMIM:615948 OROFACIODIGITAL SYNDROME XIV; OFD14
OMIM:615959 MYOPATHY, CENTRONUCLEAR, 5; CNM5
OMIM:615960 PORETTI-BOLTSHAUSER SYNDROME; PTBHS
OMIM:615973 CONE-ROD DYSTROPHY 20; CORD20
OMIM:615981 BARDET-BIEDL SYNDROME 2; BBS2
OMIM:615982 BARDET-BIEDL SYNDROME 4; BBS4
OMIM:615983 BARDET-BIEDL SYNDROME 5; BBS5
OMIM:615993 BARDET-BIEDL SYNDROME 16; BBS16
OMIM:616051 MICROCEPHALY 13, PRIMARY, AUTOSOMAL RECESSIVE; MCPH13
OMIM:616056 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 26; DEE26
OMIM:616081 PONTOCEREBELLAR HYPOPLASIA, TYPE 1C; PCH1C
OMIM:616094 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 12; MDDGC12
OMIM:616127 SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 17; SCAR17
OMIM:616140 LEUKODYSTROPHY, HYPOMYELINATING, 9; HLD9
OMIM:616155 CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2S; CMT2S
OMIM:616171 MICROCEPHALY AND CHORIORETINOPATHY, AUTOSOMAL RECESSIVE, 2; MCCRP2
OMIM:616199 POLYGLUCOSAN BODY MYOPATHY 2; PGBM2
OMIM:616211 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 28; DEE28
OMIM:616263 NEUROLOGIC, ENDOCRINE, AND PANCREATIC DISEASE, MULTISYSTEM, INFANTILE-ONSET; IMNEPD
OMIM:616266 CONGENITAL CONTRACTURES OF THE LIMBS AND FACE, HYPOTONIA, AND DEVELOPMENTAL DELAY; CLIFAHDD
OMIM:616271 3-METHYLGLUTACONIC ACIDURIA, TYPE VII; MGCA7
OMIM:616277 MITOCHONDRIAL SHORT-CHAIN ENOYL-CoA HYDRATASE 1 DEFICIENCY; ECHS1D
OMIM:616281 NEURODEVELOPMENTAL DISORDER WITH SPASTIC PARAPLEGIA AND MICROCEPHALY; NEDSPM
OMIM:616321 MYASTHENIC SYNDROME, CONGENITAL, 3A, SLOW-CHANNEL; CMS3A
OMIM:616354 SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 20; SCAR20
OMIM:616394 RETINITIS PIGMENTOSA 71; RP71
OMIM:616420 LEUKODYSTROPHY, HYPOMYELINATING, 10; HLD10
OMIM:616421 MYOCLONIC-ATONIC EPILEPSY; MAE
OMIM:616471 BETHLEM MYOPATHY 2; BTHLM2
OMIM:616490 JOUBERT SYNDROME 23; JBTS23
OMIM:616531 POLYMICROGYRIA, PERISYLVIAN, WITH CEREBELLAR HYPOPLASIA AND ARTHROGRYPOSIS; PMGYCHA
OMIM:616544 RETINITIS PIGMENTOSA 73; RP73
OMIM:616562 RETINITIS PIGMENTOSA 74; RP74
OMIM:616564 NOONAN SYNDROME 10; NS10
OMIM:616632 SEIZURES, CORTICAL BLINDNESS, AND MICROCEPHALY SYNDROME; SCBMS
OMIM:616647 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 35; DEE35
OMIM:616649 SPHEROCYTOSIS, TYPE 2; SPH2
OMIM:616651 ROIFMAN SYNDROME; RFMN
OMIM:616654 JOUBERT SYNDROME 24; JBTS24
OMIM:616657 SPASTIC TETRAPLEGIA, THIN CORPUS CALLOSUM, AND PROGRESSIVE MICROCEPHALY; SPATCCM
OMIM:616668 CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2X; CMT2X
OMIM:616683 LEUKODYSTROPHY, HYPOMYELINATING, 12; HLD12
OMIM:616721 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIn; CDG2N
OMIM:616732 OPTIC ATROPHY 10 WITH OR WITHOUT ATAXIA, MENTAL RETARDATION, AND SEIZURES; OPA10
OMIM:616738 RADIOULNAR SYNOSTOSIS WITH AMEGAKARYOCYTIC THROMBOCYTOPENIA 2; RUSAT2
OMIM:616740 IMMUNODEFICIENCY 46; IMD46
OMIM:616789 MENTAL RETARDATION AND DISTINCTIVE FACIAL FEATURES WITH OR WITHOUT CARDIAC DEFECTS; MRFACD
OMIM:616801 HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 2; IHPRF2
OMIM:616875 CEREBELLAR ATROPHY, VISUAL IMPAIRMENT, AND PSYCHOMOTOR RETARDATION; CAVIPMR
OMIM:616892 NEPHROTIC SYNDROME, TYPE 12; NPHS12
OMIM:616900 HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 3; IHPRF3
OMIM:616973 MENTAL RETARDATION, AUTOSOMAL DOMINANT 42; MRD42
OMIM:617011 MACROCEPHALY, DYSMORPHIC FACIES, AND PSYCHOMOTOR RETARDATION; MDFPMR
OMIM:617013 HYPERMANGANESEMIA WITH DYSTONIA 2; HMNDYT2
OMIM:617047 CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 26; CMH26
OMIM:617052 BONE MARROW FAILURE SYNDROME 3; BMFS3
OMIM:617053 MIRAGE SYNDROME; MIRAGE
OMIM:617093 GROWTH RETARDATION, IMPAIRED INTELLECTUAL DEVELOPMENT, HYPOTONIA, AND HEPATOPATHY; GRIDHH
OMIM:617106 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 42; DEE42
OMIM:617120 JOUBERT SYNDROME 27; JBTS27
OMIM:617121 JOUBERT SYNDROME 28; JBTS28
OMIM:617123 RETINITIS PIGMENTOSA 76; RP76
OMIM:617137 FRONTOMETAPHYSEAL DYSPLASIA 2; FMD2
OMIM:617146 ARTHROGRYPOSIS, DISTAL, WITH IMPAIRED PROPRIOCEPTION AND TOUCH; DAIPT
OMIM:617183 HAREL-YOON SYNDROME; HAYOS
OMIM:617193 ENCEPHALOPATHY, PROGRESSIVE, EARLY-ONSET, WITH BRAIN ATROPHY AND THIN CORPUS CALLOSUM; PEBAT
OMIM:617222 SUDDEN CARDIAC FAILURE, INFANTILE; SCFI
OMIM:617276 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 48; DEE48
OMIM:617330 HYPOTONIA, ATAXIA, AND DELAYED DEVELOPMENT SYNDROME; HADDS
OMIM:617350 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 52; DEE52
OMIM:617397 PSEUDO-TORCH SYNDROME 2; PTORCH2
OMIM:617433 RETINITIS PIGMENTOSA 78; RP78
OMIM:617443 BLEEDING DISORDER, PLATELET-TYPE, 21; BDPLT21
OMIM:617460 RETINITIS PIGMENTOSA 79; RP79
OMIM:617481 NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, HYPOTONIA, AND VARIABLE BRAIN ANOMALIES; NMIHBA
OMIM:617537 RAHMAN SYNDROME; RMNS
OMIM:617547 RETINAL DYSTROPHY WITH OR WITHOUT MACULAR STAPHYLOMA; RDMS
OMIM:617622 JOUBERT SYNDROME 30; JBTS30
OMIM:617675 MYOPATHY, MITOCHONDRIAL, AND ATAXIA; MMYAT
OMIM:617681 BLEPHAROCHEILODONTIC SYNDROME 2; BCDS2
OMIM:617694 AL KAISSI SYNDROME; ALKAS
OMIM:617781 RETINITIS PIGMENTOSA 80; RP80
OMIM:617805 RENAL HYPODYSPLASIA/APLASIA 3; RHDA3
OMIM:617807 NEURODEVELOPMENTAL DISORDER WITH ATAXIC GAIT, ABSENT SPEECH, AND DECREASED CORTICAL WHITE MATTER; NDAGSCW
OMIM:617829 EPILEPTIC ENCEPHALOPATHY, INFANTILE OR EARLY CHILDHOOD, 2; IECEE2
OMIM:617873 COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 35; COXPD35
OMIM:617948 ELLIPTOCYTOSIS 3; EL3
OMIM:617954 MULTIPLE MITOCHONDRIAL DYSFUNCTIONS SYNDROME 6; MMDS6
OMIM:618056 NEURODEVELOPMENTAL DISORDER WITH CEREBELLAR ATROPHY AND WITH OR WITHOUT SEIZURES; NEDCAS
OMIM:618088 NEURODEVELOPMENTAL DISORDER WITH REGRESSION, ABNORMAL MOVEMENTS, LOSS OF SPEECH, AND SEIZURES; NEDAMSS
OMIM:618129 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL DOMINANT 4; LGMDD4
OMIM:618138 MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 23; LGMDR23
OMIM:618174 CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 9; CDCBM9
OMIM:618225 MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 4; MC1DN4
OMIM:618273 MEGA-CORPUS-CALLOSUM SYNDROME WITH CEREBELLAR HYPOPLASIA AND CORTICAL MALFORMATIONS; MCCCHCM
OMIM:618316 INTELLECTUAL DEVELOPMENTAL DISORDER WITH CARDIAC DEFECTS AND DYSMORPHIC FACIES; IDDCDF
OMIM:618325 LISSENCEPHALY 9 WITH COMPLEX BRAINSTEM MALFORMATION; LIS9
OMIM:618404 LEUKODYSTROPHY, HYPOMYELINATING, 18; HLD18
OMIM:618512 O\\'DONNELL-LURIA-RODAN SYNDROME; ODLURO
OMIM:614921 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE It; CDG1T
" + }, + "url": "https://omim.org/", + "version": "0.1.0", + "name": "OMIM", + "title": "Online Mendelian Inheritance in Man", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "An online database that describes the function and phenotypes associated with human genes", + "caseSensitive": true, + "content": "fragment", + "count": 497, + "concept": [ + { + "code": "OMIM:613801", + "display": "Retinitis pigmentosa-40" + }, + { + "code": "OMIM:213300", + "display": "Joubert syndrome 1" + }, + { + "code": "OMIM:615780", + "display": "Retinitis pigmentosa 69" + }, + { + "code": "OMIM:613826", + "display": "Leber congenital amaurosis 6" + }, + { + "code": "OMIM:310200", + "display": "Duchenne muscular dystrophy" + }, + { + "code": "OMIM:617194", + "display": "Lethal congenital contracture syndrome 11" + }, + { + "code": "OMIM:105400", + "display": "AMYOTROPHIC LATERAL SCLEROSIS 1; ALS1" + }, + { + "code": "OMIM:108120", + "display": "ARTHROGRYPOSIS, DISTAL, TYPE 1A; DA1A" + }, + { + "code": "OMIM:114300", + "display": "ARTHROGRYPOSIS, DISTAL, TYPE 3; DA3" + }, + { + "code": "OMIM:115195", + "display": "CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 2; CMH2" + }, + { + "code": "OMIM:115196", + "display": "CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 3; CMH3" + }, + { + "code": "OMIM:115197", + "display": "CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 4; CMH4" + }, + { + "code": "OMIM:115200", + "display": "CARDIOMYOPATHY, DILATED, 1A; CMD1A" + }, + { + "code": "OMIM:117000", + "display": "CENTRAL CORE DISEASE OF MUSCLE; CCD" + }, + { + "code": "OMIM:117360", + "display": "SPINOCEREBELLAR ATAXIA 29; SCA29" + }, + { + "code": "OMIM:119530", + "display": "OROFACIAL CLEFT 1; OFC1" + }, + { + "code": "OMIM:122470", + "display": "CORNELIA DE LANGE SYNDROME 1; CDLS1" + }, + { + "code": "OMIM:130600", + "display": "ELLIPTOCYTOSIS 2; EL2" + }, + { + "code": "OMIM:135900", + "display": "COFFIN-SIRIS SYNDROME 1; 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DFNB18B" + }, + { + "code": "OMIM:615030", + "display": "SPASTIC PARAPLEGIA 56, AUTOSOMAL RECESSIVE; SPG56" + }, + { + "code": "OMIM:615031", + "display": "SPASTIC PARAPLEGIA 49, AUTOSOMAL RECESSIVE; SPG49" + }, + { + "code": "OMIM:615065", + "display": "ARTHROGRYPOSIS, DISTAL, TYPE 5D; DA5D" + }, + { + "code": "OMIM:615071", + "display": "ALAZAMI SYNDROME; ALAZS" + }, + { + "code": "OMIM:615095", + "display": "MICROCEPHALY 10, PRIMARY, AUTOSOMAL RECESSIVE; MCPH10" + }, + { + "code": "OMIM:615181", + "display": "MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 11; MDDGA11" + }, + { + "code": "OMIM:615190", + "display": "DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE 5; DKCB5" + }, + { + "code": "OMIM:615191", + "display": "LISSENCEPHALY 5; LIS5" + }, + { + "code": "OMIM:615268", + "display": "CEREBELLAR ATAXIA, MENTAL RETARDATION, AND DYSEQUILIBRIUM SYNDROME 4; CAMRQ4" + }, + { + "code": "OMIM:615286", + "display": "MENTAL RETARDATION, AUTOSOMAL RECESSIVE 36; MRT36" + }, + { + "code": "OMIM:615352", + "display": "MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 14; MDDGC14" + }, + { + "code": "OMIM:615411", + "display": "CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 3; CDCBM3" + }, + { + "code": "OMIM:615412", + "display": "CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 4; CDCBM4" + }, + { + "code": "OMIM:615419", + "display": "HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 1; IHPRF1" + }, + { + "code": "OMIM:615471", + "display": "MITOCHONDRIAL DNA DEPLETION SYNDROME 13 (ENCEPHALOMYOPATHIC TYPE); MTDPS13" + }, + { + "code": "OMIM:615476", + "display": "DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 18; DEE18" + }, + { + "code": "OMIM:615485", + "display": "BAINBRIDGE-ROPERS SYNDROME; BRPS" + }, + { + "code": "OMIM:615502", + "display": "MENTAL RETARDATION, AUTOSOMAL DOMINANT 21; MRD21" + }, + { + "code": "OMIM:615546", + "display": "VAN MALDERGEM SYNDROME 2; VMLDS2" + }, + { + "code": "OMIM:615574", + "display": "ASPARAGINE SYNTHETASE DEFICIENCY; ASNSD" + }, + { + "code": "OMIM:615681", + "display": "SPASTIC PARAPLEGIA 62, AUTOSOMAL RECESSIVE; SPG62" + }, + { + "code": "OMIM:615715", + "display": "BONE MARROW FAILURE SYNDROME 2; BMFS2" + }, + { + "code": "OMIM:615716", + "display": "HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 4; HPMRS4" + }, + { + "code": "OMIM:615760", + "display": "MICROCEPHALY, PROGRESSIVE, WITH SEIZURES AND CEREBRAL AND CEREBELLAR ATROPHY; MSCCA" + }, + { + "code": "OMIM:615763", + "display": "CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 5; CDCBM5" + }, + { + "code": "OMIM:615809", + "display": "PONTOCEREBELLAR HYPOPLASIA, TYPE 9; PCH9" + }, + { + "code": "OMIM:615829", + "display": "XIA-GIBBS SYNDROME; XIGIS" + }, + { + "code": "OMIM:615834", + "display": "MENTAL RETARDATION, AUTOSOMAL DOMINANT 26; MRD26" + }, + { + "code": "OMIM:615846", + "display": "AICARDI-GOUTIERES SYNDROME 7; AGS7" + }, + { + "code": "OMIM:615866", + "display": "COFFIN-SIRIS SYNDROME 9; CSS9" + }, + { + "code": "OMIM:615909", + "display": "DIAMOND-BLACKFAN ANEMIA 13; DBA13" + }, + { + "code": "OMIM:615948", + "display": "OROFACIODIGITAL SYNDROME XIV; OFD14" + }, + { + "code": "OMIM:615959", + "display": "MYOPATHY, CENTRONUCLEAR, 5; CNM5" + }, + { + "code": "OMIM:615960", + "display": "PORETTI-BOLTSHAUSER SYNDROME; PTBHS" + }, + { + "code": "OMIM:615973", + "display": "CONE-ROD DYSTROPHY 20; CORD20" + }, + { + "code": "OMIM:615981", + "display": "BARDET-BIEDL SYNDROME 2; BBS2" + }, + { + "code": "OMIM:615982", + "display": "BARDET-BIEDL SYNDROME 4; BBS4" + }, + { + "code": "OMIM:615983", + "display": "BARDET-BIEDL SYNDROME 5; BBS5" + }, + { + "code": "OMIM:615993", + "display": "BARDET-BIEDL SYNDROME 16; BBS16" + }, + { + "code": "OMIM:616051", + "display": "MICROCEPHALY 13, PRIMARY, AUTOSOMAL RECESSIVE; MCPH13" + }, + { + "code": "OMIM:616056", + "display": "DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 26; DEE26" + }, + { + "code": "OMIM:616081", + "display": "PONTOCEREBELLAR HYPOPLASIA, TYPE 1C; PCH1C" + }, + { + "code": "OMIM:616094", + "display": "MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 12; MDDGC12" + }, + { + "code": "OMIM:616127", + "display": "SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 17; SCAR17" + }, + { + "code": "OMIM:616140", + "display": "LEUKODYSTROPHY, HYPOMYELINATING, 9; HLD9" + }, + { + "code": "OMIM:616155", + "display": "CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2S; CMT2S" + }, + { + "code": "OMIM:616171", + "display": "MICROCEPHALY AND CHORIORETINOPATHY, AUTOSOMAL RECESSIVE, 2; MCCRP2" + }, + { + "code": "OMIM:616199", + "display": "POLYGLUCOSAN BODY MYOPATHY 2; PGBM2" + }, + { + "code": "OMIM:616211", + "display": "DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 28; DEE28" + }, + { + "code": "OMIM:616263", + "display": "NEUROLOGIC, ENDOCRINE, AND PANCREATIC DISEASE, MULTISYSTEM, INFANTILE-ONSET; IMNEPD" + }, + { + "code": "OMIM:616266", + "display": "CONGENITAL CONTRACTURES OF THE LIMBS AND FACE, HYPOTONIA, AND DEVELOPMENTAL DELAY; CLIFAHDD" + }, + { + "code": "OMIM:616271", + "display": "3-METHYLGLUTACONIC ACIDURIA, TYPE VII; MGCA7" + }, + { + "code": "OMIM:616277", + "display": "MITOCHONDRIAL SHORT-CHAIN ENOYL-CoA HYDRATASE 1 DEFICIENCY; ECHS1D" + }, + { + "code": "OMIM:616281", + "display": "NEURODEVELOPMENTAL DISORDER WITH SPASTIC PARAPLEGIA AND MICROCEPHALY; NEDSPM" + }, + { + "code": "OMIM:616321", + "display": "MYASTHENIC SYNDROME, CONGENITAL, 3A, SLOW-CHANNEL; CMS3A" + }, + { + "code": "OMIM:616354", + "display": "SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 20; SCAR20" + }, + { + "code": "OMIM:616394", + "display": "RETINITIS PIGMENTOSA 71; RP71" + }, + { + "code": "OMIM:616420", + "display": "LEUKODYSTROPHY, HYPOMYELINATING, 10; HLD10" + }, + { + "code": "OMIM:616421", + "display": "MYOCLONIC-ATONIC EPILEPSY; MAE" + }, + { + "code": "OMIM:616471", + "display": "BETHLEM MYOPATHY 2; BTHLM2" + }, + { + "code": "OMIM:616490", + "display": "JOUBERT SYNDROME 23; JBTS23" + }, + { + "code": "OMIM:616531", + "display": "POLYMICROGYRIA, PERISYLVIAN, WITH CEREBELLAR HYPOPLASIA AND ARTHROGRYPOSIS; PMGYCHA" + }, + { + "code": "OMIM:616544", + "display": "RETINITIS PIGMENTOSA 73; RP73" + }, + { + "code": "OMIM:616562", + "display": "RETINITIS PIGMENTOSA 74; RP74" + }, + { + "code": "OMIM:616564", + "display": "NOONAN SYNDROME 10; NS10" + }, + { + "code": "OMIM:616632", + "display": "SEIZURES, CORTICAL BLINDNESS, AND MICROCEPHALY SYNDROME; SCBMS" + }, + { + "code": "OMIM:616647", + "display": "DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 35; DEE35" + }, + { + "code": "OMIM:616649", + "display": "SPHEROCYTOSIS, TYPE 2; SPH2" + }, + { + "code": "OMIM:616651", + "display": "ROIFMAN SYNDROME; RFMN" + }, + { + "code": "OMIM:616654", + "display": "JOUBERT SYNDROME 24; JBTS24" + }, + { + "code": "OMIM:616657", + "display": "SPASTIC TETRAPLEGIA, THIN CORPUS CALLOSUM, AND PROGRESSIVE MICROCEPHALY; SPATCCM" + }, + { + "code": "OMIM:616668", + "display": "CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2X; CMT2X" + }, + { + "code": "OMIM:616683", + "display": "LEUKODYSTROPHY, HYPOMYELINATING, 12; HLD12" + }, + { + "code": "OMIM:616721", + "display": "CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIn; CDG2N" + }, + { + "code": "OMIM:616732", + "display": "OPTIC ATROPHY 10 WITH OR WITHOUT ATAXIA, MENTAL RETARDATION, AND SEIZURES; OPA10" + }, + { + "code": "OMIM:616738", + "display": "RADIOULNAR SYNOSTOSIS WITH AMEGAKARYOCYTIC THROMBOCYTOPENIA 2; RUSAT2" + }, + { + "code": "OMIM:616740", + "display": "IMMUNODEFICIENCY 46; IMD46" + }, + { + "code": "OMIM:616789", + "display": "MENTAL RETARDATION AND DISTINCTIVE FACIAL FEATURES WITH OR WITHOUT CARDIAC DEFECTS; MRFACD" + }, + { + "code": "OMIM:616801", + "display": "HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 2; IHPRF2" + }, + { + "code": "OMIM:616875", + "display": "CEREBELLAR ATROPHY, VISUAL IMPAIRMENT, AND PSYCHOMOTOR RETARDATION; CAVIPMR" + }, + { + "code": "OMIM:616892", + "display": "NEPHROTIC SYNDROME, TYPE 12; NPHS12" + }, + { + "code": "OMIM:616900", + "display": "HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 3; IHPRF3" + }, + { + "code": "OMIM:616973", + "display": "MENTAL RETARDATION, AUTOSOMAL DOMINANT 42; MRD42" + }, + { + "code": "OMIM:617011", + "display": "MACROCEPHALY, DYSMORPHIC FACIES, AND PSYCHOMOTOR RETARDATION; MDFPMR" + }, + { + "code": "OMIM:617013", + "display": "HYPERMANGANESEMIA WITH DYSTONIA 2; HMNDYT2" + }, + { + "code": "OMIM:617047", + "display": "CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 26; CMH26" + }, + { + "code": "OMIM:617052", + "display": "BONE MARROW FAILURE SYNDROME 3; BMFS3" + }, + { + "code": "OMIM:617053", + "display": "MIRAGE SYNDROME; MIRAGE" + }, + { + "code": "OMIM:617093", + "display": "GROWTH RETARDATION, IMPAIRED INTELLECTUAL DEVELOPMENT, HYPOTONIA, AND HEPATOPATHY; GRIDHH" + }, + { + "code": "OMIM:617106", + "display": "DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 42; DEE42" + }, + { + "code": "OMIM:617120", + "display": "JOUBERT SYNDROME 27; JBTS27" + }, + { + "code": "OMIM:617121", + "display": "JOUBERT SYNDROME 28; JBTS28" + }, + { + "code": "OMIM:617123", + "display": "RETINITIS PIGMENTOSA 76; RP76" + }, + { + "code": "OMIM:617137", + "display": "FRONTOMETAPHYSEAL DYSPLASIA 2; FMD2" + }, + { + "code": "OMIM:617146", + "display": "ARTHROGRYPOSIS, DISTAL, WITH IMPAIRED PROPRIOCEPTION AND TOUCH; DAIPT" + }, + { + "code": "OMIM:617183", + "display": "HAREL-YOON SYNDROME; HAYOS" + }, + { + "code": "OMIM:617193", + "display": "ENCEPHALOPATHY, PROGRESSIVE, EARLY-ONSET, WITH BRAIN ATROPHY AND THIN CORPUS CALLOSUM; PEBAT" + }, + { + "code": "OMIM:617222", + "display": "SUDDEN CARDIAC FAILURE, INFANTILE; SCFI" + }, + { + "code": "OMIM:617276", + "display": "DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 48; DEE48" + }, + { + "code": "OMIM:617330", + "display": "HYPOTONIA, ATAXIA, AND DELAYED DEVELOPMENT SYNDROME; HADDS" + }, + { + "code": "OMIM:617350", + "display": "DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 52; DEE52" + }, + { + "code": "OMIM:617397", + "display": "PSEUDO-TORCH SYNDROME 2; PTORCH2" + }, + { + "code": "OMIM:617433", + "display": "RETINITIS PIGMENTOSA 78; RP78" + }, + { + "code": "OMIM:617443", + "display": "BLEEDING DISORDER, PLATELET-TYPE, 21; BDPLT21" + }, + { + "code": "OMIM:617460", + "display": "RETINITIS PIGMENTOSA 79; RP79" + }, + { + "code": "OMIM:617481", + "display": "NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, HYPOTONIA, AND VARIABLE BRAIN ANOMALIES; NMIHBA" + }, + { + "code": "OMIM:617537", + "display": "RAHMAN SYNDROME; RMNS" + }, + { + "code": "OMIM:617547", + "display": "RETINAL DYSTROPHY WITH OR WITHOUT MACULAR STAPHYLOMA; RDMS" + }, + { + "code": "OMIM:617622", + "display": "JOUBERT SYNDROME 30; JBTS30" + }, + { + "code": "OMIM:617675", + "display": "MYOPATHY, MITOCHONDRIAL, AND ATAXIA; MMYAT" + }, + { + "code": "OMIM:617681", + "display": "BLEPHAROCHEILODONTIC SYNDROME 2; BCDS2" + }, + { + "code": "OMIM:617694", + "display": "AL KAISSI SYNDROME; ALKAS" + }, + { + "code": "OMIM:617781", + "display": "RETINITIS PIGMENTOSA 80; RP80" + }, + { + "code": "OMIM:617805", + "display": "RENAL HYPODYSPLASIA/APLASIA 3; RHDA3" + }, + { + "code": "OMIM:617807", + "display": "NEURODEVELOPMENTAL DISORDER WITH ATAXIC GAIT, ABSENT SPEECH, AND DECREASED CORTICAL WHITE MATTER; NDAGSCW" + }, + { + "code": "OMIM:617829", + "display": "EPILEPTIC ENCEPHALOPATHY, INFANTILE OR EARLY CHILDHOOD, 2; IECEE2" + }, + { + "code": "OMIM:617873", + "display": "COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 35; COXPD35" + }, + { + "code": "OMIM:617948", + "display": "ELLIPTOCYTOSIS 3; EL3" + }, + { + "code": "OMIM:617954", + "display": "MULTIPLE MITOCHONDRIAL DYSFUNCTIONS SYNDROME 6; MMDS6" + }, + { + "code": "OMIM:618056", + "display": "NEURODEVELOPMENTAL DISORDER WITH CEREBELLAR ATROPHY AND WITH OR WITHOUT SEIZURES; NEDCAS" + }, + { + "code": "OMIM:618088", + "display": "NEURODEVELOPMENTAL DISORDER WITH REGRESSION, ABNORMAL MOVEMENTS, LOSS OF SPEECH, AND SEIZURES; NEDAMSS" + }, + { + "code": "OMIM:618129", + "display": "MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL DOMINANT 4; LGMDD4" + }, + { + "code": "OMIM:618138", + "display": "MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 23; LGMDR23" + }, + { + "code": "OMIM:618174", + "display": "CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 9; CDCBM9" + }, + { + "code": "OMIM:618225", + "display": "MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 4; MC1DN4" + }, + { + "code": "OMIM:618273", + "display": "MEGA-CORPUS-CALLOSUM SYNDROME WITH CEREBELLAR HYPOPLASIA AND CORTICAL MALFORMATIONS; MCCCHCM" + }, + { + "code": "OMIM:618316", + "display": "INTELLECTUAL DEVELOPMENTAL DISORDER WITH CARDIAC DEFECTS AND DYSMORPHIC FACIES; IDDCDF" + }, + { + "code": "OMIM:618325", + "display": "LISSENCEPHALY 9 WITH COMPLEX BRAINSTEM MALFORMATION; LIS9" + }, + { + "code": "OMIM:618404", + "display": "LEUKODYSTROPHY, HYPOMYELINATING, 18; HLD18" + }, + { + "code": "OMIM:618512", + "display": "O\\'DONNELL-LURIA-RODAN SYNDROME; ODLURO" + }, + { + "code": "OMIM:614921", + "display": "CONGENITAL DISORDER OF GLYCOSYLATION, TYPE It; CDG1T" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-tbd-codes.json b/tests/fixtures/ncpi/examples/CodeSystem-tbd-codes.json new file mode 100644 index 0000000..bc6e0f7 --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-tbd-codes.json @@ -0,0 +1,136 @@ +{ + "resourceType": "CodeSystem", + "id": "tbd-codes", + "text": { + "status": "generated", + "div": "

This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes defines the following codes:

CodeDisplayDefinition
grouper grouperA means to bundle several observations such as one would find in a genetics test panel.
mode-of-inheritance mode-of-inheritanceThis is actually LOINC code 79742-3. And the IG will be updated
effect-transporter-function effect-transporter-functionPredicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.
effect-medication-efficacy Medication Efficacy
effect-medication-metabolism Medication Metabolism
effect-medication-transporter Medication Transporter Function
effect-high-risk-allele High Risk Allele
prognostic-implication Prognostic Implication componentFinding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions.
associated-cancer associated-cancer
associated-therapy Genomically linked therapyThe non-medication therapy (procedure) associated with this implication.
region-coverage region-coverageGiven as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence.
functional-annotation functional-annotationAnnotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.
exact-start-end Variant exact start and endThe genomic coordinates of the exact genomic range in which the variant resides.
inner-start-end Variant inner start and endThe genomic coordinates of the inner genomic range in which the variant might reside.
outer-start-end Variant outer start and endThe genomic coordinates of the outer genomic range in which the variant might reside.
variant-inheritance Variant inheritanceA quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.
diagnostic-implication Diagnostic ImplicationAn observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.
therapeutic-implication Therapeutic ImplicationAn observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.
" + }, + "url": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", + "version": "0.1.0", + "name": "TbdCodes", + "title": "ToBeDeterminedCodes ('TbdCodes')", + "status": "active", + "date": "2020-11-12T19:37:28+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.", + "jurisdiction": [ + { + "coding": [ + { + "system": "http://unstats.un.org/unsd/methods/m49/m49.htm", + "code": "001" + } + ] + } + ], + "content": "complete", + "count": 18, + "concept": [ + { + "code": "grouper", + "display": "grouper", + "definition": "A means to bundle several observations such as one would find in a genetics test panel." + }, + { + "code": "mode-of-inheritance", + "display": "mode-of-inheritance", + "definition": "This is actually LOINC code 79742-3. And the IG will be updated" + }, + { + "code": "effect-transporter-function", + "display": "effect-transporter-function", + "definition": "Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance." + }, + { + "code": "effect-medication-efficacy", + "display": "Medication Efficacy" + }, + { + "code": "effect-medication-metabolism", + "display": "Medication Metabolism" + }, + { + "code": "effect-medication-transporter", + "display": "Medication Transporter Function" + }, + { + "code": "effect-high-risk-allele", + "display": "High Risk Allele" + }, + { + "code": "prognostic-implication", + "display": "Prognostic Implication component", + "definition": "Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions." + }, + { + "code": "associated-cancer", + "display": "associated-cancer" + }, + { + "code": "associated-therapy", + "display": "Genomically linked therapy", + "definition": "The non-medication therapy (procedure) associated with this implication." + }, + { + "code": "region-coverage", + "display": "region-coverage", + "definition": "Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence." + }, + { + "code": "functional-annotation", + "display": "functional-annotation", + "definition": "Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537." + }, + { + "code": "exact-start-end", + "display": "Variant exact start and end", + "definition": "The genomic coordinates of the exact genomic range in which the variant resides." + }, + { + "code": "inner-start-end", + "display": "Variant inner start and end", + "definition": "The genomic coordinates of the inner genomic range in which the variant might reside." + }, + { + "code": "outer-start-end", + "display": "Variant outer start and end", + "definition": "The genomic coordinates of the outer genomic range in which the variant might reside." + }, + { + "code": "variant-inheritance", + "display": "Variant inheritance", + "definition": "A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762." + }, + { + "code": "diagnostic-implication", + "display": "Diagnostic Implication", + "definition": "An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition." + }, + { + "code": "therapeutic-implication", + "display": "Therapeutic Implication", + "definition": "An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy." + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/CodeSystem-v3-hgvs.json b/tests/fixtures/ncpi/examples/CodeSystem-v3-hgvs.json new file mode 100644 index 0000000..9910756 --- /dev/null +++ b/tests/fixtures/ncpi/examples/CodeSystem-v3-hgvs.json @@ -0,0 +1,320 @@ +{ + "resourceType": "CodeSystem", + "id": "v3-hgvs", + "text": { + "status": "generated", + "div": "

This code system http://varnomen.hgvs.org defines the following codes:

CodeDisplay
c.10283T>G c.10283T>G
c.1090delA c.1090delA
c.1100 G>T c.1100 G>T
c.1130G>A c.1130G>A
c.11521C>G c.11521C>G
c.1152_1170del c.1152_1170del
c.1243A>C c.1243A>C
c.1378C>T c.1378C>T
c.1528 G>C c.1528 G>C
c.1558C>T c.1558C>T
c.1559C>T c.1559C>T
c.158G>T c.158G>T
c.1640A>G c.1640A>G
c.1720C>T c.1720C>T
c.1823T>G c.1823T>G
c.2056+1G>T c.2056+1G>T
c.2159 A>T c.2159 A>T
c.223delG c.223delG
c.2258C>G c.2258C>G
c.226C>T c.226C>T
c.2303C>T c.2303C>T
c.2332G>A c.2332G>A
c.2405G>T c.2405G>T
c.2471T>C c.2471T>C
c.2539_2541del c.2539_2541del
c.257 G>A c.257 G>A
c.265T>A c.265T>A
c.2662G>A c.2662G>A
c.2674C>A c.2674C>A
c.26_28delAGC c.26_28delAGC
c.296 C>T c.296 C>T
c.314delA c.314delA
c.320del c.320del
c.3478G>A c.3478G>A
c.349 C>T c.349 C>T
c.350delC c.350delC
c.4009 G>A c.4009 G>A
c.416T>G c.416T>G
c.441_457del c.441_457del
c.448 C>G c.448 C>G
c.481C>G c.481C>G
c.5 A>G c.5 A>G
c.5294G>A c.5294G>A
c.5375C>T c.5375C>T
c.5380C>T c.5380C>T
c.5549C>G c.5549C>G
c.5693 G>A c.5693 G>A
c.619 G>A c.619 G>A
c.685+1G>C c.685+1G>C
c.7003C>T c.7003C>T
c.700C>A c.700C>A
c.716C>G c.716C>G
c.760 C>A c.760 C>A
c.7955G>A c.7955G>A
c.7975C>T c.7975C>T
c.8056C>G c.8056C>G
c.851G>C c.851G>C
c.863_864insACCT c.863_864insACCT
c.868G>A c.868G>A
c.931C>T c.931C>T
c.9552G>A c.9552G>A
c.959C>T c.959C>T
c.[711G>T;712C>A] c.[711G>T;712C>A]
p.(Arg2659Trp) p.(Arg2659Trp)
p.(Gln9del) p.(Gln9del)
p.(Leu3428Arg) p.(Leu3428Arg)
p.(Met3184Ile) p.(Met3184Ile)
p.(Pro460Ser) p.(Pro460Ser)
" + }, + "url": "http://varnomen.hgvs.org", + "identifier": [ + { + "system": "urn:ietf:rfc:3986", + "value": "urn:oid:2.16.840.1.113883.6.282" + } + ], + "version": "0.1.0", + "name": "Hgvs", + "title": "Human Genome Variation Society nomenclature", + "status": "active", + "experimental": false, + "date": "2019-03-20T00:00:00-04:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "HGVS nomenclatures are the guidelines for mutation nomenclature made by the Human Genome Variation Society.\n\nHGVS nomenclature can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type should be able to distinguish expressions in HGVS nomenclature from coded concepts. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, HGVS nomenclature can be used to as the observation values for DNA sequence variations. For example, OBX|1|CWE|48004-6^DNA Sequence Variation^LN||c.1129C>T^^HGVS|\n\nVersioning information: The HGVS nomenclature for the description of sequence variants was last modified Feb 20, 2008. The HGVS nomenclature for the description of protein sequence variants was last modified May 12, 2007. The HGVS nomenclature for the description of DNA sequence variants was last modified June 15, 2007 The HGVS nomenclature for the description of RNA sequence variants was last modified May 12, 2007\n\nHGVS nomenclatures can be used freely by the public.", + "content": "complete", + "count": 68, + "concept": [ + { + "code": "c.10283T>G", + "display": "c.10283T>G" + }, + { + "code": "c.1090delA", + "display": "c.1090delA" + }, + { + "code": "c.1100 G>T", + "display": "c.1100 G>T" + }, + { + "code": "c.1130G>A", + "display": "c.1130G>A" + }, + { + "code": "c.11521C>G", + "display": "c.11521C>G" + }, + { + "code": "c.1152_1170del", + "display": "c.1152_1170del" + }, + { + "code": "c.1243A>C", + "display": "c.1243A>C" + }, + { + "code": "c.1378C>T", + "display": "c.1378C>T" + }, + { + "code": "c.1528 G>C", + "display": "c.1528 G>C" + }, + { + "code": "c.1558C>T", + "display": "c.1558C>T" + }, + { + "code": "c.1559C>T", + "display": "c.1559C>T" + }, + { + "code": "c.158G>T", + "display": "c.158G>T" + }, + { + "code": "c.1640A>G", + "display": "c.1640A>G" + }, + { + "code": "c.1720C>T", + "display": "c.1720C>T" + }, + { + "code": "c.1823T>G", + "display": "c.1823T>G" + }, + { + "code": "c.2056+1G>T", + "display": "c.2056+1G>T" + }, + { + "code": "c.2159 A>T", + "display": "c.2159 A>T" + }, + { + "code": "c.223delG", + "display": "c.223delG" + }, + { + "code": "c.2258C>G", + "display": "c.2258C>G" + }, + { + "code": "c.226C>T", + "display": "c.226C>T" + }, + { + "code": "c.2303C>T", + "display": "c.2303C>T" + }, + { + "code": "c.2332G>A", + "display": "c.2332G>A" + }, + { + "code": "c.2405G>T", + "display": "c.2405G>T" + }, + { + "code": "c.2471T>C", + "display": "c.2471T>C" + }, + { + "code": "c.2539_2541del", + "display": "c.2539_2541del" + }, + { + "code": "c.257 G>A", + "display": "c.257 G>A" + }, + { + "code": "c.265T>A", + "display": "c.265T>A" + }, + { + "code": "c.2662G>A", + "display": "c.2662G>A" + }, + { + "code": "c.2674C>A", + "display": "c.2674C>A" + }, + { + "code": "c.26_28delAGC", + "display": "c.26_28delAGC" + }, + { + "code": "c.296 C>T", + "display": "c.296 C>T" + }, + { + "code": "c.314delA", + "display": "c.314delA" + }, + { + "code": "c.320del", + "display": "c.320del" + }, + { + "code": "c.3478G>A", + "display": "c.3478G>A" + }, + { + "code": "c.349 C>T", + "display": "c.349 C>T" + }, + { + "code": "c.350delC", + "display": "c.350delC" + }, + { + "code": "c.4009 G>A", + "display": "c.4009 G>A" + }, + { + "code": "c.416T>G", + "display": "c.416T>G" + }, + { + "code": "c.441_457del", + "display": "c.441_457del" + }, + { + "code": "c.448 C>G", + "display": "c.448 C>G" + }, + { + "code": "c.481C>G", + "display": "c.481C>G" + }, + { + "code": "c.5 A>G", + "display": "c.5 A>G" + }, + { + "code": "c.5294G>A", + "display": "c.5294G>A" + }, + { + "code": "c.5375C>T", + "display": "c.5375C>T" + }, + { + "code": "c.5380C>T", + "display": "c.5380C>T" + }, + { + "code": "c.5549C>G", + "display": "c.5549C>G" + }, + { + "code": "c.5693 G>A", + "display": "c.5693 G>A" + }, + { + "code": "c.619 G>A", + "display": "c.619 G>A" + }, + { + "code": "c.685+1G>C", + "display": "c.685+1G>C" + }, + { + "code": "c.7003C>T", + "display": "c.7003C>T" + }, + { + "code": "c.700C>A", + "display": "c.700C>A" + }, + { + "code": "c.716C>G", + "display": "c.716C>G" + }, + { + "code": "c.760 C>A", + "display": "c.760 C>A" + }, + { + "code": "c.7955G>A", + "display": "c.7955G>A" + }, + { + "code": "c.7975C>T", + "display": "c.7975C>T" + }, + { + "code": "c.8056C>G", + "display": "c.8056C>G" + }, + { + "code": "c.851G>C", + "display": "c.851G>C" + }, + { + "code": "c.863_864insACCT", + "display": "c.863_864insACCT" + }, + { + "code": "c.868G>A", + "display": "c.868G>A" + }, + { + "code": "c.931C>T", + "display": "c.931C>T" + }, + { + "code": "c.9552G>A", + "display": "c.9552G>A" + }, + { + "code": "c.959C>T", + "display": "c.959C>T" + }, + { + "code": "c.[711G>T;712C>A]", + "display": "c.[711G>T;712C>A]" + }, + { + "code": "p.(Arg2659Trp)", + "display": "p.(Arg2659Trp)" + }, + { + "code": "p.(Gln9del)", + "display": "p.(Gln9del)" + }, + { + "code": "p.(Leu3428Arg)", + "display": "p.(Leu3428Arg)" + }, + { + "code": "p.(Met3184Ile)", + "display": "p.(Met3184Ile)" + }, + { + "code": "p.(Pro460Ser)", + "display": "p.(Pro460Ser)" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Condition-disease-example-1.json b/tests/fixtures/ncpi/examples/Condition-disease-example-1.json new file mode 100644 index 0000000..2988ed6 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Condition-disease-example-1.json @@ -0,0 +1,89 @@ +{ + "resourceType": "Condition", + "id": "disease-example-1", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/disease" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"disease-example-1\"

Profile: NCPI Disease

clinicalStatus: Active (Condition Clinical Status Codes#active)

verificationStatus: Affected (ConditionVerificationStatus#confirmed \"Confirmed\")

category: Encounter Diagnosis (Condition Category Codes#encounter-diagnosis)

code: Neuroblastoma (NCI Thesaurus#NCIT:Neuroblastoma)

subject: Patient/patient-example-1 \" SMITH\"

recordedDate:

" + }, + "clinicalStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", + "code": "active", + "display": "Active" + } + ], + "text": "Active" + }, + "verificationStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", + "code": "confirmed", + "display": "Confirmed" + } + ], + "text": "Affected" + }, + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-category", + "code": "encounter-diagnosis", + "display": "Encounter Diagnosis" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "NCIT:Neuroblastoma", + "display": "Neuroblastoma" + } + ], + "text": "Neuroblastoma" + }, + "subject": { + "reference": "Patient/patient-example-1" + }, + "_recordedDate": { + "extension": [ + { + "extension": [ + { + "url": "target", + "valueReference": { + "reference": "Patient/patient-example-1" + } + }, + { + "url": "targetPath", + "valueString": "birthDate" + }, + { + "url": "relationship", + "valueCode": "after" + }, + { + "url": "offset", + "valueDuration": { + "value": 25, + "unit": "d", + "system": "http://unitsofmeasure.org", + "code": "days" + } + } + ], + "url": "http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Condition-phenotype-example-1.json b/tests/fixtures/ncpi/examples/Condition-phenotype-example-1.json new file mode 100644 index 0000000..de7c47b --- /dev/null +++ b/tests/fixtures/ncpi/examples/Condition-phenotype-example-1.json @@ -0,0 +1,67 @@ +{ + "resourceType": "Condition", + "id": "phenotype-example-1", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/phenotype" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"phenotype-example-1\"

Profile: NCPI Phenotype

verificationStatus: Confirmed (ConditionVerificationStatus#confirmed)

code: Present: Vesicoureteral reflux (Human Phenotype Ontology#HP:0000076 \"Vesicoureteral reflux\")

subject: Patient/patient-example-1 \" SMITH\"

recordedDate:

" + }, + "verificationStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", + "code": "confirmed", + "display": "Confirmed" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://purl.obolibrary.org/obo/hp.owl", + "code": "HP:0000076", + "display": "Vesicoureteral reflux" + } + ], + "text": "Present: Vesicoureteral reflux" + }, + "subject": { + "reference": "Patient/patient-example-1" + }, + "_recordedDate": { + "extension": [ + { + "extension": [ + { + "url": "target", + "valueReference": { + "reference": "Patient/patient-example-1" + } + }, + { + "url": "targetPath", + "valueString": "birthDate" + }, + { + "url": "relationship", + "valueCode": "after" + }, + { + "url": "offset", + "valueDuration": { + "value": 2, + "unit": "w", + "system": "http://unitsofmeasure.org", + "code": "weeks" + } + } + ], + "url": "http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/DiagnosticReport-diagnostic-report-1.json b/tests/fixtures/ncpi/examples/DiagnosticReport-diagnostic-report-1.json new file mode 100644 index 0000000..22fd892 --- /dev/null +++ b/tests/fixtures/ncpi/examples/DiagnosticReport-diagnostic-report-1.json @@ -0,0 +1,37 @@ +{ + "resourceType": "DiagnosticReport", + "id": "diagnostic-report-1", + "text": { + "status": "generated", + "div": "

Master HL7 genetic variant reporting panel

SubjectMariah Abigail Smith(OFFICIAL) ?? 2019-06-15

Report Details

CodeValue
Genetic variant assessmentPresent
Diagnostic Implication
" + }, + "extension": [ + { + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/supporting-info", + "valueReference": { + "reference": "Task/task-example-1" + } + } + ], + "status": "final", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81247-9", + "display": "Master HL7 genetic variant reporting panel" + } + ] + }, + "subject": { + "reference": "Patient/patient-example-1" + }, + "result": [ + { + "reference": "Observation/variant-example-1" + }, + { + "reference": "Observation/diagnostic-implication-1" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/DocumentReference-drs-document-reference-example-1.json b/tests/fixtures/ncpi/examples/DocumentReference-drs-document-reference-example-1.json new file mode 100644 index 0000000..b108329 --- /dev/null +++ b/tests/fixtures/ncpi/examples/DocumentReference-drs-document-reference-example-1.json @@ -0,0 +1,21 @@ +{ + "resourceType": "DocumentReference", + "id": "drs-document-reference-example-1", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-document-reference" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"drs-document-reference-example-1\"

Profile: DRS Document Reference

status: current

content

" + }, + "status": "current", + "content": [ + { + "attachment": { + "url": "drs://example.com/ga4gh/drs/v1/objects/0f8c27b9-3300-4249-bb28-f49ffb80e277" + } + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/DocumentReference-research-document-reference-example-1.json b/tests/fixtures/ncpi/examples/DocumentReference-research-document-reference-example-1.json new file mode 100644 index 0000000..12155c2 --- /dev/null +++ b/tests/fixtures/ncpi/examples/DocumentReference-research-document-reference-example-1.json @@ -0,0 +1,34 @@ +{ + "resourceType": "DocumentReference", + "id": "research-document-reference-example-1", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-research-document-reference" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"research-document-reference-example-1\"

Profile: Research Document Reference

status: current

subject: Patient/patient-example-3 \" SMITH\"

custodian: Organization/organization-example-1 \"Amazing Children's Hospital\"

content

Contexts

-Related
*Task/task-example-2
" + }, + "status": "current", + "subject": { + "reference": "Patient/patient-example-3" + }, + "custodian": { + "reference": "Organization/organization-example-1" + }, + "content": [ + { + "attachment": { + "url": "drs://example.com/ga4gh/drs/v1/objects/0f8c27b9-3300-4249-bb28-f49ffb80e277" + } + } + ], + "context": { + "related": [ + { + "reference": "Task/task-example-2" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ImplementationGuide-NCPI-FHIR-Implementation-Guide.json b/tests/fixtures/ncpi/examples/ImplementationGuide-NCPI-FHIR-Implementation-Guide.json new file mode 100644 index 0000000..ac4c47b --- /dev/null +++ b/tests/fixtures/ncpi/examples/ImplementationGuide-NCPI-FHIR-Implementation-Guide.json @@ -0,0 +1,1130 @@ +{ + "resourceType": "ImplementationGuide", + "id": "NCPI-FHIR-Implementation-Guide", + "text": { + "status": "extensions", + "div": "

NCPIFHIRImplementationGuide

The official URL for this implementation guide is: 

https://ncpi-fhir.github.io/ncpi-fhir-ig/ImplementationGuide/NCPI-FHIR-Implementation-Guide

FHIR Implementation Guide for the NIH Cloud Platform Interoperability Effort (NCPI).

