diff --git a/fsh-generated/resources/CodeSystem-component-elements.json b/fsh-generated/resources/CodeSystem-component-elements.json new file mode 100644 index 000000000..bb80c3f3a --- /dev/null +++ b/fsh-generated/resources/CodeSystem-component-elements.json @@ -0,0 +1,29 @@ +{ + "resourceType": "CodeSystem", + "status": "draft", + "content": "complete", + "name": "ComponentElements", + "id": "component-elements", + "title": "Elements of Component", + "description": "Slicing for elements of component", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/component-elements", + "concept": [ + { + "code": "ageAtOnset", + "display": "Age at Onset" + }, + { + "code": "ageAtResolution", + "display": "Age at Resolution" + }, + { + "code": "otherModifiers", + "display": "Other Modifiers" + }, + { + "code": "stage", + "display": "Stage" + } + ], + "count": 4 +} diff --git a/fsh-generated/resources/CodeSystem-condition-assertion.json b/fsh-generated/resources/CodeSystem-condition-assertion.json new file mode 100644 index 000000000..64a221321 --- /dev/null +++ b/fsh-generated/resources/CodeSystem-condition-assertion.json @@ -0,0 +1,27 @@ +{ + "resourceType": "CodeSystem", + "status": "draft", + "content": "complete", + "name": "ConditionAssertion", + "id": "condition-assertion", + "title": "Assertion of Condition Codes", + "description": "Code System for assertion of condition presence", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-assertion", + "concept": [ + { + "code": "Present", + "display": "Present" + }, + { + "code": "Absent", + "display": "Absent" + }, + { + "code": "Unknown", + "display": "Unknown" + } + ], + "experimental": false, + "caseSensitive": true, + "count": 3 +} diff --git a/fsh-generated/resources/CodeSystem-condition-type.json b/fsh-generated/resources/CodeSystem-condition-type.json new file mode 100644 index 000000000..87fca6604 --- /dev/null +++ b/fsh-generated/resources/CodeSystem-condition-type.json @@ -0,0 +1,39 @@ +{ + "resourceType": "CodeSystem", + "status": "draft", + "content": "complete", + "name": "ConditionType", + "id": "condition-type", + "title": "Type of Condition", + "description": "Code System for type of condition", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type", + "concept": [ + { + "code": "Phenotypic-Feature", + "display": "Phenotypic Feature" + }, + { + "code": "Disease", + "display": "Disease" + }, + { + "code": "Comorbidity", + "display": "Comorbidity" + }, + { + "code": "Histology", + "display": "Histology" + }, + { + "code": "Clinical-Finding", + "display": "Clinical Finding" + }, + { + "code": "EHR-Condition-Code", + "display": "EHR Condition Code" + } + ], + "experimental": false, + "caseSensitive": true, + "count": 6 +} diff --git a/fsh-generated/resources/Consent-gregor-gru-consent.json b/fsh-generated/resources/Consent-gregor-gru-consent.json new file mode 100644 index 000000000..a13f252fd --- /dev/null +++ b/fsh-generated/resources/Consent-gregor-gru-consent.json @@ -0,0 +1,64 @@ +{ + "resourceType": "Consent", + "id": "gregor-gru-consent", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + ] + }, + "category": [ + { + "coding": [ + { + "code": "research", + "system": "http://terminology.hl7.org/CodeSystem/consentcategorycodes", + "display": "Research Information Access" + } + ] + } + ], + "provision": { + "purpose": [ + { + "code": "GRU", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code", + "display": "General Research Use" + } + ], + "type": "permit" + }, + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description", + "valueMarkdown": "Use of the data is limited only by the terms of the model Data Use Certification." + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-type", + "valueCodeableConcept": { + "coding": [ + { + "code": "controlled", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type" + } + ] + } + } + ], + "status": "draft", + "scope": { + "coding": [ + { + "code": "research", + "system": "http://terminology.hl7.org/CodeSystem/consentscope" + } + ] + }, + "policyRule": { + "coding": [ + { + "code": "cric", + "system": "http://terminology.hl7.org/CodeSystem/consentpolicycodes" + } + ] + } +} diff --git a/fsh-generated/resources/DocumentReference-GF-6BAD9S7D.json b/fsh-generated/resources/DocumentReference-GF-6BAD9S7D.json new file mode 100644 index 000000000..7190ff549 --- /dev/null +++ b/fsh-generated/resources/DocumentReference-GF-6BAD9S7D.json @@ -0,0 +1,81 @@ +{ + "resourceType": "DocumentReference", + "id": "GF-6BAD9S7D", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file" + ] + }, + "identifier": [ + { + "value": "GF-6BAD9S7D" + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/content-version", + "valueString": "V1" + }, + { + "valueCodeableConcept": { + "coding": [ + { + "code": "format_3016", + "system": "http://edamontology.org", + "display": "VCF" + } + ] + }, + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-format" + }, + { + "valueQuantity": { + "value": 1044770380, + "unit": "bytes" + }, + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-size" + }, + { + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-value", + "valueString": "8f107912d862cf91fbfb77bf9c1bab36-4" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-type", + "valueCode": "etag" + } + ], + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-extension" + } + ], + "content": [ + { + "attachment": { + "url": "s3://kf-strides-study-us-east-1-prd-sd-54g4wg4r/harmonized-data/family-variants/155bb529-2e7b-474f-ba24-cd0656d5f3d0.CGP.filtered.deNovo.vep.vcf.gz" + }, + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/location-access", + "valueReference": { + "reference": "Consent/kf-gru-dac-consent" + } + } + ] + } + ], + "subject": { + "reference": "Patient/PT-006SP660" + }, + "description": "Annotated Variant Call", + "type": { + "coding": [ + { + "code": "operation_3227", + "system": "http://edamontology.org", + "display": "Variant calling" + } + ] + }, + "status": "current" +} diff --git a/fsh-generated/resources/DocumentReference-GSS123456-01-010-SG-2.json b/fsh-generated/resources/DocumentReference-GSS123456-01-010-SG-2.json new file mode 100644 index 000000000..0fb402117 --- /dev/null +++ b/fsh-generated/resources/DocumentReference-GSS123456-01-010-SG-2.json @@ -0,0 +1,81 @@ +{ + "resourceType": "DocumentReference", + "id": "GSS123456-01-010-SG-2", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file" + ] + }, + "identifier": [ + { + "value": "GSS123456-01-010-SG-2" + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/content-version", + "valueString": "V1" + }, + { + "valueCodeableConcept": { + "coding": [ + { + "code": "format_2572", + "system": "http://edamontology.org", + "display": "BAM" + } + ] + }, + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-format" + }, + { + "valueQuantity": { + "value": 1044770380, + "unit": "bytes" + }, + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-size" + }, + { + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-value", + "valueString": "9c2460c4647fdc57261f040042863fa0" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-type", + "valueCode": "md5" + } + ], + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-extension" + } + ], + "content": [ + { + "attachment": { + "url": "gs://fc-secure-a1f0e28d-c9d9-43bb-b4ba-5e0h81784fb1/GSS123456/SR_GS/GSS123456.bam" + }, + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/location-access", + "valueReference": { + "reference": "Consent/kf-gru-dac-consent" + } + } + ] + } + ], + "subject": { + "reference": "Patient/GSS123456" + }, + "description": "Aligned DNA short read", + "type": { + "coding": [ + { + "code": "operation_3198", + "system": "http://edamontology.org", + "display": "Read mapping" + } + ] + }, + "status": "current" +} diff --git a/fsh-generated/resources/Group-gregor-research-study-participants.json b/fsh-generated/resources/Group-gregor-research-study-participants.json new file mode 100644 index 000000000..ab93925a2 --- /dev/null +++ b/fsh-generated/resources/Group-gregor-research-study-participants.json @@ -0,0 +1,19 @@ +{ + "resourceType": "Group", + "id": "gregor-research-study-participants", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" + ] + }, + "identifier": [ + { + "system": "https://anvil.terra.bio/", + "value": "GREGoR Participants" + } + ], + "type": "person", + "actual": true, + "name": "Participants from the GREGoR research study GSS U08 GRU", + "quantity": 555 +} diff --git a/fsh-generated/resources/Group-gregor-study-family.json b/fsh-generated/resources/Group-gregor-study-family.json new file mode 100644 index 000000000..2b9e23798 --- /dev/null +++ b/fsh-generated/resources/Group-gregor-study-family.json @@ -0,0 +1,71 @@ +{ + "resourceType": "Group", + "id": "gregor-study-family", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-study-family" + ] + }, + "identifier": [ + { + "system": "https://anvil.terra.bio/", + "value": "GSS5555" + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/family-type", + "valueCodeableConcept": { + "coding": [ + { + "code": "Duo", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/ncpi-family-types", + "display": "Duo" + } + ] + } + } + ], + "member": [ + { + "entity": { + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/family-role", + "valueCodeableConcept": { + "coding": [ + { + "code": "CHILD", + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "display": "child" + } + ] + } + } + ], + "reference": "Patient/GSS123456" + } + }, + { + "entity": { + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/family-role", + "valueCodeableConcept": { + "coding": [ + { + "code": "MTH", + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "display": "mother" + } + ] + } + } + ], + "reference": "Patient/GSS654321" + } + } + ], + "type": "person", + "actual": true +} diff --git a/fsh-generated/resources/Observation-GSS123456-condition.json b/fsh-generated/resources/Observation-GSS123456-condition.json new file mode 100644 index 000000000..4b5fdef9b --- /dev/null +++ b/fsh-generated/resources/Observation-GSS123456-condition.json @@ -0,0 +1,85 @@ +{ + "resourceType": "Observation", + "id": "GSS123456-condition", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-condition" + ] + }, + "code": { + "coding": [ + { + "code": "HP:0006951", + "system": "http://human-phenotype-ontology.org" + } + ], + "text": "retrocerebellar cyst" + }, + "category": [ + { + "coding": [ + { + "code": "Disease", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type" + } + ] + } + ], + "component": [ + { + "code": { + "coding": [ + { + "code": "otherModifiers" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "ageAtOnset" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "HP:0011463", + "system": "http://human-phenotype-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "otherModifiers" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "HP:0012832", + "system": "http://human-phenotype-ontology.org" + } + ] + } + } + ], + "status": "final", + "subject": { + "reference": "Patient/GSS123456" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "Present", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-assertion" + } + ] + } +} diff --git a/fsh-generated/resources/Observation-PT-006SP660-condition.json b/fsh-generated/resources/Observation-PT-006SP660-condition.json new file mode 100644 index 000000000..3e4d8f69b --- /dev/null +++ b/fsh-generated/resources/Observation-PT-006SP660-condition.json @@ -0,0 +1,72 @@ +{ + "resourceType": "Observation", + "id": "PT-006SP660-condition", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-condition" + ] + }, + "code": { + "coding": [ + { + "code": "MONDO:0002203", + "system": "http://purl.obolibrary.org/obo/mondo.owl" + } + ], + "text": "ventricular ectopy" + }, + "category": [ + { + "coding": [ + { + "code": "Disease", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type" + } + ] + } + ], + "status": "final", + "subject": { + "reference": "Patient/PT-006SP660" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "Present", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-assertion" + } + ] + }, + "_effectiveDateTime": { + "extension": [ + { + "extension": [ + { + "url": "target", + "valueReference": { + "reference": "Patient/PT-006SP660" + } + }, + { + "url": "targetPath", + "valueString": "None" + }, + { + "url": "relationship", + "valueCode": "after" + }, + { + "valueDuration": { + "value": 4931, + "code": "days", + "system": "http://unitsofmeasure.org", + "unit": "d" + }, + "url": "offset" + } + ], + "url": "http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime" + } + ] + } +} diff --git a/fsh-generated/resources/Observation-gregor-example-metadata.json b/fsh-generated/resources/Observation-gregor-example-metadata.json new file mode 100644 index 000000000..54cbaefad --- /dev/null +++ b/fsh-generated/resources/Observation-gregor-example-metadata.json @@ -0,0 +1,178 @@ +{ + "resourceType": "Observation", + "id": "gregor-example-metadata", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram" + ] + }, + "focus": [ + { + "reference": "Patient/GSS123456" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "code": "AssayStrategy" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "WGS" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "PlatformInstrument" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "IlluminaHiSeq2000" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "LibraryPrep" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "polyA" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "LibrarySelection" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "PolyTEnrichment" + } + ] + } + }, + { + "valueCodeableConcept": { + "text": "Not Applicable" + }, + "code": { + "coding": [ + { + "code": "TargetRegion" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "Strandedness" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "stranded" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "ReferenceGenome" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "GRCh38" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "IsPairedEnd" + } + ] + }, + "valueBoolean": false + }, + { + "code": { + "coding": [ + { + "code": "WorkflowTool" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "bammem" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "WorkflowType" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "alignment" + } + ] + } + } + ], + "status": "final", + "code": { + "coding": [ + { + "code": "format_2572", + "system": "http://edamontology.org" + } + ] + }, + "specimen": { + "reference": "Specimen/GSS123456-01-010" + } +} diff --git a/fsh-generated/resources/Observation-gregor-family-relationship-mother.json b/fsh-generated/resources/Observation-gregor-family-relationship-mother.json new file mode 100644 index 000000000..80cd19997 --- /dev/null +++ b/fsh-generated/resources/Observation-gregor-family-relationship-mother.json @@ -0,0 +1,27 @@ +{ + "resourceType": "Observation", + "id": "gregor-family-relationship-mother", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-family-relationship" + ] + }, + "focus": [ + { + "reference": "Patient/GSS654321" + } + ], + "subject": { + "reference": "Patient/GSS123456" + }, + "code": { + "coding": [ + { + "code": "CHILD", + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "display": "child" + } + ] + }, + "status": "registered" +} diff --git a/fsh-generated/resources/Patient-GSS123456.json b/fsh-generated/resources/Patient-GSS123456.json new file mode 100644 index 000000000..34f9e3a29 --- /dev/null +++ b/fsh-generated/resources/Patient-GSS123456.json @@ -0,0 +1,59 @@ +{ + "resourceType": "Patient", + "id": "GSS123456", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + ] + }, + "identifier": [ + { + "system": "https://anvil.terra.bio/", + "value": "GSS123456" + } + ], + "extension": [ + { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", + "valueCode": "M" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "code": "2106-3", + "system": "urn:oid:2.16.840.1.113883.6.238", + "display": "White" + } + }, + { + "url": "text", + "valueString": "White" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "code": "2186-5", + "system": "urn:oid:2.16.840.1.113883.6.238", + "display": "Not Hispanic or Latino" + } + }, + { + "url": "text", + "valueString": "Not Hispanic or Latino" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-population", + "valueString": "English|Scottish" + } + ] +} diff --git a/fsh-generated/resources/Patient-GSS654321.json b/fsh-generated/resources/Patient-GSS654321.json new file mode 100644 index 000000000..170a89aba --- /dev/null +++ b/fsh-generated/resources/Patient-GSS654321.json @@ -0,0 +1,15 @@ +{ + "resourceType": "Patient", + "id": "GSS654321", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + ] + }, + "identifier": [ + { + "system": "https://anvil.terra.bio/", + "value": "GSS654321" + } + ] +} diff --git a/fsh-generated/resources/Patient-PT-006SP660.json b/fsh-generated/resources/Patient-PT-006SP660.json new file mode 100644 index 000000000..5122acd9a --- /dev/null +++ b/fsh-generated/resources/Patient-PT-006SP660.json @@ -0,0 +1,75 @@ +{ + "resourceType": "Patient", + "id": "PT-006SP660", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + ] + }, + "identifier": [ + { + "system": "https://cbtn.org/", + "value": "C21156" + }, + { + "system": "https://data.kidsfirstdrc.org", + "value": "PT-006SP660" + } + ], + "extension": [ + { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", + "valueCode": "F" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "code": "2106-3", + "system": "urn:oid:2.16.840.1.113883.6.238", + "display": "White" + } + }, + { + "url": "text", + "valueString": "White" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "code": "2186-5", + "system": "urn:oid:2.16.840.1.113883.6.238", + "display": "Not Hispanic or Latino" + } + }, + { + "url": "text", + "valueString": "Not Hispanic or Latino" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-date-of-birth-method", + "valueCoding": { + "code": "year-only", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method" + } + }, + { + "valueQuantity": { + "value": 6314, + "unit": "days", + "system": "http://unitsofmeasure.org", + "code": "d" + }, + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-age-at-last-vital-status" + } + ] +} diff --git a/fsh-generated/resources/Patient-PT-006SP675.json b/fsh-generated/resources/Patient-PT-006SP675.json new file mode 100644 index 000000000..4e3e586b6 --- /dev/null +++ b/fsh-generated/resources/Patient-PT-006SP675.json @@ -0,0 +1,91 @@ +{ + "resourceType": "Patient", + "id": "PT-006SP675", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + ] + }, + "identifier": [ + { + "system": "http://chdgenes.org/", + "value": "20757" + }, + { + "system": "http://chdgenes.org/", + "value": "PT_005B7CZ4" + } + ], + "extension": [ + { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", + "valueCode": "F" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "code": "2106-3", + "system": "urn:oid:2.16.840.1.113883.6.238", + "display": "White" + } + }, + { + "url": "text", + "valueString": "White" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race" + }, + { + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "code": "2135-2", + "system": "urn:oid:2.16.840.1.113883.6.238", + "display": "Hispanic or Latino" + } + }, + { + "url": "text", + "valueString": "Hispanic or Latino" + } + ], + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity" + } + ], + "_birthDate": { + "extension": [ + { + "extension": [ + { + "url": "target", + "valueReference": { + "reference": "Patient/PT-006SP675" + } + }, + { + "url": "targetPath", + "valueString": "birthDate" + }, + { + "url": "relationship", + "valueCode": "after" + }, + { + "valueDuration": { + "value": 2006, + "code": "days", + "system": "http://unitsofmeasure.org", + "unit": "d" + }, + "url": "offset" + } + ], + "url": "http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime" + } + ] + } +} diff --git a/fsh-generated/resources/Person-gregor-example-person.json b/fsh-generated/resources/Person-gregor-example-person.json new file mode 100644 index 000000000..abb41ae53 --- /dev/null +++ b/fsh-generated/resources/Person-gregor-example-person.json @@ -0,0 +1,22 @@ +{ + "resourceType": "Person", + "id": "gregor-example-person", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" + ] + }, + "identifier": [ + { + "system": "https://anvil.terra.bio", + "value": "PS_000" + } + ], + "link": [ + { + "target": { + "reference": "Patient/GSS123456" + } + } + ] +} diff --git a/fsh-generated/resources/Person-pcgc-example-person.json b/fsh-generated/resources/Person-pcgc-example-person.json new file mode 100644 index 000000000..cbcda4e4f --- /dev/null +++ b/fsh-generated/resources/Person-pcgc-example-person.json @@ -0,0 +1,22 @@ +{ + "resourceType": "Person", + "id": "pcgc-example-person", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" + ] + }, + "identifier": [ + { + "system": "http://chdgenes.org/", + "value": "PS_123" + } + ], + "link": [ + { + "target": { + "reference": "Patient/PT-006SP675" + } + } + ] +} diff --git a/fsh-generated/resources/ResearchStudy-research-study-gregor.json b/fsh-generated/resources/ResearchStudy-research-study-gregor.json new file mode 100644 index 000000000..4ecb02192 --- /dev/null +++ b/fsh-generated/resources/ResearchStudy-research-study-gregor.json @@ -0,0 +1,15 @@ +{ + "resourceType": "ResearchStudy", + "id": "research-study-gregor", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-study" + ] + }, + "identifier": [ + { + "value": "AnVIL_GREGoR_GSS_U08_GRU" + } + ], + "status": "completed" +} diff --git a/fsh-generated/resources/ResearchSubject-gregor-example-participantstudy.json b/fsh-generated/resources/ResearchSubject-gregor-example-participantstudy.json new file mode 100644 index 000000000..eb87dcf37 --- /dev/null +++ b/fsh-generated/resources/ResearchSubject-gregor-example-participantstudy.json @@ -0,0 +1,19 @@ +{ + "resourceType": "ResearchSubject", + "id": "gregor-example-participantstudy", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" + ] + }, + "individual": { + "reference": "Patient/GSS123456" + }, + "study": { + "reference": "ResearchStudy/research-study-gregor" + }, + "status": "candidate", + "consent": { + "reference": "Consent/gregor-gru-consent" + } +} diff --git a/fsh-generated/resources/Specimen-GSS123456-01-010.json b/fsh-generated/resources/Specimen-GSS123456-01-010.json new file mode 100644 index 000000000..35b4e5165 --- /dev/null +++ b/fsh-generated/resources/Specimen-GSS123456-01-010.json @@ -0,0 +1,25 @@ +{ + "resourceType": "Specimen", + "id": "GSS123456-01-010", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-collected-sample" + ] + }, + "identifier": [ + { + "value": "GSS123456-s1" + } + ], + "type": { + "text": "DNA" + }, + "collection": { + "method": { + "text": "DNA" + } + }, + "subject": { + "reference": "Patient/GSS123456" + } +} diff --git a/fsh-generated/resources/StructureDefinition-age-at-assertion.json b/fsh-generated/resources/StructureDefinition-age-at-assertion.json new file mode 100644 index 000000000..aee18c495 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-age-at-assertion.json @@ -0,0 +1,51 @@ +{ + "resourceType": "StructureDefinition", + "id": "age-at-assertion", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/age-at-assertion", + "name": "AgeAtAssertion", + "title": "Age at Assertion", + "status": "draft", + "description": "Age at Assertion Extension", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "effectiveDateTime" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Age at Assertion", + "definition": "Age at Assertion Extension" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/age-at-assertion" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "short": "Indicate age via relative date time extension or official date of when condition was asserted.", + "type": [ + { + "code": "Quantity" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-condition-laterality.json b/fsh-generated/resources/StructureDefinition-condition-laterality.json new file mode 100644 index 000000000..497b1eef8 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-condition-laterality.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "condition-laterality", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/condition-laterality", + "name": "ConditionLaterality", + "title": "Laterality Information", + "status": "draft", + "description": "Laterality Information", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Observation" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Laterality Information", + "definition": "Laterality Information" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/condition-laterality" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "code" + } + ], + "binding": { + "strength": "required", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-laterality-vs" + } + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-condition-location.json b/fsh-generated/resources/StructureDefinition-condition-location.json new file mode 100644 index 000000000..c66a690f8 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-condition-location.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "condition-location", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/condition-location", + "name": "ConditionLocation", + "title": "Location Information", + "status": "draft", + "description": "Location Information", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Observation.bodySite" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Location Information", + "definition": "Location Information" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/condition-location" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "code" + } + ], + "binding": { + "strength": "required", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-location-vs" + } + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-condition.json b/fsh-generated/resources/StructureDefinition-ncpi-condition.json new file mode 100644 index 000000000..003b44ac6 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-condition.json @@ -0,0 +1,306 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-condition", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-condition", + "version": "0.0.1", + "name": "NcpiCondition", + "title": "NCPI Conditon", + "status": "draft", + "description": "Information about a condition related to a research participant", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Observation", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Observation.extension", + "path": "Observation.