From a0d6e48f4a488683fa098fe642a07cea1df84f57 Mon Sep 17 00:00:00 2001 From: Ann Holmes Date: Fri, 3 Jan 2025 19:24:17 -0500 Subject: [PATCH] :lipstick: add family module diagram --- .vscode/settings.json | 7 + fsh-generated/fsh-index.json | 146 +++++++------ fsh-generated/fsh-index.txt | 65 +++--- fsh-generated/includes/fsh-link-references.md | 3 + ...ide-ncpi-fhir-implementation-guide-v2.json | 48 +++-- ...ructureDefinition-SharedDataModelFile.json | 42 ---- ...efinition-SharedDataModelFileMetadata.json | 194 ++++++++++++++++++ ...ructureDefinition-ncpi-drs-attachment.json | 33 +++ .../StructureDefinition-ncpi-drs-file.json | 54 +++++ input/pagecontent/module_family.md | 3 + 10 files changed, 449 insertions(+), 146 deletions(-) create mode 100644 .vscode/settings.json create mode 100644 fsh-generated/resources/StructureDefinition-SharedDataModelFileMetadata.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-drs-attachment.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-drs-file.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 000000000..243003193 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,7 @@ +{ + "cSpell.words": [ + "biospecimen", + "FHIR", + "NCPI" + ] +} \ No newline at end of file diff --git a/fsh-generated/fsh-index.json b/fsh-generated/fsh-index.json index 93dbe5b4b..7618571ec 100644 --- a/fsh-generated/fsh-index.json +++ b/fsh-generated/fsh-index.json @@ -4,16 +4,16 @@ "fshName": "AdaptorTrimmedCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 54, - "endLine": 60 + "startLine": 72, + "endLine": 78 }, { "outputFile": "CodeSystem-assay-strategy-cs.json", "fshName": "AssayStrategyCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 18, - "endLine": 23 + "startLine": 36, + "endLine": 41 }, { "outputFile": "CodeSystem-biospecimen-availability.json", @@ -60,32 +60,32 @@ "fshName": "HashTypeCS", "fshType": "CodeSystem", "fshFile": "modules/files.fsh", - "startLine": 28, - "endLine": 38 + "startLine": 25, + "endLine": 35 }, { "outputFile": "CodeSystem-library-prep-cs.json", "fshName": "LibraryPrepCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 32, - "endLine": 37 + "startLine": 50, + "endLine": 55 }, { "outputFile": "CodeSystem-library-selection-cs.json", "fshName": "LibrarySelectionCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 39, - "endLine": 44 + "startLine": 57, + "endLine": 62 }, { "outputFile": "CodeSystem-metadata-elements.json", "fshName": "MetadataElements", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 1, - "endLine": 16 + "startLine": 19, + "endLine": 34 }, { "outputFile": "CodeSystem-ncpi-family-types.json", @@ -108,24 +108,24 @@ "fshName": "PlatformInstrumentCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 25, - "endLine": 30 + "startLine": 43, + "endLine": 48 }, { "outputFile": "CodeSystem-reference-genome-cs.json", "fshName": "ReferenceGenomeCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 78, - "endLine": 86 + "startLine": 96, + "endLine": 104 }, { "outputFile": "CodeSystem-related-file-type-code-system.json", "fshName": "RelatedFileTypeCS", "fshType": "CodeSystem", "fshFile": "modules/files.fsh", - "startLine": 40, - "endLine": 48 + "startLine": 37, + "endLine": 45 }, { "outputFile": "CodeSystem-research-data-access-code.json", @@ -156,8 +156,8 @@ "fshName": "StrandednessCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 46, - "endLine": 52 + "startLine": 64, + "endLine": 70 }, { "outputFile": "CodeSystem-study-name-type.json", @@ -180,16 +180,16 @@ "fshName": "WorkflowToolCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 70, - "endLine": 76 + "startLine": 88, + "endLine": 94 }, { "outputFile": "CodeSystem-workflow-type-cs.json", "fshName": "WorkflowTypeCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 62, - "endLine": 68 + "startLine": 80, + "endLine": 86 }, { "outputFile": "Consent-gregor-gru-consent.json", @@ -517,7 +517,15 @@ "fshType": "Logical", "fshFile": "modules/files.fsh", "startLine": 5, - "endLine": 24 + "endLine": 21 + }, + { + "outputFile": "StructureDefinition-SharedDataModelFileMetadata.json", + "fshName": "CdmFileMetadata", + "fshType": "Logical", + "fshFile": "modules/file-metadata.fsh", + "startLine": 1, + "endLine": 17 }, { "outputFile": "StructureDefinition-SharedDataModelPerson.json", @@ -684,8 +692,8 @@ "fshName": "ContentVersion", "fshType": "Extension", "fshFile": "modules/files.fsh", - "startLine": 80, - "endLine": 