\n
" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ImplementationGuide/NCPI-FHIR-Implementation-Guide", + "version": "0.1.0", + "name": "NCPIFHIRImplementationGuide", + "title": "NCPI FHIR Implementation Guide", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "FHIR Implementation Guide for the NIH Cloud Platform Interoperability Effort (NCPI).", + "packageId": "NCPI-FHIR-Implementation-Guide", + "license": "CC0-1.0", + "fhirVersion": [ + "4.0.1" + ], + "dependsOn": [ + { + "id": "hl7_fhir_us_core", + "uri": "http://hl7.org/fhir/us/core/ImplementationGuide/hl7.fhir.us.core", + "packageId": "hl7.fhir.us.core", + "version": "3.1.1" + } + ], + "definition": { + "extension": [ + { + "extension": [ + { + "url": "code", + "valueString": "copyrightyear" + }, + { + "url": "value", + "valueString": "2021+" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "releaselabel" + }, + { + "url": "value", + "valueString": "ci-build" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "path-liquid" + }, + { + "url": "value", + "valueString": "template/liquid" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "path-liquid" + }, + { + "url": "value", + "valueString": "input/liquid" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "path-qa" + }, + { + "url": "value", + "valueString": "temp/qa" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "path-temp" + }, + { + "url": "value", + "valueString": "temp/pages" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "path-output" + }, + { + "url": "value", + "valueString": "output" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "path-suppressed-warnings" + }, + { + "url": "value", + "valueString": "input/ignoreWarnings.txt" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "path-history" + }, + { + "url": "value", + "valueString": "https://ncpi-fhir.github.io/ncpi-fhir-ig/history.html" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "template-html" + }, + { + "url": "value", + "valueString": "template-page.html" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "template-md" + }, + { + "url": "value", + "valueString": "template-page-md.html" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "apply-contact" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "apply-context" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "apply-copyright" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "apply-jurisdiction" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "apply-license" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "apply-publisher" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "apply-version" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + }, + { + "extension": [ + { + "url": "code", + "valueString": "active-tables" + }, + { + "url": "value", + "valueString": "true" + } + ], + "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter" + } + ], + "resource": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:complex-type" + } + ], + "reference": { + "reference": "StructureDefinition/ncpi-drs-attachment" + }, + "name": "DRS Attachment", + "description": "A FHIR Attachment with a DRS url.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:resource" + } + ], + "reference": { + "reference": "StructureDefinition/ncpi-drs-document-reference" + }, + "name": "DRS Document Reference", + "description": "A FHIR Document Reference with an embedded DRS URI. See https://github.com/ga4gh/data-repository-service-schemas.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:resource" + } + ], + "reference": { + "reference": "StructureDefinition/disease" + }, + "name": "NCPI Disease", + "description": "Representation for a disease under study for a given research dataset.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:resource" + } + ], + "reference": { + "reference": "StructureDefinition/family-relationship" + }, + "name": "NCPI Family Relationship", + "description": "Representation of a family relationship.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:resource" + } + ], + "reference": { + "reference": "StructureDefinition/phenotype" + }, + "name": "NCPI Phenotype", + "description": "Representation of phenotypic observations (present or absent)", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:resource" + } + ], + "reference": { + "reference": "StructureDefinition/ncpi-research-document-reference" + }, + "name": "Research Document Reference", + "description": "A FHIR Document Reference created by an analysis task. Context.related = Task ", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:resource" + } + ], + "reference": { + "reference": "StructureDefinition/ncpi-specimen-task" + }, + "name": "Research Task", + "description": "A FHIR analysis task that takes at least one specimen as input and produces at least one document.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "StructureDefinition:extension" + } + ], + "reference": { + "reference": "StructureDefinition/supporting-info" + }, + "name": "Supporting Information", + "description": "Additional information relevant to interpreting/understanding the report.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ValueSet" + } + ], + "reference": { + "reference": "ValueSet/condition-inheritance-vs" + }, + "name": "Condition Inheritance Pattern", + "description": "Value Set for specific ttransmission patterns of a condition in a pedigree", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ValueSet" + } + ], + "reference": { + "reference": "ValueSet/disease-codes" + }, + "name": "Disease Codes", + "description": "This value set includes all codes from this FHIR server's representation of OMIM, Mondo and NICt CodeSystems.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ValueSet" + } + ], + "reference": { + "reference": "ValueSet/loinc-answers" + }, + "name": "LOINC Answers", + "description": "LOINC ANSWERS used by NCPI resources", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ValueSet" + } + ], + "reference": { + "reference": "ValueSet/ncpi-vs" + }, + "name": "NCPI FHIR Codes", + "description": "Codes that would apply to NCPI projects", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ValueSet" + } + ], + "reference": { + "reference": "ValueSet/phenotype-codes" + }, + "name": "Phenotype Codes", + "description": "This value set includes all codes from Human Phenotype Ontology.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ValueSet" + } + ], + "reference": { + "reference": "ValueSet/tbd-codes" + }, + "name": "tbd-codes", + "description": "This value set includes all TBD Codes", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/ConditionInheritanceMode" + }, + "name": "Condition Inheritance Pattern", + "description": "A set of terms that describe the transmission pattern of a condition in a pedigree.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/hpo" + }, + "name": "Human Phenotype Ontology", + "description": "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Please see license of HPO at http://www.human-phenotype-ontology.org", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/v3-hgvs" + }, + "name": "Human Genome Variation Society nomenclature", + "description": "HGVS nomenclatures are the guidelines for mutation nomenclature made by the Human Genome Variation Society.\n\nHGVS nomenclature can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type should be able to distinguish expressions in HGVS nomenclature from coded concepts. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, HGVS nomenclature can be used to as the observation values for DNA sequence variations. For example, OBX|1|CWE|48004-6^DNA Sequence Variation^LN||c.1129C>T^^HGVS|\n\nVersioning information: The HGVS nomenclature for the description of sequence variants was last modified Feb 20, 2008. The HGVS nomenclature for the description of protein sequence variants was last modified May 12, 2007. The HGVS nomenclature for the description of DNA sequence variants was last modified June 15, 2007 The HGVS nomenclature for the description of RNA sequence variants was last modified May 12, 2007\n\nHGVS nomenclatures can be used freely by the public.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/loinc-answers" + }, + "name": "LOINC Answers", + "description": "LOINC ANSWERS used by NCPI resources", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/mondo" + }, + "name": "Mondo Disease Ontology", + "description": "The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. The name Mondo comes from the latin word 'mundus' and means 'for the world.'", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/ncit" + }, + "name": "NCI Thesaurus", + "description": "NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/ncpi" + }, + "name": "NCPI FHIR Codes", + "description": "Codes that would apply to NCPI projects", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/ncpi-data-types" + }, + "name": "Data Types for NCPI Research", + "description": "Data Types for NCPI Research", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/omim" + }, + "name": "Online Mendelian Inheritance in Man", + "description": "An online database that describes the function and phenotypes associated with human genes", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "CodeSystem" + } + ], + "reference": { + "reference": "CodeSystem/tbd-codes" + }, + "name": "ToBeDeterminedCodes ('TbdCodes')", + "description": "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.", + "exampleBoolean": false + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/anvil-summary-cmg" + }, + "name": "Summary detail for Center for Mendelian Genomics", + "description": "Summary detail for Center for Mendelian Genomics", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/anvil-summary-phs000711" + }, + "name": "Baylor Hopkins Center for Mendelian Genomics (BH CMG)", + "description": "Baylor Hopkins Center for Mendelian Genomics (BH CMG)", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/diagnostic-implication-1" + }, + "name": "diagnostic-implication-1", + "description": "Example representation of a known variant found during genetic testing", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "DiagnosticReport" + } + ], + "reference": { + "reference": "DiagnosticReport/diagnostic-report-1" + }, + "name": "diagnostic-report-1", + "description": "Example of a DiagnosticReport which aggregates genetic findings for a given test or run", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Condition" + } + ], + "reference": { + "reference": "Condition/disease-example-1" + }, + "name": "disease-example-1", + "description": "Example of the representation of Disease.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/disease" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "DocumentReference" + } + ], + "reference": { + "reference": "DocumentReference/drs-document-reference-example-1" + }, + "name": "drs-document-reference-example-1", + "description": "Example of the representation of DRS Document Reference.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-document-reference" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/family-relationship-example-1" + }, + "name": "family-relationship-example-1", + "description": "Example of the representation of Family Relationship.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/family-relationship-example-2" + }, + "name": "family-relationship-example-2", + "description": "Example of the representation of Family Relationship.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/family-relationship-example-3" + }, + "name": "family-relationship-example-3", + "description": "Example of the representation of Family Relationship.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/family-relationship-example-4" + }, + "name": "family-relationship-example-4", + "description": "Example of the representation of Family Relationship.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Organization" + } + ], + "reference": { + "reference": "Organization/organization-example-1" + }, + "name": "organization-example-1", + "description": "Example of the representation of Organization.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Patient" + } + ], + "reference": { + "reference": "Patient/patient-example-1" + }, + "name": "patient-example-1", + "description": "Example of the representation of Patient.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Patient" + } + ], + "reference": { + "reference": "Patient/patient-example-2" + }, + "name": "patient-example-2", + "description": "Example of the representation of Patient.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Patient" + } + ], + "reference": { + "reference": "Patient/patient-example-3" + }, + "name": "patient-example-3", + "description": "Example of the representation of Patient.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Condition" + } + ], + "reference": { + "reference": "Condition/phenotype-example-1" + }, + "name": "phenotype-example-1", + "description": "Example of the representation of observed Phenotype.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/phenotype" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Practitioner" + } + ], + "reference": { + "reference": "Practitioner/practitioner-example-1" + }, + "name": "practitioner-example-1", + "description": "Example of the representation of Practitioner.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "PractitionerRole" + } + ], + "reference": { + "reference": "PractitionerRole/practitioner-role-example-1" + }, + "name": "practitioner-role-example-1", + "description": "Example of the representation of Practitioner Role.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "DocumentReference" + } + ], + "reference": { + "reference": "DocumentReference/research-document-reference-example-1" + }, + "name": "research-document-reference-example-1", + "description": "Example of the representation of Research Document Reference.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-research-document-reference" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ResearchStudy" + } + ], + "reference": { + "reference": "ResearchStudy/research-study-cmg" + }, + "name": "research-study-cmg", + "description": "Center for Mendelian Genomics", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ResearchStudy" + } + ], + "reference": { + "reference": "ResearchStudy/research-study-example-1" + }, + "name": "research-study-example-1", + "description": "Example of the representation of Research Study.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ResearchStudy" + } + ], + "reference": { + "reference": "ResearchStudy/research-study-phs000711" + }, + "name": "research-study-phs000711", + "description": "Baylor Hopkins Center for Mendelian Genomics (BH CMG)", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ResearchSubject" + } + ], + "reference": { + "reference": "ResearchSubject/research-subject-example-1" + }, + "name": "research-subject-example-1", + "description": "Example of the representation of Research Subject.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ResearchSubject" + } + ], + "reference": { + "reference": "ResearchSubject/research-subject-example-2" + }, + "name": "research-subject-example-2", + "description": "Example of the representation of Research Subject.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "ResearchSubject" + } + ], + "reference": { + "reference": "ResearchSubject/research-subject-example-3" + }, + "name": "research-subject-example-3", + "description": "Example of the representation of Research Subject.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Specimen" + } + ], + "reference": { + "reference": "Specimen/specimen-example-1" + }, + "name": "specimen-example-1", + "description": "Example of the representation of Specimen.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Task" + } + ], + "reference": { + "reference": "Task/task-example-1" + }, + "name": "task-example-1", + "description": "Example of the representation of Task.", + "exampleBoolean": true + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Task" + } + ], + "reference": { + "reference": "Task/task-example-2" + }, + "name": "task-example-2", + "description": "Example of the representation of Task that points to a ResearchDocumentReference.", + "exampleCanonical": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-specimen-task" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information", + "valueString": "Observation" + } + ], + "reference": { + "reference": "Observation/variant-example-1" + }, + "name": "variant-example-1", + "description": "Example of a fhir representation of a variant", + "exampleBoolean": true + } + ], + "page": { + "nameUrl": "toc.html", + "title": "Table of Contents", + "generation": "html", + "page": [ + { + "nameUrl": "index.html", + "title": "Home", + "generation": "markdown" + }, + { + "nameUrl": "authors.html", + "title": "Authors", + "generation": "markdown" + }, + { + "nameUrl": "background.html", + "title": "Background", + "generation": "markdown" + }, + { + "nameUrl": "contact.html", + "title": "Contact", + "generation": "markdown" + }, + { + "nameUrl": "downloads.html", + "title": "Downloads", + "generation": "markdown" + }, + { + "nameUrl": "use_cases.html", + "title": "Use Cases", + "generation": "markdown" + } + ] + }, + "parameter": [ + { + "code": "path-resource", + "value": "input/capabilities" + }, + { + "code": "path-resource", + "value": "input/examples" + }, + { + "code": "path-resource", + "value": "input/extensions" + }, + { + "code": "path-resource", + "value": "input/models" + }, + { + "code": "path-resource", + "value": "input/operations" + }, + { + "code": "path-resource", + "value": "input/profiles" + }, + { + "code": "path-resource", + "value": "input/resources" + }, + { + "code": "path-resource", + "value": "input/vocabulary" + }, + { + "code": "path-resource", + "value": "input/maps" + }, + { + "code": "path-resource", + "value": "input/testing" + }, + { + "code": "path-resource", + "value": "input/history" + }, + { + "code": "path-resource", + "value": "fsh-generated/resources" + }, + { + "code": "path-pages", + "value": "template/config" + }, + { + "code": "path-pages", + "value": "input/images" + }, + { + "code": "path-tx-cache", + "value": "input-cache/txcache" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-anvil-summary-cmg.json b/tests/fixtures/ncpi/examples/Observation-anvil-summary-cmg.json new file mode 100644 index 0000000..8cb3bfd --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-anvil-summary-cmg.json @@ -0,0 +1,75 @@ +{ + "resourceType": "Observation", + "id": "anvil-summary-cmg", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"anvil-summary-cmg\"

status: final

code: Variable Summary (NCPI FHIR Codes#Summary)

focus: ResearchStudy/research-study-cmg

component

code: Number of Cohorts ([not stated]#CohortCount)

value: 41

component

code: Number of Samples (NCPI FHIR Codes#SampleCount)

value: 807

component

code: Number of Participants (NCPI FHIR Codes#Participant)

value: 807

component

code: Size on Disk ([not stated]#StorageSize)

value: 4.87 TR (Details: UCUM code TR = 'TR')

" + }, + "status": "final", + "code": { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "Summary", + "display": "Variable Summary" + } + ] + }, + "focus": [ + { + "reference": "ResearchStudy/research-study-cmg" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "code": "CohortCount", + "display": "Number of Cohorts" + } + ] + }, + "valueInteger": 41 + }, + { + "code": { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "SampleCount", + "display": "Number of Samples" + } + ] + }, + "valueInteger": 807 + }, + { + "code": { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "Participant", + "display": "Number of Participants" + } + ] + }, + "valueInteger": 807 + }, + { + "code": { + "coding": [ + { + "code": "StorageSize", + "display": "Size on Disk" + } + ] + }, + "valueQuantity": { + "value": 4.87, + "system": "http://unitsofmeasure.org", + "code": "TR" + } + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-anvil-summary-phs000711.json b/tests/fixtures/ncpi/examples/Observation-anvil-summary-phs000711.json new file mode 100644 index 0000000..aacc090 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-anvil-summary-phs000711.json @@ -0,0 +1,128 @@ +{ + "resourceType": "Observation", + "id": "anvil-summary-phs000711", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"anvil-summary-phs000711\"

status: final

code: Variable Summary (NCPI FHIR Codes#Summary)

focus: ResearchStudy/research-study-phs000711

component

code: Number of Samples (NCPI FHIR Codes#SampleCount)

value: 807

component

code: Number of Participants (NCPI FHIR Codes#Participant)

value: 807

component

code: Consent Codes ([not stated]#ConsentCodes)

value: HMB-IRB-NPU

component

code: Terra Workspace Name ([not stated]#TerraWorkspace)

value: AnVIL_CMG_BaylorHopkins_HMB-NPU_WES

component

code: Primary Disease ([not stated]#PrimaryDisease)

value: Mendelian

component

code: Access Type ([not stated]#AccessType)

value: Controlled Access

component

code: StudyDesign ([not stated]#StudyDesign)

value: Mendelian

component

code: DataType ([not stated]#DataType)

value: Exome

component

code: Size on Disk ([not stated]#StorageSize)

value: 4.87 TR (Details: UCUM code TR = 'TR')

" + }, + "status": "final", + "code": { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "Summary", + "display": "Variable Summary" + } + ] + }, + "focus": [ + { + "reference": "ResearchStudy/research-study-phs000711" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "SampleCount", + "display": "Number of Samples" + } + ] + }, + "valueInteger": 807 + }, + { + "code": { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "Participant", + "display": "Number of Participants" + } + ] + }, + "valueInteger": 807 + }, + { + "code": { + "coding": [ + { + "code": "ConsentCodes", + "display": "Consent Codes" + } + ] + }, + "valueString": "HMB-IRB-NPU" + }, + { + "code": { + "coding": [ + { + "code": "TerraWorkspace", + "display": "Terra Workspace Name" + } + ] + }, + "valueString": "AnVIL_CMG_BaylorHopkins_HMB-NPU_WES" + }, + { + "code": { + "coding": [ + { + "code": "PrimaryDisease", + "display": "Primary Disease" + } + ] + }, + "valueString": "Mendelian" + }, + { + "code": { + "coding": [ + { + "code": "AccessType", + "display": "Access Type" + } + ] + }, + "valueString": "Controlled Access" + }, + { + "code": { + "coding": [ + { + "code": "StudyDesign" + } + ] + }, + "valueString": "Mendelian" + }, + { + "code": { + "coding": [ + { + "code": "DataType" + } + ] + }, + "valueString": "Exome" + }, + { + "code": { + "coding": [ + { + "code": "StorageSize", + "display": "Size on Disk" + } + ] + }, + "valueQuantity": { + "value": 4.87, + "system": "http://unitsofmeasure.org", + "code": "TR" + } + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-diagnostic-implication-1.json b/tests/fixtures/ncpi/examples/Observation-diagnostic-implication-1.json new file mode 100644 index 0000000..b96535a --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-diagnostic-implication-1.json @@ -0,0 +1,75 @@ +{ + "resourceType": "Observation", + "id": "diagnostic-implication-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"diagnostic-implication-1\"

status: final

category: Laboratory (Observation Category Codes#laboratory)

code: Diagnostic Implication (ToBeDeterminedCodes ('TbdCodes')#diagnostic-implication)

derivedFrom: Observation/variant-example-1

component

code: mode-of-inheritance (ToBeDeterminedCodes ('TbdCodes')#mode-of-inheritance)

value: Autosomal recessive inheritance (condition-inheritance-vs#HP:0000007)

component

code: Genetic variation clinical significance [Imp] (LOINC#53037-8)

value: Unknown Significance (LOINC#LA6682-4)

" + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", + "code": "diagnostic-implication", + "display": "Diagnostic Implication" + } + ] + }, + "derivedFrom": [ + { + "reference": "Observation/variant-example-1" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", + "code": "mode-of-inheritance", + "display": "mode-of-inheritance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://fhir.ncpi-project-forge.io/ValueSet/condition-inheritance-vs", + "code": "HP:0000007", + "display": "Autosomal recessive inheritance" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance [Imp]" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6682-4", + "display": "Unknown Significance" + } + ] + } + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-family-relationship-example-1.json b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-1.json new file mode 100644 index 0000000..033246b --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-1.json @@ -0,0 +1,41 @@ +{ + "resourceType": "Observation", + "id": "family-relationship-example-1", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"family-relationship-example-1\"

Profile: NCPI Family Relationship

status: final

code: family member (RoleCode#FAMMEMB)

subject: Patient/patient-example-1 \" SMITH\"

focus: Patient/patient-example-2 \" SMITH\"

value: Child (RoleCode#CHILD \"child\")

" + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "FAMMEMB", + "display": "family member" + } + ] + }, + "subject": { + "reference": "Patient/patient-example-1" + }, + "focus": [ + { + "reference": "Patient/patient-example-2" + } + ], + "valueCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "CHILD", + "display": "child" + } + ], + "text": "Child" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-family-relationship-example-2.json b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-2.json new file mode 100644 index 0000000..de52ec5 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-2.json @@ -0,0 +1,41 @@ +{ + "resourceType": "Observation", + "id": "family-relationship-example-2", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"family-relationship-example-2\"

Profile: NCPI Family Relationship

status: final

code: family member (RoleCode#FAMMEMB)

subject: Patient/patient-example-1 \" SMITH\"

focus: Patient/patient-example-3 \" SMITH\"

value: Child (RoleCode#CHILD \"child\")

" + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "FAMMEMB", + "display": "family member" + } + ] + }, + "subject": { + "reference": "Patient/patient-example-1" + }, + "focus": [ + { + "reference": "Patient/patient-example-3" + } + ], + "valueCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "CHILD", + "display": "child" + } + ], + "text": "Child" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-family-relationship-example-3.json b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-3.json new file mode 100644 index 0000000..2e1dcdf --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-3.json @@ -0,0 +1,46 @@ +{ + "resourceType": "Observation", + "id": "family-relationship-example-3", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"family-relationship-example-3\"

Profile: NCPI Family Relationship

status: final

code: family member (RoleCode#FAMMEMB)

subject: Patient/patient-example-2 \" SMITH\"

focus: Patient/patient-example-1 \" SMITH\"

value: Mother (RoleCode#PRN \"parent\"; RoleCode#MTH \"mother\")

" + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "FAMMEMB", + "display": "family member" + } + ] + }, + "subject": { + "reference": "Patient/patient-example-2" + }, + "focus": [ + { + "reference": "Patient/patient-example-1" + } + ], + "valueCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "PRN", + "display": "parent" + }, + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "MTH", + "display": "mother" + } + ], + "text": "Mother" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-family-relationship-example-4.json b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-4.json new file mode 100644 index 0000000..44a95e9 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-family-relationship-example-4.json @@ -0,0 +1,46 @@ +{ + "resourceType": "Observation", + "id": "family-relationship-example-4", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"family-relationship-example-4\"

Profile: NCPI Family Relationship

status: final

code: family member (RoleCode#FAMMEMB)

subject: Patient/patient-example-3 \" SMITH\"

focus: Patient/patient-example-1 \" SMITH\"

value: Father (RoleCode#PRN \"parent\"; RoleCode#FTH \"father\")

" + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "FAMMEMB", + "display": "family member" + } + ] + }, + "subject": { + "reference": "Patient/patient-example-3" + }, + "focus": [ + { + "reference": "Patient/patient-example-1" + } + ], + "valueCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "PRN", + "display": "parent" + }, + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "FTH", + "display": "father" + } + ], + "text": "Father" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Observation-variant-example-1.json b/tests/fixtures/ncpi/examples/Observation-variant-example-1.json new file mode 100644 index 0000000..de9702a --- /dev/null +++ b/tests/fixtures/ncpi/examples/Observation-variant-example-1.json @@ -0,0 +1,215 @@ +{ + "resourceType": "Observation", + "id": "variant-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"variant-example-1\"

status: final

category: Laboratory (Observation Category Codes#laboratory)

code: Genetic variant assessment (LOINC#69548-6)

value: Present (LOINC#LA9633-4)

method: Sequencing (LOINC#LA26398-0)

specimen: Specimen/specimen-example-1: Specimen

component

code: Gene studied ID (LOINC#48018-6)

value: HGNC:6518 (gene#LBR)

component

code: Cytogenetic (chromosome) location (LOINC#48001-2)

value: Chr1 (loinc-answers#LA21254-0)

component

code: Variant exact start and end (ToBeDeterminedCodes ('TbdCodes')#exact-start-end)

value: 225592153-?

component

code: Genomic ref allele [ID] (LOINC#69547-8)

value: T

component

code: Genomic alt allele [ID] (LOINC#69551-0)

value: C

component

code: Allelic state (LOINC#53034-5)

value: Heterozygous (LOINC#LA6706-1)

component

code: Human reference sequence assembly version (LOINC#62374-4)

value: GRCh37 (LOINC#LA14029-5)

component

code: Transcript reference sequence [ID] (LOINC#51958-7)

value: NM_002296.3 (Gene Reference Sequence Collection#NM_002296.3)

component

code: DNA change (c.HGVS) (LOINC#48004-6)

value: c.1640A>G (Human Genome Variation Society nomenclature#c.1640A>G)

" + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6", + "display": "Genetic variant assessment" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA9633-4", + "display": "Present" + } + ] + }, + "method": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA26398-0", + "display": "Sequencing" + } + ] + }, + "specimen": { + "reference": "Specimen/specimen-example-1", + "display": "Specimen" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48018-6", + "display": "Gene studied ID" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/gene", + "code": "LBR", + "display": "HGNC:6518" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48001-2", + "display": "Cytogenetic (chromosome) location" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://fhir.ncpi-project-forge.io/ValueSet/loinc-answers", + "code": "LA21254-0", + "display": "Chr1" + } + ], + "text": "Chr1" + } + }, + { + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", + "code": "exact-start-end", + "display": "Variant exact start and end" + } + ] + }, + "valueRange": { + "low": { + "value": 225592153 + } + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic ref allele [ID]" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69551-0", + "display": "Genomic alt allele [ID]" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53034-5", + "display": "Allelic state" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6706-1", + "display": "Heterozygous" + } + ], + "text": "Heterozygous" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "62374-4", + "display": "Human reference sequence assembly version" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA14029-5", + "display": "GRCh37" + } + ], + "text": "GRCh37" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51958-7", + "display": "Transcript reference sequence [ID]" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.ncbi.nlm.nih.gov/refseq", + "code": "NM_002296.3", + "display": "NM_002296.3" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48004-6", + "display": "DNA change (c.HGVS)" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://varnomen.hgvs.org", + "code": "c.1640A>G", + "display": "c.1640A>G" + } + ] + } + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Organization-organization-example-1.json b/tests/fixtures/ncpi/examples/Organization-organization-example-1.json new file mode 100644 index 0000000..ce40339 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Organization-organization-example-1.json @@ -0,0 +1,43 @@ +{ + "resourceType": "Organization", + "id": "organization-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"organization-example-1\"

active: true

type: Hospital (Organization type#prov \"Healthcare Provider\")

name: Amazing Children's Hospital

telecom: ph: (555) 555-5555(WORK)

address: 3401 Civic Center Blvd., Philadelphia, PA 19104(WORK)

" + }, + "active": true, + "type": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/organization-type", + "code": "prov", + "display": "Healthcare Provider" + } + ], + "text": "Hospital" + } + ], + "name": "Amazing Children's Hospital", + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "work", + "rank": 1 + } + ], + "address": [ + { + "use": "work", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Patient-patient-example-1.json b/tests/fixtures/ncpi/examples/Patient-patient-example-1.json new file mode 100644 index 0000000..a9aaec9 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Patient-patient-example-1.json @@ -0,0 +1,182 @@ +{ + "resourceType": "Patient", + "id": "patient-example-1", + "text": { + "status": "extensions", + "div": "

Generated Narrative

Resource \"patient-example-1\"

US Core Race Extension

value: White (Details: urn:oid:2.16.840.1.113883.6.238 code 2106-3 = 'White', stated as 'White')

value: Irish (Details: urn:oid:2.16.840.1.113883.6.238 code 2113-9 = 'Irish', stated as 'Irish')

value: White

US Core Ethnicity Extension

value: Hispanic or Latino (Details: urn:oid:2.16.840.1.113883.6.238 code 2135-2 = 'Hispanic or Latino', stated as 'Hispanic or Latino')

value: Mexican (Details: urn:oid:2.16.840.1.113883.6.238 code 2148-5 = 'Mexican', stated as 'Mexican')

value: Hispanic or Latino

name: Mariah Abigail Smith(OFFICIAL)

telecom: ph: (555) 555-5555(HOME)

gender: female

birthDate: 2019-06-15

address: 3401 Civic Center Blvd., Philadelphia, PA 19104(HOME)

contact

relationship: Parent (contactRole2#C \"Emergency Contact\")

name: Jane Samantha Smith(OFFICIAL)

telecom: ph: (555) 555-5555(HOME)

address: 3401 Civic Center Blvd., Philadelphia, PA 19104(HOME)

gender: female

contact

relationship: Parent (contactRole2#C \"Emergency Contact\")

name: John Samuel Smith(OFFICIAL)

telecom: ph: (555) 555-5555(HOME)

address: 3401 Civic Center Blvd., Philadelphia, PA 19104(HOME)

gender: male

" + }, + "extension": [ + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2106-3", + "display": "White" + } + }, + { + "url": "detailed", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2113-9", + "display": "Irish" + } + }, + { + "url": "text", + "valueString": "White" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2135-2", + "display": "Hispanic or Latino" + } + }, + { + "url": "detailed", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2148-5", + "display": "Mexican" + } + }, + { + "url": "text", + "valueString": "Hispanic or Latino" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity" + } + ], + "name": [ + { + "use": "official", + "text": "Mariah Abigail Smith", + "family": "Smith", + "given": [ + "Mariah", + "Abigail" + ] + } + ], + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "home", + "rank": 1 + } + ], + "gender": "female", + "birthDate": "2019-06-15", + "address": [ + { + "use": "home", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + } + ], + "contact": [ + { + "relationship": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0131", + "code": "C", + "display": "Emergency Contact" + } + ], + "text": "Parent" + } + ], + "name": { + "use": "official", + "text": "Jane Samantha Smith", + "family": "Smith", + "given": [ + "Jane", + "Samantha" + ] + }, + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "home", + "rank": 1 + } + ], + "address": { + "use": "home", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + }, + "gender": "female" + }, + { + "relationship": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0131", + "code": "C", + "display": "Emergency Contact" + } + ], + "text": "Parent" + } + ], + "name": { + "use": "official", + "text": "John Samuel Smith", + "family": "Smith", + "given": [ + "John", + "Samuel" + ] + }, + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "home", + "rank": 1 + } + ], + "address": { + "use": "home", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + }, + "gender": "male" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Patient-patient-example-2.json b/tests/fixtures/ncpi/examples/Patient-patient-example-2.json new file mode 100644 index 0000000..a30e03f --- /dev/null +++ b/tests/fixtures/ncpi/examples/Patient-patient-example-2.json @@ -0,0 +1,130 @@ +{ + "resourceType": "Patient", + "id": "patient-example-2", + "text": { + "status": "extensions", + "div": "

Generated Narrative

Resource \"patient-example-2\"

US Core Race Extension

value: White (Details: urn:oid:2.16.840.1.113883.6.238 code 2106-3 = 'White', stated as 'White')

value: White

US Core Ethnicity Extension

value: Hispanic or Latino (Details: urn:oid:2.16.840.1.113883.6.238 code 2135-2 = 'Hispanic or Latino', stated as 'Hispanic or Latino')

value: Mexican (Details: urn:oid:2.16.840.1.113883.6.238 code 2148-5 = 'Mexican', stated as 'Mexican')

value: Hispanic or Latino

name: Jane Samantha Smith(OFFICIAL)

telecom: ph: (555) 555-5555(HOME)

gender: female

address: 3401 Civic Center Blvd., Philadelphia, PA 19104(HOME)

Contacts

-RelationshipNameTelecomAddressGender
*Spouse (contactRole2#C \"Emergency Contact\")John Samuel Smith(OFFICIAL)ph: (555) 555-5555(HOME)3401 Civic Center Blvd., Philadelphia, PA 19104(HOME)male
" + }, + "extension": [ + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2106-3", + "display": "White" + } + }, + { + "url": "text", + "valueString": "White" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2135-2", + "display": "Hispanic or Latino" + } + }, + { + "url": "detailed", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2148-5", + "display": "Mexican" + } + }, + { + "url": "text", + "valueString": "Hispanic or Latino" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity" + } + ], + "name": [ + { + "use": "official", + "text": "Jane Samantha Smith", + "family": "Smith", + "given": [ + "Jane", + "Samantha" + ] + } + ], + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "home", + "rank": 1 + } + ], + "gender": "female", + "address": [ + { + "use": "home", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + } + ], + "contact": [ + { + "relationship": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0131", + "code": "C", + "display": "Emergency Contact" + } + ], + "text": "Spouse" + } + ], + "name": { + "use": "official", + "text": "John Samuel Smith", + "family": "Smith", + "given": [ + "John", + "Samuel" + ] + }, + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "home", + "rank": 1 + } + ], + "address": { + "use": "home", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + }, + "gender": "male" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Patient-patient-example-3.json b/tests/fixtures/ncpi/examples/Patient-patient-example-3.json new file mode 100644 index 0000000..88afc25 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Patient-patient-example-3.json @@ -0,0 +1,130 @@ +{ + "resourceType": "Patient", + "id": "patient-example-3", + "text": { + "status": "extensions", + "div": "

Generated Narrative

Resource \"patient-example-3\"

US Core Race Extension

value: White (Details: urn:oid:2.16.840.1.113883.6.238 code 2106-3 = 'White', stated as 'White')

value: Irish (Details: urn:oid:2.16.840.1.113883.6.238 code 2113-9 = 'Irish', stated as 'Irish')

value: White

US Core Ethnicity Extension

value: Not Hispanic or Latino (Details: urn:oid:2.16.840.1.113883.6.238 code 2186-5 = 'Not Hispanic or Latino', stated as 'Not Hispanic or Latino')

value: Not Hispanic or Latino

name: John Samuel Smith(OFFICIAL)

telecom: ph: (555) 555-5555(HOME)

gender: male

address: 3401 Civic Center Blvd., Philadelphia, PA 19104(HOME)

Contacts

-RelationshipNameTelecomAddressGender
*Spouse (contactRole2#C \"Emergency Contact\")Jane Samantha Smith(OFFICIAL)ph: (555) 555-5555(HOME)3401 Civic Center Blvd., Philadelphia, PA 19104(HOME)female
" + }, + "extension": [ + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2106-3", + "display": "White" + } + }, + { + "url": "detailed", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2113-9", + "display": "Irish" + } + }, + { + "url": "text", + "valueString": "White" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2186-5", + "display": "Not Hispanic or Latino" + } + }, + { + "url": "text", + "valueString": "Not Hispanic or Latino" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity" + } + ], + "name": [ + { + "use": "official", + "text": "John Samuel Smith", + "family": "Smith", + "given": [ + "Jone", + "Samuel" + ] + } + ], + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "home", + "rank": 1 + } + ], + "gender": "male", + "address": [ + { + "use": "home", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + } + ], + "contact": [ + { + "relationship": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0131", + "code": "C", + "display": "Emergency Contact" + } + ], + "text": "Spouse" + } + ], + "name": { + "use": "official", + "text": "Jane Samantha Smith", + "family": "Smith", + "given": [ + "Jane", + "Samantha" + ] + }, + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "home", + "rank": 1 + } + ], + "address": { + "use": "home", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + }, + "gender": "female" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Practitioner-practitioner-example-1.json b/tests/fixtures/ncpi/examples/Practitioner-practitioner-example-1.json new file mode 100644 index 0000000..c003170 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Practitioner-practitioner-example-1.json @@ -0,0 +1,42 @@ +{ + "resourceType": "Practitioner", + "id": "practitioner-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"practitioner-example-1\"

active: true

name: Jane Samantha Smith(OFFICIAL)

telecom: ph: (555) 555-5555(WORK)

address: 3401 Civic Center Blvd., Philadelphia, PA 19104(WORK)

gender: female

" + }, + "active": true, + "name": [ + { + "use": "official", + "text": "Jane Samantha Smith", + "family": "Smith", + "given": [ + "Jane", + "Samantha" + ] + } + ], + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "work", + "rank": 1 + } + ], + "address": [ + { + "use": "work", + "type": "both", + "text": "3401 Civic Center Blvd., Philadelphia, PA 19104", + "line": [ + "3401 Civic Center Blvd." + ], + "city": "Philadelphia", + "state": "PA", + "postalCode": "19104" + } + ], + "gender": "female" +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/PractitionerRole-practitioner-role-example-1.json b/tests/fixtures/ncpi/examples/PractitionerRole-practitioner-role-example-1.json new file mode 100644 index 0000000..66028de --- /dev/null +++ b/tests/fixtures/ncpi/examples/PractitionerRole-practitioner-role-example-1.json @@ -0,0 +1,35 @@ +{ + "resourceType": "PractitionerRole", + "id": "practitioner-role-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"practitioner-role-example-1\"

active: true

practitioner: Practitioner/practitioner-example-1 \" SMITH\"

organization: Organization/organization-example-1 \"Amazing Children's Hospital\"

code: Principal Investigator (Practitioner role#researcher \"Researcher\")

telecom: ph: (555) 555-5555(WORK)

" + }, + "active": true, + "practitioner": { + "reference": "Practitioner/practitioner-example-1" + }, + "organization": { + "reference": "Organization/organization-example-1" + }, + "code": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/practitioner-role", + "code": "researcher", + "display": "Researcher" + } + ], + "text": "Principal Investigator" + } + ], + "telecom": [ + { + "system": "phone", + "value": "(555) 555-5555", + "use": "work", + "rank": 1 + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ResearchStudy-research-study-cmg.json b/tests/fixtures/ncpi/examples/ResearchStudy-research-study-cmg.json new file mode 100644 index 0000000..fdacfef --- /dev/null +++ b/tests/fixtures/ncpi/examples/ResearchStudy-research-study-cmg.json @@ -0,0 +1,33 @@ +{ + "resourceType": "ResearchStudy", + "id": "research-study-cmg", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"research-study-cmg\"

title: Center for Mendelian Genomics

status: completed

primaryPurposeType: diagnostic ([not stated]#diagnostic)

category: Study Consortium (NCPI FHIR Codes#Consortium)

condition: Mendelian ()

" + }, + "title": "Center for Mendelian Genomics", + "status": "completed", + "primaryPurposeType": { + "coding": [ + { + "code": "diagnostic" + } + ] + }, + "category": [ + { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "Consortium", + "display": "Study Consortium" + } + ] + } + ], + "condition": [ + { + "text": "Mendelian" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ResearchStudy-research-study-example-1.json b/tests/fixtures/ncpi/examples/ResearchStudy-research-study-example-1.json new file mode 100644 index 0000000..4b081da --- /dev/null +++ b/tests/fixtures/ncpi/examples/ResearchStudy-research-study-example-1.json @@ -0,0 +1,13 @@ +{ + "resourceType": "ResearchStudy", + "id": "research-study-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"research-study-example-1\"

title: NCPI Research Study Example 1

status: completed

principalInvestigator: PractitionerRole/practitioner-role-example-1

" + }, + "title": "NCPI Research Study Example 1", + "status": "completed", + "principalInvestigator": { + "reference": "PractitionerRole/practitioner-role-example-1" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ResearchStudy-research-study-phs000711.json b/tests/fixtures/ncpi/examples/ResearchStudy-research-study-phs000711.json new file mode 100644 index 0000000..3011060 --- /dev/null +++ b/tests/fixtures/ncpi/examples/ResearchStudy-research-study-phs000711.json @@ -0,0 +1,38 @@ +{ + "resourceType": "ResearchStudy", + "id": "research-study-phs000711", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"research-study-phs000711\"

title: Baylor Hopkins Center for Mendelian Genomics (BH CMG)

partOf: ResearchStudy/research-study-cmg

status: completed

primaryPurposeType: diagnostic ([not stated]#diagnostic)

category: Study Cohort (NCPI FHIR Codes#StudyCohort)

condition: Mendelian ()

" + }, + "title": "Baylor Hopkins Center for Mendelian Genomics (BH CMG)", + "partOf": [ + { + "reference": "ResearchStudy/research-study-cmg" + } + ], + "status": "completed", + "primaryPurposeType": { + "coding": [ + { + "code": "diagnostic" + } + ] + }, + "category": [ + { + "coding": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig", + "code": "StudyCohort", + "display": "Study Cohort" + } + ] + } + ], + "condition": [ + { + "text": "Mendelian" + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-1.json b/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-1.json new file mode 100644 index 0000000..a7316d8 --- /dev/null +++ b/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-1.json @@ -0,0 +1,15 @@ +{ + "resourceType": "ResearchSubject", + "id": "research-subject-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"research-subject-example-1\"

status: on-study

study: ResearchStudy/research-study-example-1

individual: Patient/patient-example-1 \" SMITH\"

" + }, + "status": "on-study", + "study": { + "reference": "ResearchStudy/research-study-example-1" + }, + "individual": { + "reference": "Patient/patient-example-1" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-2.json b/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-2.json new file mode 100644 index 0000000..ad0c37c --- /dev/null +++ b/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-2.json @@ -0,0 +1,15 @@ +{ + "resourceType": "ResearchSubject", + "id": "research-subject-example-2", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"research-subject-example-2\"

status: on-study

study: ResearchStudy/research-study-example-1

individual: Patient/patient-example-2 \" SMITH\"