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Observation.extension:condition-location", + "path": "Observation.extension", + "sliceName": "condition-location", + "short": "Any location qualifiers", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/condition-location" + ] + } + ] + }, + { + "id": "Observation.extension:condition-laterality", + "path": "Observation.extension", + "sliceName": "condition-laterality", + "short": "Laterality information for the condition site", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/condition-laterality" + ] + } + ] + }, + { + "id": "Observation.extension:condition-asserter", + "path": "Observation.extension", + "sliceName": "condition-asserter", + "short": "Who recorded this assertion about the Participant? This can support understanding the differences between self-report, doctor, trained research staff.", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/condition-asserter" + ] + } + ] + }, + { + "id": "Observation.category", + "path": "Observation.category", + "short": "Does this condition represent a specific \"type\" of condition, such as \"Phenotypic Feature\" vs \"Disease\" in a rare disease setting." + }, + { + "id": "Observation.code.coding", + "path": "Observation.code.coding", + "short": "The condition, disease, phenotypic feature, etc that this participant may have." + }, + { + "id": "Observation.code.text", + "path": "Observation.code.text", + "short": "Detailed description / free text about this condition." + }, + { + "id": "Observation.subject", + "path": "Observation.subject", + "short": "The participant we are describing", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + ] + } + ] + }, + { + "id": "Observation.effective[x]", + "path": "Observation.effective[x]", + "short": "The date or age at which this condition is being asserted. Could be expressed with a term, an age, or an age range. (for ages use http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime)", + "type": [ + { + "code": "dateTime" + } + ] + }, + { + "id": "Observation.value[x]", + "path": "Observation.value[x]", + "slicing": { + "discriminator": [ + { + "type": "type", + "path": "$this" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Observation.value[x]:valueCodeableConcept", + "path": "Observation.value[x]", + "sliceName": "valueCodeableConcept", + "short": "Does the participant have this condition?", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ], + "binding": { + "strength": "required", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-assertion-vs" + } + }, + { + "id": "Observation.bodySite", + "path": "Observation.bodySite", + "short": "Location information, such as site and/or laterality, of the condition. Multiple values should be interpreted cumulatively, so complex location information, such as \"right lung\" and \"left kidney\" may require multiple condition rows." + }, + { + "id": "Observation.method", + "path": "Observation.method", + "short": "Where or how was this this assertion about the Participant recorded? This can support understanding the differences between surveys, automated EHR extraction, manual chart abstraction, etc." + }, + { + "id": "Observation.component", + "path": "Observation.component", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "code" + } + ], + "rules": "open", + "description": "Slicing logic for observation component", + "ordered": false + } + }, + { + "id": "Observation.component:ageAtOnset", + "path": "Observation.component", + "sliceName": "ageAtOnset", + "short": "The age of onset for this condition. Could be expressed with a term, an age, or an age range.", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:ageAtOnset.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "ageAtOnset" + } + ] + } + }, + { + "id": "Observation.component:ageAtOnset.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "Quantity" + }, + { + "code": "CodeableConcept" + }, + { + "code": "Range" + }, + { + "code": "dateTime" + } + ] + }, + { + "id": "Observation.component:ageAtResolution", + "path": "Observation.component", + "sliceName": "ageAtResolution", + "short": "The age at which this condition was resolved, abated, or cured. Should be left empty in cases of current active status. Could be expressed with a term, an age, or an age range.", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:ageAtResolution.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "ageAtResolution" + } + ] + } + }, + { + "id": "Observation.component:ageAtResolution.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "Quantity" + }, + { + "code": "CodeableConcept" + }, + { + "code": "Range" + }, + { + "code": "dateTime" + } + ] + }, + { + "id": "Observation.component:otherModifiers", + "path": "Observation.component", + "sliceName": "otherModifiers", + "short": "Any additional modifiers for this condition, such as severity.", + "min": 0, + "max": "*" + }, + { + "id": "Observation.component:otherModifiers.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "otherModifiers" + } + ] + } + }, + { + "id": "Observation.component:otherModifiers.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:stage", + "path": "Observation.component", + "sliceName": "stage", + "short": "Cancer staging information", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:stage.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "stage" + } + ] + } + }, + { + "id": "Observation.component:stage.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-gene-fusion-expression.json b/fsh-generated/resources/StructureDefinition-ncpi-gene-fusion-expression.json new file mode 100644 index 000000000..2da2135ae --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-gene-fusion-expression.json @@ -0,0 +1,369 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-gene-fusion-expression", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-gene-fusion-expression", + "version": "0.0.1", + "name": "NcpiGeneFusionOrExpression", + "title": "Gene fusion or gene expression file profile", + "status": "draft", + "description": "Gene fusion or gene expression file profile", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Observation", + "baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Observation.extension", + "path": "Observation.