86 + "startLine": 77, + "endLine": 83 }, { "outputFile": "StructureDefinition-description.json", @@ -716,40 +724,40 @@ "fshName": "FileFormat", "fshType": "Extension", "fshFile": "modules/files.fsh", - "startLine": 56, - "endLine": 62 + "startLine": 53, + "endLine": 59 }, { "outputFile": "StructureDefinition-file-size.json", "fshName": "FileSize", "fshType": "Extension", "fshFile": "modules/files.fsh", - "startLine": 72, - "endLine": 78 + "startLine": 69, + "endLine": 75 }, { "outputFile": "StructureDefinition-hash-extension.json", "fshName": "HashExtension", "fshType": "Extension", "fshFile": "modules/files.fsh", - "startLine": 104, - "endLine": 112 + "startLine": 101, + "endLine": 109 }, { "outputFile": "StructureDefinition-hash-type.json", "fshName": "HashType", "fshType": "Extension", "fshFile": "modules/files.fsh", - "startLine": 96, - "endLine": 102 + "startLine": 93, + "endLine": 99 }, { "outputFile": "StructureDefinition-hash-value.json", "fshName": "HashValue", "fshType": "Extension", "fshFile": "modules/files.fsh", - "startLine": 88, - "endLine": 94 + "startLine": 85, + "endLine": 91 }, { "outputFile": "StructureDefinition-label-extension.json", @@ -764,8 +772,8 @@ "fshName": "LocationAccess", "fshType": "Extension", "fshFile": "modules/files.fsh", - "startLine": 64, - "endLine": 70 + "startLine": 61, + "endLine": 67 }, { "outputFile": "StructureDefinition-ncpi-Study-Participant.json", @@ -780,8 +788,8 @@ "fshName": "NcpiBAMCRAM", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 162, - "endLine": 209 + "startLine": 180, + "endLine": 227 }, { "outputFile": "StructureDefinition-ncpi-collected-sample.json", @@ -799,6 +807,22 @@ "startLine": 123, "endLine": 181 }, + { + "outputFile": "StructureDefinition-ncpi-drs-attachment.json", + "fshName": "DRSAttachment", + "fshType": "Profile", + "fshFile": "modules/files.fsh", + "startLine": 116, + "endLine": 123 + }, + { + "outputFile": "StructureDefinition-ncpi-drs-file.json", + "fshName": "NcpiDRSFile", + "fshType": "Profile", + "fshFile": "modules/files.fsh", + "startLine": 155, + "endLine": 169 + }, { "outputFile": "StructureDefinition-ncpi-family-relationship.json", "fshName": "NcpiFamilyRelationship", @@ -812,40 +836,40 @@ "fshName": "NcpiFASTQ", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 113, - "endLine": 160 + "startLine": 131, + "endLine": 178 }, { "outputFile": "StructureDefinition-ncpi-file-metadata.json", "fshName": "NcpiFileMetadata", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 88, - "endLine": 95 + "startLine": 106, + "endLine": 113 }, { "outputFile": "StructureDefinition-ncpi-file.json", "fshName": "NcpiFile", "fshType": "Profile", "fshFile": "modules/files.fsh", - "startLine": 116, - "endLine": 142 + "startLine": 127, + "endLine": 153 }, { "outputFile": "StructureDefinition-ncpi-gene-fusion-expression.json", "fshName": "NcpiGeneFusionOrExpression", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 309, - "endLine": 356 + "startLine": 327, + "endLine": 374 }, { "outputFile": "StructureDefinition-ncpi-maf.json", "fshName": "NcpiMAF", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 260, - "endLine": 307 + "startLine": 278, + "endLine": 325 }, { "outputFile": "StructureDefinition-ncpi-non-collected-sample.json", @@ -876,8 +900,8 @@ "fshName": "NcpiProteomics", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 358, - "endLine": 405 + "startLine": 376, + "endLine": 423 }, { "outputFile": "StructureDefinition-ncpi-research-access-policy.json", @@ -916,8 +940,8 @@ "fshName": "NcpiSpecimenCollection", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 97, - "endLine": 103 + "startLine": 115, + "endLine": 121 }, { "outputFile": "StructureDefinition-ncpi-study-family.json", @@ -932,8 +956,8 @@ "fshName": "NcpiVCF", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 211, - "endLine": 258 + "startLine": 229, + "endLine": 276 }, { "outputFile": "StructureDefinition-research-age-at-last-vital-status.json", @@ -1020,8 +1044,8 @@ "fshName": "SpecimenCollection", "fshType": "Extension", "fshFile": "modules/file-metadata.fsh", - "startLine": 105, - "endLine": 111 + "startLine": 123, + "endLine": 129 }, { "outputFile": "StructureDefinition-study-family-focus.json", @@ -1092,8 +1116,8 @@ "fshName": "EDAMOntologyTerms", "fshType": "ValueSet", "fshFile": "modules/files.fsh", - "startLine": 50, - "endLine": 54 + "startLine": 47, + "endLine": 51 }, { "outputFile": "ValueSet-mesh-terms.json", diff --git a/fsh-generated/fsh-index.txt b/fsh-generated/fsh-index.txt index d08bffef8..b64bc703d 100644 --- a/fsh-generated/fsh-index.txt +++ b/fsh-generated/fsh-index.txt @@ -1,28 +1,28 @@ Output File Name Type FSH File Lines -CodeSystem-adaptor-trimmed-cs.json AdaptorTrimmedCS CodeSystem modules/file-metadata.fsh 54 - 60 -CodeSystem-assay-strategy-cs.json AssayStrategyCS CodeSystem modules/file-metadata.fsh 18 - 23 +CodeSystem-adaptor-trimmed-cs.json AdaptorTrimmedCS CodeSystem modules/file-metadata.fsh 72 - 78 +CodeSystem-assay-strategy-cs.json AssayStrategyCS CodeSystem modules/file-metadata.fsh 36 - 41 CodeSystem-biospecimen-availability.json BiospecimenAvailability CodeSystem modules/biospecimen.fsh 53 - 58 CodeSystem-collection-type.json CollectionType CodeSystem modules/research-collection.fsh 2 - 11 CodeSystem-component-elements.json ComponentElements CodeSystem modules/condition.fsh 114 - 121 CodeSystem-condition-assertion.json ConditionAssertion CodeSystem modules/condition.fsh 50 - 59 CodeSystem-condition-type.json ConditionType CodeSystem modules/condition.fsh 31 - 43 -CodeSystem-example-hash-type-code-system.json HashTypeCS CodeSystem modules/files.fsh 28 - 38 -CodeSystem-library-prep-cs.json LibraryPrepCS CodeSystem modules/file-metadata.fsh 32 - 37 -CodeSystem-library-selection-cs.json LibrarySelectionCS CodeSystem modules/file-metadata.fsh 39 - 44 -CodeSystem-metadata-elements.json MetadataElements CodeSystem modules/file-metadata.fsh 1 - 16 +CodeSystem-example-hash-type-code-system.json HashTypeCS CodeSystem modules/files.fsh 25 - 35 +CodeSystem-library-prep-cs.json LibraryPrepCS CodeSystem modules/file-metadata.fsh 50 - 55 +CodeSystem-library-selection-cs.json LibrarySelectionCS CodeSystem modules/file-metadata.fsh 57 - 62 +CodeSystem-metadata-elements.json MetadataElements CodeSystem modules/file-metadata.fsh 19 - 34 CodeSystem-ncpi-family-types.json NcpiFamilyTypes CodeSystem modules/family.fsh 44 - 58 CodeSystem-ncpi.json Ncpi CodeSystem terminologies/ncpi.fsh 6 - 34 -CodeSystem-platform-instrument-cs.json PlatformInstrumentCS CodeSystem modules/file-metadata.fsh 25 - 30 -CodeSystem-reference-genome-cs.json ReferenceGenomeCS CodeSystem modules/file-metadata.fsh 78 - 86 -CodeSystem-related-file-type-code-system.json RelatedFileTypeCS CodeSystem modules/files.fsh 40 - 48 +CodeSystem-platform-instrument-cs.json PlatformInstrumentCS CodeSystem modules/file-metadata.fsh 43 - 48 +CodeSystem-reference-genome-cs.json ReferenceGenomeCS CodeSystem modules/file-metadata.fsh 96 - 104 +CodeSystem-related-file-type-code-system.json RelatedFileTypeCS CodeSystem modules/files.fsh 37 - 45 CodeSystem-research-data-access-code.json ResearchDataAccessCode CodeSystem modules/research-accesss-policy.fsh 6 - 22 CodeSystem-research-data-access-type.json ResearchDataAccessType CodeSystem modules/research-accesss-policy.fsh 33 - 44 CodeSystem-research-data-date-of-birth-method.json ResearchDataDateOfBirthMethod CodeSystem modules/participant.fsh 18 - 29 -CodeSystem-strandedness-cs.json StrandednessCS CodeSystem modules/file-metadata.fsh 46 - 52 +CodeSystem-strandedness-cs.json StrandednessCS CodeSystem modules/file-metadata.fsh 64 - 70 CodeSystem-study-name-type.json StudyNameType CodeSystem modules/research-study.fsh 99 - 110 CodeSystem-study-personnel-role.json StudyPersonnelRole CodeSystem modules/research-study.fsh 120 - 129 -CodeSystem-workflow-tool-cs.json WorkflowToolCS CodeSystem modules/file-metadata.fsh 70 - 76 -CodeSystem-workflow-type-cs.json WorkflowTypeCS CodeSystem modules/file-metadata.fsh 62 - 68 +CodeSystem-workflow-tool-cs.json WorkflowToolCS CodeSystem modules/file-metadata.fsh 88 - 94 +CodeSystem-workflow-type-cs.json WorkflowTypeCS CodeSystem modules/file-metadata.fsh 80 - 86 Consent-gregor-gru-consent.json gregor-gru-consent Instance examples/GREGoR_example.fsh 25 - 37 Consent-kf-gru-dac-consent.json kf-gru-dac-consent Instance examples/CBTN_example.fsh 103 - 116 Consent-kf-gru-dbgap-consent.json kf-gru-dbgap-consent Instance examples/CBTN_example.fsh 135 - 148 @@ -63,7 +63,8 @@ StructureDefinition-SharedDataModelBiospecimenCollection.json CdmBiospecimen StructureDefinition-SharedDataModelCondition.json CdmCondition Logical modules/condition.fsh 3 - 21 StructureDefinition-SharedDataModelFamilyRelationship.json CdmFamilyRelationship Logical modules/family.fsh 148 - 154 