" + }, + "status": "on-study", + "study": { + "reference": "ResearchStudy/research-study-example-1" + }, + "individual": { + "reference": "Patient/patient-example-2" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-3.json b/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-3.json new file mode 100644 index 0000000..6c076bf --- /dev/null +++ b/tests/fixtures/ncpi/examples/ResearchSubject-research-subject-example-3.json @@ -0,0 +1,15 @@ +{ + "resourceType": "ResearchSubject", + "id": "research-subject-example-3", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"research-subject-example-3\"

status: on-study

study: ResearchStudy/research-study-example-1

individual: Patient/patient-example-3 \" SMITH\"

" + }, + "status": "on-study", + "study": { + "reference": "ResearchStudy/research-study-example-1" + }, + "individual": { + "reference": "Patient/patient-example-3" + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Specimen-specimen-example-1.json b/tests/fixtures/ncpi/examples/Specimen-specimen-example-1.json new file mode 100644 index 0000000..59e0878 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Specimen-specimen-example-1.json @@ -0,0 +1,112 @@ +{ + "resourceType": "Specimen", + "id": "specimen-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"specimen-example-1\"

type: Solid Tissue (specimenType#TISS \"Tissue\")

subject: Patient/patient-example-1 \" SMITH\"

receivedTime:

Collections

-Collected[x]QuantityMethodBodySite
*50 uL (Details: UCUM code uL = 'uL')Biopsy (SNOMED CT#129314006 \"Biopsy - action\")Central Nervous System (SNOMED CT#21483005 \"Structure of central nervous system\")
" + }, + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0487", + "code": "TISS", + "display": "Tissue" + } + ], + "text": "Solid Tissue" + }, + "subject": { + "reference": "Patient/patient-example-1" + }, + "_receivedTime": { + "extension": [ + { + "extension": [ + { + "url": "target", + "valueReference": { + "reference": "Patient/patient-example-1" + } + }, + { + "url": "targetPath", + "valueString": "birthDate" + }, + { + "url": "relationship", + "valueCode": "after" + }, + { + "url": "offset", + "valueDuration": { + "value": 366, + "unit": "d", + "system": "http://unitsofmeasure.org", + "code": "days" + } + } + ], + "url": "http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime" + } + ] + }, + "collection": { + "_collectedDateTime": { + "extension": [ + { + "extension": [ + { + "url": "target", + "valueReference": { + "reference": "Patient/patient-example-1" + } + }, + { + "url": "targetPath", + "valueString": "birthDate" + }, + { + "url": "relationship", + "valueCode": "after" + }, + { + "url": "offset", + "valueDuration": { + "value": 366, + "unit": "d", + "system": "http://unitsofmeasure.org", + "code": "days" + } + } + ], + "url": "http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime" + } + ] + }, + "quantity": { + "value": 50, + "system": "http://unitsofmeasure.org", + "code": "uL" + }, + "method": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "129314006", + "display": "Biopsy - action" + } + ], + "text": "Biopsy" + }, + "bodySite": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "21483005", + "display": "Structure of central nervous system" + } + ], + "text": "Central Nervous System" + } + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-disease.json b/tests/fixtures/ncpi/examples/StructureDefinition-disease.json new file mode 100644 index 0000000..cef2014 --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-disease.json @@ -0,0 +1,2004 @@ +{ + "resourceType": "StructureDefinition", + "id": "disease", + "text": { + "status": "extensions", + "div": "
\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" Condition 0..*ConditionDetailed information about conditions, problems or diagnoses
\".\"\".\"\".\" code 0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Disease Codes (extensible)

\"doco\" Documentation for this format
" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category", + "valueString": "Clinical.Summary" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category", + "valueCode": "patient" + } + ], + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/disease", + "version": "0.1.0", + "name": "Disease", + "title": "NCPI Disease", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Representation for a disease under study for a given research dataset.", + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "workflow", + "uri": "http://hl7.org/fhir/workflow", + "name": "Workflow Pattern" + }, + { + "identity": "sct-concept", + "uri": "http://snomed.info/conceptdomain", + "name": "SNOMED CT Concept Domain Binding" + }, + { + "identity": "v2", + "uri": "http://hl7.org/v2", + "name": "HL7 v2 Mapping" + }, + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + }, + { + "identity": "w5", + "uri": "http://hl7.org/fhir/fivews", + "name": "FiveWs Pattern Mapping" + }, + { + "identity": "sct-attr", + "uri": "http://snomed.org/attributebinding", + "name": "SNOMED CT Attribute Binding" + } + ], + "kind": "resource", + "abstract": false, + "type": "Condition", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Condition", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "Condition", + "path": "Condition", + "short": "Detailed information about conditions, problems or diagnoses", + "definition": "A clinical condition, problem, diagnosis, or other event, situation, issue, or clinical concept that has risen to a level of concern.", + "min": 0, + "max": "*", + "base": { + "path": "Condition", + "min": 0, + "max": "*" + }, + "constraint": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "Most systems will expect a clinicalStatus to be valued for problem-list-items that are managed over time, but might not need a clinicalStatus for point in time encounter-diagnosis." + } + ], + "key": "con-3", + "severity": "warning", + "human": "Condition.clinicalStatus SHALL be present if verificationStatus is not entered-in-error and category is problem-list-item", + "expression": "clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.select($this='problem-list-item').empty()", + "xpath": "exists(f:clinicalStatus) or exists(f:verificationStatus/f:coding/f:code/@value='entered-in-error') or not(exists(category[@value='problem-list-item']))", + "source": "http://hl7.org/fhir/StructureDefinition/Condition" + }, + { + "key": "con-4", + "severity": "error", + "human": "If condition is abated, then clinicalStatus must be either inactive, resolved, or remission", + "expression": "abatement.empty() or clinicalStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-clinical' and (code='resolved' or code='remission' or code='inactive')).exists()", + "xpath": "not(exists(*[starts-with(local-name(.), 'abatement')])) or exists(f:clinicalStatus/f:coding[f:system/@value='http://terminology.hl7.org/CodeSystem/condition-clinical' and f:code/@value=('resolved', 'remission', 'inactive')])", + "source": "http://hl7.org/fhir/StructureDefinition/Condition" + }, + { + "key": "con-5", + "severity": "error", + "human": "Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error", + "expression": "verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').empty() or clinicalStatus.empty()", + "xpath": "not(exists(f:verificationStatus/f:coding[f:system/@value='http://terminology.hl7.org/CodeSystem/condition-ver-status' and f:code/@value='entered-in-error'])) or not(exists(f:clinicalStatus))", + "source": "http://hl7.org/fhir/StructureDefinition/Condition" + }, + { + "key": "dom-2", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources", + "expression": "contained.contained.empty()", + "xpath": "not(parent::f:contained and f:contained)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-3", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource", + "expression": "contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()", + "xpath": "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-4", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated", + "expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-5", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a security label", + "expression": "contained.meta.security.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:security))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time." + } + ], + "key": "dom-6", + "severity": "warning", + "human": "A resource should have narrative for robust management", + "expression": "text.`div`.exists()", + "xpath": "exists(f:text/h:div)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Entity. Role, or Act" + }, + { + "identity": "workflow", + "map": "Event" + }, + { + "identity": "sct-concept", + "map": "< 243796009 |Situation with explicit context| : 246090004 |Associated finding| = ( ( < 404684003 |Clinical finding| MINUS ( << 420134006 |Propensity to adverse reactions| OR << 473010000 |Hypersensitivity condition| OR << 79899007 |Drug interaction| OR << 69449002 |Drug action| OR << 441742003 |Evaluation finding| OR << 307824009 |Administrative status| OR << 385356007 |Tumor stage finding|)) OR < 272379006 |Event|)" + }, + { + "identity": "v2", + "map": "PPR message" + }, + { + "identity": "rim", + "map": "Observation[classCode=OBS, moodCode=EVN, code=ASSERTION, value id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "Condition.implicitRules", + "path": "Condition.implicitRules", + "short": "A set of rules under which this content was created", + "definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.", + "comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.implicitRules", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "uri" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation", + "isSummary": true + }, + { + "id": "Condition.language", + "path": "Condition.language", + "short": "Language of the resource content", + "definition": "The base language in which the resource is written.", + "comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).", + "min": 0, + "max": "1", + "base": { + "path": "Resource.language", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", + "valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "Language" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "preferred", + "description": "A human language.", + "valueSet": "http://hl7.org/fhir/ValueSet/languages" + } + }, + { + "id": "Condition.text", + "path": "Condition.text", + "short": "Text summary of the resource, for human interpretation", + "definition": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.", + "comment": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.", + "alias": [ + "narrative", + "html", + "xhtml", + "display" + ], + "min": 0, + "max": "1", + "base": { + "path": "DomainResource.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Narrative" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Act.text?" + } + ] + }, + { + "id": "Condition.contained", + "path": "Condition.contained", + "short": "Contained, inline Resources", + "definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.", + "comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.", + "alias": [ + "inline resources", + "anonymous resources", + "contained resources" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.contained", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Resource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.extension", + "path": "Condition.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.modifierExtension", + "path": "Condition.modifierExtension", + "short": "Extensions that cannot be ignored", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them", + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.identifier", + "path": "Condition.identifier", + "short": "External Ids for this condition", + "definition": "Business identifiers assigned to this condition by the performer or other systems which remain constant as the resource is updated and propagates from server to server.", + "comment": "This is a business identifier, not a resource identifier (see [discussion](http://hl7.org/fhir/R4/resource.html#identifiers)). It is best practice for the identifier to only appear on a single resource instance, however business practices may occasionally dictate that multiple resource instances with the same identifier can exist - possibly even with different resource types. For example, multiple Patient and a Person resource instance might share the same social insurance number.", + "requirements": "Allows identification of the condition as it is known by various participating systems and in a way that remains consistent across servers.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.identifier", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "rim", + "map": ".id" + } + ] + }, + { + "id": "Condition.clinicalStatus", + "path": "Condition.clinicalStatus", + "short": "active | recurrence | relapse | inactive | remission | resolved", + "definition": "The clinical status of the condition.", + "comment": "The data type is CodeableConcept because clinicalStatus has some clinical judgment involved, such that there might need to be more specificity than the required FHIR value set allows. For example, a SNOMED coding might allow for additional specificity.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.clinicalStatus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-3", + "con-4", + "con-5" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the status contains codes that mark the condition as no longer active.", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionClinicalStatus" + } + ], + "strength": "required", + "description": "The clinical status of the condition or diagnosis.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-clinical|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "sct-concept", + "map": "< 303105007 |Disease phases|" + }, + { + "identity": "v2", + "map": "PRB-14" + }, + { + "identity": "rim", + "map": "Observation ACT\n.inboundRelationship[typeCode=COMP].source[classCode=OBS, code=\"clinicalStatus\", moodCode=EVN].value" + } + ] + }, + { + "id": "Condition.verificationStatus", + "path": "Condition.verificationStatus", + "short": "unconfirmed | provisional | differential | confirmed | refuted | entered-in-error", + "definition": "The verification status to support the clinical status of the condition.", + "comment": "verificationStatus is not required. For example, when a patient has abdominal pain in the ED, there is not likely going to be a verification status.\nThe data type is CodeableConcept because verificationStatus has some clinical judgment involved, such that there might need to be more specificity than the required FHIR value set allows. For example, a SNOMED coding might allow for additional specificity.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.verificationStatus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-3", + "con-5" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the status contains the code refuted and entered-in-error that mark the Condition as not currently valid.", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionVerificationStatus" + } + ], + "strength": "required", + "description": "The verification status to support or decline the clinical status of the condition or diagnosis.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-ver-status|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "sct-concept", + "map": "< 410514004 |Finding context value|" + }, + { + "identity": "v2", + "map": "PRB-13" + }, + { + "identity": "rim", + "map": "Observation ACT\n.inboundRelationship[typeCode=COMP].source[classCode=OBS, code=\"verificationStatus\", moodCode=EVN].value" + }, + { + "identity": "sct-attr", + "map": "408729009" + } + ] + }, + { + "id": "Condition.category", + "path": "Condition.category", + "short": "problem-list-item | encounter-diagnosis", + "definition": "A category assigned to the condition.", + "comment": "The categorization is often highly contextual and may appear poorly differentiated or not very useful in other contexts.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.category", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionCategory" + } + ], + "strength": "extensible", + "description": "A category assigned to the condition.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-category" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "sct-concept", + "map": "< 404684003 |Clinical finding|" + }, + { + "identity": "v2", + "map": "'problem' if from PRB-3. 'diagnosis' if from DG1 segment in PV1 message" + }, + { + "identity": "rim", + "map": ".code" + } + ] + }, + { + "id": "Condition.severity", + "path": "Condition.severity", + "short": "Subjective severity of condition", + "definition": "A subjective assessment of the severity of the condition as evaluated by the clinician.", + "comment": "Coding of the severity with a terminology is preferred, where possible.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.severity", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionSeverity" + } + ], + "strength": "preferred", + "description": "A subjective assessment of the severity of the condition as evaluated by the clinician.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-severity" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.grade" + }, + { + "identity": "sct-concept", + "map": "< 272141005 |Severities|" + }, + { + "identity": "v2", + "map": "PRB-26 / ABS-3" + }, + { + "identity": "rim", + "map": "Can be pre/post-coordinated into value. Or ./inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"severity\"].value" + }, + { + "identity": "sct-attr", + "map": "246112005" + } + ] + }, + { + "id": "Condition.code", + "path": "Condition.code", + "short": "Identification of the condition, problem or diagnosis", + "definition": "Identification of the condition, problem or diagnosis.", + "requirements": "0..1 to account for primarily narrative only resources.", + "alias": [ + "type" + ], + "min": 0, + "max": "1", + "base": { + "path": "Condition.code", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "strength": "extensible", + "valueSet": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/disease-codes" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.code" + }, + { + "identity": "w5", + "map": "FiveWs.what[x]" + }, + { + "identity": "sct-concept", + "map": "code 246090004 |Associated finding| (< 404684003 |Clinical finding| MINUS\n<< 420134006 |Propensity to adverse reactions| MINUS \n<< 473010000 |Hypersensitivity condition| MINUS \n<< 79899007 |Drug interaction| MINUS\n<< 69449002 |Drug action| MINUS \n<< 441742003 |Evaluation finding| MINUS \n<< 307824009 |Administrative status| MINUS \n<< 385356007 |Tumor stage finding|) \nOR < 413350009 |Finding with explicit context|\nOR < 272379006 |Event|" + }, + { + "identity": "v2", + "map": "PRB-3" + }, + { + "identity": "rim", + "map": ".value" + }, + { + "identity": "sct-attr", + "map": "246090004" + } + ] + }, + { + "id": "Condition.bodySite", + "path": "Condition.bodySite", + "short": "Anatomical location, if relevant", + "definition": "The anatomical location where this condition manifests itself.", + "comment": "Only used if not implicit in code found in Condition.code. If the use case requires attributes from the BodySite resource (e.g. to identify and track separately) then use the standard extension [bodySite](http://hl7.org/fhir/R4/extension-bodysite.html). May be a summary code, or a reference to a very precise definition of the location, or both.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.bodySite", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "BodySite" + } + ], + "strength": "example", + "description": "Codes describing anatomical locations. May include laterality.", + "valueSet": "http://hl7.org/fhir/ValueSet/body-site" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 442083009 |Anatomical or acquired body structure|" + }, + { + "identity": "rim", + "map": ".targetBodySiteCode" + }, + { + "identity": "sct-attr", + "map": "363698007" + } + ] + }, + { + "id": "Condition.subject", + "path": "Condition.subject", + "short": "Who has the condition?", + "definition": "Indicates the patient or group who the condition record is associated with.", + "requirements": "Group is typically used for veterinary or public health use cases.", + "alias": [ + "patient" + ], + "min": 1, + "max": "1", + "base": { + "path": "Condition.subject", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/Group" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.subject" + }, + { + "identity": "w5", + "map": "FiveWs.subject[x]" + }, + { + "identity": "v2", + "map": "PID-3" + }, + { + "identity": "rim", + "map": ".participation[typeCode=SBJ].role[classCode=PAT]" + }, + { + "identity": "w5", + "map": "FiveWs.subject" + } + ] + }, + { + "id": "Condition.encounter", + "path": "Condition.encounter", + "short": "Encounter created as part of", + "definition": "The Encounter during which this Condition was created or to which the creation of this record is tightly associated.", + "comment": "This will typically be the encounter the event occurred within, but some activities may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter. This record indicates the encounter this particular record is associated with. In the case of a \"new\" diagnosis reflecting ongoing/revised information about the condition, this might be distinct from the first encounter in which the underlying condition was first \"known\".", + "min": 0, + "max": "1", + "base": { + "path": "Condition.encounter", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Encounter" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.context" + }, + { + "identity": "w5", + "map": "FiveWs.context" + }, + { + "identity": "v2", + "map": "PV1-19 (+PV1-54)" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]" + } + ] + }, + { + "id": "Condition.onset[x]", + "path": "Condition.onset[x]", + "short": "Estimated or actual date, date-time, or age", + "definition": "Estimated or actual date or date-time the condition began, in the opinion of the clinician.", + "comment": "Age is generally used when the patient reports an age at which the Condition began to occur.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.onset[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + }, + { + "code": "Age" + }, + { + "code": "Period" + }, + { + "code": "Range" + }, + { + "code": "string" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.occurrence[x]" + }, + { + "identity": "w5", + "map": "FiveWs.init" + }, + { + "identity": "v2", + "map": "PRB-16" + }, + { + "identity": "rim", + "map": ".effectiveTime.low or .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"age at onset\"].value" + } + ] + }, + { + "id": "Condition.abatement[x]", + "path": "Condition.abatement[x]", + "short": "When in resolution/remission", + "definition": "The date or estimated date that the condition resolved or went into remission. This is called \"abatement\" because of the many overloaded connotations associated with \"remission\" or \"resolution\" - Conditions are never really resolved, but they can abate.", + "comment": "There is no explicit distinction between resolution and remission because in many cases the distinction is not clear. Age is generally used when the patient reports an age at which the Condition abated. If there is no abatement element, it is unknown whether the condition has resolved or entered remission; applications and users should generally assume that the condition is still valid. When abatementString exists, it implies the condition is abated.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.abatement[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + }, + { + "code": "Age" + }, + { + "code": "Period" + }, + { + "code": "Range" + }, + { + "code": "string" + } + ], + "condition": [ + "con-4" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.done[x]" + }, + { + "identity": "rim", + "map": ".effectiveTime.high or .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"age at remission\"].value or .inboundRelationship[typeCode=SUBJ]source[classCode=CONC, moodCode=EVN].status=completed" + } + ] + }, + { + "id": "Condition.recordedDate", + "path": "Condition.recordedDate", + "short": "Date record was first recorded", + "definition": "The recordedDate represents when this particular Condition record was created in the system, which is often a system-generated date.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.recordedDate", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.recorded" + }, + { + "identity": "v2", + "map": "REL-11" + }, + { + "identity": "rim", + "map": ".participation[typeCode=AUT].time" + } + ] + }, + { + "id": "Condition.recorder", + "path": "Condition.recorder", + "short": "Who recorded the condition", + "definition": "Individual who recorded the record and takes responsibility for its content.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.recorder", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.author" + }, + { + "identity": "rim", + "map": ".participation[typeCode=AUT].role" + } + ] + }, + { + "id": "Condition.asserter", + "path": "Condition.asserter", + "short": "Person who asserts this condition", + "definition": "Individual who is making the condition statement.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.asserter", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.source" + }, + { + "identity": "v2", + "map": "REL-7.1 identifier + REL-7.12 type code" + }, + { + "identity": "rim", + "map": ".participation[typeCode=INF].role" + } + ] + }, + { + "id": "Condition.stage", + "path": "Condition.stage", + "short": "Stage/grade, usually assessed formally", + "definition": "Clinical stage or grade of a condition. May include formal severity assessments.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.stage", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "con-1", + "severity": "error", + "human": "Stage SHALL have summary or assessment", + "expression": "summary.exists() or assessment.exists()", + "xpath": "exists(f:summary) or exists(f:assessment)" + }, + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "./inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"stage/grade\"]" + } + ] + }, + { + "id": "Condition.stage.id", + "path": "Condition.stage.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.stage.extension", + "path": "Condition.stage.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.stage.modifierExtension", + "path": "Condition.stage.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.stage.summary", + "path": "Condition.stage.summary", + "short": "Simple summary (disease specific)", + "definition": "A simple summary of the stage such as \"Stage 3\". The determination of the stage is disease-specific.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.stage.summary", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-1" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionStage" + } + ], + "strength": "example", + "description": "Codes describing condition stages (e.g. Cancer stages).", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-stage" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 254291000 |Staging and scales|" + }, + { + "identity": "v2", + "map": "PRB-14" + }, + { + "identity": "rim", + "map": ".value" + } + ] + }, + { + "id": "Condition.stage.assessment", + "path": "Condition.stage.assessment", + "short": "Formal record of assessment", + "definition": "Reference to a formal record of the evidence on which the staging assessment is based.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.stage.assessment", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/ClinicalImpression", + "http://hl7.org/fhir/StructureDefinition/DiagnosticReport", + "http://hl7.org/fhir/StructureDefinition/Observation" + ] + } + ], + "condition": [ + "con-1" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": ".self" + } + ] + }, + { + "id": "Condition.stage.type", + "path": "Condition.stage.type", + "short": "Kind of staging", + "definition": "The kind of staging, such as pathological or clinical staging.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.stage.type", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionStageType" + } + ], + "strength": "example", + "description": "Codes describing the kind of condition staging (e.g. clinical or pathological).", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-stage-type" + }, + "mapping": [ + { + "identity": "rim", + "map": "./inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"stage type\"]" + } + ] + }, + { + "id": "Condition.evidence", + "path": "Condition.evidence", + "short": "Supporting evidence", + "definition": "Supporting evidence / manifestations that are the basis of the Condition's verification status, such as evidence that confirmed or refuted the condition.", + "comment": "The evidence may be a simple list of coded symptoms/manifestations, or references to observations or formal assessments, or both.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.evidence", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "con-2", + "severity": "error", + "human": "evidence SHALL have code or details", + "expression": "code.exists() or detail.exists()", + "xpath": "exists(f:code) or exists(f:detail)" + }, + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=SPRT].target[classCode=OBS, moodCode=EVN]" + } + ] + }, + { + "id": "Condition.evidence.id", + "path": "Condition.evidence.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.evidence.extension", + "path": "Condition.evidence.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.evidence.modifierExtension", + "path": "Condition.evidence.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.evidence.code", + "path": "Condition.evidence.code", + "short": "Manifestation/symptom", + "definition": "A manifestation or symptom that led to the recording of this condition.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.evidence.code", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-2" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ManifestationOrSymptom" + } + ], + "strength": "example", + "description": "Codes that describe the manifestation or symptoms of a condition.", + "valueSet": "http://hl7.org/fhir/ValueSet/manifestation-or-symptom" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.reasonCode" + }, + { + "identity": "w5", + "map": "FiveWs.why[x]" + }, + { + "identity": "sct-concept", + "map": "< 404684003 |Clinical finding|" + }, + { + "identity": "rim", + "map": "[code=\"diagnosis\"].value" + } + ] + }, + { + "id": "Condition.evidence.detail", + "path": "Condition.evidence.detail", + "short": "Supporting information found elsewhere", + "definition": "Links to other relevant information, including pathology reports.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.evidence.detail", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ], + "condition": [ + "con-2" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.why[x]" + }, + { + "identity": "rim", + "map": ".self" + } + ] + }, + { + "id": "Condition.note", + "path": "Condition.note", + "short": "Additional information about the Condition", + "definition": "Additional information about the Condition. This is a general notes/comments entry for description of the Condition, its diagnosis and prognosis.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.note", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Annotation" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.note" + }, + { + "identity": "v2", + "map": "NTE child of PRB" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"annotation\"].value" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "Condition", + "path": "Condition" + }, + { + "id": "Condition.code", + "path": "Condition.code", + "binding": { + "strength": "extensible", + "valueSet": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/disease-codes" + } + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-family-relationship.json b/tests/fixtures/ncpi/examples/StructureDefinition-family-relationship.json new file mode 100644 index 0000000..3686474 --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-family-relationship.json @@ -0,0 +1,3009 @@ +{ + "resourceType": "StructureDefinition", + "id": "family-relationship", + "text": { + "status": "extensions", + "div": "
\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" Observation 0..*ObservationMeasurements and simple assertions
\".\"\".\"\".\" code 1..1CodeableConceptType of observation (code / type)
Required Pattern: At least the following
\".\"\".\"\".\"\".\" coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\" system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v3-RoleCode
\".\"\".\"\".\"\".\"\".\" code1..1codeSymbol in syntax defined by the system
Fixed Value: FAMMEMB
\".\"\".\"\".\"\".\"\".\" display1..1stringRepresentation defined by the system
Fixed Value: family member
\".\"\".\"\".\"\".\" text 0..1stringPlain text representation of the concept
Required Pattern: Family Relationship
\".\"\".\"\".\" Slices for value[x] 0..1CodeableConceptActual result
Slice: Unordered, Open by type:$this
\".\"\".\"\".\" valueCodeableConcept 0..1CodeableConceptActual result
Binding: FamilyMember (extensible)

\"doco\" Documentation for this format
" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category", + "valueString": "Clinical.Diagnostics" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category", + "valueCode": "patient" + } + ], + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/family-relationship", + "version": "0.1.0", + "name": "FamilyRelationship", + "title": "NCPI Family Relationship", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Representation of a family relationship.", + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "workflow", + "uri": "http://hl7.org/fhir/workflow", + "name": "Workflow Pattern" + }, + { + "identity": "sct-concept", + "uri": "http://snomed.info/conceptdomain", + "name": "SNOMED CT Concept Domain Binding" + }, + { + "identity": "v2", + "uri": "http://hl7.org/v2", + "name": "HL7 v2 Mapping" + }, + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + }, + { + "identity": "w5", + "uri": "http://hl7.org/fhir/fivews", + "name": "FiveWs Pattern Mapping" + }, + { + "identity": "sct-attr", + "uri": "http://snomed.org/attributebinding", + "name": "SNOMED CT Attribute Binding" + } + ], + "kind": "resource", + "abstract": false, + "type": "Observation", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "Observation", + "path": "Observation", + "short": "Measurements and simple assertions", + "definition": "Measurements and simple assertions made about a patient, device or other subject.", + "comment": "Used for simple observations such as device measurements, laboratory atomic results, vital signs, height, weight, smoking status, comments, etc. Other resources are used to provide context for observations such as laboratory reports, etc.", + "alias": [ + "Vital Signs", + "Measurement", + "Results", + "Tests" + ], + "min": 0, + "max": "*", + "base": { + "path": "Observation", + "min": 0, + "max": "*" + }, + "constraint": [ + { + "key": "dom-2", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources", + "expression": "contained.contained.empty()", + "xpath": "not(parent::f:contained and f:contained)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-3", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource", + "expression": "contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()", + "xpath": "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-4", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated", + "expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-5", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a security label", + "expression": "contained.meta.security.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:security))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time." + } + ], + "key": "dom-6", + "severity": "warning", + "human": "A resource should have narrative for robust management", + "expression": "text.`div`.exists()", + "xpath": "exists(f:text/h:div)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "obs-6", + "severity": "error", + "human": "dataAbsentReason SHALL only be present if Observation.value[x] is not present", + "expression": "dataAbsentReason.empty() or value.empty()", + "xpath": "not(exists(f:dataAbsentReason)) or (not(exists(*[starts-with(local-name(.), 'value')])))", + "source": "http://hl7.org/fhir/StructureDefinition/Observation" + }, + { + "key": "obs-7", + "severity": "error", + "human": "If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present", + "expression": "value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()", + "xpath": "not(f:*[starts-with(local-name(.), 'value')] and (for $coding in f:code/f:coding return f:component/f:code/f:coding[f:code/@value=$coding/f:code/@value] [f:system/@value=$coding/f:system/@value]))", + "source": "http://hl7.org/fhir/StructureDefinition/Observation" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Entity. Role, or Act" + }, + { + "identity": "workflow", + "map": "Event" + }, + { + "identity": "sct-concept", + "map": "< 363787002 |Observable entity|" + }, + { + "identity": "v2", + "map": "OBX" + }, + { + "identity": "rim", + "map": "Observation[classCode=OBS, moodCode=EVN]" + } + ] + }, + { + "id": "Observation.id", + "path": "Observation.id", + "short": "Logical id of this artifact", + "definition": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.", + "comment": "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "Observation.meta", + "path": "Observation.meta", + "short": "Metadata about the resource", + "definition": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.meta", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Meta" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "Observation.implicitRules", + "path": "Observation.implicitRules", + "short": "A set of rules under which this content was created", + "definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.", + "comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.implicitRules", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "uri" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation", + "isSummary": true + }, + { + "id": "Observation.language", + "path": "Observation.language", + "short": "Language of the resource content", + "definition": "The base language in which the resource is written.", + "comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).", + "min": 0, + "max": "1", + "base": { + "path": "Resource.language", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", + "valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "Language" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "preferred", + "description": "A human language.", + "valueSet": "http://hl7.org/fhir/ValueSet/languages" + } + }, + { + "id": "Observation.text", + "path": "Observation.text", + "short": "Text summary of the resource, for human interpretation", + "definition": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.", + "comment": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.", + "alias": [ + "narrative", + "html", + "xhtml", + "display" + ], + "min": 0, + "max": "1", + "base": { + "path": "DomainResource.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Narrative" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Act.text?" + } + ] + }, + { + "id": "Observation.contained", + "path": "Observation.contained", + "short": "Contained, inline Resources", + "definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.", + "comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.", + "alias": [ + "inline resources", + "anonymous resources", + "contained resources" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.contained", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Resource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Observation.extension", + "path": "Observation.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Observation.modifierExtension", + "path": "Observation.modifierExtension", + "short": "Extensions that cannot be ignored", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them", + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Observation.identifier", + "path": "Observation.identifier", + "short": "Business Identifier for observation", + "definition": "A unique identifier assigned to this observation.", + "requirements": "Allows observations to be distinguished and referenced.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.identifier", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "v2", + "map": "OBX.21 For OBX segments from systems without OBX-21 support a combination of ORC/OBR and OBX must be negotiated between trading partners to uniquely identify the OBX segment. Depending on how V2 has been implemented each of these may be an option: 1) OBR-3 + OBX-3 + OBX-4 or 2) OBR-3 + OBR-4 + OBX-3 + OBX-4 or 2) some other way to uniquely ID the OBR/ORC + OBX-3 + OBX-4." + }, + { + "identity": "rim", + "map": "id" + } + ] + }, + { + "id": "Observation.basedOn", + "path": "Observation.basedOn", + "short": "Fulfills plan, proposal or order", + "definition": "A plan, proposal or order that is fulfilled in whole or in part by this event. For example, a MedicationRequest may require a patient to have laboratory test performed before it is dispensed.", + "requirements": "Allows tracing of authorization for the event and tracking whether proposals/recommendations were acted upon.", + "alias": [ + "Fulfills" + ], + "min": 0, + "max": "*", + "base": { + "path": "Observation.basedOn", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/CarePlan", + "http://hl7.org/fhir/StructureDefinition/DeviceRequest", + "http://hl7.org/fhir/StructureDefinition/ImmunizationRecommendation", + "http://hl7.org/fhir/StructureDefinition/MedicationRequest", + "http://hl7.org/fhir/StructureDefinition/NutritionOrder", + "http://hl7.org/fhir/StructureDefinition/ServiceRequest" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.basedOn" + }, + { + "identity": "v2", + "map": "ORC" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=COMP].source[moodCode=EVN]" + } + ] + }, + { + "id": "Observation.partOf", + "path": "Observation.partOf", + "short": "Part of referenced event", + "definition": "A larger event of which this particular Observation is a component or step. For example, an observation as part of a procedure.", + "comment": "To link an Observation to an Encounter use `encounter`. See the [Notes](http://hl7.org/fhir/R4/observation.html#obsgrouping) below for guidance on referencing another Observation.", + "alias": [ + "Container" + ], + "min": 0, + "max": "*", + "base": { + "path": "Observation.partOf", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/MedicationAdministration", + "http://hl7.org/fhir/StructureDefinition/MedicationDispense", + "http://hl7.org/fhir/StructureDefinition/MedicationStatement", + "http://hl7.org/fhir/StructureDefinition/Procedure", + "http://hl7.org/fhir/StructureDefinition/Immunization", + "http://hl7.org/fhir/StructureDefinition/ImagingStudy" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.partOf" + }, + { + "identity": "v2", + "map": "Varies by domain" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=FLFS].target" + } + ] + }, + { + "id": "Observation.status", + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-display-hint", + "valueString": "default: final" + } + ], + "path": "Observation.status", + "short": "registered | preliminary | final | amended +", + "definition": "The status of the result value.", + "comment": "This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.", + "requirements": "Need to track the status of individual results. Some results are finalized before the whole report is finalized.", + "min": 1, + "max": "1", + "base": { + "path": "Observation.status", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationStatus" + } + ], + "strength": "required", + "description": "Codes providing the status of an observation.", + "valueSet": "http://hl7.org/fhir/ValueSet/observation-status|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "sct-concept", + "map": "< 445584004 |Report by finality status|" + }, + { + "identity": "v2", + "map": "OBX-11" + }, + { + "identity": "rim", + "map": "status Amended & Final are differentiated by whether it is the subject of a ControlAct event with a type of \"revise\"" + } + ] + }, + { + "id": "Observation.category", + "path": "Observation.category", + "short": "Classification of type of observation", + "definition": "A code that classifies the general type of observation being made.", + "comment": "In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.", + "requirements": "Used for filtering what observations are retrieved and displayed.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.category", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationCategory" + } + ], + "strength": "preferred", + "description": "Codes for high level observation categories.", + "valueSet": "http://hl7.org/fhir/ValueSet/observation-category" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=\"COMP].target[classCode=\"LIST\", moodCode=\"EVN\"].code" + } + ] + }, + { + "id": "Observation.code", + "path": "Observation.code", + "short": "Type of observation (code / type)", + "definition": "Describes what was observed. Sometimes this is called the observation \"name\".", + "comment": "*All* code-value and, if present, component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.", + "requirements": "Knowing what kind of observation is being made is essential to understanding the observation.", + "alias": [ + "Name" + ], + "min": 1, + "max": "1", + "base": { + "path": "Observation.code", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "patternCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "FAMMEMB", + "display": "family member" + } + ] + }, + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationCode" + } + ], + "strength": "example", + "description": "Codes identifying names of simple observations.", + "valueSet": "http://hl7.org/fhir/ValueSet/observation-codes" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.code" + }, + { + "identity": "w5", + "map": "FiveWs.what[x]" + }, + { + "identity": "sct-concept", + "map": "< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|" + }, + { + "identity": "v2", + "map": "OBX-3" + }, + { + "identity": "rim", + "map": "code" + }, + { + "identity": "sct-attr", + "map": "116680003 |Is a|" + } + ] + }, + { + "id": "Observation.code.id", + "path": "Observation.code.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Observation.code.extension", + "path": "Observation.code.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "description": "Extensions are always sliced by (at least) url", + "rules": "open" + }, + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Observation.code.coding", + "path": "Observation.code.coding", + "short": "Code defined by a terminology system", + "definition": "A reference to a code defined by a terminology system.", + "comment": "Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.", + "requirements": "Allows for alternative encodings within a code system, and translations to other code systems.", + "min": 0, + "max": "*", + "base": { + "path": "CodeableConcept.coding", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Coding" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "C*E.1-8, C*E.10-22" + }, + { + "identity": "rim", + "map": "union(., ./translation)" + }, + { + "identity": "orim", + "map": "fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding" + } + ] + }, + { + "id": "Observation.code.text", + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable", + "valueBoolean": true + } + ], + "path": "Observation.code.text", + "short": "Plain text representation of the concept", + "definition": "A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.", + "comment": "Very often the text is the same as a displayName of one of the codings.", + "requirements": "The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.", + "min": 0, + "max": "1", + "base": { + "path": "CodeableConcept.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "string" + } + ], + "patternString": "Family Relationship", + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "C*E.9. But note many systems use C*E.2 for this" + }, + { + "identity": "rim", + "map": "./originalText[mediaType/code=\"text/plain\"]/data" + }, + { + "identity": "orim", + "map": "fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText" + } + ] + }, + { + "id": "Observation.subject", + "path": "Observation.subject", + "short": "Who and/or what the observation is about", + "definition": "The patient, or group of patients, location, or device this observation is about and into whose record the observation is placed. If the actual focus of the observation is different from the subject (or a sample of, part, or region of the subject), the `focus` element or the `code` itself specifies the actual focus of the observation.", + "comment": "One would expect this element to be a cardinality of 1..1. The only circumstance in which the subject can be missing is when the observation is made by a device that does not know the patient. In this case, the observation SHALL be matched to a patient through some context/channel matching technique, and at this point, the observation should be updated.", + "requirements": "Observations have no value if you don't know who or what they're about.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.subject", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/Group", + "http://hl7.org/fhir/StructureDefinition/Device", + "http://hl7.org/fhir/StructureDefinition/Location" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.subject" + }, + { + "identity": "w5", + "map": "FiveWs.subject[x]" + }, + { + "identity": "v2", + "map": "PID-3" + }, + { + "identity": "rim", + "map": "participation[typeCode=RTGT]" + }, + { + "identity": "w5", + "map": "FiveWs.subject" + } + ] + }, + { + "id": "Observation.focus", + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status", + "valueCode": "trial-use" + } + ], + "path": "Observation.focus", + "short": "What the observation is about, when it is not about the subject of record", + "definition": "The actual focus of an observation when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, fetus, or donor. For example, fetus observations in a mother's record. The focus of an observation could also be an existing condition, an intervention, the subject's diet, another observation of the subject, or a body structure such as tumor or implanted device. An example use case would be using the Observation resource to capture whether the mother is trained to change her child's tracheostomy tube. In this example, the child is the patient of record and the mother is the focus.", + "comment": "Typically, an observation is made about the subject - a patient, or group of patients, location, or device - and the distinction between the subject and what is directly measured for an observation is specified in the observation code itself ( e.g., \"Blood Glucose\") and does not need to be represented separately using this element. Use `specimen` if a reference to a specimen is required. If a code is required instead of a resource use either `bodysite` for bodysites or the standard extension [focusCode](http://hl7.org/fhir/R4/extension-observation-focuscode.html).", + "min": 0, + "max": "*", + "base": { + "path": "Observation.focus", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.subject[x]" + }, + { + "identity": "v2", + "map": "OBX-3" + }, + { + "identity": "rim", + "map": "participation[typeCode=SBJ]" + }, + { + "identity": "w5", + "map": "FiveWs.subject" + } + ] + }, + { + "id": "Observation.encounter", + "path": "Observation.encounter", + "short": "Healthcare event during which this observation is made", + "definition": "The healthcare event (e.g. a patient and healthcare provider interaction) during which this observation is made.", + "comment": "This will typically be the encounter the event occurred within, but some events may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter (e.g. pre-admission laboratory tests).", + "requirements": "For some observations it may be important to know the link between an observation and a particular encounter.", + "alias": [ + "Context" + ], + "min": 0, + "max": "1", + "base": { + "path": "Observation.encounter", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Encounter" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.context" + }, + { + "identity": "w5", + "map": "FiveWs.context" + }, + { + "identity": "v2", + "map": "PV1" + }, + { + "identity": "rim", + "map": "inboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]" + } + ] + }, + { + "id": "Observation.effective[x]", + "path": "Observation.effective[x]", + "short": "Clinically relevant time/time-period for observation", + "definition": "The time or time-period the observed value is asserted as being true. For biological subjects - e.g. human patients - this is usually called the \"physiologically relevant time\". This is usually either the time of the procedure or of specimen collection, but very often the source of the date/time is not known, only the date/time itself.", + "comment": "At least a date should be present unless this observation is a historical report. For recording imprecise or \"fuzzy\" times (For example, a blood glucose measurement taken \"after breakfast\") use the [Timing](http://hl7.org/fhir/R4/datatypes.html#timing) datatype which allow the measurement to be tied to regular life events.", + "requirements": "Knowing when an observation was deemed true is important to its relevance as well as determining trends.", + "alias": [ + "Occurrence" + ], + "min": 0, + "max": "1", + "base": { + "path": "Observation.effective[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + }, + { + "code": "Period" + }, + { + "code": "Timing" + }, + { + "code": "instant" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.occurrence[x]" + }, + { + "identity": "w5", + "map": "FiveWs.done[x]" + }, + { + "identity": "v2", + "map": "OBX-14, and/or OBX-19 after v2.4 (depends on who observation made)" + }, + { + "identity": "rim", + "map": "effectiveTime" + } + ] + }, + { + "id": "Observation.issued", + "path": "Observation.issued", + "short": "Date/Time this version was made available", + "definition": "The date and time this version of the observation was made available to providers, typically after the results have been reviewed and verified.", + "comment": "For Observations that don’t require review and verification, it may be the same as the [`lastUpdated` ](http://hl7.org/fhir/R4/resource-definitions.html#Meta.lastUpdated) time of the resource itself. For Observations that do require review and verification for certain updates, it might not be the same as the `lastUpdated` time of the resource itself due to a non-clinically significant update that doesn’t require the new version to be reviewed and verified again.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.issued", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "instant" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.recorded" + }, + { + "identity": "v2", + "map": "OBR.22 (or MSH.7), or perhaps OBX-19 (depends on who observation made)" + }, + { + "identity": "rim", + "map": "participation[typeCode=AUT].time" + } + ] + }, + { + "id": "Observation.performer", + "path": "Observation.performer", + "short": "Who is responsible for the observation", + "definition": "Who was responsible for asserting the observed value as \"true\".", + "requirements": "May give a degree of confidence in the observation and also indicates where follow-up questions should be directed.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.performer", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Organization", + "http://hl7.org/fhir/StructureDefinition/CareTeam", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor" + }, + { + "identity": "w5", + "map": "FiveWs.actor" + }, + { + "identity": "v2", + "map": "OBX.15 / (Practitioner) OBX-16, PRT-5:PRT-4='RO' / (Device) OBX-18 , PRT-10:PRT-4='EQUIP' / (Organization) OBX-23, PRT-8:PRT-4='PO'" + }, + { + "identity": "rim", + "map": "participation[typeCode=PRF]" + } + ] + }, + { + "id": "Observation.value[x]", + "path": "Observation.value[x]", + "slicing": { + "discriminator": [ + { + "type": "type", + "path": "$this" + } + ], + "ordered": false, + "rules": "closed" + }, + "short": "Actual result", + "definition": "The information determined as a result of making the observation, if the information has a simple value.", + "comment": "An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the [Notes section](http://hl7.org/fhir/R4/observation.html#notes) below.", + "requirements": "An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.value[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "obs-7" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 441742003 |Evaluation finding|" + }, + { + "identity": "v2", + "map": "OBX.2, OBX.5, OBX.6" + }, + { + "identity": "rim", + "map": "value" + }, + { + "identity": "sct-attr", + "map": "363714003 |Interprets|" + } + ] + }, + { + "id": "Observation.value[x]:valueCodeableConcept", + "path": "Observation.value[x]", + "sliceName": "valueCodeableConcept", + "short": "Actual result", + "definition": "The information determined as a result of making the observation, if the information has a simple value.", + "comment": "An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the [Notes section](http://hl7.org/fhir/R4/observation.html#notes) below.", + "requirements": "An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.value[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "obs-7" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "strength": "extensible", + "valueSet": "http://terminology.hl7.org/ValueSet/v3-FamilyMember" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 441742003 |Evaluation finding|" + }, + { + "identity": "v2", + "map": "OBX.2, OBX.5, OBX.6" + }, + { + "identity": "rim", + "map": "value" + }, + { + "identity": "sct-attr", + "map": "363714003 |Interprets|" + } + ] + }, + { + "id": "Observation.dataAbsentReason", + "path": "Observation.dataAbsentReason", + "short": "Why the result is missing", + "definition": "Provides a reason why the expected value in the element Observation.value[x] is missing.", + "comment": "Null or exceptional values can be represented two ways in FHIR Observations. One way is to simply include them in the value set and represent the exceptions in the value. For example, measurement values for a serology test could be \"detected\", \"not detected\", \"inconclusive\", or \"specimen unsatisfactory\". \n\nThe alternate way is to use the value element for actual observations and use the explicit dataAbsentReason element to record exceptional values. For example, the dataAbsentReason code \"error\" could be used when the measurement was not completed. Note that an observation may only be reported if there are values to report. For example differential cell counts values may be reported only when > 0. Because of these options, use-case agreements are required to interpret general observations for null or exceptional values.", + "requirements": "For many results it is necessary to handle exceptional values in measurements.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.dataAbsentReason", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "obs-6" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationValueAbsentReason" + } + ], + "strength": "extensible", + "description": "Codes specifying why the result (`Observation.value[x]`) is missing.", + "valueSet": "http://hl7.org/fhir/ValueSet/data-absent-reason" + }, + "mapping": [ + { + "identity": "v2", + "map": "N/A" + }, + { + "identity": "rim", + "map": "value.nullFlavor" + } + ] + }, + { + "id": "Observation.interpretation", + "path": "Observation.interpretation", + "short": "High, low, normal, etc.", + "definition": "A categorical assessment of an observation value. For example, high, low, normal.", + "comment": "Historically used for laboratory results (known as 'abnormal flag' ), its use extends to other use cases where coded interpretations are relevant. Often reported as one or more simple compact codes this element is often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result.", + "requirements": "For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.", + "alias": [ + "Abnormal Flag" + ], + "min": 0, + "max": "*", + "base": { + "path": "Observation.interpretation", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationInterpretation" + } + ], + "strength": "extensible", + "description": "Codes identifying interpretations of observations.", + "valueSet": "http://hl7.org/fhir/ValueSet/observation-interpretation" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 260245000 |Findings values|" + }, + { + "identity": "v2", + "map": "OBX-8" + }, + { + "identity": "rim", + "map": "interpretationCode" + }, + { + "identity": "sct-attr", + "map": "363713009 |Has interpretation|" + } + ] + }, + { + "id": "Observation.note", + "path": "Observation.note", + "short": "Comments about the observation", + "definition": "Comments about the observation or the results.", + "comment": "May include general statements about the observation, or statements about significant, unexpected or unreliable results values, or information about its source when relevant to its interpretation.", + "requirements": "Need to be able to provide free text additional information.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.note", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Annotation" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "v2", + "map": "NTE.3 (partner NTE to OBX, or sometimes another (child?) OBX)" + }, + { + "identity": "rim", + "map": "subjectOf.observationEvent[code=\"annotation\"].value" + } + ] + }, + { + "id": "Observation.bodySite", + "path": "Observation.bodySite", + "short": "Observed body part", + "definition": "Indicates the site on the subject's body where the observation was made (i.e. the target site).", + "comment": "Only used if not implicit in code found in Observation.code. In many systems, this may be represented as a related observation instead of an inline component. \n\nIf the use case requires BodySite to be handled as a separate resource (e.g. to identify and track separately) then use the standard extension[ bodySite](http://hl7.org/fhir/R4/extension-bodysite.html).", + "min": 0, + "max": "1", + "base": { + "path": "Observation.bodySite", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "BodySite" + } + ], + "strength": "example", + "description": "Codes describing anatomical locations. May include laterality.", + "valueSet": "http://hl7.org/fhir/ValueSet/body-site" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 123037004 |Body structure|" + }, + { + "identity": "v2", + "map": "OBX-20" + }, + { + "identity": "rim", + "map": "targetSiteCode" + }, + { + "identity": "sct-attr", + "map": "718497002 |Inherent location|" + } + ] + }, + { + "id": "Observation.method", + "path": "Observation.method", + "short": "How it was done", + "definition": "Indicates the mechanism used to perform the observation.", + "comment": "Only used if not implicit in code for Observation.code.", + "requirements": "In some cases, method can impact results and is thus used for determining whether results can be compared or determining significance of results.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.method", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationMethod" + } + ], + "strength": "example", + "description": "Methods for simple observations.", + "valueSet": "http://hl7.org/fhir/ValueSet/observation-methods" + }, + "mapping": [ + { + "identity": "v2", + "map": "OBX-17" + }, + { + "identity": "rim", + "map": "methodCode" + } + ] + }, + { + "id": "Observation.specimen", + "path": "Observation.specimen", + "short": "Specimen used for this observation", + "definition": "The specimen that was used when this observation was made.", + "comment": "Should only be used if not implicit in code found in `Observation.code`. Observations are not made on specimens themselves; they are made on a subject, but in many cases by the means of a specimen. Note that although specimens are often involved, they are not always tracked and reported explicitly. Also note that observation resources may be used in contexts that track the specimen explicitly (e.g. Diagnostic Report).", + "min": 0, + "max": "1", + "base": { + "path": "Observation.specimen", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 123038009 |Specimen|" + }, + { + "identity": "v2", + "map": "SPM segment" + }, + { + "identity": "rim", + "map": "participation[typeCode=SPC].specimen" + }, + { + "identity": "sct-attr", + "map": "704319004 |Inherent in|" + } + ] + }, + { + "id": "Observation.device", + "path": "Observation.device", + "short": "(Measurement) Device", + "definition": "The device used to generate the observation data.", + "comment": "Note that this is not meant to represent a device involved in the transmission of the result, e.g., a gateway. Such devices may be documented using the Provenance resource where relevant.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.device", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Device", + "http://hl7.org/fhir/StructureDefinition/DeviceMetric" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 49062001 |Device|" + }, + { + "identity": "v2", + "map": "OBX-17 / PRT -10" + }, + { + "identity": "rim", + "map": "participation[typeCode=DEV]" + }, + { + "identity": "sct-attr", + "map": "424226004 |Using device|" + } + ] + }, + { + "id": "Observation.referenceRange", + "path": "Observation.referenceRange", + "short": "Provides guide for interpretation", + "definition": "Guidance on how to interpret the value by comparison to a normal or recommended range. Multiple reference ranges are interpreted as an \"OR\". In other words, to represent two distinct target populations, two `referenceRange` elements would be used.", + "comment": "Most observations only have one generic reference range. Systems MAY choose to restrict to only supplying the relevant reference range based on knowledge about the patient (e.g., specific to the patient's age, gender, weight and other factors), but this might not be possible or appropriate. Whenever more than one reference range is supplied, the differences between them SHOULD be provided in the reference range and/or age properties.", + "requirements": "Knowing what values are considered \"normal\" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.referenceRange", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "obs-3", + "severity": "error", + "human": "Must have at least a low or a high or text", + "expression": "low.exists() or high.exists() or text.exists()", + "xpath": "(exists(f:low) or exists(f:high)or exists(f:text))" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "v2", + "map": "OBX.7" + }, + { + "identity": "rim", + "map": "outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]" + } + ] + }, + { + "id": "Observation.referenceRange.id", + "path": "Observation.referenceRange.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Observation.referenceRange.extension", + "path": "Observation.referenceRange.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Observation.referenceRange.modifierExtension", + "path": "Observation.referenceRange.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Observation.referenceRange.low", + "path": "Observation.referenceRange.low", + "short": "Low Range, if relevant", + "definition": "The value of the low bound of the reference range. The low bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the low bound is omitted, it is assumed to be meaningless (e.g. reference range is <=2.3).", + "min": 0, + "max": "1", + "base": { + "path": "Observation.referenceRange.low", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Quantity", + "profile": [ + "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" + ] + } + ], + "condition": [ + "obs-3" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "v2", + "map": "OBX-7" + }, + { + "identity": "rim", + "map": "value:IVL_PQ.low" + } + ] + }, + { + "id": "Observation.referenceRange.high", + "path": "Observation.referenceRange.high", + "short": "High Range, if relevant", + "definition": "The value of the high bound of the reference range. The high bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the high bound is omitted, it is assumed to be meaningless (e.g. reference range is >= 2.3).", + "min": 0, + "max": "1", + "base": { + "path": "Observation.referenceRange.high", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Quantity", + "profile": [ + "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" + ] + } + ], + "condition": [ + "obs-3" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "v2", + "map": "OBX-7" + }, + { + "identity": "rim", + "map": "value:IVL_PQ.high" + } + ] + }, + { + "id": "Observation.referenceRange.type", + "path": "Observation.referenceRange.type", + "short": "Reference range qualifier", + "definition": "Codes to indicate the what part of the targeted reference population it applies to. For example, the normal or therapeutic range.", + "comment": "This SHOULD be populated if there is more than one range. If this element is not present then the normal range is assumed.", + "requirements": "Need to be able to say what kind of reference range this is - normal, recommended, therapeutic, etc., - for proper interpretation.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.referenceRange.type", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationRangeMeaning" + } + ], + "strength": "preferred", + "description": "Code for the meaning of a reference range.", + "valueSet": "http://hl7.org/fhir/ValueSet/referencerange-meaning" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 260245000 |Findings values| OR \r< 365860008 |General clinical state finding| \rOR \r< 250171008 |Clinical history or observation findings| OR \r< 415229000 |Racial group| OR \r< 365400002 |Finding of puberty stage| OR\r< 443938003 |Procedure carried out on subject|" + }, + { + "identity": "v2", + "map": "OBX-10" + }, + { + "identity": "rim", + "map": "interpretationCode" + } + ] + }, + { + "id": "Observation.referenceRange.appliesTo", + "path": "Observation.referenceRange.appliesTo", + "short": "Reference range population", + "definition": "Codes to indicate the target population this reference range applies to. For example, a reference range may be based on the normal population or a particular sex or race. Multiple `appliesTo` are interpreted as an \"AND\" of the target populations. For example, to represent a target population of African American females, both a code of female and a code for African American would be used.", + "comment": "This SHOULD be populated if there is more than one range. If this element is not present then the normal population is assumed.", + "requirements": "Need to be able to identify the target population for proper interpretation.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.referenceRange.appliesTo", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationRangeType" + } + ], + "strength": "example", + "description": "Codes identifying the population the reference range applies to.", + "valueSet": "http://hl7.org/fhir/ValueSet/referencerange-appliesto" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 260245000 |Findings values| OR \r< 365860008 |General clinical state finding| \rOR \r< 250171008 |Clinical history or observation findings| OR \r< 415229000 |Racial group| OR \r< 365400002 |Finding of puberty stage| OR\r< 443938003 |Procedure carried out on subject|" + }, + { + "identity": "v2", + "map": "OBX-10" + }, + { + "identity": "rim", + "map": "interpretationCode" + } + ] + }, + { + "id": "Observation.referenceRange.age", + "path": "Observation.referenceRange.age", + "short": "Applicable age range, if relevant", + "definition": "The age at which this reference range is applicable. This is a neonatal age (e.g. number of weeks at term) if the meaning says so.", + "requirements": "Some analytes vary greatly over age.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.referenceRange.age", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Range" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "outboundRelationship[typeCode=PRCN].targetObservationCriterion[code=\"age\"].value" + } + ] + }, + { + "id": "Observation.referenceRange.text", + "path": "Observation.referenceRange.text", + "short": "Text based reference range in an observation", + "definition": "Text based reference range in an observation which may be used when a quantitative range is not appropriate for an observation. An example would be a reference value of \"Negative\" or a list or table of \"normals\".", + "min": 0, + "max": "1", + "base": { + "path": "Observation.referenceRange.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "string" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "v2", + "map": "OBX-7" + }, + { + "identity": "rim", + "map": "value:ST" + } + ] + }, + { + "id": "Observation.hasMember", + "path": "Observation.hasMember", + "short": "Related resource that belongs to the Observation group", + "definition": "This observation is a group observation (e.g. a battery, a panel of tests, a set of vital sign measurements) that includes the target as a member of the group.", + "comment": "When using this element, an observation will typically have either a value or a set of related resources, although both may be present in some cases. For a discussion on the ways Observations can assembled in groups together, see [Notes](http://hl7.org/fhir/R4/observation.html#obsgrouping) below. Note that a system may calculate results from [QuestionnaireResponse](http://hl7.org/fhir/R4/questionnaireresponse.html) into a final score and represent the score as an Observation.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.hasMember", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Observation", + "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse", + "http://hl7.org/fhir/StructureDefinition/MolecularSequence" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "Relationships established by OBX-4 usage" + }, + { + "identity": "rim", + "map": "outBoundRelationship" + } + ] + }, + { + "id": "Observation.derivedFrom", + "path": "Observation.derivedFrom", + "short": "Related measurements the observation is made from", + "definition": "The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.", + "comment": "All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see [Notes](http://hl7.org/fhir/R4/observation.html#obsgrouping) below.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.derivedFrom", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/DocumentReference", + "http://hl7.org/fhir/StructureDefinition/ImagingStudy", + "http://hl7.org/fhir/StructureDefinition/Media", + "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse", + "http://hl7.org/fhir/StructureDefinition/Observation", + "http://hl7.org/fhir/StructureDefinition/MolecularSequence" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "Relationships established by OBX-4 usage" + }, + { + "identity": "rim", + "map": ".targetObservation" + } + ] + }, + { + "id": "Observation.component", + "path": "Observation.component", + "short": "Component results", + "definition": "Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.", + "comment": "For a discussion on the ways Observations can be assembled in groups together see [Notes](http://hl7.org/fhir/R4/observation.html#notes) below.", + "requirements": "Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.component", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "containment by OBX-4?" + }, + { + "identity": "rim", + "map": "outBoundRelationship[typeCode=COMP]" + } + ] + }, + { + "id": "Observation.component.id", + "path": "Observation.component.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Observation.component.extension", + "path": "Observation.component.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Observation.component.modifierExtension", + "path": "Observation.component.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Observation.component.code", + "path": "Observation.component.code", + "short": "Type of component observation (code / type)", + "definition": "Describes what was observed. Sometimes this is called the observation \"code\".", + "comment": "*All* code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.", + "requirements": "Knowing what kind of observation is being made is essential to understanding the observation.", + "min": 1, + "max": "1", + "base": { + "path": "Observation.component.code", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationCode" + } + ], + "strength": "example", + "description": "Codes identifying names of simple observations.", + "valueSet": "http://hl7.org/fhir/ValueSet/observation-codes" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.what[x]" + }, + { + "identity": "sct-concept", + "map": "< 363787002 |Observable entity| OR \r< 386053000 |Evaluation procedure|" + }, + { + "identity": "v2", + "map": "OBX-3" + }, + { + "identity": "rim", + "map": "code" + } + ] + }, + { + "id": "Observation.component.value[x]", + "path": "Observation.component.value[x]", + "short": "Actual component result", + "definition": "The information determined as a result of making the observation, if the information has a simple value.", + "comment": "Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the [Notes section](http://hl7.org/fhir/R4/observation.html#notes) below.", + "requirements": "An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.component.value[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Quantity" + }, + { + "code": "CodeableConcept" + }, + { + "code": "string" + }, + { + "code": "boolean" + }, + { + "code": "integer" + }, + { + "code": "Range" + }, + { + "code": "Ratio" + }, + { + "code": "SampledData" + }, + { + "code": "time" + }, + { + "code": "dateTime" + }, + { + "code": "Period" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "sct-concept", + "map": "363714003 |Interprets| < 441742003 |Evaluation finding|" + }, + { + "identity": "v2", + "map": "OBX.2, OBX.5, OBX.6" + }, + { + "identity": "rim", + "map": "value" + }, + { + "identity": "sct-attr", + "map": "363714003 |Interprets|" + } + ] + }, + { + "id": "Observation.component.dataAbsentReason", + "path": "Observation.component.dataAbsentReason", + "short": "Why the component result is missing", + "definition": "Provides a reason why the expected value in the element Observation.component.value[x] is missing.", + "comment": "\"Null\" or exceptional values can be represented two ways in FHIR Observations. One way is to simply include them in the value set and represent the exceptions in the value. For example, measurement values for a serology test could be \"detected\", \"not detected\", \"inconclusive\", or \"test not done\". \n\nThe alternate way is to use the value element for actual observations and use the explicit dataAbsentReason element to record exceptional values. For example, the dataAbsentReason code \"error\" could be used when the measurement was not completed. Because of these options, use-case agreements are required to interpret general observations for exceptional values.", + "requirements": "For many results it is necessary to handle exceptional values in measurements.", + "min": 0, + "max": "1", + "base": { + "path": "Observation.component.dataAbsentReason", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "obs-6" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationValueAbsentReason" + } + ], + "strength": "extensible", + "description": "Codes specifying why the result (`Observation.value[x]`) is missing.", + "valueSet": "http://hl7.org/fhir/ValueSet/data-absent-reason" + }, + "mapping": [ + { + "identity": "v2", + "map": "N/A" + }, + { + "identity": "rim", + "map": "value.nullFlavor" + } + ] + }, + { + "id": "Observation.component.interpretation", + "path": "Observation.component.interpretation", + "short": "High, low, normal, etc.", + "definition": "A categorical assessment of an observation value. For example, high, low, normal.", + "comment": "Historically used for laboratory results (known as 'abnormal flag' ), its use extends to other use cases where coded interpretations are relevant. Often reported as one or more simple compact codes this element is often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result.", + "requirements": "For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.", + "alias": [ + "Abnormal Flag" + ], + "min": 0, + "max": "*", + "base": { + "path": "Observation.component.interpretation", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ObservationInterpretation" + } + ], + "strength": "extensible", + "description": "Codes identifying interpretations of observations.", + "valueSet": "http://hl7.org/fhir/ValueSet/observation-interpretation" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 260245000 |Findings values|" + }, + { + "identity": "v2", + "map": "OBX-8" + }, + { + "identity": "rim", + "map": "interpretationCode" + }, + { + "identity": "sct-attr", + "map": "363713009 |Has interpretation|" + } + ] + }, + { + "id": "Observation.component.referenceRange", + "path": "Observation.component.referenceRange", + "short": "Provides guide for interpretation of component result", + "definition": "Guidance on how to interpret the value by comparison to a normal or recommended range.", + "comment": "Most observations only have one generic reference range. Systems MAY choose to restrict to only supplying the relevant reference range based on knowledge about the patient (e.g., specific to the patient's age, gender, weight and other factors), but this might not be possible or appropriate. Whenever more than one reference range is supplied, the differences between them SHOULD be provided in the reference range and/or age properties.", + "requirements": "Knowing what values are considered \"normal\" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.", + "min": 0, + "max": "*", + "base": { + "path": "Observation.component.referenceRange", + "min": 0, + "max": "*" + }, + "contentReference": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.referenceRange", + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "v2", + "map": "OBX.7" + }, + { + "identity": "rim", + "map": "outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "Observation", + "path": "Observation" + }, + { + "id": "Observation.code", + "path": "Observation.code", + "patternCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "FAMMEMB", + "display": "family member" + } + ] + } + }, + { + "id": "Observation.code.text", + "path": "Observation.code.text", + "patternString": "Family Relationship" + }, + { + "id": "Observation.value[x]", + "path": "Observation.value[x]", + "slicing": { + "discriminator": [ + { + "type": "type", + "path": "$this" + } + ], + "ordered": false, + "rules": "open" + }, + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.valueCodeableConcept", + "path": "Observation.valueCodeableConcept", + "min": 0, + "max": "1", + "binding": { + "strength": "extensible", + "valueSet": "http://terminology.hl7.org/ValueSet/v3-FamilyMember" + } + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-attachment.json b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-attachment.json new file mode 100644 index 0000000..16964ec --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-attachment.json @@ -0,0 +1,603 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-drs-attachment", + "text": { + "status": "extensions", + "div": "
\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" Attachment I0..*AttachmentContent in a format defined elsewhere
must-be-drs-uri: attachment.url must start with ^drs://. A drs:// hostname-based URI, as defined in the DRS documentation, that tells clients how to access this object. The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around. For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the `self_uri` presents you with a hostname and properly encoded DRS ID for use in subsequent `access` endpoint calls.