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Observation.extension:specimen-collection", + "path": "Observation.extension", + "sliceName": "specimen-collection", + "short": "Linkage for related samples", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection" + ] + } + ] + }, + { + "id": "Observation.component", + "path": "Observation.component", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "code" + } + ], + "rules": "open", + "ordered": false, + "description": "Slice pattern for component.code" + }, + "min": 8 + }, + { + "id": "Observation.component:assay_strategy", + "path": "Observation.component", + "sliceName": "assay_strategy", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:assay_strategy.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "AssayStrategy" + } + ] + } + }, + { + "id": "Observation.component:assay_strategy.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:platform_instrument", + "path": "Observation.component", + "sliceName": "platform_instrument", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:platform_instrument.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "PlatformInstrument" + } + ] + } + }, + { + "id": "Observation.component:platform_instrument.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:library_prep", + "path": "Observation.component", + "sliceName": "library_prep", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:library_prep.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "LibraryPrep" + } + ] + } + }, + { + "id": "Observation.component:library_prep.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:library_selection", + "path": "Observation.component", + "sliceName": "library_selection", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:library_selection.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "LibrarySelection" + } + ] + } + }, + { + "id": "Observation.component:library_selection.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:strandedness", + "path": "Observation.component", + "sliceName": "strandedness", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:strandedness.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "Strandedness" + } + ] + } + }, + { + "id": "Observation.component:strandedness.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:target_region", + "path": "Observation.component", + "sliceName": "target_region", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:target_region.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "TargetRegion" + } + ] + } + }, + { + "id": "Observation.component:target_region.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:is_paired_end", + "path": "Observation.component", + "sliceName": "is_paired_end", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:is_paired_end.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "IsPairedEnd" + } + ] + } + }, + { + "id": "Observation.component:is_paired_end.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + }, + { + "code": "boolean" + } + ] + }, + { + "id": "Observation.component:adaptor_trimmed", + "path": "Observation.component", + "sliceName": "adaptor_trimmed", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:adaptor_trimmed.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "AdaptorTrimmed" + } + ] + } + }, + { + "id": "Observation.component:adaptor_trimmed.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + }, + { + "code": "boolean" + } + ] + }, + { + "id": "Observation.component:reference_genome", + "path": "Observation.component", + "sliceName": "reference_genome", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:reference_genome.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "ReferenceGenome" + } + ] + } + }, + { + "id": "Observation.component:reference_genome.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:workflow_type", + "path": "Observation.component", + "sliceName": "workflow_type", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:workflow_type.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "WorkflowType" + } + ] + } + }, + { + "id": "Observation.component:workflow_type.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:workflow_tool", + "path": "Observation.component", + "sliceName": "workflow_tool", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:workflow_tool.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "WorkflowTool" + } + ] + } + }, + { + "id": "Observation.component:workflow_tool.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-maf.json b/fsh-generated/resources/StructureDefinition-ncpi-maf.json new file mode 100644 index 000000000..f759a8300 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-maf.json @@ -0,0 +1,369 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-maf", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-maf", + "version": "0.0.1", + "name": "NcpiMAF", + "title": "MAF (Somatic Mutation) file profile", + "status": "draft", + "description": "MAF (Somatic Mutation) file profile", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Observation", + "baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Observation.extension", + "path": "Observation.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Observation.extension:specimen-collection", + "path": "Observation.extension", + "sliceName": "specimen-collection", + "short": "Linkage for related samples", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection" + ] + } + ] + }, + { + "id": "Observation.component", + "path": "Observation.component", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "code" + } + ], + "rules": "open", + "ordered": false, + "description": "Slice pattern for component.code" + }, + "min": 5 + }, + { + "id": "Observation.component:assay_strategy", + "path": "Observation.component", + "sliceName": "assay_strategy", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:assay_strategy.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "AssayStrategy" + } + ] + } + }, + { + "id": "Observation.component:assay_strategy.