StructureDefinition-SharedDataModelFamilyRole.json CdmFamilyRole Logical modules/family.fsh 25 - 31 -StructureDefinition-SharedDataModelFile.json CdmFile Logical modules/files.fsh 5 - 24 +StructureDefinition-SharedDataModelFile.json CdmFile Logical modules/files.fsh 5 - 21 +StructureDefinition-SharedDataModelFileMetadata.json CdmFileMetadata Logical modules/file-metadata.fsh 1 - 17 StructureDefinition-SharedDataModelPerson.json CdmPerson Logical modules/participant.fsh 93 - 98 StructureDefinition-SharedDataModelResearchCollection.json CdmResearchCollection Logical modules/research-collection.fsh 39 - 48 StructureDefinition-SharedDataModelResearchDataAccessPolicy.json CdmResearchDataAccessPolicy Logical modules/research-accesss-policy.fsh 113 - 120 @@ -84,38 +85,40 @@ StructureDefinition-condition-asserter.json ConditionAsser StructureDefinition-condition-laterality.json ConditionLaterality Extension modules/condition.fsh 105 - 111 StructureDefinition-condition-location.json ConditionLocation Extension modules/condition.fsh 97 - 103 StructureDefinition-consanguinity.json Consanguinity Extension modules/family.fsh 93 - 99 -StructureDefinition-content-version.json ContentVersion Extension modules/files.fsh 80 - 86 +StructureDefinition-content-version.json ContentVersion Extension modules/files.fsh 77 - 83 StructureDefinition-description.json Description Extension modules/family.fsh 76 - 81 StructureDefinition-family-role.json FamilyRole Extension modules/family.fsh 34 - 42 StructureDefinition-family-type.json FamilyType Extension modules/family.fsh 68 - 74 -StructureDefinition-file-format.json FileFormat Extension modules/files.fsh 56 - 62 -StructureDefinition-file-size.json FileSize Extension modules/files.fsh 72 - 78 -StructureDefinition-hash-extension.json HashExtension Extension modules/files.fsh 104 - 112 -StructureDefinition-hash-type.json HashType Extension modules/files.fsh 96 - 102 -StructureDefinition-hash-value.json HashValue Extension modules/files.fsh 88 - 94 +StructureDefinition-file-format.json FileFormat Extension modules/files.fsh 53 - 59 +StructureDefinition-file-size.json FileSize Extension modules/files.fsh 69 - 75 +StructureDefinition-hash-extension.json HashExtension Extension modules/files.fsh 101 - 109 +StructureDefinition-hash-type.json HashType Extension modules/files.fsh 93 - 99 +StructureDefinition-hash-value.json HashValue Extension modules/files.fsh 85 - 91 StructureDefinition-label-extension.json Label Extension extensions/Label.fsh 1 - 13 -StructureDefinition-location-access.json LocationAccess Extension modules/files.fsh 64 - 70 +StructureDefinition-location-access.json LocationAccess Extension modules/files.fsh 61 - 67 StructureDefinition-ncpi-Study-Participant.json NcpiStudyParticipant Profile modules/participant.fsh 133 - 145 -StructureDefinition-ncpi-bamcram.json NcpiBAMCRAM Profile modules/file-metadata.fsh 162 - 209 +StructureDefinition-ncpi-bamcram.json NcpiBAMCRAM Profile modules/file-metadata.fsh 180 - 227 StructureDefinition-ncpi-collected-sample.json NCPICollectedSample Profile modules/biospecimen.fsh 133 - 140 StructureDefinition-ncpi-condition.json NcpiCondition Profile modules/condition.fsh 123 - 181 +StructureDefinition-ncpi-drs-attachment.json DRSAttachment Profile modules/files.fsh 116 - 123 +StructureDefinition-ncpi-drs-file.json NcpiDRSFile Profile modules/files.fsh 155 - 169 StructureDefinition-ncpi-family-relationship.json NcpiFamilyRelationship Profile modules/family.fsh 156 - 170 -StructureDefinition-ncpi-fastq.json NcpiFASTQ Profile modules/file-metadata.fsh 113 - 160 -StructureDefinition-ncpi-file-metadata.json NcpiFileMetadata Profile modules/file-metadata.fsh 88 - 95 -StructureDefinition-ncpi-file.json NcpiFile Profile modules/files.fsh 116 - 142 -StructureDefinition-ncpi-gene-fusion-expression.json NcpiGeneFusionOrExpression Profile modules/file-metadata.fsh 309 - 356 -StructureDefinition-ncpi-maf.json NcpiMAF Profile modules/file-metadata.fsh 260 - 307 +StructureDefinition-ncpi-fastq.json NcpiFASTQ Profile modules/file-metadata.fsh 131 - 178 +StructureDefinition-ncpi-file-metadata.json NcpiFileMetadata Profile modules/file-metadata.fsh 106 - 113 +StructureDefinition-ncpi-file.json NcpiFile Profile modules/files.fsh 127 - 153 +StructureDefinition-ncpi-gene-fusion-expression.json NcpiGeneFusionOrExpression Profile modules/file-metadata.fsh 327 - 374 +StructureDefinition-ncpi-maf.json NcpiMAF Profile