\"doco\" Documentation for this format
" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment", + "version": "0.1.0", + "name": "DRSAttachment", + "title": "DRS Attachment", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "A FHIR Attachment with a DRS url.", + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "v2", + "uri": "http://hl7.org/v2", + "name": "HL7 v2 Mapping" + }, + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + } + ], + "kind": "complex-type", + "abstract": false, + "type": "Attachment", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Attachment", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "Attachment", + "path": "Attachment", + "short": "Content in a format defined elsewhere", + "definition": "For referring to data content defined in other formats.", + "comment": "When providing a summary view (for example with Observation.value[x]) Attachment should be represented with a brief display text such as \"Signed Procedure Consent\".", + "min": 0, + "max": "*", + "base": { + "path": "Attachment", + "min": 0, + "max": "*" + }, + "condition": [ + "ele-1" + ], + "constraint": [ + { + "key": "att-1", + "severity": "error", + "human": "If the Attachment has data, it SHALL have a contentType", + "expression": "data.empty() or contentType.exists()", + "xpath": "not(exists(f:data)) or exists(f:contentType)", + "source": "http://hl7.org/fhir/StructureDefinition/Attachment" + }, + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "must-be-drs-uri", + "severity": "error", + "human": "attachment.url must start with ^drs://. A drs:// hostname-based URI, as defined in the DRS documentation, that tells clients how to access this object. The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around. For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the `self_uri` presents you with a hostname and properly encoded DRS ID for use in subsequent `access` endpoint calls.", + "expression": "$this.url.matches('^drs://.*')", + "source": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + } + ], + "isModifier": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + }, + { + "identity": "v2", + "map": "ED/RP" + }, + { + "identity": "rim", + "map": "ED" + } + ] + }, + { + "id": "Attachment.id", + "path": "Attachment.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Attachment.extension", + "path": "Attachment.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "description": "Extensions are always sliced by (at least) url", + "rules": "open" + }, + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Attachment.contentType", + "path": "Attachment.contentType", + "short": "Mime type of the content, with charset etc.", + "definition": "Identifies the type of the data in the attachment and allows a method to be chosen to interpret or render the data. Includes mime type parameters such as charset where appropriate.", + "requirements": "Processors of the data need to be able to know how to interpret the data.", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.contentType", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "example": [ + { + "label": "General", + "valueCode": "text/plain; charset=UTF-8, image/png" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "MimeType" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "required", + "description": "The mime type of an attachment. Any valid mime type is allowed.", + "valueSet": "http://hl7.org/fhir/ValueSet/mimetypes|4.0.1" + }, + "mapping": [ + { + "identity": "v2", + "map": "ED.2+ED.3/RP.2+RP.3. Note conversion may be needed if old style values are being used" + }, + { + "identity": "rim", + "map": "./mediaType, ./charset" + } + ] + }, + { + "id": "Attachment.language", + "path": "Attachment.language", + "short": "Human language of the content (BCP-47)", + "definition": "The human language of the content. The value can be any valid value according to BCP 47.", + "requirements": "Users need to be able to choose between the languages in a set of attachments.", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.language", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "example": [ + { + "label": "General", + "valueCode": "en-AU" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", + "valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "Language" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "preferred", + "description": "A human language.", + "valueSet": "http://hl7.org/fhir/ValueSet/languages" + }, + "mapping": [ + { + "identity": "rim", + "map": "./language" + } + ] + }, + { + "id": "Attachment.data", + "path": "Attachment.data", + "short": "Data inline, base64ed", + "definition": "The actual data of the attachment - a sequence of bytes, base64 encoded.", + "comment": "The base64-encoded data SHALL be expressed in the same character set as the base resource XML or JSON.", + "requirements": "The data needs to able to be transmitted inline.", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.data", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "base64Binary" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "v2", + "map": "ED.5" + }, + { + "identity": "rim", + "map": "./data" + } + ] + }, + { + "id": "Attachment.url", + "path": "Attachment.url", + "short": "Uri where the data can be found", + "definition": "A location where the data can be accessed.", + "comment": "If both data and url are provided, the url SHALL point to the same content as the data contains. Urls may be relative references or may reference transient locations such as a wrapping envelope using cid: though this has ramifications for using signatures. Relative URLs are interpreted relative to the service url, like a resource reference, rather than relative to the resource itself. If a URL is provided, it SHALL resolve to actual data.", + "requirements": "The data needs to be transmitted by reference.", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.url", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "url" + } + ], + "example": [ + { + "label": "General", + "valueUrl": "http://www.acme.com/logo-small.png" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "RP.1+RP.2 - if they refer to a URL (see v2.6)" + }, + { + "identity": "rim", + "map": "./reference/literal" + } + ] + }, + { + "id": "Attachment.size", + "path": "Attachment.size", + "short": "Number of bytes of content (if url provided)", + "definition": "The number of bytes of data that make up this attachment (before base64 encoding, if that is done).", + "comment": "The number of bytes is redundant if the data is provided as a base64binary, but is useful if the data is provided as a url reference.", + "requirements": "Representing the size allows applications to determine whether they should fetch the content automatically in advance, or refuse to fetch it at all.", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.size", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "unsignedInt" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A (needs data type R3 proposal)" + } + ] + }, + { + "id": "Attachment.hash", + "path": "Attachment.hash", + "short": "Hash of the data (sha-1, base64ed)", + "definition": "The calculated hash of the data using SHA-1. Represented using base64.", + "comment": "The hash is calculated on the data prior to base64 encoding, if the data is based64 encoded. The hash is not intended to support digital signatures. Where protection against malicious threats a digital signature should be considered, see [Provenance.signature](http://hl7.org/fhir/R4/provenance-definitions.html#Provenance.signature) for mechanism to protect a resource with a digital signature.", + "requirements": "Included so that applications can verify that the contents of a location have not changed due to technical failures (e.g., storage rot, transport glitch, incorrect version).", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.hash", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "base64Binary" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": ".integrityCheck[parent::ED/integrityCheckAlgorithm=\"SHA-1\"]" + } + ] + }, + { + "id": "Attachment.title", + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable", + "valueBoolean": true + } + ], + "path": "Attachment.title", + "short": "Label to display in place of the data", + "definition": "A label or set of text to display in place of the data.", + "requirements": "Applications need a label to display to a human user in place of the actual data if the data cannot be rendered or perceived by the viewer.", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.title", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "string" + } + ], + "example": [ + { + "label": "General", + "valueString": "Official Corporate Logo" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "./title/data" + } + ] + }, + { + "id": "Attachment.creation", + "path": "Attachment.creation", + "short": "Date attachment was first created", + "definition": "The date that the attachment was first created.", + "requirements": "This is often tracked as an integrity issue for use of the attachment.", + "min": 0, + "max": "1", + "base": { + "path": "Attachment.creation", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A (needs data type R3 proposal)" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "Attachment", + "path": "Attachment", + "constraint": [ + { + "key": "must-be-drs-uri", + "severity": "error", + "human": "attachment.url must start with ^drs://. A drs:// hostname-based URI, as defined in the DRS documentation, that tells clients how to access this object. The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around. For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the `self_uri` presents you with a hostname and properly encoded DRS ID for use in subsequent `access` endpoint calls.", + "expression": "$this.url.matches('^drs://.*')", + "source": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + } + ] + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-document-reference.json b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-document-reference.json new file mode 100644 index 0000000..ca0e1fb --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-drs-document-reference.json @@ -0,0 +1,2453 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-drs-document-reference", + "text": { + "status": "extensions", + "div": "
\r\n\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" DocumentReference 0..*DocumentReferenceA reference to a document
\".\"\".\"\".\" content
\".\"\".\"\".\"\".\" attachment 1..1DRSAttachmentContent in a format defined elsewhere

\"doco\" Documentation for this format
" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category", + "valueString": "Foundation.Documents" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category", + "valueCode": "not-classified" + } + ], + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-document-reference", + "version": "0.1.0", + "name": "DRSDocumentReference", + "title": "DRS Document Reference", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "A FHIR Document Reference with an embedded DRS URI. See https://github.com/ga4gh/data-repository-service-schemas.", + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "workflow", + "uri": "http://hl7.org/fhir/workflow", + "name": "Workflow Pattern" + }, + { + "identity": "fhircomposition", + "uri": "http://hl7.org/fhir/composition", + "name": "FHIR Composition" + }, + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + }, + { + "identity": "cda", + "uri": "http://hl7.org/v3/cda", + "name": "CDA (R2)" + }, + { + "identity": "w5", + "uri": "http://hl7.org/fhir/fivews", + "name": "FiveWs Pattern Mapping" + }, + { + "identity": "v2", + "uri": "http://hl7.org/v2", + "name": "HL7 v2 Mapping" + }, + { + "identity": "xds", + "uri": "http://ihe.net/xds", + "name": "XDS metadata equivalent" + } + ], + "kind": "resource", + "abstract": false, + "type": "DocumentReference", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/DocumentReference", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "DocumentReference", + "path": "DocumentReference", + "short": "A reference to a document", + "definition": "A reference to a document of any kind for any purpose. Provides metadata about the document so that the document can be discovered and managed. The scope of a document is any seralized object with a mime-type, so includes formal patient centric documents (CDA), cliical notes, scanned paper, and non-patient specific documents like policy text.", + "comment": "Usually, this is used for documents other than those defined by FHIR.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference", + "min": 0, + "max": "*" + }, + "constraint": [ + { + "key": "dom-2", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources", + "expression": "contained.contained.empty()", + "xpath": "not(parent::f:contained and f:contained)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-3", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource", + "expression": "contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()", + "xpath": "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-4", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated", + "expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-5", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a security label", + "expression": "contained.meta.security.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:security))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time." + } + ], + "key": "dom-6", + "severity": "warning", + "human": "A resource should have narrative for robust management", + "expression": "text.`div`.exists()", + "xpath": "exists(f:text/h:div)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Entity. Role, or Act" + }, + { + "identity": "workflow", + "map": "Event" + }, + { + "identity": "fhircomposition", + "map": "when describing a Composition" + }, + { + "identity": "rim", + "map": "Document[classCode=\"DOC\" and moodCode=\"EVN\"]" + }, + { + "identity": "cda", + "map": "when describing a CDA" + } + ] + }, + { + "id": "DocumentReference.id", + "path": "DocumentReference.id", + "short": "Logical id of this artifact", + "definition": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.", + "comment": "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "DocumentReference.meta", + "path": "DocumentReference.meta", + "short": "Metadata about the resource", + "definition": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.meta", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Meta" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "DocumentReference.implicitRules", + "path": "DocumentReference.implicitRules", + "short": "A set of rules under which this content was created", + "definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.", + "comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.implicitRules", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "uri" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation", + "isSummary": true + }, + { + "id": "DocumentReference.language", + "path": "DocumentReference.language", + "short": "Language of the resource content", + "definition": "The base language in which the resource is written.", + "comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).", + "min": 0, + "max": "1", + "base": { + "path": "Resource.language", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", + "valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "Language" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "preferred", + "description": "A human language.", + "valueSet": "http://hl7.org/fhir/ValueSet/languages" + } + }, + { + "id": "DocumentReference.text", + "path": "DocumentReference.text", + "short": "Text summary of the resource, for human interpretation", + "definition": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.", + "comment": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.", + "alias": [ + "narrative", + "html", + "xhtml", + "display" + ], + "min": 0, + "max": "1", + "base": { + "path": "DomainResource.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Narrative" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Act.text?" + } + ] + }, + { + "id": "DocumentReference.contained", + "path": "DocumentReference.contained", + "short": "Contained, inline Resources", + "definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.", + "comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.", + "alias": [ + "inline resources", + "anonymous resources", + "contained resources" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.contained", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Resource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.extension", + "path": "DocumentReference.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.modifierExtension", + "path": "DocumentReference.modifierExtension", + "short": "Extensions that cannot be ignored", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them", + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.masterIdentifier", + "path": "DocumentReference.masterIdentifier", + "short": "Master Version Specific Identifier", + "definition": "Document identifier as assigned by the source of the document. This identifier is specific to this version of the document. This unique identifier may be used elsewhere to identify this version of the document.", + "comment": "CDA Document Id extension and root.", + "requirements": "The structure and format of this Id shall be consistent with the specification corresponding to the formatCode attribute. (e.g. for a DICOM standard document a 64-character numeric UID, for an HL7 CDA format a serialization of the CDA Document Id extension and root in the form \"oid^extension\", where OID is a 64 digits max, and the Id is a 16 UTF-8 char max. If the OID is coded without the extension then the '^' character shall not be included.).", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.masterIdentifier", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "fhircomposition", + "map": "Composition.identifier" + }, + { + "identity": "v2", + "map": "TXA-12" + }, + { + "identity": "rim", + "map": ".id" + }, + { + "identity": "xds", + "map": "DocumentEntry.uniqueId" + }, + { + "identity": "cda", + "map": "ClinicalDocument/id" + } + ] + }, + { + "id": "DocumentReference.identifier", + "path": "DocumentReference.identifier", + "short": "Other identifiers for the document", + "definition": "Other identifiers associated with the document, including version independent identifiers.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.identifier", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "v2", + "map": "TXA-16?" + }, + { + "identity": "rim", + "map": ".id / .setId" + }, + { + "identity": "xds", + "map": "DocumentEntry.entryUUID" + } + ] + }, + { + "id": "DocumentReference.status", + "path": "DocumentReference.status", + "short": "current | superseded | entered-in-error", + "definition": "The status of this document reference.", + "comment": "This is the status of the DocumentReference object, which might be independent from the docStatus element.\n\nThis element is labeled as a modifier because the status contains the codes that mark the document or reference as not currently valid.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.status", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labelled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentReferenceStatus" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "required", + "description": "The status of the document reference.", + "valueSet": "http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "v2", + "map": "TXA-19" + }, + { + "identity": "rim", + "map": "interim: .completionCode=\"IN\" & ./statusCode[isNormalDatatype()]=\"active\"; final: .completionCode=\"AU\" && ./statusCode[isNormalDatatype()]=\"complete\" and not(./inboundRelationship[typeCode=\"SUBJ\" and isNormalActRelationship()]/source[subsumesCode(\"ActClass#CACT\") and moodCode=\"EVN\" and domainMember(\"ReviseDocument\", code) and isNormalAct()]); amended: .completionCode=\"AU\" && ./statusCode[isNormalDatatype()]=\"complete\" and ./inboundRelationship[typeCode=\"SUBJ\" and isNormalActRelationship()]/source[subsumesCode(\"ActClass#CACT\") and moodCode=\"EVN\" and domainMember(\"ReviseDocument\", code) and isNormalAct() and statusCode=\"completed\"]; withdrawn : .completionCode=NI && ./statusCode[isNormalDatatype()]=\"obsolete\"" + }, + { + "identity": "xds", + "map": "DocumentEntry.availabilityStatus" + } + ] + }, + { + "id": "DocumentReference.docStatus", + "path": "DocumentReference.docStatus", + "short": "preliminary | final | amended | entered-in-error", + "definition": "The status of the underlying document.", + "comment": "The document that is pointed to might be in various lifecycle states.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.docStatus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ReferredDocumentStatus" + } + ], + "strength": "required", + "description": "Status of the underlying document.", + "valueSet": "http://hl7.org/fhir/ValueSet/composition-status|4.0.1" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "fhircomposition", + "map": "Composition.status" + }, + { + "identity": "v2", + "map": "TXA-17" + }, + { + "identity": "rim", + "map": ".statusCode" + } + ] + }, + { + "id": "DocumentReference.type", + "path": "DocumentReference.type", + "short": "Kind of document (LOINC if possible)", + "definition": "Specifies the particular kind of document referenced (e.g. History and Physical, Discharge Summary, Progress Note). This usually equates to the purpose of making the document referenced.", + "comment": "Key metadata element describing the document that describes he exact type of document. Helps humans to assess whether the document is of interest when viewing a list of documents.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.type", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80Type" + } + ], + "strength": "preferred", + "description": "Precise type of clinical document.", + "valueSet": "http://hl7.org/fhir/ValueSet/c80-doc-typecodes" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.code" + }, + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "fhircomposition", + "map": "Composition.type" + }, + { + "identity": "v2", + "map": "TXA-2" + }, + { + "identity": "rim", + "map": "./code" + }, + { + "identity": "xds", + "map": "DocumentEntry.type" + }, + { + "identity": "cda", + "map": "ClinicalDocument/code/@code \n\nThe typeCode should be mapped from the ClinicalDocument/code element to a set of document type codes configured in the affinity domain. One suggested coding system to use for typeCode is LOINC, in which case the mapping step can be omitted." + } + ] + }, + { + "id": "DocumentReference.category", + "path": "DocumentReference.category", + "short": "Categorization of document", + "definition": "A categorization for the type of document referenced - helps for indexing and searching. This may be implied by or derived from the code specified in the DocumentReference.type.", + "comment": "Key metadata element describing the the category or classification of the document. This is a broader perspective that groups similar documents based on how they would be used. This is a primary key used in searching.", + "alias": [ + "claxs" + ], + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.category", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80Class" + } + ], + "strength": "example", + "description": "High-level kind of a clinical document at a macro level.", + "valueSet": "http://hl7.org/fhir/ValueSet/document-classcodes" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "fhircomposition", + "map": "Composition.class" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=\"COMP].target[classCode=\"LIST\", moodCode=\"EVN\"].code" + }, + { + "identity": "xds", + "map": "DocumentEntry.class" + }, + { + "identity": "cda", + "map": "Derived from a mapping of /ClinicalDocument/code/@code to an Affinity Domain specified coded value to use and coding system. Affinity Domains are encouraged to use the appropriate value for Type of Service, based on the LOINC Type of Service (see Page 53 of the LOINC User's Manual). Must be consistent with /ClinicalDocument/code/@code" + } + ] + }, + { + "id": "DocumentReference.subject", + "path": "DocumentReference.subject", + "short": "Who/what is the subject of the document", + "definition": "Who or what the document is about. The document can be about a person, (patient or healthcare practitioner), a device (e.g. a machine) or even a group of subjects (such as a document about a herd of farm animals, or a set of patients that share a common exposure).", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.subject", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/Group", + "http://hl7.org/fhir/StructureDefinition/Device" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.subject" + }, + { + "identity": "w5", + "map": "FiveWs.subject[x]" + }, + { + "identity": "fhircomposition", + "map": "Composition.subject" + }, + { + "identity": "v2", + "map": "PID-3 (No standard way to define a Practitioner or Group subject in HL7 v2 MDM message)" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"SBJ\"].role[typeCode=\"PAT\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.patientId" + }, + { + "identity": "cda", + "map": "ClinicalDocument/recordTarget/" + }, + { + "identity": "w5", + "map": "FiveWs.subject" + } + ] + }, + { + "id": "DocumentReference.date", + "path": "DocumentReference.date", + "short": "When this document reference was created", + "definition": "When the document reference was created.", + "comment": "Referencing/indexing time is used for tracking, organizing versions and searching.", + "alias": [ + "indexed" + ], + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.date", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "instant" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.occurrence[x]" + }, + { + "identity": "w5", + "map": "FiveWs.recorded" + }, + { + "identity": "fhircomposition", + "map": "Composition.date" + }, + { + "identity": "rim", + "map": ".availabilityTime[type=\"TS\"]" + } + ] + }, + { + "id": "DocumentReference.author", + "path": "DocumentReference.author", + "short": "Who and/or what authored the document", + "definition": "Identifies who is responsible for adding the information to the document.", + "comment": "Not necessarily who did the actual data entry (i.e. typist) or who was the source (informant).", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.author", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Organization", + "http://hl7.org/fhir/StructureDefinition/Device", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor" + }, + { + "identity": "fhircomposition", + "map": "Composition.author" + }, + { + "identity": "v2", + "map": "TXA-9 (No standard way to indicate a Device in HL7 v2 MDM message)" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"AUT\"].role[classCode=\"ASSIGNED\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.author" + }, + { + "identity": "cda", + "map": "ClinicalDocument/author" + } + ] + }, + { + "id": "DocumentReference.authenticator", + "path": "DocumentReference.authenticator", + "short": "Who/what authenticated the document", + "definition": "Which person or organization authenticates that this document is valid.", + "comment": "Represents a participant within the author institution who has legally authenticated or attested the document. Legal authentication implies that a document has been signed manually or electronically by the legal Authenticator.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.authenticator", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor" + }, + { + "identity": "w5", + "map": "FiveWs.witness" + }, + { + "identity": "fhircomposition", + "map": "Composition.attester" + }, + { + "identity": "v2", + "map": "TXA-10" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"AUTHEN\"].role[classCode=\"ASSIGNED\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.legalAuthenticator" + }, + { + "identity": "cda", + "map": "ClinicalDocument/legalAuthenticator" + } + ] + }, + { + "id": "DocumentReference.custodian", + "path": "DocumentReference.custodian", + "short": "Organization which maintains the document", + "definition": "Identifies the organization or group who is responsible for ongoing maintenance of and access to the document.", + "comment": "Identifies the logical organization (software system, vendor, or department) to go to find the current version, where to report issues, etc. This is different from the physical location (URL, disk drive, or server) of the document, which is the technical location of the document, which host may be delegated to the management of some other organization.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.custodian", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor" + }, + { + "identity": "fhircomposition", + "map": "Composition.custodian" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"RCV\"].role[classCode=\"CUST\"].scoper[classCode=\"ORG\" and determinerCode=\"INST\"]" + } + ] + }, + { + "id": "DocumentReference.relatesTo", + "path": "DocumentReference.relatesTo", + "short": "Relationships to other documents", + "definition": "Relationships that this document has with other document references that already exist.", + "comment": "This element is labeled as a modifier because documents that append to other documents are incomplete on their own.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.relatesTo", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.relatesTo" + }, + { + "identity": "rim", + "map": ".outboundRelationship" + }, + { + "identity": "xds", + "map": "DocumentEntry Associations" + } + ] + }, + { + "id": "DocumentReference.relatesTo.id", + "path": "DocumentReference.relatesTo.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.relatesTo.extension", + "path": "DocumentReference.relatesTo.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.relatesTo.modifierExtension", + "path": "DocumentReference.relatesTo.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.relatesTo.code", + "path": "DocumentReference.relatesTo.code", + "short": "replaces | transforms | signs | appends", + "definition": "The type of relationship that this document has with anther document.", + "comment": "If this document appends another document, then the document cannot be fully understood without also accessing the referenced document.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.relatesTo.code", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentRelationshipType" + } + ], + "strength": "required", + "description": "The type of relationship between documents.", + "valueSet": "http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.relatesTo.code" + }, + { + "identity": "rim", + "map": ".outboundRelationship.typeCode" + }, + { + "identity": "xds", + "map": "DocumentEntry Associations type" + } + ] + }, + { + "id": "DocumentReference.relatesTo.target", + "path": "DocumentReference.relatesTo.target", + "short": "Target of the relationship", + "definition": "The target document of this relationship.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.relatesTo.target", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/DocumentReference" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.relatesTo.target" + }, + { + "identity": "rim", + "map": ".target[classCode=\"DOC\", moodCode=\"EVN\"].id" + }, + { + "identity": "xds", + "map": "DocumentEntry Associations reference" + } + ] + }, + { + "id": "DocumentReference.description", + "path": "DocumentReference.description", + "short": "Human-readable description", + "definition": "Human-readable description of the source document.", + "comment": "What the document is about, a terse summary of the document.", + "requirements": "Helps humans to assess whether the document is of interest.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.description", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "string" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "TXA-25" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=\"SUBJ\"].target.text" + }, + { + "identity": "xds", + "map": "DocumentEntry.comments" + } + ] + }, + { + "id": "DocumentReference.securityLabel", + "path": "DocumentReference.securityLabel", + "short": "Document security-tags", + "definition": "A set of Security-Tag codes specifying the level of privacy/security of the Document. Note that DocumentReference.meta.security contains the security labels of the \"reference\" to the document, while DocumentReference.securityLabel contains a snapshot of the security labels on the document the reference refers to.", + "comment": "The confidentiality codes can carry multiple vocabulary items. HL7 has developed an understanding of security and privacy tags that might be desirable in a Document Sharing environment, called HL7 Healthcare Privacy and Security Classification System (HCS). The following specification is recommended but not mandated, as the vocabulary bindings are an administrative domain responsibility. The use of this method is up to the policy domain such as the XDS Affinity Domain or other Trust Domain where all parties including sender and recipients are trusted to appropriately tag and enforce. \n\nIn the HL7 Healthcare Privacy and Security Classification (HCS) there are code systems specific to Confidentiality, Sensitivity, Integrity, and Handling Caveats. Some values would come from a local vocabulary as they are related to workflow roles and special projects.", + "requirements": "Use of the Health Care Privacy/Security Classification (HCS) system of security-tag use is recommended.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.securityLabel", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "SecurityLabels" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "extensible", + "description": "Security Labels from the Healthcare Privacy and Security Classification System.", + "valueSet": "http://hl7.org/fhir/ValueSet/security-labels" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.confidentiality, Composition.meta.security" + }, + { + "identity": "v2", + "map": "TXA-18" + }, + { + "identity": "rim", + "map": ".confidentialityCode" + }, + { + "identity": "xds", + "map": "DocumentEntry.confidentialityCode" + }, + { + "identity": "cda", + "map": "ClinicalDocument/confidentialityCode/@code" + } + ] + }, + { + "id": "DocumentReference.content", + "path": "DocumentReference.content", + "short": "Document referenced", + "definition": "The document and format referenced. There may be multiple content element repetitions, each with a different format.", + "min": 1, + "max": "*", + "base": { + "path": "DocumentReference.content", + "min": 1, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Bundle(Composition+*)" + }, + { + "identity": "rim", + "map": "document.text" + } + ] + }, + { + "id": "DocumentReference.content.id", + "path": "DocumentReference.content.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.content.extension", + "path": "DocumentReference.content.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.content.modifierExtension", + "path": "DocumentReference.content.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.content.attachment", + "path": "DocumentReference.content.attachment", + "short": "Content in a format defined elsewhere", + "definition": "For referring to data content defined in other formats.", + "comment": "When providing a summary view (for example with Observation.value[x]) Attachment should be represented with a brief display text such as \"Signed Procedure Consent\".", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.content.attachment", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "Attachment", + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + ] + } + ], + "condition": [ + "ele-1" + ], + "constraint": [ + { + "key": "att-1", + "severity": "error", + "human": "If the Attachment has data, it SHALL have a contentType", + "expression": "data.empty() or contentType.exists()", + "xpath": "not(exists(f:data)) or exists(f:contentType)", + "source": "http://hl7.org/fhir/StructureDefinition/Attachment" + }, + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "must-be-drs-uri", + "severity": "error", + "human": "attachment.url must start with ^drs://. A drs:// hostname-based URI, as defined in the DRS documentation, that tells clients how to access this object. The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around. For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the `self_uri` presents you with a hostname and properly encoded DRS ID for use in subsequent `access` endpoint calls.", + "expression": "$this.url.matches('^drs://.*')", + "source": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + } + ], + "isModifier": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + }, + { + "identity": "v2", + "map": "ED/RP" + }, + { + "identity": "rim", + "map": "ED" + } + ] + }, + { + "id": "DocumentReference.content.format", + "path": "DocumentReference.content.format", + "short": "Format/content rules for the document", + "definition": "An identifier of the document encoding, structure, and template that the document conforms to beyond the base format indicated in the mimeType.", + "comment": "Note that while IHE mostly issues URNs for format types, not all documents can be identified by a URI.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.content.format", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Coding" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentFormat" + } + ], + "strength": "preferred", + "description": "Document Format Codes.", + "valueSet": "http://hl7.org/fhir/ValueSet/formatcodes" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.meta.profile" + }, + { + "identity": "rim", + "map": "document.text" + }, + { + "identity": "xds", + "map": "DocumentEntry.formatCode" + }, + { + "identity": "cda", + "map": "derived from the IHE Profile or Implementation Guide templateID" + } + ] + }, + { + "id": "DocumentReference.context", + "path": "DocumentReference.context", + "short": "Clinical context of document", + "definition": "The clinical context in which the document was prepared.", + "comment": "These values are primarily added to help with searching for interesting/relevant documents.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "outboundRelationship[typeCode=\"SUBJ\"].target[classCode<'ACT']" + } + ] + }, + { + "id": "DocumentReference.context.id", + "path": "DocumentReference.context.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.context.extension", + "path": "DocumentReference.context.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.context.modifierExtension", + "path": "DocumentReference.context.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.context.encounter", + "path": "DocumentReference.context.encounter", + "short": "Context of the document content", + "definition": "Describes the clinical encounter or type of care that the document content is associated with.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.context.encounter", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Encounter", + "http://hl7.org/fhir/StructureDefinition/EpisodeOfCare" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.context" + }, + { + "identity": "w5", + "map": "FiveWs.context" + }, + { + "identity": "fhircomposition", + "map": "Composition.encounter" + }, + { + "identity": "rim", + "map": "unique(highest(./outboundRelationship[typeCode=\"SUBJ\" and isNormalActRelationship()], priorityNumber)/target[moodCode=\"EVN\" and classCode=(\"ENC\", \"PCPR\") and isNormalAct])" + } + ] + }, + { + "id": "DocumentReference.context.event", + "path": "DocumentReference.context.event", + "short": "Main clinical acts documented", + "definition": "This list of codes represents the main clinical acts, such as a colonoscopy or an appendectomy, being documented. In some cases, the event is inherent in the type Code, such as a \"History and Physical Report\" in which the procedure being documented is necessarily a \"History and Physical\" act.", + "comment": "An event can further specialize the act inherent in the type, such as where it is simply \"Procedure Report\" and the procedure was a \"colonoscopy\". If one or more event codes are included, they shall not conflict with the values inherent in the class or type elements as such a conflict would create an ambiguous situation.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.context.event", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentEventType" + } + ], + "strength": "example", + "description": "This list of codes represents the main clinical acts being documented.", + "valueSet": "http://terminology.hl7.org/ValueSet/v3-ActCode" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.event.code" + }, + { + "identity": "rim", + "map": ".code" + }, + { + "identity": "xds", + "map": "DocumentEntry.eventCodeList" + } + ] + }, + { + "id": "DocumentReference.context.period", + "path": "DocumentReference.context.period", + "short": "Time of service that is being documented", + "definition": "The time period over which the service that is described by the document was provided.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.period", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Period" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.event.period" + }, + { + "identity": "rim", + "map": ".effectiveTime" + }, + { + "identity": "xds", + "map": "DocumentEntry.serviceStartTime, DocumentEntry.serviceStopTime" + }, + { + "identity": "cda", + "map": "ClinicalDocument/documentationOf/\nserviceEvent/effectiveTime/low/\n@value --> ClinicalDocument/documentationOf/\nserviceEvent/effectiveTime/high/\n@value" + } + ] + }, + { + "id": "DocumentReference.context.facilityType", + "path": "DocumentReference.context.facilityType", + "short": "Kind of facility where patient was seen", + "definition": "The kind of facility where the patient was seen.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.facilityType", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80FacilityType" + } + ], + "strength": "example", + "description": "XDS Facility Type.", + "valueSet": "http://hl7.org/fhir/ValueSet/c80-facilitycodes" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "usually from a mapping to a local ValueSet" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"LOC\"].role[classCode=\"DSDLOC\"].code" + }, + { + "identity": "xds", + "map": "DocumentEntry.healthcareFacilityTypeCode" + }, + { + "identity": "cda", + "map": "usually a mapping to a local ValueSet. Must be consistent with /clinicalDocument/code" + } + ] + }, + { + "id": "DocumentReference.context.practiceSetting", + "path": "DocumentReference.context.practiceSetting", + "short": "Additional details about where the content was created (e.g. clinical specialty)", + "definition": "This property may convey specifics about the practice setting where the content was created, often reflecting the clinical specialty.", + "comment": "This element should be based on a coarse classification system for the class of specialty practice. Recommend the use of the classification system for Practice Setting, such as that described by the Subject Matter Domain in LOINC.", + "requirements": "This is an important piece of metadata that providers often rely upon to quickly sort and/or filter out to find specific content.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.practiceSetting", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80PracticeSetting" + } + ], + "strength": "example", + "description": "Additional details about where the content was created (e.g. clinical specialty).", + "valueSet": "http://hl7.org/fhir/ValueSet/c80-practice-codes" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "usually from a mapping to a local ValueSet" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"LOC\"].role[classCode=\"DSDLOC\"].code" + }, + { + "identity": "xds", + "map": "DocumentEntry.practiceSettingCode" + }, + { + "identity": "cda", + "map": "usually from a mapping to a local ValueSet" + } + ] + }, + { + "id": "DocumentReference.context.sourcePatientInfo", + "path": "DocumentReference.context.sourcePatientInfo", + "short": "Patient demographics from source", + "definition": "The Patient Information as known when the document was published. May be a reference to a version specific, or contained.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.sourcePatientInfo", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.subject" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"SBJ\"].role[typeCode=\"PAT\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.sourcePatientInfo, DocumentEntry.sourcePatientId" + }, + { + "identity": "cda", + "map": "ClinicalDocument/recordTarget/" + } + ] + }, + { + "id": "DocumentReference.context.related", + "path": "DocumentReference.context.related", + "short": "Related identifiers or resources", + "definition": "Related identifiers or resources associated with the DocumentReference.", + "comment": "May be identifiers or resources that caused the DocumentReference or referenced Document to be created.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.context.related", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.event.detail" + }, + { + "identity": "rim", + "map": "./outboundRelationship[typeCode=\"PERT\" and isNormalActRelationship()] / target[isNormalAct]" + }, + { + "identity": "xds", + "map": "DocumentEntry.referenceIdList" + }, + { + "identity": "cda", + "map": "ClinicalDocument/relatedDocument" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "DocumentReference", + "path": "DocumentReference" + }, + { + "id": "DocumentReference.content.attachment", + "path": "DocumentReference.content.attachment", + "type": [ + { + "code": "Attachment", + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + ] + } + ] + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-research-document-reference.json b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-research-document-reference.json new file mode 100644 index 0000000..d7654d5 --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-research-document-reference.json @@ -0,0 +1,2480 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-research-document-reference", + "text": { + "status": "extensions", + "div": "
\r\n\r\n\r\n\r\n\r\n\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" DocumentReference 0..*DocumentReferenceA reference to a document
\".\"\".\"\".\" subject 1..1Reference(Patient | Practitioner | Group | Device)Who/what is the subject of the document
\".\"\".\"\".\" custodian 1..1Reference(Organization)Organization which maintains the document
\".\"\".\"\".\" content
\".\"\".\"\".\"\".\" attachment 1..1DRSAttachmentContent in a format defined elsewhere
\".\"\".\"\".\" context 1..1BackboneElementClinical context of document
\".\"\".\"\".\"\".\" related 0..*Reference(Task)Related identifiers or resources