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:platform_instrument", + "path": "Observation.component", + "sliceName": "platform_instrument", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:platform_instrument.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "PlatformInstrument" + } + ] + } + }, + { + "id": "Observation.component:platform_instrument.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:library_prep", + "path": "Observation.component", + "sliceName": "library_prep", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:library_prep.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "LibraryPrep" + } + ] + } + }, + { + "id": "Observation.component:library_prep.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:library_selection", + "path": "Observation.component", + "sliceName": "library_selection", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:library_selection.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "LibrarySelection" + } + ] + } + }, + { + "id": "Observation.component:library_selection.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:strandedness", + "path": "Observation.component", + "sliceName": "strandedness", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:strandedness.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "Strandedness" + } + ] + } + }, + { + "id": "Observation.component:strandedness.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:target_region", + "path": "Observation.component", + "sliceName": "target_region", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:target_region.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "TargetRegion" + } + ] + } + }, + { + "id": "Observation.component:target_region.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:is_paired_end", + "path": "Observation.component", + "sliceName": "is_paired_end", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:is_paired_end.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "IsPairedEnd" + } + ] + } + }, + { + "id": "Observation.component:is_paired_end.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + }, + { + "code": "boolean" + } + ] + }, + { + "id": "Observation.component:adaptor_trimmed", + "path": "Observation.component", + "sliceName": "adaptor_trimmed", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:adaptor_trimmed.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "AdaptorTrimmed" + } + ] + } + }, + { + "id": "Observation.component:adaptor_trimmed.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + }, + { + "code": "boolean" + } + ] + }, + { + "id": "Observation.component:reference_genome", + "path": "Observation.component", + "sliceName": "reference_genome", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:reference_genome.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "ReferenceGenome" + } + ] + } + }, + { + "id": "Observation.component:reference_genome.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:workflow_type", + "path": "Observation.component", + "sliceName": "workflow_type", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:workflow_type.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "WorkflowType" + } + ] + } + }, + { + "id": "Observation.component:workflow_type.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:workflow_tool", + "path": "Observation.component", + "sliceName": "workflow_tool", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:workflow_tool.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "WorkflowTool" + } + ] + } + }, + { + "id": "Observation.component:workflow_tool.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-proteomics.json b/fsh-generated/resources/StructureDefinition-ncpi-proteomics.json new file mode 100644 index 000000000..5fc131570 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-proteomics.json @@ -0,0 +1,369 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-proteomics", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-proteomics", + "version": "0.0.1", + "name": "NcpiProteomics", + "title": "Proteomics file profile", + "status": "draft", + "description": "Proteomics file profile", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Observation", + "baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Observation.extension", + "path": "Observation.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Observation.extension:specimen-collection", + "path": "Observation.extension", + "sliceName": "specimen-collection", + "short": "Linkage for related samples", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection" + ] + } + ] + }, + { + "id": "Observation.component", + "path": "Observation.component", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "code" + } + ], + "rules": "open", + "ordered": false, + "description": "Slice pattern for component.code" + }, + "min": 5 + }, + { + "id": "Observation.component:assay_strategy", + "path": "Observation.component", + "sliceName": "assay_strategy", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:assay_strategy.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "AssayStrategy" + } + ] + } + }, + { + "id": "Observation.component:assay_strategy.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:platform_instrument", + "path": "Observation.component", + "sliceName": "platform_instrument", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:platform_instrument.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "PlatformInstrument" + } + ] + } + }, + { + "id": "Observation.component:platform_instrument.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:library_prep", + "path": "Observation.component", + "sliceName": "library_prep", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:library_prep.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "LibraryPrep" + } + ] + } + }, + { + "id": "Observation.component:library_prep.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:library_selection", + "path": "Observation.component", + "sliceName": "library_selection", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:library_selection.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "LibrarySelection" + } + ] + } + }, + { + "id": "Observation.component:library_selection.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:strandedness", + "path": "Observation.component", + "sliceName": "strandedness", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:strandedness.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "Strandedness" + } + ] + } + }, + { + "id": "Observation.component:strandedness.