modules/file-metadata.fsh 278 - 325 StructureDefinition-ncpi-non-collected-sample.json NCPINonCollectedSample Profile modules/biospecimen.fsh 142 - 149 StructureDefinition-ncpi-participant.json NcpiParticipant Profile modules/participant.fsh 62 - 87 StructureDefinition-ncpi-person.json NcpiPerson Profile modules/participant.fsh 101 - 112 -StructureDefinition-ncpi-proteomics.json NcpiProteomics Profile modules/file-metadata.fsh 358 - 405 +StructureDefinition-ncpi-proteomics.json NcpiProteomics Profile modules/file-metadata.fsh 376 - 423 StructureDefinition-ncpi-research-access-policy.json NcpiResearchAccessPolicy Profile modules/research-accesss-policy.fsh 92 - 110 StructureDefinition-ncpi-research-collection.json NcpiResearchCollection Profile modules/research-collection.fsh 20 - 37 StructureDefinition-ncpi-research-study.json NcpiResearchStudy Profile modules/research-study.fsh 60 - 86 StructureDefinition-ncpi-sample.json NCPISample Profile modules/biospecimen.fsh 90 - 130 -StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.json NcpiSpecimenCollection Profile modules/file-metadata.fsh 97 - 103 +StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.json NcpiSpecimenCollection Profile modules/file-metadata.fsh 115 - 121 StructureDefinition-ncpi-study-family.json NcpiStudyFamily Profile modules/family.fsh 108 - 131 -StructureDefinition-ncpi-vcf.json NcpiVCF Profile modules/file-metadata.fsh 211 - 258 +StructureDefinition-ncpi-vcf.json NcpiVCF Profile modules/file-metadata.fsh 229 - 276 StructureDefinition-research-age-at-last-vital-status.json AgeAtLastVitalStatus Extension modules/participant.fsh 53 - 60 StructureDefinition-research-date-of-birth-method.json ResearchDateOfBirthMethod Extension modules/participant.fsh 45 - 51 StructureDefinition-research-disease-use-limitation.json ResearchDiseaseUseLimitation Extension modules/research-accesss-policy.fsh 67 - 73 @@ -126,7 +129,7 @@ StructureDefinition-research-study-design.json ResearchStudyD StructureDefinition-research-study-group.json ResearchStudyGroup Profile modules/research-study-group.fsh 1 - 12 StructureDefinition-research-study-result.json ResearchStudyResult Extension modules/research-study.fsh 15 - 20 StructureDefinition-research-web-Link.json ResearchWebLink Extension extensions/ResearchWebLink.fsh 2 - 9 -StructureDefinition-specimen-collection.json SpecimenCollection Extension modules/file-metadata.fsh 105 - 111 +StructureDefinition-specimen-collection.json SpecimenCollection Extension modules/file-metadata.fsh 123 - 129 StructureDefinition-study-family-focus.json StudyFamilyFocus Extension modules/family.fsh 101 - 106 ValueSet-collection-type-vs.json CollectionTypeVS ValueSet modules/research-collection.fsh 13 - 18 ValueSet-condition-assertion-vs.json ConditionAssertionVS ValueSet modules/condition.fsh 61 - 64 @@ -135,7 +138,7 @@ ValueSet-condition-laterality-vs.json LateralityQual ValueSet-condition-location-vs.json BodyLocationQualifierVS ValueSet modules/condition.fsh 66 - 70 ValueSet-condition-type-vs.json ConditionTypeVS ValueSet modules/condition.fsh 45 - 48 ValueSet-consanguinity-assertion-vs.json ConsanguinityAssertionVS ValueSet modules/family.fsh 83 - 91 -ValueSet-edam-ontology-terms.json EDAMOntologyTerms ValueSet modules/files.fsh 50 - 54 +ValueSet-edam-ontology-terms.json EDAMOntologyTerms ValueSet modules/files.fsh 47 - 51 ValueSet-mesh-terms.json MeshTerms ValueSet modules/research-accesss-policy.fsh 54 - 60 ValueSet-ncpi-family-types-vs.json NcpiFamilyTypesVS ValueSet modules/family.fsh 60 - 66 ValueSet-research-data-access-code-vs.json ResearchDataAccessCodeVS ValueSet modules/research-accesss-policy.fsh 25 - 30 diff --git a/fsh-generated/includes/fsh-link-references.md b/fsh-generated/includes/fsh-link-references.md index 83ac47bc7..a5dfa13fc 100644 --- a/fsh-generated/includes/fsh-link-references.md +++ b/fsh-generated/includes/fsh-link-references.md @@ -26,6 +26,7 @@ [ConsanguinityAssertionVS]: ValueSet-consanguinity-assertion-vs.html [kf-research-study-personnel-role-pi]: PractitionerRole-kf-research-study-personnel-role-pi.html [kf-research-study-personnel-role-pi-x01]: PractitionerRole-kf-research-study-personnel-role-pi-x01.html +[DRSAttachment]: StructureDefinition-ncpi-drs-attachment.html [ComponentElements]: CodeSystem-component-elements.html [ResearchDataDateOfBirthMethodVS]: ValueSet-research-data-date-of-birth-method-vs.html [ResearchDataDateOfBirthMethod]: CodeSystem-research-data-date-of-birth-method.html @@ -73,6 +74,7 @@ [NCPICollectedSample]: StructureDefinition-ncpi-collected-sample.html [NCPINonCollectedSample]: StructureDefinition-ncpi-non-collected-sample.html [NcpiCondition]: StructureDefinition-ncpi-condition.html +[NcpiDRSFile]: StructureDefinition-ncpi-drs-file.html [NcpiFamilyTypes]: CodeSystem-ncpi-family-types.html [NcpiFASTQ]: StructureDefinition-ncpi-fastq.html [Ncpi]: CodeSystem-ncpi.html @@ -116,6 +118,7 @@ [CdmFamilyRelationship]: StructureDefinition-SharedDataModelFamilyRelationship.html [CdmFamilyRole]: StructureDefinition-SharedDataModelFamilyRole.html [CdmFile]: StructureDefinition-SharedDataModelFile.html +[CdmFileMetadata]: StructureDefinition-SharedDataModelFileMetadata.html [CdmResearchCollection]: StructureDefinition-SharedDataModelResearchCollection.html [CdmResearchDataAccessPolicy]: StructureDefinition-SharedDataModelResearchDataAccessPolicy.html [CdmStudyParticipant]: StructureDefinition-SharedDataModelStudyParticipant.html diff --git a/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json b/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json index 14fc1bf42..44891a920 100644 --- a/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json +++ b/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json @@ -113,8 +113,8 @@ "reference": { "reference": "Observation/gregor-family-relationship-mother" }, - "name": "An example family relationship based on data from CBTN", - "description": "An example family relationship based on data from CBTN.", + "name": "An example family relationship based on data from GREGoR", + "description": "An example family relationship based on data from GREGoR.", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-family-relationship" }, { @@ -260,6 +260,14 @@ "description": "dbGaP PI, X01 FY 2021", "exampleBoolean": true }, + { + "reference": { + "reference": "StructureDefinition/ncpi-drs-attachment" + }, + "name": "DRS Attachment", + "description": "A FHIR Attachment with a DRS url.", + "exampleBoolean": false + }, { "reference": { "reference": "CodeSystem/component-elements" @@ -344,8 +352,8 @@ "reference": { "reference": "DocumentReference/GSS123456-01-010-SG-2" }, - "name": "Example file based on CBTN", - "description": "Use case of file information from CBTN", + "name": "Example file based on GREGoR", + "description": "Use case of file information from GREGor", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file" }, { @@ -360,8 +368,8 @@ "reference": { "reference": "Observation/FASTQ-example" }, - "name": "Example file metadata for a FASTQ file", - "description": "Example file metadata for a FASTQ file", + "name": "Example file metadata from CBTN", + "description": "Example file metadata from CBTN", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-fastq" }, { @@ -636,6 +644,14 @@ "description": "Information about a condition related to a research participant", "exampleBoolean": false }, + { + "reference": { + "reference": "StructureDefinition/ncpi-drs-file" + }, + "name": "NCPI DRS File", + "description": "Information about a DRS file related to a research participant", + "exampleBoolean": false + }, { "reference": { "reference": "CodeSystem/ncpi-family-types" @@ -760,8 +776,8 @@ "reference": { "reference": "Group/gregor-research-study-participants" }, - "name": "Participants from the CBTN research study", - "description": "Participants from the CBTN research study", + "name": "Participants from the GREGoR research study", + "description": "Participants from the GREGoR research study", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" }, { @@ -980,6 +996,14 @@ "description": "The **Shared Data Model for File**", "exampleBoolean": false }, + { + "reference": { + "reference": "StructureDefinition/SharedDataModelFileMetadata" + }, + "name": "Shared data model for File Metadata", + "description": "The **Shared Data Model for File Metadata**", + "exampleBoolean": false + }, { "reference": { "reference": "StructureDefinition/SharedDataModelResearchCollection" @@ -1224,13 +1248,13 @@ "generation": "markdown" }, { - "nameUrl": "example_cbtn.html", - "title": "Example Cbtn", + "nameUrl": "example_CBTN.html", + "title": "Example CBTN", "generation": "markdown" }, { - "nameUrl": "example_gregor.html", - "title": "Example Gregor", + "nameUrl": "example_GREGoR.html", + "title": "Example GRE Go