\"doco\" Documentation for this format
" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category", + "valueString": "Foundation.Documents" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category", + "valueCode": "not-classified" + } + ], + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-research-document-reference", + "version": "0.1.0", + "name": "ResearchDocumentReference", + "title": "Research Document Reference", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "A FHIR Document Reference created by an analysis task. Context.related = Task ", + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "workflow", + "uri": "http://hl7.org/fhir/workflow", + "name": "Workflow Pattern" + }, + { + "identity": "fhircomposition", + "uri": "http://hl7.org/fhir/composition", + "name": "FHIR Composition" + }, + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + }, + { + "identity": "cda", + "uri": "http://hl7.org/v3/cda", + "name": "CDA (R2)" + }, + { + "identity": "w5", + "uri": "http://hl7.org/fhir/fivews", + "name": "FiveWs Pattern Mapping" + }, + { + "identity": "v2", + "uri": "http://hl7.org/v2", + "name": "HL7 v2 Mapping" + }, + { + "identity": "xds", + "uri": "http://ihe.net/xds", + "name": "XDS metadata equivalent" + } + ], + "kind": "resource", + "abstract": false, + "type": "DocumentReference", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/DocumentReference", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "DocumentReference", + "path": "DocumentReference", + "short": "A reference to a document", + "definition": "A reference to a document of any kind for any purpose. Provides metadata about the document so that the document can be discovered and managed. The scope of a document is any seralized object with a mime-type, so includes formal patient centric documents (CDA), cliical notes, scanned paper, and non-patient specific documents like policy text.", + "comment": "Usually, this is used for documents other than those defined by FHIR.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference", + "min": 0, + "max": "*" + }, + "constraint": [ + { + "key": "dom-2", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources", + "expression": "contained.contained.empty()", + "xpath": "not(parent::f:contained and f:contained)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-3", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource", + "expression": "contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()", + "xpath": "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-4", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated", + "expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-5", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a security label", + "expression": "contained.meta.security.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:security))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time." + } + ], + "key": "dom-6", + "severity": "warning", + "human": "A resource should have narrative for robust management", + "expression": "text.`div`.exists()", + "xpath": "exists(f:text/h:div)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Entity. Role, or Act" + }, + { + "identity": "workflow", + "map": "Event" + }, + { + "identity": "fhircomposition", + "map": "when describing a Composition" + }, + { + "identity": "rim", + "map": "Document[classCode=\"DOC\" and moodCode=\"EVN\"]" + }, + { + "identity": "cda", + "map": "when describing a CDA" + } + ] + }, + { + "id": "DocumentReference.id", + "path": "DocumentReference.id", + "short": "Logical id of this artifact", + "definition": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.", + "comment": "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "DocumentReference.meta", + "path": "DocumentReference.meta", + "short": "Metadata about the resource", + "definition": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.meta", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Meta" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "DocumentReference.implicitRules", + "path": "DocumentReference.implicitRules", + "short": "A set of rules under which this content was created", + "definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.", + "comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.implicitRules", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "uri" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation", + "isSummary": true + }, + { + "id": "DocumentReference.language", + "path": "DocumentReference.language", + "short": "Language of the resource content", + "definition": "The base language in which the resource is written.", + "comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).", + "min": 0, + "max": "1", + "base": { + "path": "Resource.language", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", + "valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "Language" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "preferred", + "description": "A human language.", + "valueSet": "http://hl7.org/fhir/ValueSet/languages" + } + }, + { + "id": "DocumentReference.text", + "path": "DocumentReference.text", + "short": "Text summary of the resource, for human interpretation", + "definition": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.", + "comment": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.", + "alias": [ + "narrative", + "html", + "xhtml", + "display" + ], + "min": 0, + "max": "1", + "base": { + "path": "DomainResource.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Narrative" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Act.text?" + } + ] + }, + { + "id": "DocumentReference.contained", + "path": "DocumentReference.contained", + "short": "Contained, inline Resources", + "definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.", + "comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.", + "alias": [ + "inline resources", + "anonymous resources", + "contained resources" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.contained", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Resource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.extension", + "path": "DocumentReference.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.modifierExtension", + "path": "DocumentReference.modifierExtension", + "short": "Extensions that cannot be ignored", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them", + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.masterIdentifier", + "path": "DocumentReference.masterIdentifier", + "short": "Master Version Specific Identifier", + "definition": "Document identifier as assigned by the source of the document. This identifier is specific to this version of the document. This unique identifier may be used elsewhere to identify this version of the document.", + "comment": "CDA Document Id extension and root.", + "requirements": "The structure and format of this Id shall be consistent with the specification corresponding to the formatCode attribute. (e.g. for a DICOM standard document a 64-character numeric UID, for an HL7 CDA format a serialization of the CDA Document Id extension and root in the form \"oid^extension\", where OID is a 64 digits max, and the Id is a 16 UTF-8 char max. If the OID is coded without the extension then the '^' character shall not be included.).", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.masterIdentifier", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "fhircomposition", + "map": "Composition.identifier" + }, + { + "identity": "v2", + "map": "TXA-12" + }, + { + "identity": "rim", + "map": ".id" + }, + { + "identity": "xds", + "map": "DocumentEntry.uniqueId" + }, + { + "identity": "cda", + "map": "ClinicalDocument/id" + } + ] + }, + { + "id": "DocumentReference.identifier", + "path": "DocumentReference.identifier", + "short": "Other identifiers for the document", + "definition": "Other identifiers associated with the document, including version independent identifiers.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.identifier", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "v2", + "map": "TXA-16?" + }, + { + "identity": "rim", + "map": ".id / .setId" + }, + { + "identity": "xds", + "map": "DocumentEntry.entryUUID" + } + ] + }, + { + "id": "DocumentReference.status", + "path": "DocumentReference.status", + "short": "current | superseded | entered-in-error", + "definition": "The status of this document reference.", + "comment": "This is the status of the DocumentReference object, which might be independent from the docStatus element.\n\nThis element is labeled as a modifier because the status contains the codes that mark the document or reference as not currently valid.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.status", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labelled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentReferenceStatus" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "required", + "description": "The status of the document reference.", + "valueSet": "http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "v2", + "map": "TXA-19" + }, + { + "identity": "rim", + "map": "interim: .completionCode=\"IN\" & ./statusCode[isNormalDatatype()]=\"active\"; final: .completionCode=\"AU\" && ./statusCode[isNormalDatatype()]=\"complete\" and not(./inboundRelationship[typeCode=\"SUBJ\" and isNormalActRelationship()]/source[subsumesCode(\"ActClass#CACT\") and moodCode=\"EVN\" and domainMember(\"ReviseDocument\", code) and isNormalAct()]); amended: .completionCode=\"AU\" && ./statusCode[isNormalDatatype()]=\"complete\" and ./inboundRelationship[typeCode=\"SUBJ\" and isNormalActRelationship()]/source[subsumesCode(\"ActClass#CACT\") and moodCode=\"EVN\" and domainMember(\"ReviseDocument\", code) and isNormalAct() and statusCode=\"completed\"]; withdrawn : .completionCode=NI && ./statusCode[isNormalDatatype()]=\"obsolete\"" + }, + { + "identity": "xds", + "map": "DocumentEntry.availabilityStatus" + } + ] + }, + { + "id": "DocumentReference.docStatus", + "path": "DocumentReference.docStatus", + "short": "preliminary | final | amended | entered-in-error", + "definition": "The status of the underlying document.", + "comment": "The document that is pointed to might be in various lifecycle states.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.docStatus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ReferredDocumentStatus" + } + ], + "strength": "required", + "description": "Status of the underlying document.", + "valueSet": "http://hl7.org/fhir/ValueSet/composition-status|4.0.1" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "fhircomposition", + "map": "Composition.status" + }, + { + "identity": "v2", + "map": "TXA-17" + }, + { + "identity": "rim", + "map": ".statusCode" + } + ] + }, + { + "id": "DocumentReference.type", + "path": "DocumentReference.type", + "short": "Kind of document (LOINC if possible)", + "definition": "Specifies the particular kind of document referenced (e.g. History and Physical, Discharge Summary, Progress Note). This usually equates to the purpose of making the document referenced.", + "comment": "Key metadata element describing the document that describes he exact type of document. Helps humans to assess whether the document is of interest when viewing a list of documents.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.type", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80Type" + } + ], + "strength": "preferred", + "description": "Precise type of clinical document.", + "valueSet": "http://hl7.org/fhir/ValueSet/c80-doc-typecodes" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.code" + }, + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "fhircomposition", + "map": "Composition.type" + }, + { + "identity": "v2", + "map": "TXA-2" + }, + { + "identity": "rim", + "map": "./code" + }, + { + "identity": "xds", + "map": "DocumentEntry.type" + }, + { + "identity": "cda", + "map": "ClinicalDocument/code/@code \n\nThe typeCode should be mapped from the ClinicalDocument/code element to a set of document type codes configured in the affinity domain. One suggested coding system to use for typeCode is LOINC, in which case the mapping step can be omitted." + } + ] + }, + { + "id": "DocumentReference.category", + "path": "DocumentReference.category", + "short": "Categorization of document", + "definition": "A categorization for the type of document referenced - helps for indexing and searching. This may be implied by or derived from the code specified in the DocumentReference.type.", + "comment": "Key metadata element describing the the category or classification of the document. This is a broader perspective that groups similar documents based on how they would be used. This is a primary key used in searching.", + "alias": [ + "claxs" + ], + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.category", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80Class" + } + ], + "strength": "example", + "description": "High-level kind of a clinical document at a macro level.", + "valueSet": "http://hl7.org/fhir/ValueSet/document-classcodes" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "fhircomposition", + "map": "Composition.class" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=\"COMP].target[classCode=\"LIST\", moodCode=\"EVN\"].code" + }, + { + "identity": "xds", + "map": "DocumentEntry.class" + }, + { + "identity": "cda", + "map": "Derived from a mapping of /ClinicalDocument/code/@code to an Affinity Domain specified coded value to use and coding system. Affinity Domains are encouraged to use the appropriate value for Type of Service, based on the LOINC Type of Service (see Page 53 of the LOINC User's Manual). Must be consistent with /ClinicalDocument/code/@code" + } + ] + }, + { + "id": "DocumentReference.subject", + "path": "DocumentReference.subject", + "short": "Who/what is the subject of the document", + "definition": "Who or what the document is about. The document can be about a person, (patient or healthcare practitioner), a device (e.g. a machine) or even a group of subjects (such as a document about a herd of farm animals, or a set of patients that share a common exposure).", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.subject", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/Group", + "http://hl7.org/fhir/StructureDefinition/Device" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.subject" + }, + { + "identity": "w5", + "map": "FiveWs.subject[x]" + }, + { + "identity": "fhircomposition", + "map": "Composition.subject" + }, + { + "identity": "v2", + "map": "PID-3 (No standard way to define a Practitioner or Group subject in HL7 v2 MDM message)" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"SBJ\"].role[typeCode=\"PAT\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.patientId" + }, + { + "identity": "cda", + "map": "ClinicalDocument/recordTarget/" + }, + { + "identity": "w5", + "map": "FiveWs.subject" + } + ] + }, + { + "id": "DocumentReference.date", + "path": "DocumentReference.date", + "short": "When this document reference was created", + "definition": "When the document reference was created.", + "comment": "Referencing/indexing time is used for tracking, organizing versions and searching.", + "alias": [ + "indexed" + ], + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.date", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "instant" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.occurrence[x]" + }, + { + "identity": "w5", + "map": "FiveWs.recorded" + }, + { + "identity": "fhircomposition", + "map": "Composition.date" + }, + { + "identity": "rim", + "map": ".availabilityTime[type=\"TS\"]" + } + ] + }, + { + "id": "DocumentReference.author", + "path": "DocumentReference.author", + "short": "Who and/or what authored the document", + "definition": "Identifies who is responsible for adding the information to the document.", + "comment": "Not necessarily who did the actual data entry (i.e. typist) or who was the source (informant).", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.author", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Organization", + "http://hl7.org/fhir/StructureDefinition/Device", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor" + }, + { + "identity": "fhircomposition", + "map": "Composition.author" + }, + { + "identity": "v2", + "map": "TXA-9 (No standard way to indicate a Device in HL7 v2 MDM message)" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"AUT\"].role[classCode=\"ASSIGNED\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.author" + }, + { + "identity": "cda", + "map": "ClinicalDocument/author" + } + ] + }, + { + "id": "DocumentReference.authenticator", + "path": "DocumentReference.authenticator", + "short": "Who/what authenticated the document", + "definition": "Which person or organization authenticates that this document is valid.", + "comment": "Represents a participant within the author institution who has legally authenticated or attested the document. Legal authentication implies that a document has been signed manually or electronically by the legal Authenticator.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.authenticator", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor" + }, + { + "identity": "w5", + "map": "FiveWs.witness" + }, + { + "identity": "fhircomposition", + "map": "Composition.attester" + }, + { + "identity": "v2", + "map": "TXA-10" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"AUTHEN\"].role[classCode=\"ASSIGNED\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.legalAuthenticator" + }, + { + "identity": "cda", + "map": "ClinicalDocument/legalAuthenticator" + } + ] + }, + { + "id": "DocumentReference.custodian", + "path": "DocumentReference.custodian", + "short": "Organization which maintains the document", + "definition": "Identifies the organization or group who is responsible for ongoing maintenance of and access to the document.", + "comment": "Identifies the logical organization (software system, vendor, or department) to go to find the current version, where to report issues, etc. This is different from the physical location (URL, disk drive, or server) of the document, which is the technical location of the document, which host may be delegated to the management of some other organization.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.custodian", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor" + }, + { + "identity": "fhircomposition", + "map": "Composition.custodian" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"RCV\"].role[classCode=\"CUST\"].scoper[classCode=\"ORG\" and determinerCode=\"INST\"]" + } + ] + }, + { + "id": "DocumentReference.relatesTo", + "path": "DocumentReference.relatesTo", + "short": "Relationships to other documents", + "definition": "Relationships that this document has with other document references that already exist.", + "comment": "This element is labeled as a modifier because documents that append to other documents are incomplete on their own.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.relatesTo", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.relatesTo" + }, + { + "identity": "rim", + "map": ".outboundRelationship" + }, + { + "identity": "xds", + "map": "DocumentEntry Associations" + } + ] + }, + { + "id": "DocumentReference.relatesTo.id", + "path": "DocumentReference.relatesTo.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.relatesTo.extension", + "path": "DocumentReference.relatesTo.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.relatesTo.modifierExtension", + "path": "DocumentReference.relatesTo.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.relatesTo.code", + "path": "DocumentReference.relatesTo.code", + "short": "replaces | transforms | signs | appends", + "definition": "The type of relationship that this document has with anther document.", + "comment": "If this document appends another document, then the document cannot be fully understood without also accessing the referenced document.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.relatesTo.code", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentRelationshipType" + } + ], + "strength": "required", + "description": "The type of relationship between documents.", + "valueSet": "http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.relatesTo.code" + }, + { + "identity": "rim", + "map": ".outboundRelationship.typeCode" + }, + { + "identity": "xds", + "map": "DocumentEntry Associations type" + } + ] + }, + { + "id": "DocumentReference.relatesTo.target", + "path": "DocumentReference.relatesTo.target", + "short": "Target of the relationship", + "definition": "The target document of this relationship.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.relatesTo.target", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/DocumentReference" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.relatesTo.target" + }, + { + "identity": "rim", + "map": ".target[classCode=\"DOC\", moodCode=\"EVN\"].id" + }, + { + "identity": "xds", + "map": "DocumentEntry Associations reference" + } + ] + }, + { + "id": "DocumentReference.description", + "path": "DocumentReference.description", + "short": "Human-readable description", + "definition": "Human-readable description of the source document.", + "comment": "What the document is about, a terse summary of the document.", + "requirements": "Helps humans to assess whether the document is of interest.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.description", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "string" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "v2", + "map": "TXA-25" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=\"SUBJ\"].target.text" + }, + { + "identity": "xds", + "map": "DocumentEntry.comments" + } + ] + }, + { + "id": "DocumentReference.securityLabel", + "path": "DocumentReference.securityLabel", + "short": "Document security-tags", + "definition": "A set of Security-Tag codes specifying the level of privacy/security of the Document. Note that DocumentReference.meta.security contains the security labels of the \"reference\" to the document, while DocumentReference.securityLabel contains a snapshot of the security labels on the document the reference refers to.", + "comment": "The confidentiality codes can carry multiple vocabulary items. HL7 has developed an understanding of security and privacy tags that might be desirable in a Document Sharing environment, called HL7 Healthcare Privacy and Security Classification System (HCS). The following specification is recommended but not mandated, as the vocabulary bindings are an administrative domain responsibility. The use of this method is up to the policy domain such as the XDS Affinity Domain or other Trust Domain where all parties including sender and recipients are trusted to appropriately tag and enforce. \n\nIn the HL7 Healthcare Privacy and Security Classification (HCS) there are code systems specific to Confidentiality, Sensitivity, Integrity, and Handling Caveats. Some values would come from a local vocabulary as they are related to workflow roles and special projects.", + "requirements": "Use of the Health Care Privacy/Security Classification (HCS) system of security-tag use is recommended.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.securityLabel", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "SecurityLabels" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "extensible", + "description": "Security Labels from the Healthcare Privacy and Security Classification System.", + "valueSet": "http://hl7.org/fhir/ValueSet/security-labels" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.confidentiality, Composition.meta.security" + }, + { + "identity": "v2", + "map": "TXA-18" + }, + { + "identity": "rim", + "map": ".confidentialityCode" + }, + { + "identity": "xds", + "map": "DocumentEntry.confidentialityCode" + }, + { + "identity": "cda", + "map": "ClinicalDocument/confidentialityCode/@code" + } + ] + }, + { + "id": "DocumentReference.content", + "path": "DocumentReference.content", + "short": "Document referenced", + "definition": "The document and format referenced. There may be multiple content element repetitions, each with a different format.", + "min": 1, + "max": "*", + "base": { + "path": "DocumentReference.content", + "min": 1, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Bundle(Composition+*)" + }, + { + "identity": "rim", + "map": "document.text" + } + ] + }, + { + "id": "DocumentReference.content.id", + "path": "DocumentReference.content.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.content.extension", + "path": "DocumentReference.content.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.content.modifierExtension", + "path": "DocumentReference.content.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.content.attachment", + "path": "DocumentReference.content.attachment", + "short": "Content in a format defined elsewhere", + "definition": "For referring to data content defined in other formats.", + "comment": "When providing a summary view (for example with Observation.value[x]) Attachment should be represented with a brief display text such as \"Signed Procedure Consent\".", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.content.attachment", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "Attachment", + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + ] + } + ], + "condition": [ + "ele-1" + ], + "constraint": [ + { + "key": "att-1", + "severity": "error", + "human": "If the Attachment has data, it SHALL have a contentType", + "expression": "data.empty() or contentType.exists()", + "xpath": "not(exists(f:data)) or exists(f:contentType)", + "source": "http://hl7.org/fhir/StructureDefinition/Attachment" + }, + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "must-be-drs-uri", + "severity": "error", + "human": "attachment.url must start with ^drs://. A drs:// hostname-based URI, as defined in the DRS documentation, that tells clients how to access this object. The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around. For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the `self_uri` presents you with a hostname and properly encoded DRS ID for use in subsequent `access` endpoint calls.", + "expression": "$this.url.matches('^drs://.*')", + "source": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + } + ], + "isModifier": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + }, + { + "identity": "v2", + "map": "ED/RP" + }, + { + "identity": "rim", + "map": "ED" + } + ] + }, + { + "id": "DocumentReference.content.format", + "path": "DocumentReference.content.format", + "short": "Format/content rules for the document", + "definition": "An identifier of the document encoding, structure, and template that the document conforms to beyond the base format indicated in the mimeType.", + "comment": "Note that while IHE mostly issues URNs for format types, not all documents can be identified by a URI.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.content.format", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Coding" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentFormat" + } + ], + "strength": "preferred", + "description": "Document Format Codes.", + "valueSet": "http://hl7.org/fhir/ValueSet/formatcodes" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.meta.profile" + }, + { + "identity": "rim", + "map": "document.text" + }, + { + "identity": "xds", + "map": "DocumentEntry.formatCode" + }, + { + "identity": "cda", + "map": "derived from the IHE Profile or Implementation Guide templateID" + } + ] + }, + { + "id": "DocumentReference.context", + "path": "DocumentReference.context", + "short": "Clinical context of document", + "definition": "The clinical context in which the document was prepared.", + "comment": "These values are primarily added to help with searching for interesting/relevant documents.", + "min": 1, + "max": "1", + "base": { + "path": "DocumentReference.context", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "outboundRelationship[typeCode=\"SUBJ\"].target[classCode<'ACT']" + } + ] + }, + { + "id": "DocumentReference.context.id", + "path": "DocumentReference.context.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.context.extension", + "path": "DocumentReference.context.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "DocumentReference.context.modifierExtension", + "path": "DocumentReference.context.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "DocumentReference.context.encounter", + "path": "DocumentReference.context.encounter", + "short": "Context of the document content", + "definition": "Describes the clinical encounter or type of care that the document content is associated with.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.context.encounter", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Encounter", + "http://hl7.org/fhir/StructureDefinition/EpisodeOfCare" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.context" + }, + { + "identity": "w5", + "map": "FiveWs.context" + }, + { + "identity": "fhircomposition", + "map": "Composition.encounter" + }, + { + "identity": "rim", + "map": "unique(highest(./outboundRelationship[typeCode=\"SUBJ\" and isNormalActRelationship()], priorityNumber)/target[moodCode=\"EVN\" and classCode=(\"ENC\", \"PCPR\") and isNormalAct])" + } + ] + }, + { + "id": "DocumentReference.context.event", + "path": "DocumentReference.context.event", + "short": "Main clinical acts documented", + "definition": "This list of codes represents the main clinical acts, such as a colonoscopy or an appendectomy, being documented. In some cases, the event is inherent in the type Code, such as a \"History and Physical Report\" in which the procedure being documented is necessarily a \"History and Physical\" act.", + "comment": "An event can further specialize the act inherent in the type, such as where it is simply \"Procedure Report\" and the procedure was a \"colonoscopy\". If one or more event codes are included, they shall not conflict with the values inherent in the class or type elements as such a conflict would create an ambiguous situation.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.context.event", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentEventType" + } + ], + "strength": "example", + "description": "This list of codes represents the main clinical acts being documented.", + "valueSet": "http://terminology.hl7.org/ValueSet/v3-ActCode" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.event.code" + }, + { + "identity": "rim", + "map": ".code" + }, + { + "identity": "xds", + "map": "DocumentEntry.eventCodeList" + } + ] + }, + { + "id": "DocumentReference.context.period", + "path": "DocumentReference.context.period", + "short": "Time of service that is being documented", + "definition": "The time period over which the service that is described by the document was provided.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.period", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Period" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.event.period" + }, + { + "identity": "rim", + "map": ".effectiveTime" + }, + { + "identity": "xds", + "map": "DocumentEntry.serviceStartTime, DocumentEntry.serviceStopTime" + }, + { + "identity": "cda", + "map": "ClinicalDocument/documentationOf/\nserviceEvent/effectiveTime/low/\n@value --> ClinicalDocument/documentationOf/\nserviceEvent/effectiveTime/high/\n@value" + } + ] + }, + { + "id": "DocumentReference.context.facilityType", + "path": "DocumentReference.context.facilityType", + "short": "Kind of facility where patient was seen", + "definition": "The kind of facility where the patient was seen.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.facilityType", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80FacilityType" + } + ], + "strength": "example", + "description": "XDS Facility Type.", + "valueSet": "http://hl7.org/fhir/ValueSet/c80-facilitycodes" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "usually from a mapping to a local ValueSet" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"LOC\"].role[classCode=\"DSDLOC\"].code" + }, + { + "identity": "xds", + "map": "DocumentEntry.healthcareFacilityTypeCode" + }, + { + "identity": "cda", + "map": "usually a mapping to a local ValueSet. Must be consistent with /clinicalDocument/code" + } + ] + }, + { + "id": "DocumentReference.context.practiceSetting", + "path": "DocumentReference.context.practiceSetting", + "short": "Additional details about where the content was created (e.g. clinical specialty)", + "definition": "This property may convey specifics about the practice setting where the content was created, often reflecting the clinical specialty.", + "comment": "This element should be based on a coarse classification system for the class of specialty practice. Recommend the use of the classification system for Practice Setting, such as that described by the Subject Matter Domain in LOINC.", + "requirements": "This is an important piece of metadata that providers often rely upon to quickly sort and/or filter out to find specific content.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.practiceSetting", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "DocumentC80PracticeSetting" + } + ], + "strength": "example", + "description": "Additional details about where the content was created (e.g. clinical specialty).", + "valueSet": "http://hl7.org/fhir/ValueSet/c80-practice-codes" + }, + "mapping": [ + { + "identity": "fhircomposition", + "map": "usually from a mapping to a local ValueSet" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"LOC\"].role[classCode=\"DSDLOC\"].code" + }, + { + "identity": "xds", + "map": "DocumentEntry.practiceSettingCode" + }, + { + "identity": "cda", + "map": "usually from a mapping to a local ValueSet" + } + ] + }, + { + "id": "DocumentReference.context.sourcePatientInfo", + "path": "DocumentReference.context.sourcePatientInfo", + "short": "Patient demographics from source", + "definition": "The Patient Information as known when the document was published. May be a reference to a version specific, or contained.", + "min": 0, + "max": "1", + "base": { + "path": "DocumentReference.context.sourcePatientInfo", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.subject" + }, + { + "identity": "rim", + "map": ".participation[typeCode=\"SBJ\"].role[typeCode=\"PAT\"]" + }, + { + "identity": "xds", + "map": "DocumentEntry.sourcePatientInfo, DocumentEntry.sourcePatientId" + }, + { + "identity": "cda", + "map": "ClinicalDocument/recordTarget/" + } + ] + }, + { + "id": "DocumentReference.context.related", + "path": "DocumentReference.context.related", + "short": "Related identifiers or resources", + "definition": "Related identifiers or resources associated with the DocumentReference.", + "comment": "May be identifiers or resources that caused the DocumentReference or referenced Document to be created.", + "min": 0, + "max": "*", + "base": { + "path": "DocumentReference.context.related", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Task" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "fhircomposition", + "map": "Composition.event.detail" + }, + { + "identity": "rim", + "map": "./outboundRelationship[typeCode=\"PERT\" and isNormalActRelationship()] / target[isNormalAct]" + }, + { + "identity": "xds", + "map": "DocumentEntry.referenceIdList" + }, + { + "identity": "cda", + "map": "ClinicalDocument/relatedDocument" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "DocumentReference", + "path": "DocumentReference" + }, + { + "id": "DocumentReference.subject", + "path": "DocumentReference.subject", + "min": 1 + }, + { + "id": "DocumentReference.custodian", + "path": "DocumentReference.custodian", + "min": 1 + }, + { + "id": "DocumentReference.content.attachment", + "path": "DocumentReference.content.attachment", + "type": [ + { + "code": "Attachment", + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-attachment" + ] + } + ] + }, + { + "id": "DocumentReference.context", + "path": "DocumentReference.context", + "min": 1 + }, + { + "id": "DocumentReference.context.related", + "path": "DocumentReference.context.related", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Task" + ] + } + ] + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-specimen-task.json b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-specimen-task.json new file mode 100644 index 0000000..9996266 --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-ncpi-specimen-task.json @@ -0,0 +1,2996 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-specimen-task", + "text": { + "status": "extensions", + "div": "
\r\n\r\n\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" Task 0..*TaskA task to be performed
\".\"\".\"\".\" focus 1..1Reference(Specimen)What task is acting on
\".\"\".\"\".\" for 1..1Reference(Patient)Beneficiary of the Task
\".\"\".\"\".\" owner 1..1Reference(Organization)Responsible individual

