diff --git a/fsh-generated/fsh-index.json b/fsh-generated/fsh-index.json index c2f0bf347..bd1116784 100644 --- a/fsh-generated/fsh-index.json +++ b/fsh-generated/fsh-index.json @@ -4,8 +4,8 @@ "fshName": "AdaptorTrimmedCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 49, - "endLine": 54 + "startLine": 54, + "endLine": 60 }, { "outputFile": "CodeSystem-assay-strategy-cs.json", @@ -13,7 +13,7 @@ "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", "startLine": 18, - "endLine": 22 + "endLine": 23 }, { "outputFile": "CodeSystem-biospecimen-availability.json", @@ -68,16 +68,16 @@ "fshName": "LibraryPrepCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 30, - "endLine": 34 + "startLine": 32, + "endLine": 37 }, { "outputFile": "CodeSystem-library-selection-cs.json", "fshName": "LibrarySelectionCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 36, - "endLine": 40 + "startLine": 39, + "endLine": 44 }, { "outputFile": "CodeSystem-metadata-elements.json", @@ -108,16 +108,16 @@ "fshName": "PlatformInstrumentCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 24, - "endLine": 28 + "startLine": 25, + "endLine": 30 }, { "outputFile": "CodeSystem-reference-genome-cs.json", "fshName": "ReferenceGenomeCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 70, - "endLine": 77 + "startLine": 78, + "endLine": 86 }, { "outputFile": "CodeSystem-related-file-type-code-system.json", @@ -156,8 +156,8 @@ "fshName": "StrandednessCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 42, - "endLine": 47 + "startLine": 46, + "endLine": 52 }, { "outputFile": "CodeSystem-study-name-type.json", @@ -180,32 +180,24 @@ "fshName": "WorkflowToolCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 63, - "endLine": 68 + "startLine": 70, + "endLine": 76 }, { "outputFile": "CodeSystem-workflow-type-cs.json", "fshName": "WorkflowTypeCS", "fshType": "CodeSystem", "fshFile": "modules/file-metadata.fsh", - "startLine": 56, - "endLine": 61 - }, - { - "outputFile": "Consent-GRU.json", - "fshName": "GRU", - "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 88, - "endLine": 101 + "startLine": 62, + "endLine": 68 }, { - "outputFile": "Consent-HMB.json", - "fshName": "HMB", + "outputFile": "Consent-gregor-gru-consent.json", + "fshName": "gregor-gru-consent", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 178, - "endLine": 191 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 25, + "endLine": 37 }, { "outputFile": "Consent-hmb-irb-npu-consent.json", @@ -227,49 +219,57 @@ "outputFile": "Consent-kf-gru-dac-consent.json", "fshName": "kf-gru-dac-consent", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 105, - "endLine": 118 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 103, + "endLine": 116 }, { "outputFile": "Consent-kf-gru-dbgap-consent.json", "fshName": "kf-gru-dbgap-consent", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 135, - "endLine": 148 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 133, + "endLine": 146 }, { "outputFile": "Consent-kf-gsr-allowed-access.json", "fshName": "kf-gsr-allowed-access", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 165, - "endLine": 176 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 163, + "endLine": 174 }, { "outputFile": "Consent-kf-registered-allowed-access.json", "fshName": "kf-registered-allowed-access", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 193, - "endLine": 204 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 191, + "endLine": 202 }, { - "outputFile": "DocumentReference-PT-006SP660.json", - "fshName": "PT-006SP660", + "outputFile": "DocumentReference-GF-6BAD9S7D.json", + "fshName": "GF-6BAD9S7D", "fshType": "Instance", - "fshFile": "examples/files.fsh", - "startLine": 1, - "endLine": 22 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 342, + "endLine": 363 + }, + { + "outputFile": "DocumentReference-GSS123456-01-010-SG-2.json", + "fshName": "GSS123456-01-010-SG-2", + "fshType": "Instance", + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 147, + "endLine": 168 }, { "outputFile": "Group-cbtn-study-family.json", "fshName": "FM-00C8Y7DG", "fshType": "Instance", "fshFile": "examples/family.fsh", - "startLine": 12, - "endLine": 31 + "startLine": 11, + "endLine": 30 }, { "outputFile": "Group-cmg-research-study-bhcmg-consent-group-hmb-npu.json", @@ -287,13 +287,29 @@ "startLine": 135, "endLine": 146 }, + { + "outputFile": "Group-gregor-research-study-participants.json", + "fshName": "gregor-research-study-participants", + "fshType": "Instance", + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 12, + "endLine": 23 + }, + { + "outputFile": "Group-gregor-study-family.json", + "fshName": "GSS5555", + "fshType": "Instance", + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 91, + "endLine": 106 + }, { "outputFile": "Group-kf-research-study-cbtn-participants.json", "fshName": "kf-research-study-cbtn-participants", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 92, - "endLine": 103 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 90, + "endLine": 101 }, { "outputFile": "List-ncpi-research-collection-cmg.json", @@ -307,161 +323,137 @@ "outputFile": "List-ncpi-research-collection-kfx01.json", "fshName": "ncpi-research-collection-kfx01", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 236, - "endLine": 246 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 234, + "endLine": 244 }, { "outputFile": "List-ncpi-research-collection-pbta.json", "fshName": "ncpi-research-collection-pbta", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 222, - "endLine": 234 - }, - { - "outputFile": "Observation-BAM-CRAM-example.json", - "fshName": "BAM-CRAM-example", - "fshType": "Instance", - "fshFile": "examples/file-metadata.fsh", - "startLine": 29, - "endLine": 58 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 220, + "endLine": 232 }, { "outputFile": "Observation-FASTQ-example.json", "fshName": "FASTQ-example", "fshType": "Instance", - "fshFile": "examples/file-metadata.fsh", - "startLine": 1, - "endLine": 26 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 366, + "endLine": 388 }, { - "outputFile": "Observation-PT-006SP660-condition.json", - "fshName": "PT-006SP660-condition", + "outputFile": "Observation-GSS123456-condition.json", + "fshName": "GSS123456-condition", "fshType": "Instance", - "fshFile": "examples/condition.fsh", - "startLine": 2, - "endLine": 34 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 119, + "endLine": 133 }, { - "outputFile": "Observation-VCF-example.json", - "fshName": "VCF-example", + "outputFile": "Observation-PT-006SP660-condition.json", + "fshName": "PT-006SP660-condition", "fshType": "Instance", - "fshFile": "examples/file-metadata.fsh", - "startLine": 60, - "endLine": 89 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 276, + "endLine": 308 }, { "outputFile": "Observation-cbtn-family-relationship-mother.json", "fshName": "cbtn-family-relationship-mother", "fshType": "Instance", "fshFile": "examples/family.fsh", - "startLine": 33, - "endLine": 41 + "startLine": 32, + "endLine": 40 }, { "outputFile": "Observation-cbtn-family-relationship-son.json", "fshName": "cbtn-family-relationship-son", "fshType": "Instance", "fshFile": "examples/family.fsh", - "startLine": 48, - "endLine": 56 + "startLine": 47, + "endLine": 55 }, { - "outputFile": "Organization-kf-research-study-organization-chop.json", - "fshName": "kf-research-study-organization-chop", + "outputFile": "Observation-gregor-example-metadata.json", + "fshName": "gregor-example-metadata", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 4, - "endLine": 11 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 171, + "endLine": 197 }, { - "outputFile": "Patient-6812345.json", - "fshName": "6812345", + "outputFile": "Observation-gregor-family-relationship-mother.json", + "fshName": "gregor-family-relationship-mother", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 222, - "endLine": 255 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 108, + "endLine": 116 }, { - "outputFile": "Patient-PT-005B7CZ4.json", - "fshName": "PT-005B7CZ4", + "outputFile": "Organization-kf-research-study-organization-chop.json", + "fshName": "kf-research-study-organization-chop", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 132, - "endLine": 164 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 2, + "endLine": 9 }, { - "outputFile": "Patient-PT-KZG2CZ95.json", - "fshName": "PT-KZG2CZ95", + "outputFile": "Patient-GSS123456.json", + "fshName": "GSS123456", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 15, - "endLine": 54 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 50, + "endLine": 66 }, { - "outputFile": "Person-cbtn-example-person.json", - "fshName": "cbtn-example-person", + "outputFile": "Patient-GSS654321.json", + "fshName": "GSS654321", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 77, - "endLine": 86 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 40, + "endLine": 48 }, { - "outputFile": "Person-emerge-example-person.json", - "fshName": "emerge-example-person", + "outputFile": "Patient-PT-006SP660.json", + "fshName": "PT-006SP660", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 257, - "endLine": 266 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 247, + "endLine": 271 }, { - "outputFile": "Person-pcgc-example-person.json", - "fshName": "pcgc-example-person", + "outputFile": "Person-gregor-example-person.json", + "fshName": "gregor-example-person", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 167, - "endLine": 176 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 