R", "generation": "markdown" }, { diff --git a/fsh-generated/resources/StructureDefinition-SharedDataModelFile.json b/fsh-generated/resources/StructureDefinition-SharedDataModelFile.json index 8beafc7b5..ee34bff50 100644 --- a/fsh-generated/resources/StructureDefinition-SharedDataModelFile.json +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelFile.json @@ -194,48 +194,6 @@ "code": "code" } ] - }, - { - "id": "SharedDataModelFile.relatedFile", - "path": "SharedDataModelFile.relatedFile", - "short": "Provides a reference to another file that is related to this one", - "definition": "Provides a reference to another file that is related to this one", - "min": 0, - "max": "1", - "type": [ - { - "code": "List" - } - ] - }, - { - "id": "SharedDataModelFile.relatedFile.file", - "path": "SharedDataModelFile.relatedFile.file", - "short": "The file to which this related file is related", - "definition": "The file to which this related file is related", - "min": 0, - "max": "1", - "type": [ - { - "code": "Extension", - "profile": [ - "http://hl7.org/fhir/StructureDefinition/valueset-reference" - ] - } - ] - }, - { - "id": "SharedDataModelFile.relatedFile.type", - "path": "SharedDataModelFile.relatedFile.type", - "short": "The relationship of the file to the parent file in reference", - "definition": "The relationship of the file to the parent file in reference", - "min": 0, - "max": "1", - "type": [ - { - "code": "code" - } - ] } ] } diff --git a/fsh-generated/resources/StructureDefinition-SharedDataModelFileMetadata.json b/fsh-generated/resources/StructureDefinition-SharedDataModelFileMetadata.json new file mode 100644 index 000000000..93f2a66ee --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelFileMetadata.json @@ -0,0 +1,194 @@ +{ + "resourceType": "StructureDefinition", + "id": "SharedDataModelFileMetadata", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelFileMetadata", + "name": "CdmFileMetadata", + "title": "Shared data model for File Metadata", + "status": "draft", + "description": "The **Shared Data Model for File Metadata**", + "fhirVersion": "4.3.0", + "kind": "logical", + "abstract": false, + "type": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelFileMetadata", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Base", + "derivation": "specialization", + "differential": { + "element": [ + { + "id": "SharedDataModelFileMetadata", + "path": "SharedDataModelFileMetadata", + "short": "Shared data model for File Metadata", + "definition": "The **Shared Data Model for File Metadata**" + }, + { + "id": "SharedDataModelFileMetadata.parentFile", + "path": "SharedDataModelFileMetadata.parentFile", + "short": "The file which this metadata refers to", + "definition": "The file which this metadata refers to", + "min": 1, + "max": "1", + "type": [ + { + "code": "Reference" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.assayStrategy", + "path": "SharedDataModelFileMetadata.assayStrategy", + "short": "Assay strategy employed for this file", + "definition": "Assay strategy employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.platformInstrument", + "path": "SharedDataModelFileMetadata.platformInstrument", + "short": "The platform instrument employed for this file", + "definition": "The platform instrument employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.relatedSamples", + "path": "SharedDataModelFileMetadata.relatedSamples", + "short": "Any samples (biospecimen) related to the file", + "definition": "Any samples (biospecimen) related to the file", + "min": 0, + "max": "*", + "type": [ + { + "code": "Reference" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.libraryPrep", + "path": "SharedDataModelFileMetadata.libraryPrep", + "short": "The library preparation employed for this file", + "definition": "The library preparation employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.librarySelection", + "path": "SharedDataModelFileMetadata.librarySelection", + "short": "The library selection employed for this file", + "definition": "The library selection employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.strandedness", + "path": "SharedDataModelFileMetadata.strandedness", + "short": "The strandedness of the file", + "definition": "The strandedness of the file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.targetRegion", + "path": "SharedDataModelFileMetadata.targetRegion", + "short": "The