\"doco\" Documentation for this format
" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category", + "valueString": "Base.Workflow" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category", + "valueCode": "not-classified" + } + ], + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-specimen-task", + "version": "0.1.0", + "name": "SpecimenTask", + "title": "Research Task", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "A FHIR analysis task that takes at least one specimen as input and produces at least one document.", + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "workflow", + "uri": "http://hl7.org/fhir/workflow", + "name": "Workflow Pattern" + }, + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + }, + { + "identity": "w5", + "uri": "http://hl7.org/fhir/fivews", + "name": "FiveWs Pattern Mapping" + }, + { + "identity": "v2", + "uri": "http://hl7.org/v2", + "name": "HL7 v2 Mapping" + } + ], + "kind": "resource", + "abstract": false, + "type": "Task", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Task", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "Task", + "path": "Task", + "short": "A task to be performed", + "definition": "A task to be performed.", + "min": 0, + "max": "*", + "base": { + "path": "Task", + "min": 0, + "max": "*" + }, + "constraint": [ + { + "key": "dom-2", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources", + "expression": "contained.contained.empty()", + "xpath": "not(parent::f:contained and f:contained)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-3", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource", + "expression": "contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()", + "xpath": "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-4", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated", + "expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-5", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a security label", + "expression": "contained.meta.security.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:security))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time." + } + ], + "key": "dom-6", + "severity": "warning", + "human": "A resource should have narrative for robust management", + "expression": "text.`div`.exists()", + "xpath": "exists(f:text/h:div)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "inv-1", + "severity": "error", + "human": "Last modified date must be greater than or equal to authored-on date.", + "expression": "lastModified.exists().not() or authoredOn.exists().not() or lastModified >= authoredOn", + "xpath": "not(exists(f:lastModified/@value)) or not(exists(f:authoredOn/@value)) or f:lastModified/@value >= f:authoredOn/@value", + "source": "http://hl7.org/fhir/StructureDefinition/Task" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Entity. Role, or Act" + }, + { + "identity": "workflow", + "map": "Request, Event" + }, + { + "identity": "rim", + "map": "ControlAct[moodCode=INT]" + } + ] + }, + { + "id": "Task.id", + "path": "Task.id", + "short": "Logical id of this artifact", + "definition": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.", + "comment": "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "Task.meta", + "path": "Task.meta", + "short": "Metadata about the resource", + "definition": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.meta", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Meta" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "Task.implicitRules", + "path": "Task.implicitRules", + "short": "A set of rules under which this content was created", + "definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.", + "comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.implicitRules", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "uri" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation", + "isSummary": true + }, + { + "id": "Task.language", + "path": "Task.language", + "short": "Language of the resource content", + "definition": "The base language in which the resource is written.", + "comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).", + "min": 0, + "max": "1", + "base": { + "path": "Resource.language", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", + "valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "Language" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "preferred", + "description": "A human language.", + "valueSet": "http://hl7.org/fhir/ValueSet/languages" + } + }, + { + "id": "Task.text", + "path": "Task.text", + "short": "Text summary of the resource, for human interpretation", + "definition": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.", + "comment": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.", + "alias": [ + "narrative", + "html", + "xhtml", + "display" + ], + "min": 0, + "max": "1", + "base": { + "path": "DomainResource.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Narrative" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Act.text?" + } + ] + }, + { + "id": "Task.contained", + "path": "Task.contained", + "short": "Contained, inline Resources", + "definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.", + "comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.", + "alias": [ + "inline resources", + "anonymous resources", + "contained resources" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.contained", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Resource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Task.extension", + "path": "Task.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Task.modifierExtension", + "path": "Task.modifierExtension", + "short": "Extensions that cannot be ignored", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them", + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Task.identifier", + "path": "Task.identifier", + "short": "Task Instance Identifier", + "definition": "The business identifier for this task.", + "min": 0, + "max": "*", + "base": { + "path": "Task.identifier", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Request.identifier, Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "rim", + "map": ".id" + } + ] + }, + { + "id": "Task.instantiatesCanonical", + "path": "Task.instantiatesCanonical", + "short": "Formal definition of task", + "definition": "The URL pointing to a *FHIR*-defined protocol, guideline, orderset or other definition that is adhered to in whole or in part by this Task.", + "requirements": "Enables a formal definition of how he task is to be performed, enabling automation.", + "min": 0, + "max": "1", + "base": { + "path": "Task.instantiatesCanonical", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "canonical", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/ActivityDefinition" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Request.instantiatesCanonical, Event.instantiatesCanonical" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=DEFN].target" + } + ] + }, + { + "id": "Task.instantiatesUri", + "path": "Task.instantiatesUri", + "short": "Formal definition of task", + "definition": "The URL pointing to an *externally* maintained protocol, guideline, orderset or other definition that is adhered to in whole or in part by this Task.", + "requirements": "Enables a formal definition of how he task is to be performed (e.g. using BPMN, BPEL, XPDL or other formal notation to be associated with a task), enabling automation.", + "min": 0, + "max": "1", + "base": { + "path": "Task.instantiatesUri", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "uri" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.instantiatesUrl" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=DEFN].target" + } + ] + }, + { + "id": "Task.basedOn", + "path": "Task.basedOn", + "short": "Request fulfilled by this task", + "definition": "BasedOn refers to a higher-level authorization that triggered the creation of the task. It references a \"request\" resource such as a ServiceRequest, MedicationRequest, ServiceRequest, CarePlan, etc. which is distinct from the \"request\" resource the task is seeking to fulfill. This latter resource is referenced by FocusOn. For example, based on a ServiceRequest (= BasedOn), a task is created to fulfill a procedureRequest ( = FocusOn ) to collect a specimen from a patient.", + "min": 0, + "max": "*", + "base": { + "path": "Task.basedOn", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Request.basedOn, Event.basedOn" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=FLFS].target[moodCode=INT]" + } + ] + }, + { + "id": "Task.groupIdentifier", + "path": "Task.groupIdentifier", + "short": "Requisition or grouper id", + "definition": "An identifier that links together multiple tasks and other requests that were created in the same context.", + "requirements": "Billing and/or reporting can be linked to whether multiple requests were created as a single unit.", + "min": 0, + "max": "1", + "base": { + "path": "Task.groupIdentifier", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Request.groupIdentifier" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=COMP].source[moodCode=INT].id" + } + ] + }, + { + "id": "Task.partOf", + "path": "Task.partOf", + "short": "Composite task", + "definition": "Task that this particular task is part of.", + "comment": "This should usually be 0..1.", + "requirements": "Allows tasks to be broken down into sub-steps (and this division can occur independent of the original task).", + "min": 0, + "max": "*", + "base": { + "path": "Task.partOf", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Task" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.partOf" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=COMP].source[moodCode=INT]" + } + ] + }, + { + "id": "Task.status", + "path": "Task.status", + "short": "draft | requested | received | accepted | +", + "definition": "The current status of the task.", + "requirements": "These states enable coordination of task status with off-the-shelf workflow solutions that support automation of tasks.", + "min": 1, + "max": "1", + "base": { + "path": "Task.status", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskStatus" + } + ], + "strength": "required", + "description": "The current status of the task.", + "valueSet": "http://hl7.org/fhir/ValueSet/task-status|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Request.status, Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "rim", + "map": ".statusCode" + } + ] + }, + { + "id": "Task.statusReason", + "path": "Task.statusReason", + "short": "Reason for current status", + "definition": "An explanation as to why this task is held, failed, was refused, etc.", + "comment": "This applies to the current status. Look at the history of the task to see reasons for past statuses.", + "min": 0, + "max": "1", + "base": { + "path": "Task.statusReason", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskStatusReason" + } + ], + "strength": "example", + "description": "Codes to identify the reason for current status. These will typically be specific to a particular workflow." + }, + "mapping": [ + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=SUBJ].source[classCode=CACT, moodCode=EVN, code=\"status change\"].reasonCode" + } + ] + }, + { + "id": "Task.businessStatus", + "path": "Task.businessStatus", + "short": "E.g. \"Specimen collected\", \"IV prepped\"", + "definition": "Contains business-specific nuances of the business state.", + "requirements": "There's often a need to track substates of a task - this is often variable by specific workflow implementation.", + "min": 0, + "max": "1", + "base": { + "path": "Task.businessStatus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskBusinessStatus" + } + ], + "strength": "example", + "description": "The domain-specific business-contextual sub-state of the task. For example: \"Blood drawn\", \"IV inserted\", \"Awaiting physician signature\", etc." + }, + "mapping": [ + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"business status\"]" + } + ] + }, + { + "id": "Task.intent", + "path": "Task.intent", + "short": "unknown | proposal | plan | order | original-order | reflex-order | filler-order | instance-order | option", + "definition": "Indicates the \"level\" of actionability associated with the Task, i.e. i+R[9]Cs this a proposed task, a planned task, an actionable task, etc.", + "comment": "This element is immutable. Proposed tasks, planned tasks, etc. must be distinct instances.\n\nIn most cases, Tasks will have an intent of \"order\".", + "min": 1, + "max": "1", + "base": { + "path": "Task.intent", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskIntent" + } + ], + "strength": "required", + "description": "Distinguishes whether the task is a proposal, plan or full order.", + "valueSet": "http://hl7.org/fhir/ValueSet/task-intent|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Request.intent" + }, + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "rim", + "map": ".moodCode" + } + ] + }, + { + "id": "Task.priority", + "path": "Task.priority", + "short": "routine | urgent | asap | stat", + "definition": "Indicates how quickly the Task should be addressed with respect to other requests.", + "requirements": "Used to identify the service level expected while performing a task.", + "min": 0, + "max": "1", + "base": { + "path": "Task.priority", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "meaningWhenMissing": "If missing, this task should be performed with normal priority", + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskPriority" + } + ], + "strength": "required", + "description": "The task's priority.", + "valueSet": "http://hl7.org/fhir/ValueSet/request-priority|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Request.priority" + }, + { + "identity": "w5", + "map": "FiveWs.grade" + }, + { + "identity": "rim", + "map": ".priorityCode" + } + ] + }, + { + "id": "Task.code", + "path": "Task.code", + "short": "Task Type", + "definition": "A name or code (or both) briefly describing what the task involves.", + "comment": "The title (eg \"My Tasks\", \"Outstanding Tasks for Patient X\") should go into the code.", + "min": 0, + "max": "1", + "base": { + "path": "Task.code", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskCode" + } + ], + "strength": "example", + "description": "Codes to identify what the task involves. These will typically be specific to a particular workflow.", + "valueSet": "http://hl7.org/fhir/ValueSet/task-code" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Request.code, Event.code" + }, + { + "identity": "w5", + "map": "FiveWs.what[x]" + }, + { + "identity": "rim", + "map": ".code" + } + ] + }, + { + "id": "Task.description", + "path": "Task.description", + "short": "Human-readable explanation of task", + "definition": "A free-text description of what is to be performed.", + "min": 0, + "max": "1", + "base": { + "path": "Task.description", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "string" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": ".text" + } + ] + }, + { + "id": "Task.focus", + "path": "Task.focus", + "short": "What task is acting on", + "definition": "The request being actioned or the resource being manipulated by this task.", + "comment": "If multiple resources need to be manipulated, use sub-tasks. (This ensures that status can be tracked independently for each referenced resource.).", + "requirements": "Used to identify the thing to be done.", + "min": 1, + "max": "1", + "base": { + "path": "Task.focus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.what[x]" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=SUBJ].target" + } + ] + }, + { + "id": "Task.for", + "path": "Task.for", + "short": "Beneficiary of the Task", + "definition": "The entity who benefits from the performance of the service specified in the task (e.g., the patient).", + "requirements": "Used to track tasks outstanding for a beneficiary. Do not use to track the task owner or creator (see owner and creator respectively). This can also affect access control.", + "alias": [ + "Patient" + ], + "min": 1, + "max": "1", + "base": { + "path": "Task.for", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Request.subject, Event.subject" + }, + { + "identity": "w5", + "map": "FiveWs.subject[x]" + }, + { + "identity": "rim", + "map": ".participation[typeCode=RCT].role" + }, + { + "identity": "w5", + "map": "FiveWs.subject" + } + ] + }, + { + "id": "Task.encounter", + "path": "Task.encounter", + "short": "Healthcare event during which this task originated", + "definition": "The healthcare event (e.g. a patient and healthcare provider interaction) during which this task was created.", + "requirements": "For some tasks it may be important to know the link between the encounter the task originated within.", + "min": 0, + "max": "1", + "base": { + "path": "Task.encounter", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Encounter" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Request.context, Event.context" + }, + { + "identity": "w5", + "map": "FiveWs.context" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=COMP].source[classCode=PCPR, moodCode=EVN]" + } + ] + }, + { + "id": "Task.executionPeriod", + "path": "Task.executionPeriod", + "short": "Start and end time of execution", + "definition": "Identifies the time action was first taken against the task (start) and/or the time final action was taken against the task prior to marking it as completed (end).", + "min": 0, + "max": "1", + "base": { + "path": "Task.executionPeriod", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Period" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.occurrence[x]" + }, + { + "identity": "w5", + "map": "FiveWs.done[x]" + }, + { + "identity": "rim", + "map": ".effectiveTime" + } + ] + }, + { + "id": "Task.authoredOn", + "path": "Task.authoredOn", + "short": "Task Creation Date", + "definition": "The date and time this task was created.", + "requirements": "Most often used along with lastUpdated to track duration of task to supporting monitoring and management.", + "alias": [ + "Created Date" + ], + "min": 0, + "max": "1", + "base": { + "path": "Task.authoredOn", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + } + ], + "condition": [ + "inv-1" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Request.authoredOn" + }, + { + "identity": "w5", + "map": "FiveWs.recorded" + }, + { + "identity": "rim", + "map": ".participation[typeCode=AUT].time" + } + ] + }, + { + "id": "Task.lastModified", + "path": "Task.lastModified", + "short": "Task Last Modified Date", + "definition": "The date and time of last modification to this task.", + "requirements": "Used along with history to track task activity and time in a particular task state. This enables monitoring and management.", + "alias": [ + "Update Date" + ], + "min": 0, + "max": "1", + "base": { + "path": "Task.lastModified", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + } + ], + "condition": [ + "inv-1" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=SUBJ, ].source[classCode=CACT, moodCode=EVN].effectiveTime" + } + ] + }, + { + "id": "Task.requester", + "path": "Task.requester", + "short": "Who is asking for task to be done", + "definition": "The creator of the task.", + "requirements": "Identifies who created this task. May be used by access control mechanisms (e.g., to ensure that only the creator can cancel a task).", + "min": 0, + "max": "1", + "base": { + "path": "Task.requester", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Device", + "http://hl7.org/fhir/StructureDefinition/Organization", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Request.requester" + }, + { + "identity": "w5", + "map": "FiveWs.author" + }, + { + "identity": "rim", + "map": ".participation[typeCode=AUT].role" + } + ] + }, + { + "id": "Task.performerType", + "path": "Task.performerType", + "short": "Requested performer", + "definition": "The kind of participant that should perform the task.", + "requirements": "Use to distinguish tasks on different activity queues.", + "min": 0, + "max": "*", + "base": { + "path": "Task.performerType", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskPerformerType" + } + ], + "strength": "preferred", + "description": "The type(s) of task performers allowed.", + "valueSet": "http://hl7.org/fhir/ValueSet/performer-role" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.role, Request.performerType" + }, + { + "identity": "w5", + "map": "FiveWs.actor" + }, + { + "identity": "rim", + "map": ".participation[typeCode=PRF].role.code" + } + ] + }, + { + "id": "Task.owner", + "path": "Task.owner", + "short": "Responsible individual", + "definition": "Individual organization or Device currently responsible for task execution.", + "comment": "Tasks may be created with an owner not yet identified.", + "requirements": "Identifies who is expected to perform this task.", + "alias": [ + "Performer", + "Executer" + ], + "min": 1, + "max": "1", + "base": { + "path": "Task.owner", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.performer.actor, Request.performer" + }, + { + "identity": "w5", + "map": "FiveWs.actor" + }, + { + "identity": "rim", + "map": ".participation[typeCode=PRF].role" + } + ] + }, + { + "id": "Task.location", + "path": "Task.location", + "short": "Where task occurs", + "definition": "Principal physical location where the this task is performed.", + "requirements": "Ties the event to where the records are likely kept and provides context around the event occurrence (e.g. if it occurred inside or outside a dedicated healthcare setting).", + "min": 0, + "max": "1", + "base": { + "path": "Task.location", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Location" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Request.reasonCode, Event.reasonCode" + }, + { + "identity": "w5", + "map": "FiveWs.where[x]" + }, + { + "identity": "rim", + "map": ".participation[typeCode=LOC].role" + } + ] + }, + { + "id": "Task.reasonCode", + "path": "Task.reasonCode", + "short": "Why task is needed", + "definition": "A description or code indicating why this task needs to be performed.", + "comment": "This should only be included if there is no focus or if it differs from the reason indicated on the focus.", + "min": 0, + "max": "1", + "base": { + "path": "Task.reasonCode", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskReason" + } + ], + "strength": "example", + "description": "Indicates why the task is needed. E.g. Suspended because patient admitted to hospital." + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.location" + }, + { + "identity": "w5", + "map": "FiveWs.why[x]" + }, + { + "identity": "v2", + "map": "EVN.7" + }, + { + "identity": "rim", + "map": ".reasonCode" + } + ] + }, + { + "id": "Task.reasonReference", + "path": "Task.reasonReference", + "short": "Why task is needed", + "definition": "A resource reference indicating why this task needs to be performed.", + "comment": "Tasks might be justified based on an Observation, a Condition, a past or planned procedure, etc. This should only be included if there is no focus or if it differs from the reason indicated on the focus. Use the CodeableConcept text element in `Task.reasonCode` if the data is free (uncoded) text.", + "min": 0, + "max": "1", + "base": { + "path": "Task.reasonReference", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Request.reasonReference, Event.reasonReference" + }, + { + "identity": "w5", + "map": "FiveWs.why[x]" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=RSON].target" + } + ] + }, + { + "id": "Task.insurance", + "path": "Task.insurance", + "short": "Associated insurance coverage", + "definition": "Insurance plans, coverage extensions, pre-authorizations and/or pre-determinations that may be relevant to the Task.", + "min": 0, + "max": "*", + "base": { + "path": "Task.insurance", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Coverage", + "http://hl7.org/fhir/StructureDefinition/ClaimResponse" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Request.insurance" + }, + { + "identity": "v2", + "map": "IN1/IN2" + }, + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=COVBY].target" + } + ] + }, + { + "id": "Task.note", + "path": "Task.note", + "short": "Comments made about the task", + "definition": "Free-text information captured about the task as it progresses.", + "min": 0, + "max": "*", + "base": { + "path": "Task.note", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Annotation" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Request.note, Event.note" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=SUBJ, ].source[classCode=OBS, moodCode=EVN, code=\"annotation\"].value(string)" + } + ] + }, + { + "id": "Task.relevantHistory", + "path": "Task.relevantHistory", + "short": "Key events in history of the Task", + "definition": "Links to Provenance records for past versions of this Task that identify key state transitions or updates that are likely to be relevant to a user looking at the current version of the task.", + "comment": "This element does not point to the Provenance associated with the *current* version of the resource - as it would be created after this version existed. The Provenance for the current version can be retrieved with a _revinclude.", + "alias": [ + "Status History" + ], + "min": 0, + "max": "*", + "base": { + "path": "Task.relevantHistory", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Provenance" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Request.relevantHistory" + }, + { + "identity": "rim", + "map": ".inboundRelationship(typeCode=SUBJ].source[classCode=CACT, moodCode=EVN]" + } + ] + }, + { + "id": "Task.restriction", + "path": "Task.restriction", + "short": "Constraints on fulfillment tasks", + "definition": "If the Task.focus is a request resource and the task is seeking fulfillment (i.e. is asking for the request to be actioned), this element identifies any limitations on what parts of the referenced request should be actioned.", + "requirements": "Sometimes when fulfillment is sought, you don't want full fulfillment.", + "min": 0, + "max": "1", + "base": { + "path": "Task.restriction", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Instead of pointing to request, would point to component of request, having these characteristics" + } + ] + }, + { + "id": "Task.restriction.id", + "path": "Task.restriction.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Task.restriction.extension", + "path": "Task.restriction.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Task.restriction.modifierExtension", + "path": "Task.restriction.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Task.restriction.repetitions", + "path": "Task.restriction.repetitions", + "short": "How many times to repeat", + "definition": "Indicates the number of times the requested action should occur.", + "requirements": "E.g. order that requests monthly lab tests, fulfillment is sought for 1.", + "min": 0, + "max": "1", + "base": { + "path": "Task.restriction.repetitions", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "positiveInt" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": ".repeatNumber" + } + ] + }, + { + "id": "Task.restriction.period", + "path": "Task.restriction.period", + "short": "When fulfillment sought", + "definition": "Over what time-period is fulfillment sought.", + "comment": "Note that period.high is the due date representing the time by which the task should be completed.", + "requirements": "E.g. order that authorizes 1 year's services. Fulfillment is sought for next 3 months.", + "min": 0, + "max": "1", + "base": { + "path": "Task.restriction.period", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Period" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": ".effectiveTime(IVL)" + } + ] + }, + { + "id": "Task.restriction.recipient", + "path": "Task.restriction.recipient", + "short": "For whom is fulfillment sought?", + "definition": "For requests that are targeted to more than on potential recipient/target, for whom is fulfillment sought?", + "min": 0, + "max": "*", + "base": { + "path": "Task.restriction.recipient", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson", + "http://hl7.org/fhir/StructureDefinition/Group", + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": ".participation[typeCode=SBJ].role" + } + ] + }, + { + "id": "Task.input", + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name", + "valueString": "Parameter" + } + ], + "path": "Task.input", + "short": "Information used to perform task", + "definition": "Additional information that may be needed in the execution of the task.", + "requirements": "Resources and data used to perform the task. This data is used in the business logic of task execution, and is stored separately because it varies between workflows.", + "alias": [ + "Supporting Information" + ], + "min": 0, + "max": "*", + "base": { + "path": "Task.input", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "???" + } + ] + }, + { + "id": "Task.input.id", + "path": "Task.input.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Task.input.extension", + "path": "Task.input.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Task.input.modifierExtension", + "path": "Task.input.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Task.input.type", + "path": "Task.input.type", + "short": "Label for the input", + "definition": "A code or description indicating how the input is intended to be used as part of the task execution.", + "comment": "If referencing a BPMN workflow or Protocol, the \"system\" is the URL for the workflow definition and the code is the \"name\" of the required input.", + "requirements": "Inputs are named to enable task automation to bind data and pass it from one task to the next.", + "alias": [ + "Name" + ], + "min": 1, + "max": "1", + "base": { + "path": "Task.input.type", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskInputParameterType" + } + ], + "strength": "example", + "description": "Codes to identify types of input parameters. These will typically be specific to a particular workflow. E.g. \"Comparison source\", \"Applicable consent\", \"Concomitent Medications\", etc." + }, + "mapping": [ + { + "identity": "rim", + "map": "???" + } + ] + }, + { + "id": "Task.input.value[x]", + "path": "Task.input.value[x]", + "short": "Content to use in performing the task", + "definition": "The value of the input parameter as a basic type.", + "min": 1, + "max": "1", + "base": { + "path": "Task.input.value[x]", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "base64Binary" + }, + { + "code": "boolean" + }, + { + "code": "canonical" + }, + { + "code": "code" + }, + { + "code": "date" + }, + { + "code": "dateTime" + }, + { + "code": "decimal" + }, + { + "code": "id" + }, + { + "code": "instant" + }, + { + "code": "integer" + }, + { + "code": "markdown" + }, + { + "code": "oid" + }, + { + "code": "positiveInt" + }, + { + "code": "string" + }, + { + "code": "time" + }, + { + "code": "unsignedInt" + }, + { + "code": "uri" + }, + { + "code": "url" + }, + { + "code": "uuid" + }, + { + "code": "Address" + }, + { + "code": "Age" + }, + { + "code": "Annotation" + }, + { + "code": "Attachment" + }, + { + "code": "CodeableConcept" + }, + { + "code": "Coding" + }, + { + "code": "ContactPoint" + }, + { + "code": "Count" + }, + { + "code": "Distance" + }, + { + "code": "Duration" + }, + { + "code": "HumanName" + }, + { + "code": "Identifier" + }, + { + "code": "Money" + }, + { + "code": "Period" + }, + { + "code": "Quantity" + }, + { + "code": "Range" + }, + { + "code": "Ratio" + }, + { + "code": "Reference" + }, + { + "code": "SampledData" + }, + { + "code": "Signature" + }, + { + "code": "Timing" + }, + { + "code": "ContactDetail" + }, + { + "code": "Contributor" + }, + { + "code": "DataRequirement" + }, + { + "code": "Expression" + }, + { + "code": "ParameterDefinition" + }, + { + "code": "RelatedArtifact" + }, + { + "code": "TriggerDefinition" + }, + { + "code": "UsageContext" + }, + { + "code": "Dosage" + }, + { + "code": "Meta" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "???" + } + ] + }, + { + "id": "Task.output", + "path": "Task.output", + "short": "Information produced as part of task", + "definition": "Outputs produced by the Task.", + "requirements": "Resources and data produced during the execution the task. This data is generated by the business logic of task execution, and is stored separately because it varies between workflows.", + "min": 0, + "max": "*", + "base": { + "path": "Task.output", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "???" + } + ] + }, + { + "id": "Task.output.id", + "path": "Task.output.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Task.output.extension", + "path": "Task.output.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Task.output.modifierExtension", + "path": "Task.output.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Task.output.type", + "path": "Task.output.type", + "short": "Label for output", + "definition": "The name of the Output parameter.", + "requirements": "Outputs are named to enable task automation to bind data and pass it from one task to the next.", + "alias": [ + "Name" + ], + "min": 1, + "max": "1", + "base": { + "path": "Task.output.type", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "TaskOutputParameterType" + } + ], + "strength": "example", + "description": "Codes to identify types of input parameters. These will typically be specific to a particular workflow. E.g. \"Identified issues\", \"Preliminary results\", \"Filler order\", \"Final results\", etc." + }, + "mapping": [ + { + "identity": "rim", + "map": "???" + } + ] + }, + { + "id": "Task.output.value[x]", + "path": "Task.output.value[x]", + "short": "Result of output", + "definition": "The value of the Output parameter as a basic type.", + "requirements": "Task outputs can take any form.", + "min": 1, + "max": "1", + "base": { + "path": "Task.output.value[x]", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "base64Binary" + }, + { + "code": "boolean" + }, + { + "code": "canonical" + }, + { + "code": "code" + }, + { + "code": "date" + }, + { + "code": "dateTime" + }, + { + "code": "decimal" + }, + { + "code": "id" + }, + { + "code": "instant" + }, + { + "code": "integer" + }, + { + "code": "markdown" + }, + { + "code": "oid" + }, + { + "code": "positiveInt" + }, + { + "code": "string" + }, + { + "code": "time" + }, + { + "code": "unsignedInt" + }, + { + "code": "uri" + }, + { + "code": "url" + }, + { + "code": "uuid" + }, + { + "code": "Address" + }, + { + "code": "Age" + }, + { + "code": "Annotation" + }, + { + "code": "Attachment" + }, + { + "code": "CodeableConcept" + }, + { + "code": "Coding" + }, + { + "code": "ContactPoint" + }, + { + "code": "Count" + }, + { + "code": "Distance" + }, + { + "code": "Duration" + }, + { + "code": "HumanName" + }, + { + "code": "Identifier" + }, + { + "code": "Money" + }, + { + "code": "Period" + }, + { + "code": "Quantity" + }, + { + "code": "Range" + }, + { + "code": "Ratio" + }, + { + "code": "Reference" + }, + { + "code": "SampledData" + }, + { + "code": "Signature" + }, + { + "code": "Timing" + }, + { + "code": "ContactDetail" + }, + { + "code": "Contributor" + }, + { + "code": "DataRequirement" + }, + { + "code": "Expression" + }, + { + "code": "ParameterDefinition" + }, + { + "code": "RelatedArtifact" + }, + { + "code": "TriggerDefinition" + }, + { + "code": "UsageContext" + }, + { + "code": "Dosage" + }, + { + "code": "Meta" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "???" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "Task", + "path": "Task" + }, + { + "id": "Task.focus", + "path": "Task.focus", + "min": 1, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + } + ] + }, + { + "id": "Task.for", + "path": "Task.for", + "min": 1, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient" + ] + } + ] + }, + { + "id": "Task.owner", + "path": "Task.owner", + "min": 1, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ] + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-phenotype.json b/tests/fixtures/ncpi/examples/StructureDefinition-phenotype.json new file mode 100644 index 0000000..e70083e --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-phenotype.json @@ -0,0 +1,2004 @@ +{ + "resourceType": "StructureDefinition", + "id": "phenotype", + "text": { + "status": "extensions", + "div": "
\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" Condition 0..*ConditionDetailed information about conditions, problems or diagnoses
\".\"\".\"\".\" code 0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Phenotype Codes (required)

\"doco\" Documentation for this format
" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category", + "valueString": "Clinical.Summary" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category", + "valueCode": "patient" + } + ], + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/phenotype", + "version": "0.1.0", + "name": "Phenotype", + "title": "NCPI Phenotype", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Representation of phenotypic observations (present or absent)", + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "workflow", + "uri": "http://hl7.org/fhir/workflow", + "name": "Workflow Pattern" + }, + { + "identity": "sct-concept", + "uri": "http://snomed.info/conceptdomain", + "name": "SNOMED CT Concept Domain Binding" + }, + { + "identity": "v2", + "uri": "http://hl7.org/v2", + "name": "HL7 v2 Mapping" + }, + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + }, + { + "identity": "w5", + "uri": "http://hl7.org/fhir/fivews", + "name": "FiveWs Pattern Mapping" + }, + { + "identity": "sct-attr", + "uri": "http://snomed.org/attributebinding", + "name": "SNOMED CT Attribute Binding" + } + ], + "kind": "resource", + "abstract": false, + "type": "Condition", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Condition", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "Condition", + "path": "Condition", + "short": "Detailed information about conditions, problems or diagnoses", + "definition": "A clinical condition, problem, diagnosis, or other event, situation, issue, or clinical concept that has risen to a level of concern.", + "min": 0, + "max": "*", + "base": { + "path": "Condition", + "min": 0, + "max": "*" + }, + "constraint": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "Most systems will expect a clinicalStatus to be valued for problem-list-items that are managed over time, but might not need a clinicalStatus for point in time encounter-diagnosis." + } + ], + "key": "con-3", + "severity": "warning", + "human": "Condition.clinicalStatus SHALL be present if verificationStatus is not entered-in-error and category is problem-list-item", + "expression": "clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.select($this='problem-list-item').empty()", + "xpath": "exists(f:clinicalStatus) or exists(f:verificationStatus/f:coding/f:code/@value='entered-in-error') or not(exists(category[@value='problem-list-item']))", + "source": "http://hl7.org/fhir/StructureDefinition/Condition" + }, + { + "key": "con-4", + "severity": "error", + "human": "If condition is abated, then clinicalStatus must be either inactive, resolved, or remission", + "expression": "abatement.empty() or clinicalStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-clinical' and (code='resolved' or code='remission' or code='inactive')).exists()", + "xpath": "not(exists(*[starts-with(local-name(.), 'abatement')])) or exists(f:clinicalStatus/f:coding[f:system/@value='http://terminology.hl7.org/CodeSystem/condition-clinical' and f:code/@value=('resolved', 'remission', 'inactive')])", + "source": "http://hl7.org/fhir/StructureDefinition/Condition" + }, + { + "key": "con-5", + "severity": "error", + "human": "Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error", + "expression": "verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').empty() or clinicalStatus.empty()", + "xpath": "not(exists(f:verificationStatus/f:coding[f:system/@value='http://terminology.hl7.org/CodeSystem/condition-ver-status' and f:code/@value='entered-in-error'])) or not(exists(f:clinicalStatus))", + "source": "http://hl7.org/fhir/StructureDefinition/Condition" + }, + { + "key": "dom-2", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources", + "expression": "contained.contained.empty()", + "xpath": "not(parent::f:contained and f:contained)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-3", + "severity": "error", + "human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource", + "expression": "contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()", + "xpath": "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-4", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated", + "expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "key": "dom-5", + "severity": "error", + "human": "If a resource is contained in another resource, it SHALL NOT have a security label", + "expression": "contained.meta.security.empty()", + "xpath": "not(exists(f:contained/*/f:meta/f:security))", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + }, + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice", + "valueBoolean": true + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation", + "valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time." + } + ], + "key": "dom-6", + "severity": "warning", + "human": "A resource should have narrative for robust management", + "expression": "text.`div`.exists()", + "xpath": "exists(f:text/h:div)", + "source": "http://hl7.org/fhir/StructureDefinition/DomainResource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Entity. Role, or Act" + }, + { + "identity": "workflow", + "map": "Event" + }, + { + "identity": "sct-concept", + "map": "< 243796009 |Situation with explicit context| : 246090004 |Associated finding| = ( ( < 404684003 |Clinical finding| MINUS ( << 420134006 |Propensity to adverse reactions| OR << 473010000 |Hypersensitivity condition| OR << 79899007 |Drug interaction| OR << 69449002 |Drug action| OR << 441742003 |Evaluation finding| OR << 307824009 |Administrative status| OR << 385356007 |Tumor stage finding|)) OR < 272379006 |Event|)" + }, + { + "identity": "v2", + "map": "PPR message" + }, + { + "identity": "rim", + "map": "Observation[classCode=OBS, moodCode=EVN, code=ASSERTION, value id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true + }, + { + "id": "Condition.implicitRules", + "path": "Condition.implicitRules", + "short": "A set of rules under which this content was created", + "definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.", + "comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.", + "min": 0, + "max": "1", + "base": { + "path": "Resource.implicitRules", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "uri" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation", + "isSummary": true + }, + { + "id": "Condition.language", + "path": "Condition.language", + "short": "Language of the resource content", + "definition": "The base language in which the resource is written.", + "comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).", + "min": 0, + "max": "1", + "base": { + "path": "Resource.language", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "code" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", + "valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "Language" + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", + "valueBoolean": true + } + ], + "strength": "preferred", + "description": "A human language.", + "valueSet": "http://hl7.org/fhir/ValueSet/languages" + } + }, + { + "id": "Condition.text", + "path": "Condition.text", + "short": "Text summary of the resource, for human interpretation", + "definition": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.", + "comment": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.", + "alias": [ + "narrative", + "html", + "xhtml", + "display" + ], + "min": 0, + "max": "1", + "base": { + "path": "DomainResource.text", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Narrative" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "Act.text?" + } + ] + }, + { + "id": "Condition.contained", + "path": "Condition.contained", + "short": "Contained, inline Resources", + "definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.", + "comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.", + "alias": [ + "inline resources", + "anonymous resources", + "contained resources" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.contained", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Resource" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.extension", + "path": "Condition.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.modifierExtension", + "path": "Condition.modifierExtension", + "short": "Extensions that cannot be ignored", + "definition": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "DomainResource.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them", + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.identifier", + "path": "Condition.identifier", + "short": "External Ids for this condition", + "definition": "Business identifiers assigned to this condition by the performer or other systems which remain constant as the resource is updated and propagates from server to server.", + "comment": "This is a business identifier, not a resource identifier (see [discussion](http://hl7.org/fhir/R4/resource.html#identifiers)). It is best practice for the identifier to only appear on a single resource instance, however business practices may occasionally dictate that multiple resource instances with the same identifier can exist - possibly even with different resource types. For example, multiple Patient and a Person resource instance might share the same social insurance number.", + "requirements": "Allows identification of the condition as it is known by various participating systems and in a way that remains consistent across servers.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.identifier", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Identifier" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.identifier" + }, + { + "identity": "w5", + "map": "FiveWs.identifier" + }, + { + "identity": "rim", + "map": ".id" + } + ] + }, + { + "id": "Condition.clinicalStatus", + "path": "Condition.clinicalStatus", + "short": "active | recurrence | relapse | inactive | remission | resolved", + "definition": "The clinical status of the condition.", + "comment": "The data type is CodeableConcept because clinicalStatus has some clinical judgment involved, such that there might need to be more specificity than the required FHIR value set allows. For example, a SNOMED coding might allow for additional specificity.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.clinicalStatus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-3", + "con-4", + "con-5" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the status contains codes that mark the condition as no longer active.", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionClinicalStatus" + } + ], + "strength": "required", + "description": "The clinical status of the condition or diagnosis.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-clinical|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "sct-concept", + "map": "< 303105007 |Disease phases|" + }, + { + "identity": "v2", + "map": "PRB-14" + }, + { + "identity": "rim", + "map": "Observation ACT\n.inboundRelationship[typeCode=COMP].source[classCode=OBS, code=\"clinicalStatus\", moodCode=EVN].value" + } + ] + }, + { + "id": "Condition.verificationStatus", + "path": "Condition.verificationStatus", + "short": "unconfirmed | provisional | differential | confirmed | refuted | entered-in-error", + "definition": "The verification status to support the clinical status of the condition.", + "comment": "verificationStatus is not required. For example, when a patient has abdominal pain in the ED, there is not likely going to be a verification status.\nThe data type is CodeableConcept because verificationStatus has some clinical judgment involved, such that there might need to be more specificity than the required FHIR value set allows. For example, a SNOMED coding might allow for additional specificity.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.verificationStatus", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-3", + "con-5" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": true, + "isModifierReason": "This element is labeled as a modifier because the status contains the code refuted and entered-in-error that mark the Condition as not currently valid.", + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionVerificationStatus" + } + ], + "strength": "required", + "description": "The verification status to support or decline the clinical status of the condition or diagnosis.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-ver-status|4.0.1" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.status" + }, + { + "identity": "w5", + "map": "FiveWs.status" + }, + { + "identity": "sct-concept", + "map": "< 410514004 |Finding context value|" + }, + { + "identity": "v2", + "map": "PRB-13" + }, + { + "identity": "rim", + "map": "Observation ACT\n.inboundRelationship[typeCode=COMP].source[classCode=OBS, code=\"verificationStatus\", moodCode=EVN].value" + }, + { + "identity": "sct-attr", + "map": "408729009" + } + ] + }, + { + "id": "Condition.category", + "path": "Condition.category", + "short": "problem-list-item | encounter-diagnosis", + "definition": "A category assigned to the condition.", + "comment": "The categorization is often highly contextual and may appear poorly differentiated or not very useful in other contexts.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.category", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionCategory" + } + ], + "strength": "extensible", + "description": "A category assigned to the condition.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-category" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.class" + }, + { + "identity": "sct-concept", + "map": "< 404684003 |Clinical finding|" + }, + { + "identity": "v2", + "map": "'problem' if from PRB-3. 'diagnosis' if from DG1 segment in PV1 message" + }, + { + "identity": "rim", + "map": ".code" + } + ] + }, + { + "id": "Condition.severity", + "path": "Condition.severity", + "short": "Subjective severity of condition", + "definition": "A subjective assessment of the severity of the condition as evaluated by the clinician.", + "comment": "Coding of the severity with a terminology is preferred, where possible.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.severity", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionSeverity" + } + ], + "strength": "preferred", + "description": "A subjective assessment of the severity of the condition as evaluated by the clinician.", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-severity" + }, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.grade" + }, + { + "identity": "sct-concept", + "map": "< 272141005 |Severities|" + }, + { + "identity": "v2", + "map": "PRB-26 / ABS-3" + }, + { + "identity": "rim", + "map": "Can be pre/post-coordinated into value. Or ./inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"severity\"].value" + }, + { + "identity": "sct-attr", + "map": "246112005" + } + ] + }, + { + "id": "Condition.code", + "path": "Condition.code", + "short": "Identification of the condition, problem or diagnosis", + "definition": "Identification of the condition, problem or diagnosis.", + "requirements": "0..1 to account for primarily narrative only resources.", + "alias": [ + "type" + ], + "min": 0, + "max": "1", + "base": { + "path": "Condition.code", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "strength": "required", + "valueSet": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/phenotype-codes" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.code" + }, + { + "identity": "w5", + "map": "FiveWs.what[x]" + }, + { + "identity": "sct-concept", + "map": "code 246090004 |Associated finding| (< 404684003 |Clinical finding| MINUS\n<< 420134006 |Propensity to adverse reactions| MINUS \n<< 473010000 |Hypersensitivity condition| MINUS \n<< 79899007 |Drug interaction| MINUS\n<< 69449002 |Drug action| MINUS \n<< 441742003 |Evaluation finding| MINUS \n<< 307824009 |Administrative status| MINUS \n<< 385356007 |Tumor stage finding|) \nOR < 413350009 |Finding with explicit context|\nOR < 272379006 |Event|" + }, + { + "identity": "v2", + "map": "PRB-3" + }, + { + "identity": "rim", + "map": ".value" + }, + { + "identity": "sct-attr", + "map": "246090004" + } + ] + }, + { + "id": "Condition.bodySite", + "path": "Condition.bodySite", + "short": "Anatomical location, if relevant", + "definition": "The anatomical location where this condition manifests itself.", + "comment": "Only used if not implicit in code found in Condition.code. If the use case requires attributes from the BodySite resource (e.g. to identify and track separately) then use the standard extension [bodySite](http://hl7.org/fhir/R4/extension-bodysite.html). May be a summary code, or a reference to a very precise definition of the location, or both.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.bodySite", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "BodySite" + } + ], + "strength": "example", + "description": "Codes describing anatomical locations. May include laterality.", + "valueSet": "http://hl7.org/fhir/ValueSet/body-site" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 442083009 |Anatomical or acquired body structure|" + }, + { + "identity": "rim", + "map": ".targetBodySiteCode" + }, + { + "identity": "sct-attr", + "map": "363698007" + } + ] + }, + { + "id": "Condition.subject", + "path": "Condition.subject", + "short": "Who has the condition?", + "definition": "Indicates the patient or group who the condition record is associated with.", + "requirements": "Group is typically used for veterinary or public health use cases.", + "alias": [ + "patient" + ], + "min": 1, + "max": "1", + "base": { + "path": "Condition.subject", + "min": 1, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/Group" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.subject" + }, + { + "identity": "w5", + "map": "FiveWs.subject[x]" + }, + { + "identity": "v2", + "map": "PID-3" + }, + { + "identity": "rim", + "map": ".participation[typeCode=SBJ].role[classCode=PAT]" + }, + { + "identity": "w5", + "map": "FiveWs.subject" + } + ] + }, + { + "id": "Condition.encounter", + "path": "Condition.encounter", + "short": "Encounter created as part of", + "definition": "The Encounter during which this Condition was created or to which the creation of this record is tightly associated.", + "comment": "This will typically be the encounter the event occurred within, but some activities may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter. This record indicates the encounter this particular record is associated with. In the case of a \"new\" diagnosis reflecting ongoing/revised information about the condition, this might be distinct from the first encounter in which the underlying condition was first \"known\".", + "min": 0, + "max": "1", + "base": { + "path": "Condition.encounter", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Encounter" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.context" + }, + { + "identity": "w5", + "map": "FiveWs.context" + }, + { + "identity": "v2", + "map": "PV1-19 (+PV1-54)" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]" + } + ] + }, + { + "id": "Condition.onset[x]", + "path": "Condition.onset[x]", + "short": "Estimated or actual date, date-time, or age", + "definition": "Estimated or actual date or date-time the condition began, in the opinion of the clinician.", + "comment": "Age is generally used when the patient reports an age at which the Condition began to occur.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.onset[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + }, + { + "code": "Age" + }, + { + "code": "Period" + }, + { + "code": "Range" + }, + { + "code": "string" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "workflow", + "map": "Event.occurrence[x]" + }, + { + "identity": "w5", + "map": "FiveWs.init" + }, + { + "identity": "v2", + "map": "PRB-16" + }, + { + "identity": "rim", + "map": ".effectiveTime.low or .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"age at onset\"].value" + } + ] + }, + { + "id": "Condition.abatement[x]", + "path": "Condition.abatement[x]", + "short": "When in resolution/remission", + "definition": "The date or estimated date that the condition resolved or went into remission. This is called \"abatement\" because of the many overloaded connotations associated with \"remission\" or \"resolution\" - Conditions are never really resolved, but they can abate.", + "comment": "There is no explicit distinction between resolution and remission because in many cases the distinction is not clear. Age is generally used when the patient reports an age at which the Condition abated. If there is no abatement element, it is unknown whether the condition has resolved or entered remission; applications and users should generally assume that the condition is still valid. When abatementString exists, it implies the condition is abated.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.abatement[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + }, + { + "code": "Age" + }, + { + "code": "Period" + }, + { + "code": "Range" + }, + { + "code": "string" + } + ], + "condition": [ + "con-4" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.done[x]" + }, + { + "identity": "rim", + "map": ".effectiveTime.high or .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"age at remission\"].value or .inboundRelationship[typeCode=SUBJ]source[classCode=CONC, moodCode=EVN].status=completed" + } + ] + }, + { + "id": "Condition.recordedDate", + "path": "Condition.recordedDate", + "short": "Date record was first recorded", + "definition": "The recordedDate represents when this particular Condition record was created in the system, which is often a system-generated date.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.recordedDate", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "dateTime" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.recorded" + }, + { + "identity": "v2", + "map": "REL-11" + }, + { + "identity": "rim", + "map": ".participation[typeCode=AUT].time" + } + ] + }, + { + "id": "Condition.recorder", + "path": "Condition.recorder", + "short": "Who recorded the condition", + "definition": "Individual who recorded the record and takes responsibility for its content.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.recorder", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.author" + }, + { + "identity": "rim", + "map": ".participation[typeCode=AUT].role" + } + ] + }, + { + "id": "Condition.asserter", + "path": "Condition.asserter", + "short": "Person who asserts this condition", + "definition": "Individual who is making the condition statement.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.asserter", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Patient", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.source" + }, + { + "identity": "v2", + "map": "REL-7.1 identifier + REL-7.12 type code" + }, + { + "identity": "rim", + "map": ".participation[typeCode=INF].role" + } + ] + }, + { + "id": "Condition.stage", + "path": "Condition.stage", + "short": "Stage/grade, usually assessed formally", + "definition": "Clinical stage or grade of a condition. May include formal severity assessments.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.stage", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "con-1", + "severity": "error", + "human": "Stage SHALL have summary or assessment", + "expression": "summary.exists() or assessment.exists()", + "xpath": "exists(f:summary) or exists(f:assessment)" + }, + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "./inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"stage/grade\"]" + } + ] + }, + { + "id": "Condition.stage.id", + "path": "Condition.stage.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.stage.extension", + "path": "Condition.stage.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.stage.modifierExtension", + "path": "Condition.stage.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.stage.summary", + "path": "Condition.stage.summary", + "short": "Simple summary (disease specific)", + "definition": "A simple summary of the stage such as \"Stage 3\". The determination of the stage is disease-specific.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.stage.summary", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-1" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionStage" + } + ], + "strength": "example", + "description": "Codes describing condition stages (e.g. Cancer stages).", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-stage" + }, + "mapping": [ + { + "identity": "sct-concept", + "map": "< 254291000 |Staging and scales|" + }, + { + "identity": "v2", + "map": "PRB-14" + }, + { + "identity": "rim", + "map": ".value" + } + ] + }, + { + "id": "Condition.stage.assessment", + "path": "Condition.stage.assessment", + "short": "Formal record of assessment", + "definition": "Reference to a formal record of the evidence on which the staging assessment is based.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.stage.assessment", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/ClinicalImpression", + "http://hl7.org/fhir/StructureDefinition/DiagnosticReport", + "http://hl7.org/fhir/StructureDefinition/Observation" + ] + } + ], + "condition": [ + "con-1" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": ".self" + } + ] + }, + { + "id": "Condition.stage.type", + "path": "Condition.stage.type", + "short": "Kind of staging", + "definition": "The kind of staging, such as pathological or clinical staging.", + "min": 0, + "max": "1", + "base": { + "path": "Condition.stage.type", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ConditionStageType" + } + ], + "strength": "example", + "description": "Codes describing the kind of condition staging (e.g. clinical or pathological).", + "valueSet": "http://hl7.org/fhir/ValueSet/condition-stage-type" + }, + "mapping": [ + { + "identity": "rim", + "map": "./inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"stage type\"]" + } + ] + }, + { + "id": "Condition.evidence", + "path": "Condition.evidence", + "short": "Supporting evidence", + "definition": "Supporting evidence / manifestations that are the basis of the Condition's verification status, such as evidence that confirmed or refuted the condition.", + "comment": "The evidence may be a simple list of coded symptoms/manifestations, or references to observations or formal assessments, or both.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.evidence", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "BackboneElement" + } + ], + "constraint": [ + { + "key": "con-2", + "severity": "error", + "human": "evidence SHALL have code or details", + "expression": "code.exists() or detail.exists()", + "xpath": "exists(f:code) or exists(f:detail)" + }, + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": ".outboundRelationship[typeCode=SPRT].target[classCode=OBS, moodCode=EVN]" + } + ] + }, + { + "id": "Condition.evidence.id", + "path": "Condition.evidence.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.evidence.extension", + "path": "Condition.evidence.extension", + "short": "Additional content defined by implementations", + "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "alias": [ + "extensions", + "user content" + ], + "min": 0, + "max": "*", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Condition.evidence.modifierExtension", + "path": "Condition.evidence.modifierExtension", + "short": "Extensions that cannot be ignored even if unrecognized", + "definition": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).", + "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", + "requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).", + "alias": [ + "extensions", + "user content", + "modifiers" + ], + "min": 0, + "max": "*", + "base": { + "path": "BackboneElement.modifierExtension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": true, + "isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them", + "isSummary": true, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Condition.evidence.code", + "path": "Condition.evidence.code", + "short": "Manifestation/symptom", + "definition": "A manifestation or symptom that led to the recording of this condition.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.evidence.code", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "CodeableConcept" + } + ], + "condition": [ + "con-2" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "binding": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", + "valueString": "ManifestationOrSymptom" + } + ], + "strength": "example", + "description": "Codes that describe the manifestation or symptoms of a condition.", + "valueSet": "http://hl7.org/fhir/ValueSet/manifestation-or-symptom" + }, + "mapping": [ + { + "identity": "workflow", + "map": "Event.reasonCode" + }, + { + "identity": "w5", + "map": "FiveWs.why[x]" + }, + { + "identity": "sct-concept", + "map": "< 404684003 |Clinical finding|" + }, + { + "identity": "rim", + "map": "[code=\"diagnosis\"].value" + } + ] + }, + { + "id": "Condition.evidence.detail", + "path": "Condition.evidence.detail", + "short": "Supporting information found elsewhere", + "definition": "Links to other relevant information, including pathology reports.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.evidence.detail", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ], + "condition": [ + "con-2" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": true, + "mapping": [ + { + "identity": "w5", + "map": "FiveWs.why[x]" + }, + { + "identity": "rim", + "map": ".self" + } + ] + }, + { + "id": "Condition.note", + "path": "Condition.note", + "short": "Additional information about the Condition", + "definition": "Additional information about the Condition. This is a general notes/comments entry for description of the Condition, its diagnosis and prognosis.", + "min": 0, + "max": "*", + "base": { + "path": "Condition.note", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Annotation" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "workflow", + "map": "Event.note" + }, + { + "identity": "v2", + "map": "NTE child of PRB" + }, + { + "identity": "rim", + "map": ".inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"annotation\"].value" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "Condition", + "path": "Condition" + }, + { + "id": "Condition.code", + "path": "Condition.code", + "binding": { + "strength": "required", + "valueSet": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/phenotype-codes" + } + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/StructureDefinition-supporting-info.json b/tests/fixtures/ncpi/examples/StructureDefinition-supporting-info.json new file mode 100644 index 0000000..b4cb8f4 --- /dev/null +++ b/tests/fixtures/ncpi/examples/StructureDefinition-supporting-info.json @@ -0,0 +1,296 @@ +{ + "resourceType": "StructureDefinition", + "id": "supporting-info", + "text": { + "status": "extensions", + "div": "
\r\n\r\n\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" Extension 0..*ExtensionSupporting Information
\".\"\".\"\".\" extension 0..0
\".\"\".\"\".\" url 1..1uri"https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/supporting-info"
\".\"\".\"\".\" value[x] 0..1Reference(Resource)Value of extension