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:target_region", + "path": "Observation.component", + "sliceName": "target_region", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:target_region.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "TargetRegion" + } + ] + } + }, + { + "id": "Observation.component:target_region.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:is_paired_end", + "path": "Observation.component", + "sliceName": "is_paired_end", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:is_paired_end.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "IsPairedEnd" + } + ] + } + }, + { + "id": "Observation.component:is_paired_end.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + }, + { + "code": "boolean" + } + ] + }, + { + "id": "Observation.component:adaptor_trimmed", + "path": "Observation.component", + "sliceName": "adaptor_trimmed", + "min": 0, + "max": "1" + }, + { + "id": "Observation.component:adaptor_trimmed.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "AdaptorTrimmed" + } + ] + } + }, + { + "id": "Observation.component:adaptor_trimmed.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + }, + { + "code": "boolean" + } + ] + }, + { + "id": "Observation.component:reference_genome", + "path": "Observation.component", + "sliceName": "reference_genome", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:reference_genome.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "ReferenceGenome" + } + ] + } + }, + { + "id": "Observation.component:reference_genome.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:workflow_type", + "path": "Observation.component", + "sliceName": "workflow_type", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:workflow_type.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "WorkflowType" + } + ] + } + }, + { + "id": "Observation.component:workflow_type.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "Observation.component:workflow_tool", + "path": "Observation.component", + "sliceName": "workflow_tool", + "min": 1, + "max": "1" + }, + { + "id": "Observation.component:workflow_tool.code", + "path": "Observation.component.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "WorkflowTool" + } + ] + } + }, + { + "id": "Observation.component:workflow_tool.value[x]", + "path": "Observation.component.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.json b/fsh-generated/resources/StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.json new file mode 100644 index 000000000..3a54631f8 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.json @@ -0,0 +1,24 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-specimen-NcpiSpecimenCollection", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-specimen-NcpiSpecimenCollection", + "name": "NcpiSpecimenCollection", + "title": "Linkage for related samples", + "status": "draft", + "description": "Linkage for related samples", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "List", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/List", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "List.subject", + "path": "List.subject", + "short": "Reference to any subjects or other samples related to a subject" + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-specimen-collection.json b/fsh-generated/resources/StructureDefinition-specimen-collection.json new file mode 100644 index 000000000..ee9d4c388 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-specimen-collection.json @@ -0,0 +1,51 @@ +{ + "resourceType": "StructureDefinition", + "id": "specimen-collection", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection", + "name": "SpecimenCollection", + "title": "Linkage for related samples", + "status": "draft", + "description": "Linkage for related samples", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "NcpiSpecimenCollection.subject" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Linkage for related samples", + "definition": "Linkage for related samples" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "short": "Reference to other samples related to this sample", + "type": [ + { + "code": "Reference" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-condition-assertion-vs.json b/fsh-generated/resources/ValueSet-condition-assertion-vs.json new file mode 100644 index 000000000..df5ef3223 --- /dev/null +++ b/fsh-generated/resources/ValueSet-condition-assertion-vs.json @@ -0,0 +1,15 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "ConditionAssertionVS", + "id": "condition-assertion-vs", + "title": "Assertion of Condition Codes", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-assertion-vs", + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-assertion" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-condition-laterality-vs.json b/fsh-generated/resources/ValueSet-condition-laterality-vs.json new file mode 100644 index 000000000..6115722d6 --- /dev/null +++ b/fsh-generated/resources/ValueSet-condition-laterality-vs.json @@ -0,0 +1,16 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "LateralityQualifierVS", + "id": "condition-laterality-vs", + "title": "Laterality Information", + "description": "Laterality Information", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-laterality-vs", + "compose": { + "include": [ + { + "system": "http://hl7.org/fhir/us/mcode/ValueSet/mcode-laterality-qualifier-vs" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-condition-location-vs.json b/fsh-generated/resources/ValueSet-condition-location-vs.json new file mode 100644 index 000000000..e90661b45 --- /dev/null +++ b/fsh-generated/resources/ValueSet-condition-location-vs.json @@ -0,0 +1,16 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "BodyLocationQualifierVS", + "id": "condition-location-vs", + "title": "Location Information", + "description": "Location Information", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-location-vs", + "compose": { + "include": [ + { + "system": "http://hl7.org/fhir/us/mcode/ValueSet/mcode-body-location-qualifier-vs" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-condition-type-vs.json b/fsh-generated/resources/ValueSet-condition-type-vs.json new file mode 100644 index 000000000..deccfc8e0 --- /dev/null +++ b/fsh-generated/resources/ValueSet-condition-type-vs.json @@ -0,0 +1,15 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "ConditionTypeVS", + "id": "condition-type-vs", + "title": "Type of Condition", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-type-vs", + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type" + } + ] + } +}