target region employed for this file", + "definition": "The target region employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.referenceGenome", + "path": "SharedDataModelFileMetadata.referenceGenome", + "short": "The reference genome employed for this file", + "definition": "The reference genome employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.isPairedEnd", + "path": "SharedDataModelFileMetadata.isPairedEnd", + "short": "Does this file represent paired end data?", + "definition": "Does this file represent paired end data?", + "min": 0, + "max": "1", + "type": [ + { + "code": "boolean" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.workflowType", + "path": "SharedDataModelFileMetadata.workflowType", + "short": "The workflow type employed for this file", + "definition": "The workflow type employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.workflowTool", + "path": "SharedDataModelFileMetadata.workflowTool", + "short": "The workflow tool employed for this file", + "definition": "The workflow tool employed for this file", + "min": 0, + "max": "1", + "type": [ + { + "code": "CodeableConcept" + } + ] + }, + { + "id": "SharedDataModelFileMetadata.adaptorTrimmed", + "path": "SharedDataModelFileMetadata.adaptorTrimmed", + "short": "Does this file indicate that an adaptor is trimmed?", + "definition": "Does this file indicate that an adaptor is trimmed?", + "min": 0, + "max": "1", + "type": [ + { + "code": "boolean" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-drs-attachment.json b/fsh-generated/resources/StructureDefinition-ncpi-drs-attachment.json new file mode 100644 index 000000000..08f48d1fc --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-drs-attachment.json @@ -0,0 +1,33 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-drs-attachment", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-drs-attachment", + "version": "0.1.0", + "name": "DRSAttachment", + "title": "DRS Attachment", + "status": "draft", + "description": "A FHIR Attachment with a DRS url.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "type": "Attachment", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Attachment", + "derivation": "constraint", + "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://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-drs-attachment" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-drs-file.json b/fsh-generated/resources/StructureDefinition-ncpi-drs-file.json new file mode 100644 index 000000000..912db5be4 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-drs-file.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-drs-file", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-drs-file", + "version": "0.0.1", + "name": "NcpiDRSFile", + "title": "NCPI DRS File", + "status": "draft", + "description": "Information about a DRS file related to a research participant", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "DocumentReference", + "baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "DocumentReference.content", + "path": "DocumentReference.content", + "slicing": { + "discriminator": [ + { + "type": "pattern", + "path": "code" + } + ], + "rules": "openAtEnd", + "ordered": true, + "description": "Slicing pattern to make content.attachment require a DRS file type and allow other file types" + } + }, + { + "id": "DocumentReference.content:DRS", + "path": "DocumentReference.content", + "sliceName": "DRS", + "min": 1, + "max": "1" + }, + { + "id": "DocumentReference.content:DRS.attachment", + "path": "DocumentReference.content.attachment", + "type": [ + { + "code": "Attachment", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-drs-attachment" + ] + } + ] + } + ] + } +} diff --git a/input/pagecontent/module_family.md b/input/pagecontent/module_family.md index 9f0d78066..932f31719 100644 --- a/input/pagecontent/module_family.md +++ b/input/pagecontent/module_family.md @@ -1,5 +1,8 @@ # Family +
+ Family Model Diagram +
## Overview This module describes family groups and family relationships, often used in genomic analyses to aid in identification of causal variants. We include several articulations of these: Family Study is an entity that describes a collection of participants in the context of a research study. Family Relationships describe the relationship of two Participants, and should be sufficient for generating a pedigree if the source information is present.