\"doco\" Documentation for this format
" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/supporting-info", + "version": "0.1.0", + "name": "SupportingInformation", + "title": "Supporting Information", + "status": "active", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Additional information relevant to interpreting/understanding the report.", + "jurisdiction": [ + { + "coding": [ + { + "system": "http://unstats.un.org/unsd/methods/m49/m49.htm", + "code": "001" + } + ] + } + ], + "fhirVersion": "4.0.1", + "mapping": [ + { + "identity": "rim", + "uri": "http://hl7.org/v3", + "name": "RIM Mapping" + } + ], + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Element" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "snapshot": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Supporting Information", + "definition": "Additional information relevant to interpreting/understanding the report.", + "min": 0, + "max": "*", + "base": { + "path": "Extension", + "min": 0, + "max": "*" + }, + "condition": [ + "ele-1" + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false + }, + { + "id": "Extension.id", + "path": "Extension.id", + "representation": [ + "xmlAttr" + ], + "short": "Unique id for inter-element referencing", + "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", + "min": 0, + "max": "1", + "base": { + "path": "Element.id", + "min": 0, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "string" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "n/a" + } + ] + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "description": "Extensions are always sliced by (at least) url", + "rules": "open" + }, + "short": "Extension", + "definition": "An Extension", + "min": 0, + "max": "0", + "base": { + "path": "Element.extension", + "min": 0, + "max": "*" + }, + "type": [ + { + "code": "Extension" + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + }, + { + "key": "ext-1", + "severity": "error", + "human": "Must have either extensions or value[x], not both", + "expression": "extension.exists() != value.exists()", + "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", + "source": "http://hl7.org/fhir/StructureDefinition/Extension" + } + ], + "isModifier": false, + "isSummary": false + }, + { + "id": "Extension.url", + "path": "Extension.url", + "representation": [ + "xmlAttr" + ], + "short": "identifies the meaning of the extension", + "definition": "Source of the definition for the extension code - a logical name or a URL.", + "comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.", + "min": 1, + "max": "1", + "base": { + "path": "Extension.url", + "min": 1, + "max": "1" + }, + "type": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", + "valueUrl": "uri" + } + ], + "code": "http://hl7.org/fhirpath/System.String" + } + ], + "fixedUri": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/supporting-info", + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "short": "Value of extension", + "definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).", + "min": 0, + "max": "1", + "base": { + "path": "Extension.value[x]", + "min": 0, + "max": "1" + }, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ], + "constraint": [ + { + "key": "ele-1", + "severity": "error", + "human": "All FHIR elements must have a @value or children", + "expression": "hasValue() or (children().count() > id.count())", + "xpath": "@value|f:*|h:div", + "source": "http://hl7.org/fhir/StructureDefinition/Element" + } + ], + "isModifier": false, + "isSummary": false, + "mapping": [ + { + "identity": "rim", + "map": "N/A" + } + ] + } + ] + }, + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Supporting Information", + "definition": "Additional information relevant to interpreting/understanding the report." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/supporting-info" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Resource" + ] + } + ] + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Task-task-example-1.json b/tests/fixtures/ncpi/examples/Task-task-example-1.json new file mode 100644 index 0000000..002c04a --- /dev/null +++ b/tests/fixtures/ncpi/examples/Task-task-example-1.json @@ -0,0 +1,30 @@ +{ + "resourceType": "Task", + "id": "task-example-1", + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"task-example-1\"

status: completed

intent: order

Inputs

-TypeValue[x]
*Specimen ()Specimen/specimen-example-1

Outputs

-TypeValue[x]
*DocumentReference ()DocumentReference/drs-document-reference-example-1
" + }, + "status": "completed", + "intent": "order", + "input": [ + { + "type": { + "text": "Specimen" + }, + "valueReference": { + "reference": "Specimen/specimen-example-1" + } + } + ], + "output": [ + { + "type": { + "text": "DocumentReference" + }, + "valueReference": { + "reference": "DocumentReference/drs-document-reference-example-1" + } + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/Task-task-example-2.json b/tests/fixtures/ncpi/examples/Task-task-example-2.json new file mode 100644 index 0000000..5ea3c86 --- /dev/null +++ b/tests/fixtures/ncpi/examples/Task-task-example-2.json @@ -0,0 +1,44 @@ +{ + "resourceType": "Task", + "id": "task-example-2", + "meta": { + "profile": [ + "https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-specimen-task" + ] + }, + "text": { + "status": "generated", + "div": "

Generated Narrative

Resource \"task-example-2\"

Profile: Research Task

status: completed

intent: order

focus: Specimen/specimen-example-1

for: Patient/patient-example-3 \" SMITH\"

owner: Organization/organization-example-1 \"Amazing Children's Hospital\"

Inputs

-TypeValue[x]
*Specimen ()Specimen/specimen-example-1

Outputs

-TypeValue[x]
*DocumentReference ()DocumentReference/research-document-reference-example-1
" + }, + "status": "completed", + "intent": "order", + "focus": { + "reference": "Specimen/specimen-example-1" + }, + "for": { + "reference": "Patient/patient-example-3" + }, + "owner": { + "reference": "Organization/organization-example-1" + }, + "input": [ + { + "type": { + "text": "Specimen" + }, + "valueReference": { + "reference": "Specimen/specimen-example-1" + } + } + ], + "output": [ + { + "type": { + "text": "DocumentReference" + }, + "valueReference": { + "reference": "DocumentReference/research-document-reference-example-1" + } + } + ] +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ValueSet-condition-inheritance-vs.json b/tests/fixtures/ncpi/examples/ValueSet-condition-inheritance-vs.json new file mode 100644 index 0000000..0acfaf5 --- /dev/null +++ b/tests/fixtures/ncpi/examples/ValueSet-condition-inheritance-vs.json @@ -0,0 +1,54 @@ +{ + "resourceType": "ValueSet", + "id": "condition-inheritance-vs", + "text": { + "status": "generated", + "div": "" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/condition-inheritance-vs", + "version": "0.1.0", + "name": "ConditionInheritanceModeVS", + "title": "Condition Inheritance Pattern", + "status": "active", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Value Set for specific ttransmission patterns of a condition in a pedigree", + "jurisdiction": [ + { + "coding": [ + { + "system": "http://unstats.un.org/unsd/methods/m49/m49.htm", + "code": "001" + } + ] + } + ], + "compose": { + "include": [ + { + "system": "https://ncpi-fhir.github.io/ncpi-fhir-ig/CodeSystem/ConditionInheritanceMode" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ValueSet-disease-codes.json b/tests/fixtures/ncpi/examples/ValueSet-disease-codes.json new file mode 100644 index 0000000..9d97067 --- /dev/null +++ b/tests/fixtures/ncpi/examples/ValueSet-disease-codes.json @@ -0,0 +1,51 @@ +{ + "resourceType": "ValueSet", + "id": "disease-codes", + "text": { + "status": "generated", + "div": "

This value set includes codes based on the following rules:

" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/disease-codes", + "version": "0.1.0", + "name": "DiseaseCodes", + "title": "Disease Codes", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "This value set includes all codes from this FHIR server's representation of OMIM, Mondo and NICt CodeSystems.", + "compose": { + "include": [ + { + "system": "https://omim.org/" + }, + { + "system": "http://purl.obolibrary.org/obo/mondo.owl" + }, + { + "system": "http://purl.obolibrary.org/obo/ncit.owl" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ValueSet-loinc-answers.json b/tests/fixtures/ncpi/examples/ValueSet-loinc-answers.json new file mode 100644 index 0000000..a22591a --- /dev/null +++ b/tests/fixtures/ncpi/examples/ValueSet-loinc-answers.json @@ -0,0 +1,45 @@ +{ + "resourceType": "ValueSet", + "id": "loinc-answers", + "text": { + "status": "generated", + "div": "
" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/loinc-answers", + "version": "0.1.0", + "name": "LoincAnswers", + "title": "LOINC Answers", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "LOINC ANSWERS used by NCPI resources", + "compose": { + "include": [ + { + "system": "ncpi:loinc-answers" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ValueSet-ncpi-vs.json b/tests/fixtures/ncpi/examples/ValueSet-ncpi-vs.json new file mode 100644 index 0000000..cebfc1a --- /dev/null +++ b/tests/fixtures/ncpi/examples/ValueSet-ncpi-vs.json @@ -0,0 +1,47 @@ +{ + "resourceType": "ValueSet", + "id": "ncpi-vs", + "text": { + "status": "generated", + "div": "

This value set includes codes based on the following rules:

" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/ncpi-vs", + "version": "0.1.0", + "name": "Ncpi_VS", + "title": "NCPI FHIR Codes", + "status": "draft", + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "Codes that would apply to NCPI projects", + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig" + }, + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig/datatypes" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ValueSet-phenotype-codes.json b/tests/fixtures/ncpi/examples/ValueSet-phenotype-codes.json new file mode 100644 index 0000000..f0e2d1a --- /dev/null +++ b/tests/fixtures/ncpi/examples/ValueSet-phenotype-codes.json @@ -0,0 +1,45 @@ +{ + "resourceType": "ValueSet", + "id": "phenotype-codes", + "text": { + "status": "generated", + "div": "
" + }, + "url": "https://ncpi-fhir.github.io/ncpi-fhir-ig/ValueSet/phenotype-codes", + "version": "0.1.0", + "name": "PhenotypeCodes", + "title": "Phenotype Codes", + "status": "draft", + "experimental": false, + "date": "2021-12-13T19:24:22+00:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "This value set includes all codes from Human Phenotype Ontology.", + "compose": { + "include": [ + { + "system": "http://purl.obolibrary.org/obo/hp.owl" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/examples/ValueSet-tbd-codes.json b/tests/fixtures/ncpi/examples/ValueSet-tbd-codes.json new file mode 100644 index 0000000..cd6fb03 --- /dev/null +++ b/tests/fixtures/ncpi/examples/ValueSet-tbd-codes.json @@ -0,0 +1,56 @@ +{ + "resourceType": "ValueSet", + "id": "tbd-codes", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/shareablevalueset" + ] + }, + "text": { + "status": "generated", + "div": "" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg", + "valueCode": "cg" + } + ], + "url": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes", + "version": "0.1.0", + "name": "ToBeDeterminedCodes", + "title": "tbd-codes", + "status": "active", + "experimental": false, + "date": "2019-08-21T00:00:00-04:00", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "https://github.com/ncpi-fhir" + } + ] + }, + { + "name": "Meen Chul Kim", + "telecom": [ + { + "system": "email", + "value": "meenchul@d3b.center", + "use": "work" + } + ] + } + ], + "description": "This value set includes all TBD Codes", + "compose": { + "include": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" + } + ] + } +} \ No newline at end of file diff --git a/tests/fixtures/ncpi/output/gen3/_definitions.yaml b/tests/fixtures/ncpi/output/gen3/_definitions.yaml new file mode 100644 index 0000000..da80111 --- /dev/null +++ b/tests/fixtures/ncpi/output/gen3/_definitions.yaml @@ -0,0 +1,252 @@ +id: _definitions + +UUID: + term: + $ref: "_terms.yaml#/UUID" + type: string + pattern: "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$" + +parent_uuids: + type: array + minItems: 1 + items: + $ref: "#/UUID" + uniqueItems: true + +foreign_key_project: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: true + #Can either use 'id' which are Gen3 IDs (UUID) or 'code' + #which is the user defined ID for project + properties: + id: + $ref: "#/UUID" + code: + type: string + +to_one_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key_project" + +to_many_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + - $ref: "#/foreign_key_project" + +foreign_key: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: True + #Can either use 'id' which are GDC IDs (UUID) or 'submitter_id' + #which are user defined IDs ("submitter IDs in the backend") + properties: + id: + $ref: "#/UUID" + submitter_id: + type: string + +to_one: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key" + +to_many: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + - $ref: "#/foreign_key" + +datetime: + oneOf: + - type: string + format: date-time + - type: 'null' + term: + $ref: "_terms.yaml#/datetime" + +file_name: + type: string + term: + $ref: "_terms.yaml#/file_name" + +file_size: + type: integer + term: + $ref: "_terms.yaml#/file_size" + +file_format: + type: string + term: + $ref: "_terms.yaml#/file_format" + +ga4gh_drs_uri: + type: string + term: + $ref: "_terms.yaml#/ga4gh_drs_uri" + +md5sum: + type: string + term: + $ref: "_terms.yaml#/md5sum" + pattern: "^[a-f0-9]{32}$" + +object_id: + type: string + description: "The GUID of the object in the index service." + +release_state: + description: "Release state of an entity." + default: unreleased + enum: + - unreleased + - released + - redacted + +data_bundle_state: + description: "State of a data bundle." + default: submitted + enum: + - submitted + - validated + - error + - released + - suppressed + - redacted + +data_file_error_type: + term: + $ref: "_terms.yaml#/data_file_error_type" + enum: + - file_size + - file_format + - md5sum + +state: + term: + $ref: "_terms.yaml#/state" + default: validated + downloadable: + - uploaded + - md5summed + - validating + - validated + - error + - invalid + - released + public: + - live + oneOf: + - enum: #This list covers legacy data + - uploading + - uploaded + - md5summing + - md5summed + - validating + - error + - invalid + - suppressed + - redacted + - live + - enum: #This list covers all future data 1/15/16 + - validated + - submitted + - released + +file_state: + term: + $ref: "_terms.yaml#/file_state" + default: registered + enum: + - registered + - uploading + - uploaded + - validating + - validated + - submitted + - processing + - processed + - released + - error + +qc_metrics_state: + term: + $ref: "_terms.yaml#/qc_metric_state" + enum: + - FAIL + - PASS + - WARN + +project_id: + type: string + term: + $ref: "_terms.yaml#/project_id" + +data_file_properties: + $ref: "#/ubiquitous_properties" + file_name: + $ref: "#/file_name" + file_size: + $ref: "#/file_size" + file_format: + $ref: "#/file_format" + md5sum: + $ref: "#/md5sum" + object_id: + $ref: "#/object_id" + file_state: + $ref: "#/file_state" + error_type: + $ref: "#/data_file_error_type" + ga4gh_drs_uri: + $ref: "#/ga4gh_drs_uri" + +workflow_properties: + $ref: "#/ubiquitous_properties" + workflow_link: + description: "Link to Github hash for the CWL workflow used." + type: string + workflow_version: + description: "Major version for a GDC workflow." + type: string + workflow_start_datetime: + $ref: "#/datetime" + workflow_end_datetime: + $ref: "#/datetime" + +ubiquitous_properties: + type: + type: string + id: + $ref: "#/UUID" + systemAlias: node_id + submitter_id: + type: + - string + description: > + A project-specific identifier for a node. This property is the calling card/nickname/alias for + a unit of submission. It can be used in place of the UUID for identifying or recalling a node. + state: + $ref: "#/state" + project_id: + $ref: "#/project_id" + created_datetime: + $ref: "#/datetime" + updated_datetime: + $ref: "#/datetime" diff --git a/tests/fixtures/ncpi/output/gen3/_settings.yaml b/tests/fixtures/ncpi/output/gen3/_settings.yaml new file mode 100644 index 0000000..d7e2171 --- /dev/null +++ b/tests/fixtures/ncpi/output/gen3/_settings.yaml @@ -0,0 +1,6 @@ +# Global settings for the graph + +# Is the graph case centric, that we want +# to create a link between all children to case +# to expedite case filter on nodes +enable_case_cache: false diff --git a/tests/fixtures/ncpi/output/gen3/_terms.yaml b/tests/fixtures/ncpi/output/gen3/_terms.yaml new file mode 100644 index 0000000..6024d85 --- /dev/null +++ b/tests/fixtures/ncpi/output/gen3/_terms.yaml @@ -0,0 +1,1938 @@ +id: _terms + + + +28s_16s_ribosomal_rna_ratio: + description: > + The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA. + termDef: + term: "28s/18s Ribosomal RNA Ratio" + source: null + cde_id: null + cde_version: null + term_url: null + + + + + +a260_a280_ratio: + description: > + Numeric value that represents the sample ratio of nucleic acid absorbance at 260 nm and 280 nm, + used to determine a measure of DNA purity. + termDef: + term: Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value + source: caDSR + cde_id: 5432595 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" + +age: + description: > + Age at last visit. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Age at last visit. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +family_onset: + description: > + Typical age of onset for the family. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Typical age of onset for the family. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +disease_omim_id: + description: > + The ID of the term from OMIM which represents a disease. (CMG) + termDef: + term: The ID of the term from OMIM which represents a disease. (CMG) + source: OMIM + cde_id: OMIM + cde_version: 1.0 + term_url: "https://www.ncbi.nlm.nih.gov/omim" + +phenotype_hpo_id: + description: > + The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + termDef: + term: The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + source: HPO + cde_id: HPO + cde_version: 1.0 + term_url: "https://hpo.jax.org/app/" + +adapter_name: # TOREVIEW + description: > + Name of the sequencing adapter. + +adapter_sequence: # TOREVIEW + description: > + Base sequence of the sequencing adapter. + +age_of_onset: + description: > + Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + termDef: + term: Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +age_at_event_days_gt89: + description: > + Indicate whether the 'Age at the time an event occurs expressed in the number of days since birth' is greater than 32872 days (89 years). + +age_at_diagnosis: + description: > + Age at the time of diagnosis expressed in number of days since birth. If the age at diagnosis is greater than 32872 days (89 years), then see 'age_at_diagnosis_gt89'. + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +age_at_diagnosis_gt89: + description: > + Indicate whether the age at the time of diagnosis expressed in number of days since birth is greater than 32872 days (89 years). + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +ajcc_clinical_m: + description: > + Extent of the distant metastasis for the cancer based on evidence obtained from clinical + assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage + source: caDSR + cde_id: 3440331 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0" + +ajcc_clinical_n: + description: > + Extent of the regional lymph node involvement for the cancer based on evidence obtained from + clinical assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage + source: caDSR + cde_id: 3440330 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0" + +ajcc_clinical_stage: + description: > + Stage group determined from clinical information on the tumor (T), regional node (N) and + metastases (M) and by grouping cases with similar prognosis for cancer. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Group Stage + source: caDSR + cde_id: 3440332 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0" + +ajcc_clinical_t: + description: > + Extent of the primary cancer based on evidence obtained from clinical assessment parameters + determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage + source: caDSR + cde_id: 3440328 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0" + +ajcc_pathologic_m: + description: > + Code to represent the defined absence or presence of distant spread or metastases (M) to + locations via vascular channels or lymphatics beyond the regional lymph nodes, using + criteria established by the American Joint Committee on Cancer (AJCC). + termDef: + term: American Joint Committee on Cancer Metastasis Stage Code + source: caDSR + cde_id: 3045439 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0" + +ajcc_pathologic_n: + description: > + The codes that represent the stage of cancer based on the nodes present (N stage) according + to criteria based on multiple editions of the AJCC's Cancer Staging Manual. + termDef: + term: Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203106 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0" + +ajcc_pathologic_stage: + description: > + The extent of a cancer, especially whether the disease has spread from the original site to + other parts of the body based on AJCC staging criteria. + termDef: + term: Neoplasm Disease Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203222 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0" + +ajcc_pathologic_t: + description: > + Code of pathological T (primary tumor) to define the size or contiguous extension of the + primary tumor (T), using staging criteria from the American Joint Committee on Cancer + (AJCC). + termDef: + term: American Joint Committee on Cancer Tumor Stage Code + source: caDSR + cde_id: 3045435 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0" + +alcohol_history: + description: > + A response to a question that asks whether the participant has consumed at least 12 drinks of + any kind of alcoholic beverage in their lifetime. + termDef: + term: Alcohol Lifetime History Indicator + source: caDSR + cde_id: 2201918 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0" + +drink_number: + description: > + Units of drink consumed during Drink Period (DRNKPRD). (GTEx) + +aliquot_quantity: + description: > + The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +aliquot_volume: + description: > + The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Volume + source: null + cde_id: null + cde_version: null + term_url: null + +amount: # TOREVIEW + description: > + Weight in grams or volume in mL. + +analyte_quantity: + description: > + The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +analyte_type: + description: > + Text term that represents the kind of molecular specimen analyte. + termDef: + term: Molecular Specimen Type Text Name + source: caDSR + cde_id: 2513915 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" + +analyte_type_id: + description: > + A single letter code used to identify a type of molecular analyte. + termDef: + term: Molecular Analyte Identification Code + source: caDSR + cde_id: 5432508 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0" + +analyte_volume: + description: > + The volume in microliters (ml) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Volume + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_b_symptoms: + description: > + Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical + record. + termDef: + term: Lymphoma B-Symptoms Medical Record Documented Indicator + source: caDSR + cde_id: 2902402 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0" + +ann_arbor_clinical_stage: + description: > + The classification of the clinically confirmed anatomic disease extent of lymphoma (Hodgkin's + and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Clinical Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_extranodal_involvement: + description: > + Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement + of an extranodal site. + termDef: + term: Lymphomatous Extranodal Site Involvement Indicator + source: caDSR + cde_id: 3364582 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0" + +ann_arbor_pathologic_stage: + description: > + The classification of the pathologically confirmed anatomic disease extent of lymphoma + (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Pathologic Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_tumor_stage: + description: > + The classification of the anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based + on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Tumor Stage + source: null + cde_id: null + cde_version: null + term_url: null + +base_caller_name: # TOREVIEW + description: > + Name of the base caller. + +base_caller_version: # TOREVIEW + description: > + Version of the base caller. + +biomarker_name: + description: > + The name of the biomarker being tested for this specimen and set of test results. + termDef: + term: Biomarker Name + source: caDSR + cde_id: 5473 + cde_version: 11.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31" + +biomarker_result: + description: > + Text term to define the results of genetic testing. + termDef: + term: Laboratory Procedure Genetic Abnormality Test Result Type + source: caDSR + cde_id: 3234680 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0" + +biomarker_test_method: + description: > + Text descriptor of a molecular analysis method used for an individual. + termDef: + term: Disease Detection Molecular Analysis Method Type + source: caDSR + cde_id: 3121575 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0" + +biospecimen_anatomic_site_id: + description: > + Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +biospecimen_anatomic_site_label: + description: > + Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +bmi: + description: > + Autocalculated field of BMI: general indicator of the body fat an individual is carrying based upon the ratio of weight to height. BMI = 703 * weight in pounds/height in inches squared. (GTEx) + termDef: + term: Body Mass Index (BMI) + source: caDSR + cde_id: 4973892 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" + +burkitt_lymphoma_clinical_variant: + description: > + Burkitt's lymphoma categorization based on clinical features that differ from other forms of the + same disease. + termDef: + term: Burkitt Lymphoma Clinical Variant Type + source: caDSR + cde_id: 3770421 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" + +cause_of_death: + description: > + Text term to identify the cause of death for a patient. + termDef: + term: Patient Death Reason + source: caDSR + cde_id: 2554674 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0" + +cea_level_preoperative: + description: > + Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. [Manually- + curated] + termDef: + term: Preoperative Carcinoembryonic Antigen Result Value + source: caDSR + cde_id: 2716510 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0" + +cigarettes_per_day: + description: > + The average number of cigarettes smoked per day. + termDef: + term: Smoking Use Average Number + source: caDSR + cde_id: 2001716 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0" + +circumferential_resection_margin: + description: > + A value in millimeters indicating the measured length between a malignant lesion of the + colon or rectum and the nearest radial (or circumferential) border of tissue removed during + cancer surgery. + termDef: + term: Colorectal Surgical Margin Circumferential Distance Measurement + source: caDSR + cde_id: 64202 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0" + +classification_of_tumor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +colon_polyps_history: + description: > + Yes/No indicator to describe if the subject had a previous history of colon polyps as noted + in the history/physical or previous endoscopic report (s). + termDef: + term: Colon Carcinoma Polyp Occurrence Indicator + source: caDSR + cde_id: 3107197 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0" + +composition: + description: > + Text term that represents the cellular composition of the sample. + termDef: + term: Biospecimen Cellular Composition Type + source: caDSR + cde_id: 5432591 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" + +concentration: + description: > + Numeric value that represents the concentration of an analyte or aliquot extracted from the + sample or sample portion, measured in milligrams per milliliter. + termDef: + term: Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value + source: caDSR + cde_id: 5432594 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" + +creation_datetime: + description: > + The datetime of portion creation encoded as seconds from epoch. + termDef: + term: Biospecimen Portion Creation Seconds Date/Time + source: caDSR + cde_id: 5432592 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0" + +current_weight: + description: > + Numeric value that represents the current weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Current Weight Milligram Value + source: caDSR + cde_id: 5432606 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" + +data_category: # TOREVIEW + description: > + Broad categorization of the contents of the data file. + +data_file_error_type: # TOREVIEW + description: > + Type of error for the data file object. + +data_format: # TOREVIEW + description: > + Format of the data files. + +data_type: # TOREVIEW + description: > + Specific content type of the data file. (CMG) + +datetime: + description: > + A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] + +days_to_birth: + description: > + Time interval from a person's date of birth to the date of initial pathologic diagnosis, + represented as a calculated negative number of days. + termDef: + term: Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0" + +days_to_collection: + description: > + Time interval from the date of biospecimen collection to the date of initial pathologic + diagnosis, represented as a calculated number of days. + termDef: + term: Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008340 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0" + +days_to_death: + description: > + Time interval from a person's date of death to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Death Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3165475 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0" + +days_to_hiv_diagnosis: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of human + immunodeficiency diagnosis, represented as a calculated number of days. + termDef: + term: Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value + source: caDSR + cde_id: 4618491 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0" + +days_to_last_follow_up: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_last_known_disease_status: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_new_event: + description: > + Time interval from the date of new tumor event including progression, recurrence and new + primary malignacies to the date of initial pathologic diagnosis, represented as a calculated + number of days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_recurrence: + description: > + Time interval from the date of new tumor event including progression, recurrence and new primary + malignancies to the date of initial pathologic diagnosis, represented as a calculated number of + days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_sample_procurement: + description: > + The number of days from the date the patient was diagnosed to the date of the procedure that + produced the sample. + +days_to_treatment: + description: > + Number of days from date of initial pathologic diagnosis that treatment began. + termDef: + term: Days to Treatment Start + source: null + cde_id: null + cde_version: null + term_url: null + +days_to_treatment_end: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of treatment end, + represented as a calculated number of days. + termDef: + term: Treatment End Subtract First Pathologic Diagnosis Day Calculation Value + source: caDSR + cde_id: 5102431 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0" + +days_to_treatment_start: + description: > + Time interval from the date of the initial pathologic diagnosis to the start of treatment, + represented as a calculated number of days. + termDef: + term: Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value + source: caDSR + cde_id: 5102411 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0" + +diagnosis_pathologically_confirmed: + description: > + The histologic description of tissue or cells confirmed by a pathology review of frozen or + formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used + to extract analyte(s). + termDef: + term: Post-Diagnostic Pathology Review Confirmation + source: null + cde_id: null + cde_version: null + term_url: null + +dlco_ref_predictive_percent: + description: > + The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide + detected in a patient's lungs. + termDef: + term: Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value + source: caDSR + cde_id: 2180255 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0" + +encoding: + description: > + Version of ASCII encoding of quality values found in the file. + termDef: + term: Encoding + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +estrogen_receptor_percent_positive_ihc: + description: > + Classification to represent ER Positive results expressed as a percentage value. + termDef: + term: ER Level Cell Percentage Category + source: caDSR + cde_id: 3128341 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0" + +estrogen_receptor_result_ihc: + description: > + Text term to represent the overall result of Estrogen Receptor (ER) testing. + termDef: + term: Breast Carcinoma Estrogen Receptor Status + source: caDSR + cde_id: 2957359 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0" + +ethnicity: + description: > + An individual's self-described social and cultural grouping, specifically whether an individual + describes themselves as Hispanic or Latino (HARMONIZED). The provided values are based on the categories + defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (CMG, GTEx) + termDef: + term: Ethnic Group Category Text + source: caDSR + cde_id: 2192217 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" + +experiment_name: # TOREVIEW + description: > + Submitter-defined name for the experiment. + +experimental_strategy: # TOREVIEW + description: > + The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri. + +fastq_name: # TOREVIEW + description: > + Names of FASTQs. + +fev1_ref_post_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second post-bronchodilator. + termDef: + term: Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302948 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0" + +fev1_ref_pre_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second pre-bronchodilator. + termDef: + term: Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302947 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" + +fev1_fvc_post_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) post-bronchodilator. + termDef: + term: Post Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302956 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0" + +fev1_fvc_pre_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) pre-bronchodilator. + termDef: + term: Pre Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302955 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0" + +figo_stage: + description: > + The extent of a cervical or endometrial cancer within the body, especially whether the + disease has spread from the original site to other parts of the body, as described by the + International Federation of Gynecology and Obstetrics (FIGO) stages. + termDef: + term: Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage + source: caDSR + cde_id: 3225684 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" + +file_format: + description: > + The format of the data file object. + +file_name: # TOREVIEW + description: > + The name (or part of a name) of a file (of any type). + +file_size: # TOREVIEW + description: > + The size of the data file (object) in bytes. + +file_state: # TOREVIEW + description: > + The current state of the data file object. + +flow_cell_barcode: # TOREVIEW + description: > + Flow Cell Barcode. + +freezing_method: + description: > + Text term that represents the method used for freezing the sample. + termDef: + term: Tissue Sample Freezing Method Type + source: caDSR + cde_id: 5432607 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" + +ga4gh_drs_uri: + description: > + DRS URI as defined by GA4GH DRS spec for pointers to file objects. + +sex: + description: > + Text designations that identify gender (HARMONIZED). Gender is described as the assemblage of properties that + distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification + of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] (CMG) + termDef: + term: Person Gender Text Type + source: caDSR + cde_id: 2200604 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" + +height: + description: > + The height of Donor in inches as reported by Donor, family/next of kin, or medical record abstraction. (GTEx) + termDef: + term: Patient Height Measurement + source: caDSR + cde_id: 649 + cde_version: 4.1 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" + +her2_erbb2_percent_positive_ihc: + description: > + Classification to represent the number of positive HER2/ERBB2 cells in a specimen or sample. + termDef: + term: HER2 ERBB Positive Finding Cell Percentage Category + source: caDSR + cde_id: 3086980 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0" + +her2_erbb2_result_fish: + description: > + the type of outcome for HER2 as determined by an in situ hybridization (ISH) assay. + termDef: + term: Laboratory Procedure HER2/neu in situ Hybridization Outcome Type + source: caDSR + cde_id: 2854089 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0" + +her2_erbb2_result_ihc: + description: > + Text term to signify the result of the medical procedure that involves testing a sample of + blood or tissue for HER2 by histochemical localization of immunoreactive substances using + labeled antibodies as reagents. + termDef: + term: Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status + source: caDSR + cde_id: 2957563 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0" + +hiv_positive: + description: > + Text term to signify whether a physician has diagnosed HIV infection in a patient. + termDef: + term: Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator + source: caDSR + cde_id: 4030799 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0" + +hpv_positive_type: + description: > + Text classification to represent the strain or type of human papillomavirus identified in an + individual. + termDef: + term: Human Papillomavirus Type + source: caDSR + cde_id: 2922649 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0" + +hpv_status: + description: > + The findings of the oncogenic HPV. + termDef: + term: Oncogenic Human Papillomavirus Result Type + source: caDSR + cde_id: 2230033 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" + +includes_spike_ins: # TOREVIEW + description: > + Spike-in included? + +initial_weight: + description: > + Numeric value that represents the initial weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Initial Weight Milligram Value + source: caDSR + cde_id: 5432605 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0" + +instrument_model: + description: > + Numeric value that represents the sample dimension that is greater than the shortest + dimension and less than the longest dimension, measured in millimeters. + termDef: + term: Tissue Sample Intermediate Dimension Millimeter Measurement + source: caDSR + cde_id: 5432604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" + +intermediate_dimension: # TOREVIEW + description: > + Intermediate dimension of the sample, in millimeters. + +is_ffpe: + description: > + Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in + paraffin (FFPE). + termDef: + term: Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator + source: caDSR + cde_id: 4170557 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" + +is_paired_end: # TOREVIEW + description: > + Are the reads paired end? + +is_proband: # TOREVIEW + description: > + Boolean value to determine if the case is the proband. + +last_known_disease_status: + description: > + Text term that describes the last known state or condition of an individual's neoplasm. + termDef: + term: Person Last Known Neoplasm Status + source: caDSR + cde_id: 5424231 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0" + +laterality: + description: > + For tumors in paired organs, designates the side on which the cancer originates. + termDef: + term: Primary Tumor Laterality + source: caDSR + cde_id: 827 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0" + +ldh_level_at_diagnosis: + description: > + The 2 decimal place numeric laboratory value measured, assigned or computed related to the + assessment of lactate dehydrogenase in a specimen. + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value + source: caDSR + cde_id: 2798766 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0" + +ldh_normal_range_upper: + description: > + The top value of the range of statistical characteristics that are supposed to represent + accepted standard, non-pathological pattern for lactate dehydrogenase (units not specified). + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value + source: caDSR + cde_id: 2597015 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" + +library_strategy: # TOREVIEW + description: > + Library strategy. + +library_selection: # TOREVIEW + description: > + Library Selection Method + +library_name: # TOREVIEW + description: > + Name of the library. + +library_preparation_kit_name: # TOREVIEW + description: > + Name of Library Preparation Kit + +library_preparation_kit_vendor: # TOREVIEW + description: > + Vendor of Library Preparation Kit + +library_preparation_kit_catalog_number: # TOREVIEW + description: > + Catalog of Library Preparation Kit + +library_preparation_kit_version: # TOREVIEW + description: > + Version of Library Preparation Kit + +library_strand: # TOREVIEW + description: > + Library stranded-ness. + +longest_dimension: + description: > + Numeric value that represents the longest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Longest Dimension Millimeter Measurement + source: caDSR + cde_id: 5432602 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0" + +lymph_nodes_positive: + description: > + The number of lymph nodes involved with disease as determined by pathologic examination. + termDef: + term: Lymph Node(s) Positive Number + source: caDSR + cde_id: 89 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0" + +lymphatic_invasion_present: + description: > + A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating + lymphatic involvement + termDef: + term: Lymphatic/Small vessel Invasion Ind + source: caDSR + cde_id: 64171 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" + +method_of_diagnosis: + description: > + The method used to initially the patient's diagnosis. + termDef: + term: Method of Diagnosis + source: null + cde_id: null + cde_version: null + term_url: null + +method_of_sample_procurement: + description: > + The method used to procure the sample used to extract analyte(s). + termDef: + term: Method of Sample Procurement + source: null + cde_id: null + cde_version: null + term_url: null + +md5sum: # TOREVIEW + description: > + The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital + fingerprint. + +microsatellite_instability_abnormal: + description: > + The yes/no indicator to signify the status of a tumor for microsatellite instability. + termDef: + term: Microsatellite Instability Occurrence Indicator + source: caDSR + cde_id: 3123142 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0" + +morphology: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000 used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The study of the structure of the cells and their + arrangement to constitute tissues and, finally, the association among these to form organs. In + pathology, the microscopic process of identifying normal and abnormal morphologic + characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A + system of numbered categories for representation of data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code + source: caDSR + cde_id: 3226275 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0" + +new_event_anatomic_site: + description: > + Text term to specify the anatomic location of the return of tumor after treatment. + termDef: + term: New Neoplasm Event Occurrence Anatomic Site + source: caDSR + cde_id: 3108271 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0" + +new_event_type: + description: > + Text term to identify a new tumor event. + termDef: + term: New Neoplasm Event Type + source: caDSR + cde_id: 3119721 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0" + +normal_tumor_genotype_snp_match: + description: > + Text term that represents whether or not the genotype of the normal tumor matches or if the data + is not available. + termDef: + term: Normal Tumor Genotype Match Indicator + source: caDSR + cde_id: 4588156 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0" + +number_proliferating_cells: + description: > + Numeric value that represents the count of proliferating cells determined during pathologic + review of the sample slide(s). + termDef: + term: Pathology Review Slide Proliferating Cell Count + source: caDSR + cde_id: 5432636 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0" + +oct_embedded: + description: > + Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound. + termDef: + term: Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator + source: caDSR + cde_id: 5432538 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" + +years_smoked: + description: > + Number of years the Donor smoked. (GTEx) + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +percent_eosinophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or + specimen. + termDef: + term: Specimen Eosinophilia Percentage Value + source: caDSR + cde_id: 2897700 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0" + +percent_gc_content: + description: > + The overall %GC of all bases in all sequences. + termDef: + term: "%GC" + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +percent_granulocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or + specimen. + termDef: + term: Specimen Granulocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897705 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0" + +percent_inflam_infiltration: + description: > + Numeric value to represent local response to cellular injury, marked by capillary dilatation, + edema and leukocyte infiltration; clinically, inflammation is manifest by reddness, heat, pain, + swelling and loss of function, with the need to heal damaged tissue. + termDef: + term: Specimen Inflammation Change Percentage Value + source: caDSR + cde_id: 2897695 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0" + +percent_lymphocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue + normal sample or specimen. + termDef: + term: Specimen Lymphocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897710 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0" + +percent_monocyte_infiltration: + description: > + Numeric value to represent the percentage of monocyte infiltration in a sample or specimen. + termDef: + term: Specimen Monocyte Infiltration Percentage Value + source: caDSR + cde_id: 5455535 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0" + +percent_necrosis: + description: > + Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen. + termDef: + term: Malignant Neoplasm Necrosis Percentage Value + source: caDSR + cde_id: 2841237 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0" + +percent_neutrophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value + source: caDSR + cde_id: 2841267 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0" + +percent_normal_cells: + description: > + Numeric value to represent the percentage of normal cell content in a malignant tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Normal Cell Percentage Value + source: caDSR + cde_id: 2841233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0" + +percent_stromal_cells: + description: > + Numeric value to represent the percentage of reactive cells that are present in a malignant + tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc. + termDef: + term: Malignant Neoplasm Stromal Cell Percentage Value + source: caDSR + cde_id: 2841241 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0" + +percent_tumor_cells: + description: > + Numeric value that represents the percentage of infiltration by granulocytes in a sample. + termDef: + term: Specimen Tumor Cell Percentage Value + source: caDSR + cde_id: 5432686 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0" + +percent_tumor_nuclei: + description: > + Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen. + termDef: + term: Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value + source: caDSR + cde_id: 2841225 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0" + +perineural_invasion_present: + description: > + a yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is + present. + termDef: + term: Tumor Perineural Invasion Ind + source: caDSR + cde_id: 64181 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" + +platform: # TOREVIEW + description: > + Name of the platform used to obtain data. + +portion_number: + description: > + Numeric value that represents the sequential number assigned to a portion of the sample. + termDef: + term: Biospecimen Portion Sequence Number + source: caDSR + cde_id: 5432711 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0" + +portion_weight: + description: > + Numeric value that represents the sample portion weight, measured in milligrams. + termDef: + term: Biospecimen Portion Weight Milligram Value + source: caDSR + cde_id: 5432593 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0" + +preservation_method: + description: > + Text term that represents the method used to preserve the sample. + termDef: + term: Tissue Sample Preservation Method Type + source: caDSR + cde_id: 5432521 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" + + +prior_malignancy: + description: > + Text term to describe the patient's history of prior cancer diagnosis and the spatial location + of any previous cancer occurrence. + termDef: + term: Prior Cancer Diagnosis Occurrence Description Text + source: caDSR + cde_id: 3382736 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0" + +prior_treatment: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +progesterone_receptor_percent_positive_ihc: + description: > + Classification to represent Progesterone Receptor Positive results expressed as a percentage + value. + termDef: + term: Progesterone Receptor Level Cell Percentage Category + source: caDSR + cde_id: 3128342 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0" + +progesterone_receptor_result_ihc: + description: > + Text term to represent the overall result of Progresterone Receptor (PR) testing. + termDef: + term: Breast Carcinoma Progesterone Receptor Status + source: caDSR + cde_id: 2957357 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0" + +progression_or_recurrence: + description: > + Yes/No/Unknown indicator to identify whether a patient has had a new tumor event + after initial treatment. + termDef: + term: New Neoplasm Event Post Initial Therapy Indicator + source: caDSR + cde_id: 3121376 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" + +project_id: # TOREVIEW + description: > + Unique ID for any specific defined piece of work that is undertaken or attempted to + meet a single requirement. + +qc_metric_state: + description: > + State classification given by FASTQC for the metric. Metric specific details about the states + are available on their website. + termDef: + term: QC Metric State + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" + +race: + description: > + An arbitrary classification of a taxonomic group that is a division of a species (HARMONIZED). It usually + arises as a consequence of geographical isolation within a species and is characterized by + shared heredity, physical attributes and behavior, and in the case of humans, by common history, + nationality, or geographic distribution. The provided values are based on the categories defined + by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (GTEx) + termDef: + term: Race Category Text + source: caDSR + cde_id: 2192199 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" + +read_length: # TOREVIEW + description: > + The length of the reads. + +read_group_name: # TOREVIEW + description: > + The name of the read group. + +relationship_age_at_diagnosis: + description: > + The age (in years) when the patient's relative was first diagnosed. + termDef: + term: Relative Diagnosis Age Value + source: caDSR + cde_id: 5300571 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0" + +relationship_to_proband: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relationship_type: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relative_with_cancer_history: + description: > + Indicator to signify whether or not an individual's biological relative has been diagnosed with + another type of cancer. + termDef: + term: Other Cancer Biological Relative History Indicator + source: caDSR + cde_id: 3901752 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0" + +residual_disease: + description: > + Text terms to describe the status of a tissue margin following surgical resection. + termDef: + term: Surgical Margin Resection Status + source: caDSR + cde_id: 2608702 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" + +RIN: + description: > + A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the + RNA sample including the presence or absence of degradation products. + termDef: + term: Biospecimen RNA Integrity Number Value + source: caDSR + cde_id: 5278775 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" + +sample_type: + description: > + Text term to describe the source of a biospecimen used for a laboratory test. + termDef: + term: Specimen Type Collection Biospecimen Type + source: caDSR + cde_id: 3111302 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" + +sample_type_id: # TOREVIEW + description: > + The accompanying sample type id for the sample type. + +section_location: # TOREVIEW + description: > + Tissue source of the slide. + +sequencing_center: # TOREVIEW + description: > + Name of the center that provided the sequence files. + +shortest_dimension: + description: > + Numeric value that represents the shortest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Short Dimension Millimeter Measurement + source: caDSR + cde_id: 5432603 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0" + +site_of_resection_or_biopsy: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000, used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The description of an anatomical region or of a body part. + Named locations of, or within, the body. A system of numbered categories for representation of + data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code + source: caDSR + cde_id: 3226281 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" + +size_selection_range: # TOREVIEW + description: > + Range of size selection. + +smoking_history: + description: > + Category describing current smoking status and smoking history as self-reported by a patient. + termDef: + term: Smoking History + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +smoking_intensity: + description: > + Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes + smoked per day x number of years smoked divided by 20 + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +source_center: # TOREVIEW + description: > + Name of the center that provided the item. + +spectrophotometer_method: + description: > + Name of the method used to determine the concentration of purified nucleic acid within a + solution. + termDef: + term: Purification Nucleic Acid Solution Concentration Determination Method Type + source: caDSR + cde_id: 3008378 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" + +spike_ins_fasta: # TOREVIEW + description: > + Name of the FASTA file that contains the spike-in sequences. + +spike_ins_concentration: # TOREVIEW + description: > + Spike in concentration. + +state: # TOREVIEW + description: > + The current state of the object. + +target_capture_kit_name: # TOREVIEW + description: > + Name of Target Capture Kit. + +target_capture_kit_vendor: # TOREVIEW + description: > + Vendor of Target Capture Kit. + +target_capture_kit_catalog_number: # TOREVIEW + description: > + Catalog of Target Capture Kit. + +target_capture_kit_version: # TOREVIEW + description: > + Version of Target Capture Kit. + +target_capture_kit_target_region: # TOREVIEW + description: > + Target Capture Kit BED file. + +therapeutic_agents: + description: > + Text identification of the individual agent(s) used as part of a prior treatment regimen. + termDef: + term: Prior Therapy Regimen Text + source: caDSR + cde_id: 2975232 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0" + +time_between_clamping_and_freezing: + description: > + Numeric representation of the elapsed time between the surgical clamping of blood supply and + freezing of the sample, measured in minutes. + termDef: + term: Tissue Sample Clamping and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432611 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0" + +time_between_excision_and_freezing: + description: > + Numeric representation of the elapsed time between the excision and freezing of the sample, + measured in minutes. + termDef: + term: Tissue Sample Excision and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432612 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0" + +tissue_or_organ_of_origin: + description: > + Text term that describes the anatomic site of the tumor or disease. + termDef: + term: Tumor Disease Anatomic Site + source: caDSR + cde_id: 3427536 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0" + +tissue_type: + description: > + Text term that represents a description of the kind of tissue collected with respect to disease + status or proximity to tumor tissue. + termDef: + term: Tissue Sample Description Type + source: caDSR + cde_id: 5432687 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" + +to_trim_adapter_sequence: # TOREVIEW + description: > + Does the user suggest adapter trimming? + +tobacco_smoking_onset_year: + description: > + The year in which the participant began smoking. + termDef: + term: Started Smoking Year + source: caDSR + cde_id: 2228604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0" + +tobacco_smoking_quit_year: + description: > + The year in which the participant quit smoking. + termDef: + term: Stopped Smoking Year + source: caDSR + cde_id: 2228610 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0" + +tobacco_smoking_status: + description: > + Category describing current smoking status and smoking history as self-reported by a + patient. + termDef: + term: Patient Smoking History Category + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +total_sequences: + description: > + A count of the total number of sequences processed. + termDef: + term: Total Sequences + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +treatment_anatomic_site: + description: > + The anatomic site or field targeted by a treatment regimen or single agent therapy. + termDef: + term: Treatment Anatomic Site + source: null + cde_id: null + cde_version: null + term_url: null + +treatment_intent_type: + description: > + Text term to identify the reason for the administration of a treatment regimen. [Manually-curated] + termDef: + term: Treatment Regimen Intent Type + source: caDSR + cde_id: 2793511 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0" + +treatment_or_therapy: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +treatment_outcome: + description: > + Text term that describes the patient¿s final outcome after the treatment was administered. + termDef: + term: Treatment Outcome Type + source: caDSR + cde_id: 5102383 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0" + +treatment_type: + description: > + Text term that describes the kind of treatment administered. + termDef: + term: Treatment Method Type + source: caDSR + cde_id: 5102381 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" + +tumor_grade: + description: > + Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation + and aggressiveness. + termDef: + term: Neoplasm Histologic Grade + source: caDSR + cde_id: 2785839 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" + +tumor_code: # TOREVIEW + description: > + Diagnostic tumor code of the tissue sample source. + +tumor_code_id: # TOREVIEW + description: > + BCR-defined id code for the tumor sample. + +tumor_descriptor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +tumor_stage: + description: > + The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether + lymph nodes contain cancer, and whether the cancer has spread from the original site to other + parts of the body. The accepted values for tumor_stage depend on the tumor site, type, and + accepted staging system. These items should accompany the tumor_stage value as associated + metadata. + termDef: + term: Tumor Stage + source: NCIt + cde_id: C16899 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" + +UUID: + description: > + A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to + be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be + different. Its relatively small size lends itself well to sorting, ordering, and hashing of all + sorts, storing in databases, simple allocation, and ease of programming in general. + termDef: + term: Universally Unique Identifier + source: NCIt + cde_id: C54100 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" + +vascular_invasion_present: + description: > + The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or + presence in a tumor specimen. + termDef: + term: Tumor Vascular Invasion Ind-3 + source: caDSR + cde_id: 64358 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0" + +vital_status: + description: > + The survival state of the person registered on the protocol. + termDef: + term: Patient Vital Status + source: caDSR + cde_id: 5 + cde_version: 5.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" + +weight: + description: > + The weight of the patient measured in lbs (HARMONIZED). + termDef: + term: Patient Weight Measurement + source: caDSR + cde_id: 651 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" + +well_number: + description: > + Numeric value that represents the the well location within a plate for the analyte or + aliquot from the sample. + termDef: + term: Biospecimen Analyte or Aliquot Plate Well Number + source: caDSR + cde_id: 5432613 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0" + +workflow_type: + description: > + Generic name for the workflow used to analyze a data set. + +year_of_birth: + description: > + Numeric value to represent the calendar year in which an individual was born. + termDef: + term: Year Birth Date Number + source: caDSR + cde_id: 2896954 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" + +year_of_diagnosis: + description: > + Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. + termDef: + term: Year of initial pathologic diagnosis + source: caDSR + cde_id: 2896960 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" + +year_of_death: + description: > + Numeric value to represent the year of the death of an individual. + termDef: + term: Year Death Number + source: caDSR + cde_id: 2897030 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" + +years_smoked: + description: > + Numeric value (or unknown) to represent the number of years a person has been smoking (HARMONIZED). If the number of years is greater than 89, see 'years_smoked_gt89'. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" + +years_smoked_gt89: + description: > + Indicate whether the numeric value to represent the number of years a person has been smoking (HARMONIZED) is greater than 89 years. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" diff --git a/tests/fixtures/synthea/.gitignore b/tests/fixtures/synthea/.gitignore new file mode 100644 index 0000000..480dcf6 --- /dev/null +++ b/tests/fixtures/synthea/.gitignore @@ -0,0 +1 @@ +raw/ diff --git a/tests/fixtures/synthea/filtered/Condition.ndjson b/tests/fixtures/synthea/filtered/Condition.ndjson new file mode 100644 index 0000000..94511e8 --- /dev/null +++ b/tests/fixtures/synthea/filtered/Condition.ndjson @@ -0,0 +1,370 @@ +{"resourceType":"Condition","id":"8b010866-9eb9-4135-1d1c-e9406a8e571f","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition"]},"clinicalStatus":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/condition-clinical","code":"resolved"}]},"verificationStatus":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/condition-ver-status","code":"confirmed"}]},"category":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/condition-category","code":"encounter-diagnosis","display":"Encounter Diagnosis"}]}],"code":{"coding":[{"system":"http://snomed.info/sct","code":"24079001","display":"Atopic dermatitis"}],"text":"Atopic 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(procedure)"},"subject":{"reference":"Patient/2878a2e6-80cc-96c0-0596-00c411d5afd7"},"encounter":{"reference":"Encounter/5f2ab988-4794-3c47-1140-8eb6efdf1c45"},"performedPeriod":{"start":"2021-10-21T10:51:26-07:00","end":"2021-10-21T11:19:52-07:00"},"location":{"reference":"Location?identifier=https://github.com/synthetichealth/synthea|2b9a3124-afdb-3959-bd52-991104897d1b","display":"PCP53949"}} diff --git a/tests/fixtures/synthea/output/gen3/_definitions.yaml b/tests/fixtures/synthea/output/gen3/_definitions.yaml new file mode 100644 index 0000000..da80111 --- /dev/null +++ b/tests/fixtures/synthea/output/gen3/_definitions.yaml @@ -0,0 +1,252 @@ +id: _definitions + +UUID: + term: + $ref: "_terms.yaml#/UUID" + type: string + pattern: "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$" + +parent_uuids: + type: array + minItems: 1 + items: + $ref: "#/UUID" + uniqueItems: true + +foreign_key_project: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: true + #Can either use 'id' which are Gen3 IDs (UUID) or 'code' + #which is the user defined ID for project + properties: + id: + $ref: "#/UUID" + code: + type: string + +to_one_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key_project" + +to_many_project: + anyOf: + - type: array + items: + $ref: "#/foreign_key_project" + minItems: 1 + - $ref: "#/foreign_key_project" + +foreign_key: + type: object + # Allow true here because we can have other unique keys defined on + # a target type + additionalProperties: True + #Can either use 'id' which are GDC IDs (UUID) or 'submitter_id' + #which are user defined IDs ("submitter IDs in the backend") + properties: + id: + $ref: "#/UUID" + submitter_id: + type: string + +to_one: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + maxItems: 1 + - $ref: "#/foreign_key" + +to_many: + anyOf: + - type: array + items: + $ref: "#/foreign_key" + minItems: 1 + - $ref: "#/foreign_key" + +datetime: + oneOf: + - type: string + format: date-time + - type: 'null' + term: + $ref: "_terms.yaml#/datetime" + +file_name: + type: string + term: + $ref: "_terms.yaml#/file_name" + +file_size: + type: integer + term: + $ref: "_terms.yaml#/file_size" + +file_format: + type: string + term: + $ref: "_terms.yaml#/file_format" + +ga4gh_drs_uri: + type: string + term: + $ref: "_terms.yaml#/ga4gh_drs_uri" + +md5sum: + type: string + term: + $ref: "_terms.yaml#/md5sum" + pattern: "^[a-f0-9]{32}$" + +object_id: + type: string + description: "The GUID of the object in the index service." + +release_state: + description: "Release state of an entity." + default: unreleased + enum: + - unreleased + - released + - redacted + +data_bundle_state: + description: "State of a data bundle." + default: submitted + enum: + - submitted + - validated + - error + - released + - suppressed + - redacted + +data_file_error_type: + term: + $ref: "_terms.yaml#/data_file_error_type" + enum: + - file_size + - file_format + - md5sum + +state: + term: + $ref: "_terms.yaml#/state" + default: validated + downloadable: + - uploaded + - md5summed + - validating + - validated + - error + - invalid + - released + public: + - live + oneOf: + - enum: #This list covers legacy data + - uploading + - uploaded + - md5summing + - md5summed + - validating + - error + - invalid + - suppressed + - redacted + - live + - enum: #This list covers all future data 1/15/16 + - validated + - submitted + - released + +file_state: + term: + $ref: "_terms.yaml#/file_state" + default: registered + enum: + - registered + - uploading + - uploaded + - validating + - validated + - submitted + - processing + - processed + - released + - error + +qc_metrics_state: + term: + $ref: "_terms.yaml#/qc_metric_state" + enum: + - FAIL + - PASS + - WARN + +project_id: + type: string + term: + $ref: "_terms.yaml#/project_id" + +data_file_properties: + $ref: "#/ubiquitous_properties" + file_name: + $ref: "#/file_name" + file_size: + $ref: "#/file_size" + file_format: + $ref: "#/file_format" + md5sum: + $ref: "#/md5sum" + object_id: + $ref: "#/object_id" + file_state: + $ref: "#/file_state" + error_type: + $ref: "#/data_file_error_type" + ga4gh_drs_uri: + $ref: "#/ga4gh_drs_uri" + +workflow_properties: + $ref: "#/ubiquitous_properties" + workflow_link: + description: "Link to Github hash for the CWL workflow used." + type: string + workflow_version: + description: "Major version for a GDC workflow." + type: string + workflow_start_datetime: + $ref: "#/datetime" + workflow_end_datetime: + $ref: "#/datetime" + +ubiquitous_properties: + type: + type: string + id: + $ref: "#/UUID" + systemAlias: node_id + submitter_id: + type: + - string + description: > + A project-specific identifier for a node. This property is the calling card/nickname/alias for + a unit of submission. It can be used in place of the UUID for identifying or recalling a node. + state: + $ref: "#/state" + project_id: + $ref: "#/project_id" + created_datetime: + $ref: "#/datetime" + updated_datetime: + $ref: "#/datetime" diff --git a/tests/fixtures/synthea/output/gen3/_settings.yaml b/tests/fixtures/synthea/output/gen3/_settings.yaml new file mode 100644 index 0000000..d7e2171 --- /dev/null +++ b/tests/fixtures/synthea/output/gen3/_settings.yaml @@ -0,0 +1,6 @@ +# Global settings for the graph + +# Is the graph case centric, that we want +# to create a link between all children to case +# to expedite case filter on nodes +enable_case_cache: false diff --git a/tests/fixtures/synthea/output/gen3/_terms.yaml b/tests/fixtures/synthea/output/gen3/_terms.yaml new file mode 100644 index 0000000..6024d85 --- /dev/null +++ b/tests/fixtures/synthea/output/gen3/_terms.yaml @@ -0,0 +1,1938 @@ +id: _terms + + + +28s_16s_ribosomal_rna_ratio: + description: > + The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA. + termDef: + term: "28s/18s Ribosomal RNA Ratio" + source: null + cde_id: null + cde_version: null + term_url: null + + + + + +a260_a280_ratio: + description: > + Numeric value that represents the sample ratio of nucleic acid absorbance at 260 nm and 280 nm, + used to determine a measure of DNA purity. + termDef: + term: Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value + source: caDSR + cde_id: 5432595 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" + +age: + description: > + Age at last visit. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Age at last visit. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +family_onset: + description: > + Typical age of onset for the family. Age is encoded as ISO8601 duration. (CMG) + termDef: + term: Typical age of onset for the family. Age is encoded as ISO8601 duration. + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +disease_omim_id: + description: > + The ID of the term from OMIM which represents a disease. (CMG) + termDef: + term: The ID of the term from OMIM which represents a disease. (CMG) + source: OMIM + cde_id: OMIM + cde_version: 1.0 + term_url: "https://www.ncbi.nlm.nih.gov/omim" + +phenotype_hpo_id: + description: > + The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + termDef: + term: The ID of the term from Human Phenotype Ontology which represents a harmonized phenotype. (CMG) + source: HPO + cde_id: HPO + cde_version: 1.0 + term_url: "https://hpo.jax.org/app/" + +adapter_name: # TOREVIEW + description: > + Name of the sequencing adapter. + +adapter_sequence: # TOREVIEW + description: > + Base sequence of the sequencing adapter. + +age_of_onset: + description: > + Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + termDef: + term: Age of onset (if affected). Otherwise age of last exam or phenotype transfer. (CMG) + source: Phenopackets + cde_id: ISO8601 + cde_version: 1.0 + term_url: "https://phenopackets-schema.readthedocs.io/en/latest/age.html#rstage" + +age_at_event_days_gt89: + description: > + Indicate whether the 'Age at the time an event occurs expressed in the number of days since birth' is greater than 32872 days (89 years). + +age_at_diagnosis: + description: > + Age at the time of diagnosis expressed in number of days since birth. If the age at diagnosis is greater than 32872 days (89 years), then see 'age_at_diagnosis_gt89'. + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +age_at_diagnosis_gt89: + description: > + Indicate whether the age at the time of diagnosis expressed in number of days since birth is greater than 32872 days (89 years). + termDef: + term: Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + +ajcc_clinical_m: + description: > + Extent of the distant metastasis for the cancer based on evidence obtained from clinical + assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage + source: caDSR + cde_id: 3440331 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0" + +ajcc_clinical_n: + description: > + Extent of the regional lymph node involvement for the cancer based on evidence obtained from + clinical assessment parameters determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage + source: caDSR + cde_id: 3440330 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0" + +ajcc_clinical_stage: + description: > + Stage group determined from clinical information on the tumor (T), regional node (N) and + metastases (M) and by grouping cases with similar prognosis for cancer. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Group Stage + source: caDSR + cde_id: 3440332 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0" + +ajcc_clinical_t: + description: > + Extent of the primary cancer based on evidence obtained from clinical assessment parameters + determined prior to treatment. + termDef: + term: Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage + source: caDSR + cde_id: 3440328 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0" + +ajcc_pathologic_m: + description: > + Code to represent the defined absence or presence of distant spread or metastases (M) to + locations via vascular channels or lymphatics beyond the regional lymph nodes, using + criteria established by the American Joint Committee on Cancer (AJCC). + termDef: + term: American Joint Committee on Cancer Metastasis Stage Code + source: caDSR + cde_id: 3045439 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0" + +ajcc_pathologic_n: + description: > + The codes that represent the stage of cancer based on the nodes present (N stage) according + to criteria based on multiple editions of the AJCC's Cancer Staging Manual. + termDef: + term: Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203106 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0" + +ajcc_pathologic_stage: + description: > + The extent of a cancer, especially whether the disease has spread from the original site to + other parts of the body based on AJCC staging criteria. + termDef: + term: Neoplasm Disease Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203222 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0" + +ajcc_pathologic_t: + description: > + Code of pathological T (primary tumor) to define the size or contiguous extension of the + primary tumor (T), using staging criteria from the American Joint Committee on Cancer + (AJCC). + termDef: + term: American Joint Committee on Cancer Tumor Stage Code + source: caDSR + cde_id: 3045435 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0" + +alcohol_history: + description: > + A response to a question that asks whether the participant has consumed at least 12 drinks of + any kind of alcoholic beverage in their lifetime. + termDef: + term: Alcohol Lifetime History Indicator + source: caDSR + cde_id: 2201918 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0" + +drink_number: + description: > + Units of drink consumed during Drink Period (DRNKPRD). (GTEx) + +aliquot_quantity: + description: > + The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +aliquot_volume: + description: > + The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Aliquot Volume + source: null + cde_id: null + cde_version: null + term_url: null + +amount: # TOREVIEW + description: > + Weight in grams or volume in mL. + +analyte_quantity: + description: > + The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Quantity + source: null + cde_id: null + cde_version: null + term_url: null + +analyte_type: + description: > + Text term that represents the kind of molecular specimen analyte. + termDef: + term: Molecular Specimen Type Text Name + source: caDSR + cde_id: 2513915 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" + +analyte_type_id: + description: > + A single letter code used to identify a type of molecular analyte. + termDef: + term: Molecular Analyte Identification Code + source: caDSR + cde_id: 5432508 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0" + +analyte_volume: + description: > + The volume in microliters (ml) of the analyte(s) derived from the analyte(s) shipped for + sequencing and characterization. + termDef: + term: Biospecimen Analyte Volume + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_b_symptoms: + description: > + Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical + record. + termDef: + term: Lymphoma B-Symptoms Medical Record Documented Indicator + source: caDSR + cde_id: 2902402 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0" + +ann_arbor_clinical_stage: + description: > + The classification of the clinically confirmed anatomic disease extent of lymphoma (Hodgkin's + and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Clinical Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_extranodal_involvement: + description: > + Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement + of an extranodal site. + termDef: + term: Lymphomatous Extranodal Site Involvement Indicator + source: caDSR + cde_id: 3364582 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0" + +ann_arbor_pathologic_stage: + description: > + The classification of the pathologically confirmed anatomic disease extent of lymphoma + (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Pathologic Stage + source: null + cde_id: null + cde_version: null + term_url: null + +ann_arbor_tumor_stage: + description: > + The classification of the anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based + on the Ann Arbor Staging System. + termDef: + term: Ann Arbor Tumor Stage + source: null + cde_id: null + cde_version: null + term_url: null + +base_caller_name: # TOREVIEW + description: > + Name of the base caller. + +base_caller_version: # TOREVIEW + description: > + Version of the base caller. + +biomarker_name: + description: > + The name of the biomarker being tested for this specimen and set of test results. + termDef: + term: Biomarker Name + source: caDSR + cde_id: 5473 + cde_version: 11.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31" + +biomarker_result: + description: > + Text term to define the results of genetic testing. + termDef: + term: Laboratory Procedure Genetic Abnormality Test Result Type + source: caDSR + cde_id: 3234680 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0" + +biomarker_test_method: + description: > + Text descriptor of a molecular analysis method used for an individual. + termDef: + term: Disease Detection Molecular Analysis Method Type + source: caDSR + cde_id: 3121575 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0" + +biospecimen_anatomic_site_id: + description: > + Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +biospecimen_anatomic_site_label: + description: > + Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + termDef: + term: Uberon Label, anatomical location as described by the Uber Anatomy Ontology (UBERON). (CMG) + source: Uberon + cde_id: Uberon + cde_version: 1.0 + term_url: "https://www.ebi.ac.uk/ols/ontologies/uberon" + +bmi: + description: > + Autocalculated field of BMI: general indicator of the body fat an individual is carrying based upon the ratio of weight to height. BMI = 703 * weight in pounds/height in inches squared. (GTEx) + termDef: + term: Body Mass Index (BMI) + source: caDSR + cde_id: 4973892 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" + +burkitt_lymphoma_clinical_variant: + description: > + Burkitt's lymphoma categorization based on clinical features that differ from other forms of the + same disease. + termDef: + term: Burkitt Lymphoma Clinical Variant Type + source: caDSR + cde_id: 3770421 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" + +cause_of_death: + description: > + Text term to identify the cause of death for a patient. + termDef: + term: Patient Death Reason + source: caDSR + cde_id: 2554674 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0" + +cea_level_preoperative: + description: > + Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. [Manually- + curated] + termDef: + term: Preoperative Carcinoembryonic Antigen Result Value + source: caDSR + cde_id: 2716510 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0" + +cigarettes_per_day: + description: > + The average number of cigarettes smoked per day. + termDef: + term: Smoking Use Average Number + source: caDSR + cde_id: 2001716 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0" + +circumferential_resection_margin: + description: > + A value in millimeters indicating the measured length between a malignant lesion of the + colon or rectum and the nearest radial (or circumferential) border of tissue removed during + cancer surgery. + termDef: + term: Colorectal Surgical Margin Circumferential Distance Measurement + source: caDSR + cde_id: 64202 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0" + +classification_of_tumor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +colon_polyps_history: + description: > + Yes/No indicator to describe if the subject had a previous history of colon polyps as noted + in the history/physical or previous endoscopic report (s). + termDef: + term: Colon Carcinoma Polyp Occurrence Indicator + source: caDSR + cde_id: 3107197 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0" + +composition: + description: > + Text term that represents the cellular composition of the sample. + termDef: + term: Biospecimen Cellular Composition Type + source: caDSR + cde_id: 5432591 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" + +concentration: + description: > + Numeric value that represents the concentration of an analyte or aliquot extracted from the + sample or sample portion, measured in milligrams per milliliter. + termDef: + term: Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value + source: caDSR + cde_id: 5432594 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" + +creation_datetime: + description: > + The datetime of portion creation encoded as seconds from epoch. + termDef: + term: Biospecimen Portion Creation Seconds Date/Time + source: caDSR + cde_id: 5432592 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0" + +current_weight: + description: > + Numeric value that represents the current weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Current Weight Milligram Value + source: caDSR + cde_id: 5432606 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" + +data_category: # TOREVIEW + description: > + Broad categorization of the contents of the data file. + +data_file_error_type: # TOREVIEW + description: > + Type of error for the data file object. + +data_format: # TOREVIEW + description: > + Format of the data files. + +data_type: # TOREVIEW + description: > + Specific content type of the data file. (CMG) + +datetime: + description: > + A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] + +days_to_birth: + description: > + Time interval from a person's date of birth to the date of initial pathologic diagnosis, + represented as a calculated negative number of days. + termDef: + term: Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0" + +days_to_collection: + description: > + Time interval from the date of biospecimen collection to the date of initial pathologic + diagnosis, represented as a calculated number of days. + termDef: + term: Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008340 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0" + +days_to_death: + description: > + Time interval from a person's date of death to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Death Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3165475 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0" + +days_to_hiv_diagnosis: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of human + immunodeficiency diagnosis, represented as a calculated number of days. + termDef: + term: Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value + source: caDSR + cde_id: 4618491 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0" + +days_to_last_follow_up: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_last_known_disease_status: + description: > + Time interval from the date of last follow up to the date of initial pathologic diagnosis, + represented as a calculated number of days. + termDef: + term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + +days_to_new_event: + description: > + Time interval from the date of new tumor event including progression, recurrence and new + primary malignacies to the date of initial pathologic diagnosis, represented as a calculated + number of days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_recurrence: + description: > + Time interval from the date of new tumor event including progression, recurrence and new primary + malignancies to the date of initial pathologic diagnosis, represented as a calculated number of + days. + termDef: + term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + +days_to_sample_procurement: + description: > + The number of days from the date the patient was diagnosed to the date of the procedure that + produced the sample. + +days_to_treatment: + description: > + Number of days from date of initial pathologic diagnosis that treatment began. + termDef: + term: Days to Treatment Start + source: null + cde_id: null + cde_version: null + term_url: null + +days_to_treatment_end: + description: > + Time interval from the date of the initial pathologic diagnosis to the date of treatment end, + represented as a calculated number of days. + termDef: + term: Treatment End Subtract First Pathologic Diagnosis Day Calculation Value + source: caDSR + cde_id: 5102431 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0" + +days_to_treatment_start: + description: > + Time interval from the date of the initial pathologic diagnosis to the start of treatment, + represented as a calculated number of days. + termDef: + term: Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value + source: caDSR + cde_id: 5102411 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0" + +diagnosis_pathologically_confirmed: + description: > + The histologic description of tissue or cells confirmed by a pathology review of frozen or + formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used + to extract analyte(s). + termDef: + term: Post-Diagnostic Pathology Review Confirmation + source: null + cde_id: null + cde_version: null + term_url: null + +dlco_ref_predictive_percent: + description: > + The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide + detected in a patient's lungs. + termDef: + term: Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value + source: caDSR + cde_id: 2180255 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0" + +encoding: + description: > + Version of ASCII encoding of quality values found in the file. + termDef: + term: Encoding + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +estrogen_receptor_percent_positive_ihc: + description: > + Classification to represent ER Positive results expressed as a percentage value. + termDef: + term: ER Level Cell Percentage Category + source: caDSR + cde_id: 3128341 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0" + +estrogen_receptor_result_ihc: + description: > + Text term to represent the overall result of Estrogen Receptor (ER) testing. + termDef: + term: Breast Carcinoma Estrogen Receptor Status + source: caDSR + cde_id: 2957359 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0" + +ethnicity: + description: > + An individual's self-described social and cultural grouping, specifically whether an individual + describes themselves as Hispanic or Latino (HARMONIZED). The provided values are based on the categories + defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (CMG, GTEx) + termDef: + term: Ethnic Group Category Text + source: caDSR + cde_id: 2192217 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" + +experiment_name: # TOREVIEW + description: > + Submitter-defined name for the experiment. + +experimental_strategy: # TOREVIEW + description: > + The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri. + +fastq_name: # TOREVIEW + description: > + Names of FASTQs. + +fev1_ref_post_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second post-bronchodilator. + termDef: + term: Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302948 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0" + +fev1_ref_pre_bronch_percent: + description: > + The percentage comparison to a normal value reference range of the volume of air that a + patient can forcibly exhale from the lungs in one second pre-bronchodilator. + termDef: + term: Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302947 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" + +fev1_fvc_post_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) post-bronchodilator. + termDef: + term: Post Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302956 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0" + +fev1_fvc_pre_bronch_percent: + description: > + Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided + by the Forced Vital Capacity (FVC) pre-bronchodilator. + termDef: + term: Pre Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302955 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0" + +figo_stage: + description: > + The extent of a cervical or endometrial cancer within the body, especially whether the + disease has spread from the original site to other parts of the body, as described by the + International Federation of Gynecology and Obstetrics (FIGO) stages. + termDef: + term: Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage + source: caDSR + cde_id: 3225684 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" + +file_format: + description: > + The format of the data file object. + +file_name: # TOREVIEW + description: > + The name (or part of a name) of a file (of any type). + +file_size: # TOREVIEW + description: > + The size of the data file (object) in bytes. + +file_state: # TOREVIEW + description: > + The current state of the data file object. + +flow_cell_barcode: # TOREVIEW + description: > + Flow Cell Barcode. + +freezing_method: + description: > + Text term that represents the method used for freezing the sample. + termDef: + term: Tissue Sample Freezing Method Type + source: caDSR + cde_id: 5432607 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" + +ga4gh_drs_uri: + description: > + DRS URI as defined by GA4GH DRS spec for pointers to file objects. + +sex: + description: > + Text designations that identify gender (HARMONIZED). Gender is described as the assemblage of properties that + distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification + of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] (CMG) + termDef: + term: Person Gender Text Type + source: caDSR + cde_id: 2200604 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" + +height: + description: > + The height of Donor in inches as reported by Donor, family/next of kin, or medical record abstraction. (GTEx) + termDef: + term: Patient Height Measurement + source: caDSR + cde_id: 649 + cde_version: 4.1 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" + +her2_erbb2_percent_positive_ihc: + description: > + Classification to represent the number of positive HER2/ERBB2 cells in a specimen or sample. + termDef: + term: HER2 ERBB Positive Finding Cell Percentage Category + source: caDSR + cde_id: 3086980 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0" + +her2_erbb2_result_fish: + description: > + the type of outcome for HER2 as determined by an in situ hybridization (ISH) assay. + termDef: + term: Laboratory Procedure HER2/neu in situ Hybridization Outcome Type + source: caDSR + cde_id: 2854089 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0" + +her2_erbb2_result_ihc: + description: > + Text term to signify the result of the medical procedure that involves testing a sample of + blood or tissue for HER2 by histochemical localization of immunoreactive substances using + labeled antibodies as reagents. + termDef: + term: Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status + source: caDSR + cde_id: 2957563 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0" + +hiv_positive: + description: > + Text term to signify whether a physician has diagnosed HIV infection in a patient. + termDef: + term: Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator + source: caDSR + cde_id: 4030799 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0" + +hpv_positive_type: + description: > + Text classification to represent the strain or type of human papillomavirus identified in an + individual. + termDef: + term: Human Papillomavirus Type + source: caDSR + cde_id: 2922649 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0" + +hpv_status: + description: > + The findings of the oncogenic HPV. + termDef: + term: Oncogenic Human Papillomavirus Result Type + source: caDSR + cde_id: 2230033 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" + +includes_spike_ins: # TOREVIEW + description: > + Spike-in included? + +initial_weight: + description: > + Numeric value that represents the initial weight of the sample, measured in milligrams. + termDef: + term: Tissue Sample Initial Weight Milligram Value + source: caDSR + cde_id: 5432605 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0" + +instrument_model: + description: > + Numeric value that represents the sample dimension that is greater than the shortest + dimension and less than the longest dimension, measured in millimeters. + termDef: + term: Tissue Sample Intermediate Dimension Millimeter Measurement + source: caDSR + cde_id: 5432604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" + +intermediate_dimension: # TOREVIEW + description: > + Intermediate dimension of the sample, in millimeters. + +is_ffpe: + description: > + Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in + paraffin (FFPE). + termDef: + term: Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator + source: caDSR + cde_id: 4170557 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" + +is_paired_end: # TOREVIEW + description: > + Are the reads paired end? + +is_proband: # TOREVIEW + description: > + Boolean value to determine if the case is the proband. + +last_known_disease_status: + description: > + Text term that describes the last known state or condition of an individual's neoplasm. + termDef: + term: Person Last Known Neoplasm Status + source: caDSR + cde_id: 5424231 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0" + +laterality: + description: > + For tumors in paired organs, designates the side on which the cancer originates. + termDef: + term: Primary Tumor Laterality + source: caDSR + cde_id: 827 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0" + +ldh_level_at_diagnosis: + description: > + The 2 decimal place numeric laboratory value measured, assigned or computed related to the + assessment of lactate dehydrogenase in a specimen. + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value + source: caDSR + cde_id: 2798766 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0" + +ldh_normal_range_upper: + description: > + The top value of the range of statistical characteristics that are supposed to represent + accepted standard, non-pathological pattern for lactate dehydrogenase (units not specified). + termDef: + term: Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value + source: caDSR + cde_id: 2597015 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" + +library_strategy: # TOREVIEW + description: > + Library strategy. + +library_selection: # TOREVIEW + description: > + Library Selection Method + +library_name: # TOREVIEW + description: > + Name of the library. + +library_preparation_kit_name: # TOREVIEW + description: > + Name of Library Preparation Kit + +library_preparation_kit_vendor: # TOREVIEW + description: > + Vendor of Library Preparation Kit + +library_preparation_kit_catalog_number: # TOREVIEW + description: > + Catalog of Library Preparation Kit + +library_preparation_kit_version: # TOREVIEW + description: > + Version of Library Preparation Kit + +library_strand: # TOREVIEW + description: > + Library stranded-ness. + +longest_dimension: + description: > + Numeric value that represents the longest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Longest Dimension Millimeter Measurement + source: caDSR + cde_id: 5432602 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0" + +lymph_nodes_positive: + description: > + The number of lymph nodes involved with disease as determined by pathologic examination. + termDef: + term: Lymph Node(s) Positive Number + source: caDSR + cde_id: 89 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0" + +lymphatic_invasion_present: + description: > + A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating + lymphatic involvement + termDef: + term: Lymphatic/Small vessel Invasion Ind + source: caDSR + cde_id: 64171 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" + +method_of_diagnosis: + description: > + The method used to initially the patient's diagnosis. + termDef: + term: Method of Diagnosis + source: null + cde_id: null + cde_version: null + term_url: null + +method_of_sample_procurement: + description: > + The method used to procure the sample used to extract analyte(s). + termDef: + term: Method of Sample Procurement + source: null + cde_id: null + cde_version: null + term_url: null + +md5sum: # TOREVIEW + description: > + The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital + fingerprint. + +microsatellite_instability_abnormal: + description: > + The yes/no indicator to signify the status of a tumor for microsatellite instability. + termDef: + term: Microsatellite Instability Occurrence Indicator + source: caDSR + cde_id: 3123142 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0" + +morphology: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000 used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The study of the structure of the cells and their + arrangement to constitute tissues and, finally, the association among these to form organs. In + pathology, the microscopic process of identifying normal and abnormal morphologic + characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A + system of numbered categories for representation of data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code + source: caDSR + cde_id: 3226275 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0" + +new_event_anatomic_site: + description: > + Text term to specify the anatomic location of the return of tumor after treatment. + termDef: + term: New Neoplasm Event Occurrence Anatomic Site + source: caDSR + cde_id: 3108271 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0" + +new_event_type: + description: > + Text term to identify a new tumor event. + termDef: + term: New Neoplasm Event Type + source: caDSR + cde_id: 3119721 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0" + +normal_tumor_genotype_snp_match: + description: > + Text term that represents whether or not the genotype of the normal tumor matches or if the data + is not available. + termDef: + term: Normal Tumor Genotype Match Indicator + source: caDSR + cde_id: 4588156 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0" + +number_proliferating_cells: + description: > + Numeric value that represents the count of proliferating cells determined during pathologic + review of the sample slide(s). + termDef: + term: Pathology Review Slide Proliferating Cell Count + source: caDSR + cde_id: 5432636 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0" + +oct_embedded: + description: > + Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound. + termDef: + term: Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator + source: caDSR + cde_id: 5432538 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" + +years_smoked: + description: > + Number of years the Donor smoked. (GTEx) + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +percent_eosinophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or + specimen. + termDef: + term: Specimen Eosinophilia Percentage Value + source: caDSR + cde_id: 2897700 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0" + +percent_gc_content: + description: > + The overall %GC of all bases in all sequences. + termDef: + term: "%GC" + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +percent_granulocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or + specimen. + termDef: + term: Specimen Granulocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897705 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0" + +percent_inflam_infiltration: + description: > + Numeric value to represent local response to cellular injury, marked by capillary dilatation, + edema and leukocyte infiltration; clinically, inflammation is manifest by reddness, heat, pain, + swelling and loss of function, with the need to heal damaged tissue. + termDef: + term: Specimen Inflammation Change Percentage Value + source: caDSR + cde_id: 2897695 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0" + +percent_lymphocyte_infiltration: + description: > + Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue + normal sample or specimen. + termDef: + term: Specimen Lymphocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897710 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0" + +percent_monocyte_infiltration: + description: > + Numeric value to represent the percentage of monocyte infiltration in a sample or specimen. + termDef: + term: Specimen Monocyte Infiltration Percentage Value + source: caDSR + cde_id: 5455535 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0" + +percent_necrosis: + description: > + Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen. + termDef: + term: Malignant Neoplasm Necrosis Percentage Value + source: caDSR + cde_id: 2841237 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0" + +percent_neutrophil_infiltration: + description: > + Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value + source: caDSR + cde_id: 2841267 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0" + +percent_normal_cells: + description: > + Numeric value to represent the percentage of normal cell content in a malignant tumor sample or + specimen. + termDef: + term: Malignant Neoplasm Normal Cell Percentage Value + source: caDSR + cde_id: 2841233 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0" + +percent_stromal_cells: + description: > + Numeric value to represent the percentage of reactive cells that are present in a malignant + tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc. + termDef: + term: Malignant Neoplasm Stromal Cell Percentage Value + source: caDSR + cde_id: 2841241 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0" + +percent_tumor_cells: + description: > + Numeric value that represents the percentage of infiltration by granulocytes in a sample. + termDef: + term: Specimen Tumor Cell Percentage Value + source: caDSR + cde_id: 5432686 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0" + +percent_tumor_nuclei: + description: > + Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen. + termDef: + term: Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value + source: caDSR + cde_id: 2841225 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0" + +perineural_invasion_present: + description: > + a yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is + present. + termDef: + term: Tumor Perineural Invasion Ind + source: caDSR + cde_id: 64181 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" + +platform: # TOREVIEW + description: > + Name of the platform used to obtain data. + +portion_number: + description: > + Numeric value that represents the sequential number assigned to a portion of the sample. + termDef: + term: Biospecimen Portion Sequence Number + source: caDSR + cde_id: 5432711 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0" + +portion_weight: + description: > + Numeric value that represents the sample portion weight, measured in milligrams. + termDef: + term: Biospecimen Portion Weight Milligram Value + source: caDSR + cde_id: 5432593 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0" + +preservation_method: + description: > + Text term that represents the method used to preserve the sample. + termDef: + term: Tissue Sample Preservation Method Type + source: caDSR + cde_id: 5432521 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" + + +prior_malignancy: + description: > + Text term to describe the patient's history of prior cancer diagnosis and the spatial location + of any previous cancer occurrence. + termDef: + term: Prior Cancer Diagnosis Occurrence Description Text + source: caDSR + cde_id: 3382736 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0" + +prior_treatment: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +progesterone_receptor_percent_positive_ihc: + description: > + Classification to represent Progesterone Receptor Positive results expressed as a percentage + value. + termDef: + term: Progesterone Receptor Level Cell Percentage Category + source: caDSR + cde_id: 3128342 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0" + +progesterone_receptor_result_ihc: + description: > + Text term to represent the overall result of Progresterone Receptor (PR) testing. + termDef: + term: Breast Carcinoma Progesterone Receptor Status + source: caDSR + cde_id: 2957357 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0" + +progression_or_recurrence: + description: > + Yes/No/Unknown indicator to identify whether a patient has had a new tumor event + after initial treatment. + termDef: + term: New Neoplasm Event Post Initial Therapy Indicator + source: caDSR + cde_id: 3121376 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" + +project_id: # TOREVIEW + description: > + Unique ID for any specific defined piece of work that is undertaken or attempted to + meet a single requirement. + +qc_metric_state: + description: > + State classification given by FASTQC for the metric. Metric specific details about the states + are available on their website. + termDef: + term: QC Metric State + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" + +race: + description: > + An arbitrary classification of a taxonomic group that is a division of a species (HARMONIZED). It usually + arises as a consequence of geographical isolation within a species and is characterized by + shared heredity, physical attributes and behavior, and in the case of humans, by common history, + nationality, or geographic distribution. The provided values are based on the categories defined + by the U.S. Office of Management and Business and used by the U.S. Census Bureau. (GTEx) + termDef: + term: Race Category Text + source: caDSR + cde_id: 2192199 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" + +read_length: # TOREVIEW + description: > + The length of the reads. + +read_group_name: # TOREVIEW + description: > + The name of the read group. + +relationship_age_at_diagnosis: + description: > + The age (in years) when the patient's relative was first diagnosed. + termDef: + term: Relative Diagnosis Age Value + source: caDSR + cde_id: 5300571 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0" + +relationship_to_proband: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relationship_type: + description: > + The subgroup that describes the state of connectedness between members of the unit of society + organized around kinship ties. + termDef: + term: Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + +relative_with_cancer_history: + description: > + Indicator to signify whether or not an individual's biological relative has been diagnosed with + another type of cancer. + termDef: + term: Other Cancer Biological Relative History Indicator + source: caDSR + cde_id: 3901752 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0" + +residual_disease: + description: > + Text terms to describe the status of a tissue margin following surgical resection. + termDef: + term: Surgical Margin Resection Status + source: caDSR + cde_id: 2608702 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" + +RIN: + description: > + A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the + RNA sample including the presence or absence of degradation products. + termDef: + term: Biospecimen RNA Integrity Number Value + source: caDSR + cde_id: 5278775 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" + +sample_type: + description: > + Text term to describe the source of a biospecimen used for a laboratory test. + termDef: + term: Specimen Type Collection Biospecimen Type + source: caDSR + cde_id: 3111302 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" + +sample_type_id: # TOREVIEW + description: > + The accompanying sample type id for the sample type. + +section_location: # TOREVIEW + description: > + Tissue source of the slide. + +sequencing_center: # TOREVIEW + description: > + Name of the center that provided the sequence files. + +shortest_dimension: + description: > + Numeric value that represents the shortest dimension of the sample, measured in millimeters. + termDef: + term: Tissue Sample Short Dimension Millimeter Measurement + source: caDSR + cde_id: 5432603 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0" + +site_of_resection_or_biopsy: + description: > + The third edition of the International Classification of Diseases for Oncology, published in + 2000, used principally in tumor and cancer registries for coding the site (topography) and the + histology (morphology) of neoplasms. The description of an anatomical region or of a body part. + Named locations of, or within, the body. A system of numbered categories for representation of + data. + termDef: + term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code + source: caDSR + cde_id: 3226281 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" + +size_selection_range: # TOREVIEW + description: > + Range of size selection. + +smoking_history: + description: > + Category describing current smoking status and smoking history as self-reported by a patient. + termDef: + term: Smoking History + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +smoking_intensity: + description: > + Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes + smoked per day x number of years smoked divided by 20 + termDef: + term: Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +source_center: # TOREVIEW + description: > + Name of the center that provided the item. + +spectrophotometer_method: + description: > + Name of the method used to determine the concentration of purified nucleic acid within a + solution. + termDef: + term: Purification Nucleic Acid Solution Concentration Determination Method Type + source: caDSR + cde_id: 3008378 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" + +spike_ins_fasta: # TOREVIEW + description: > + Name of the FASTA file that contains the spike-in sequences. + +spike_ins_concentration: # TOREVIEW + description: > + Spike in concentration. + +state: # TOREVIEW + description: > + The current state of the object. + +target_capture_kit_name: # TOREVIEW + description: > + Name of Target Capture Kit. + +target_capture_kit_vendor: # TOREVIEW + description: > + Vendor of Target Capture Kit. + +target_capture_kit_catalog_number: # TOREVIEW + description: > + Catalog of Target Capture Kit. + +target_capture_kit_version: # TOREVIEW + description: > + Version of Target Capture Kit. + +target_capture_kit_target_region: # TOREVIEW + description: > + Target Capture Kit BED file. + +therapeutic_agents: + description: > + Text identification of the individual agent(s) used as part of a prior treatment regimen. + termDef: + term: Prior Therapy Regimen Text + source: caDSR + cde_id: 2975232 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0" + +time_between_clamping_and_freezing: + description: > + Numeric representation of the elapsed time between the surgical clamping of blood supply and + freezing of the sample, measured in minutes. + termDef: + term: Tissue Sample Clamping and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432611 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0" + +time_between_excision_and_freezing: + description: > + Numeric representation of the elapsed time between the excision and freezing of the sample, + measured in minutes. + termDef: + term: Tissue Sample Excision and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432612 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0" + +tissue_or_organ_of_origin: + description: > + Text term that describes the anatomic site of the tumor or disease. + termDef: + term: Tumor Disease Anatomic Site + source: caDSR + cde_id: 3427536 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0" + +tissue_type: + description: > + Text term that represents a description of the kind of tissue collected with respect to disease + status or proximity to tumor tissue. + termDef: + term: Tissue Sample Description Type + source: caDSR + cde_id: 5432687 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" + +to_trim_adapter_sequence: # TOREVIEW + description: > + Does the user suggest adapter trimming? + +tobacco_smoking_onset_year: + description: > + The year in which the participant began smoking. + termDef: + term: Started Smoking Year + source: caDSR + cde_id: 2228604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0" + +tobacco_smoking_quit_year: + description: > + The year in which the participant quit smoking. + termDef: + term: Stopped Smoking Year + source: caDSR + cde_id: 2228610 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0" + +tobacco_smoking_status: + description: > + Category describing current smoking status and smoking history as self-reported by a + patient. + termDef: + term: Patient Smoking History Category + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + +total_sequences: + description: > + A count of the total number of sequences processed. + termDef: + term: Total Sequences + source: FastQC + cde_id: null + cde_version: null + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + +treatment_anatomic_site: + description: > + The anatomic site or field targeted by a treatment regimen or single agent therapy. + termDef: + term: Treatment Anatomic Site + source: null + cde_id: null + cde_version: null + term_url: null + +treatment_intent_type: + description: > + Text term to identify the reason for the administration of a treatment regimen. [Manually-curated] + termDef: + term: Treatment Regimen Intent Type + source: caDSR + cde_id: 2793511 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0" + +treatment_or_therapy: + description: > + A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents + received before the body specimen was collected. + termDef: + term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + +treatment_outcome: + description: > + Text term that describes the patient¿s final outcome after the treatment was administered. + termDef: + term: Treatment Outcome Type + source: caDSR + cde_id: 5102383 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0" + +treatment_type: + description: > + Text term that describes the kind of treatment administered. + termDef: + term: Treatment Method Type + source: caDSR + cde_id: 5102381 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" + +tumor_grade: + description: > + Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation + and aggressiveness. + termDef: + term: Neoplasm Histologic Grade + source: caDSR + cde_id: 2785839 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" + +tumor_code: # TOREVIEW + description: > + Diagnostic tumor code of the tissue sample source. + +tumor_code_id: # TOREVIEW + description: > + BCR-defined id code for the tumor sample. + +tumor_descriptor: + description: > + Text that describes the kind of disease present in the tumor specimen as related to a specific + timepoint. + termDef: + term: Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + +tumor_stage: + description: > + The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether + lymph nodes contain cancer, and whether the cancer has spread from the original site to other + parts of the body. The accepted values for tumor_stage depend on the tumor site, type, and + accepted staging system. These items should accompany the tumor_stage value as associated + metadata. + termDef: + term: Tumor Stage + source: NCIt + cde_id: C16899 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" + +UUID: + description: > + A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to + be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be + different. Its relatively small size lends itself well to sorting, ordering, and hashing of all + sorts, storing in databases, simple allocation, and ease of programming in general. + termDef: + term: Universally Unique Identifier + source: NCIt + cde_id: C54100 + cde_version: null + term_url: "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" + +vascular_invasion_present: + description: > + The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or + presence in a tumor specimen. + termDef: + term: Tumor Vascular Invasion Ind-3 + source: caDSR + cde_id: 64358 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0" + +vital_status: + description: > + The survival state of the person registered on the protocol. + termDef: + term: Patient Vital Status + source: caDSR + cde_id: 5 + cde_version: 5.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" + +weight: + description: > + The weight of the patient measured in lbs (HARMONIZED). + termDef: + term: Patient Weight Measurement + source: caDSR + cde_id: 651 + cde_version: 4.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" + +well_number: + description: > + Numeric value that represents the the well location within a plate for the analyte or + aliquot from the sample. + termDef: + term: Biospecimen Analyte or Aliquot Plate Well Number + source: caDSR + cde_id: 5432613 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0" + +workflow_type: + description: > + Generic name for the workflow used to analyze a data set. + +year_of_birth: + description: > + Numeric value to represent the calendar year in which an individual was born. + termDef: + term: Year Birth Date Number + source: caDSR + cde_id: 2896954 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" + +year_of_diagnosis: + description: > + Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. + termDef: + term: Year of initial pathologic diagnosis + source: caDSR + cde_id: 2896960 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" + +year_of_death: + description: > + Numeric value to represent the year of the death of an individual. + termDef: + term: Year Death Number + source: caDSR + cde_id: 2897030 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" + +years_smoked: + description: > + Numeric value (or unknown) to represent the number of years a person has been smoking (HARMONIZED). If the number of years is greater than 89, see 'years_smoked_gt89'. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" + +years_smoked_gt89: + description: > + Indicate whether the numeric value to represent the number of years a person has been smoking (HARMONIZED) is greater than 89 years. + termDef: + term: Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0"