68, + "endLine": 77 }, { "outputFile": "PractitionerRole-kf-research-study-personnel-role-op-lead.json", "fshName": "kf-research-study-personnel-role-op-lead", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 29, - "endLine": 35 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 27, + "endLine": 33 }, { "outputFile": "PractitionerRole-kf-research-study-personnel-role-pi-x01.json", "fshName": "kf-research-study-personnel-role-pi-x01", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 13, - "endLine": 19 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 11, + "endLine": 17 }, { "outputFile": "PractitionerRole-kf-research-study-personnel-role-pi.json", "fshName": "kf-research-study-personnel-role-pi", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 21, - "endLine": 27 - }, - { - "outputFile": "ResearchStudy-SD-BHJXBDQK.json", - "fshName": "SD-BHJXBDQK", - "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 103, - "endLine": 116 - }, - { - "outputFile": "ResearchStudy-SD-PREASA7S.json", - "fshName": "SD-PREASA7S", - "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 193, - "endLine": 206 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 19, + "endLine": 25 }, { "outputFile": "ResearchStudy-cmg-research-study-bhcmg.json", @@ -491,81 +483,73 @@ "outputFile": "ResearchStudy-kf-research-study-cbtn.json", "fshName": "kf-research-study-cbtn", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 37, - "endLine": 88 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 35, + "endLine": 86 }, { "outputFile": "ResearchStudy-kf-research-study-subject-gru-dac.json", "fshName": "kf-research-study-subject-gru-dac", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 120, - "endLine": 133 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 118, + "endLine": 131 }, { "outputFile": "ResearchStudy-kf-research-study-subject-gru-dbgap.json", "fshName": "kf-research-study-subject-gru-dbgap", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 150, - "endLine": 163 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 148, + "endLine": 161 }, { "outputFile": "ResearchStudy-kf-research-study-subject-gsr-allowed.json", "fshName": "kf-research-study-subject-gsr-allowed", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 178, - "endLine": 191 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 176, + "endLine": 189 }, { "outputFile": "ResearchStudy-kf-research-study-subject-registered.json", "fshName": "kf-research-study-subject-registered", "fshType": "Instance", - "fshFile": "examples/ResearchStudy-CBTN.fsh", - "startLine": 206, - "endLine": 219 - }, - { - "outputFile": "ResearchStudy-phv00407460.v2.json", - "fshName": "phv00407460.v2", - "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 270, - "endLine": 283 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 204, + "endLine": 217 }, { - "outputFile": "ResearchSubject-cbtn-example-participantstudy.json", - "fshName": "cbtn-example-participantstudy", + "outputFile": "ResearchStudy-research-study-gregor.json", + "fshName": "research-study-gregor", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 118, - "endLine": 126 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 2, + "endLine": 10 }, { - "outputFile": "ResearchSubject-emerge-example-participantstudy.json", - "fshName": "emerge-example-participantstudy", + "outputFile": "ResearchSubject-gregor-example-participantstudy.json", + "fshName": "gregor-example-participantstudy", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 285, - "endLine": 293 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 79, + "endLine": 87 }, { - "outputFile": "ResearchSubject-pcgc-example-participantstudy.json", - "fshName": "pcgc-example-participantstudy", + "outputFile": "Specimen-GSS123456-01-010.json", + "fshName": "GSS123456-01-010", "fshType": "Instance", - "fshFile": "examples/participant.fsh", - "startLine": 208, - "endLine": 216 + "fshFile": "examples/GREGoR_example.fsh", + "startLine": 136, + "endLine": 144 }, { "outputFile": "Specimen-SA-000.json", "fshName": "SA-000", "fshType": "Instance", - "fshFile": "examples/biospecimen.fsh", - "startLine": 3, - "endLine": 31 + "fshFile": "examples/CBTN_example.fsh", + "startLine": 311, + "endLine": 339 }, { "outputFile": "StructureDefinition-SharedDataModelAliquot.json", @@ -596,8 +580,8 @@ "fshName": "CdmFamilyRelationship", "fshType": "Logical", "fshFile": "modules/family.fsh", - "startLine": 149, - "endLine": 155 + "startLine": 148, + "endLine": 154 }, { "outputFile": "StructureDefinition-SharedDataModelFamilyRole.json", @@ -876,8 +860,8 @@ "fshName": "NcpiBAMCRAM", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 153, - "endLine": 200 + "startLine": 162, + "endLine": 209 }, { "outputFile": "StructureDefinition-ncpi-collected-sample.json", @@ -900,24 +884,24 @@ "fshName": "NcpiFamilyRelationship", "fshType": "Profile", "fshFile": "modules/family.fsh", - "startLine": 157, - "endLine": 171 + "startLine": 156, + "endLine": 170 }, { "outputFile": "StructureDefinition-ncpi-fastq.json", "fshName": "NcpiFASTQ", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 104, - "endLine": 151 + "startLine": 113, + "endLine": 160 }, { "outputFile": "StructureDefinition-ncpi-file-metadata.json", "fshName": "NcpiFileMetadata", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 79, - "endLine": 86 + "startLine": 88, + "endLine": 95 }, { "outputFile": "StructureDefinition-ncpi-file.json", @@ -932,16 +916,16 @@ "fshName": "NcpiGeneFusionOrExpression", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 300, - "endLine": 347 + "startLine": 309, + "endLine": 356 }, { "outputFile": "StructureDefinition-ncpi-maf.json", "fshName": "NcpiMAF", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 251, - "endLine": 298 + "startLine": 260, + "endLine": 307 }, { "outputFile": "StructureDefinition-ncpi-non-collected-sample.json", @@ -972,8 +956,8 @@ "fshName": "NcpiProteomics", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 349, - "endLine": 396 + "startLine": 358, + "endLine": 405 }, { "outputFile": "StructureDefinition-ncpi-research-access-policy.json", @@ -1012,8 +996,8 @@ "fshName": "NcpiSpecimenCollection", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 88, - "endLine": 94 + "startLine": 97, + "endLine": 103 }, { "outputFile": "StructureDefinition-ncpi-study-family.json", @@ -1028,8 +1012,8 @@ "fshName": "NcpiVCF", "fshType": "Profile", "fshFile": "modules/file-metadata.fsh", - "startLine": 202, - "endLine": 249 + "startLine": 211, + "endLine": 258 }, { "outputFile": "StructureDefinition-research-age-at-last-vital-status.json", @@ -1132,8 +1116,8 @@ "fshName": "SpecimenCollection", "fshType": "Extension", "fshFile": "modules/file-metadata.fsh", - "startLine": 96, - "endLine": 102 + "startLine": 105, + "endLine": 111 }, { "outputFile": "StructureDefinition-study-family-focus.json", diff --git a/fsh-generated/fsh-index.txt b/fsh-generated/fsh-index.txt index 8482a0e77..94eaf46ad 100644 --- a/fsh-generated/fsh-index.txt +++ b/fsh-generated/fsh-index.txt @@ -1,79 +1,77 @@ Output File Name Type FSH File Lines -CodeSystem-adaptor-trimmed-cs.json AdaptorTrimmedCS CodeSystem modules/file-metadata.fsh 49 - 54 -CodeSystem-assay-strategy-cs.json AssayStrategyCS CodeSystem modules/file-metadata.fsh 18 - 22 +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-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 30 - 34 -CodeSystem-library-selection-cs.json LibrarySelectionCS CodeSystem modules/file-metadata.fsh 36 - 40 +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-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 24 - 28 -CodeSystem-reference-genome-cs.json ReferenceGenomeCS CodeSystem modules/file-metadata.fsh 70 - 77 +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-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 42 - 47 +CodeSystem-strandedness-cs.json StrandednessCS CodeSystem modules/file-metadata.fsh 46 - 52 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 63 - 68 -CodeSystem-workflow-type-cs.json WorkflowTypeCS CodeSystem modules/file-metadata.fsh 56 - 61 -Consent-GRU.json GRU Instance examples/participant.fsh 88 - 101 -Consent-HMB.json HMB Instance examples/participant.fsh 178 - 191 +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 +Consent-gregor-gru-consent.json gregor-gru-consent Instance examples/GREGoR_example.fsh 25 - 37 Consent-hmb-irb-npu-consent.json hmb-irb-npu-consent Instance examples/ResearchStudy-BH-CMG.fsh 117 - 133 Consent-hmb-npu-consent.json hmb-npu-consent Instance examples/ResearchStudy-BH-CMG.fsh 71 - 86 -Consent-kf-gru-dac-consent.json kf-gru-dac-consent Instance examples/ResearchStudy-CBTN.fsh 105 - 118 -Consent-kf-gru-dbgap-consent.json kf-gru-dbgap-consent Instance examples/ResearchStudy-CBTN.fsh 135 - 148 -Consent-kf-gsr-allowed-access.json kf-gsr-allowed-access Instance examples/ResearchStudy-CBTN.fsh 165 - 176 -Consent-kf-registered-allowed-access.json kf-registered-allowed-access Instance examples/ResearchStudy-CBTN.fsh 193 - 204 -DocumentReference-PT-006SP660.json PT-006SP660 Instance examples/files.fsh 1 - 22 -Group-cbtn-study-family.json FM-00C8Y7DG Instance examples/family.fsh 12 - 31 +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 133 - 146 +Consent-kf-gsr-allowed-access.json kf-gsr-allowed-access Instance examples/CBTN_example.fsh 163 - 174 +Consent-kf-registered-allowed-access.json kf-registered-allowed-access Instance examples/CBTN_example.fsh 191 - 202 +DocumentReference-GF-6BAD9S7D.json GF-6BAD9S7D Instance examples/CBTN_example.fsh 342 - 363 +DocumentReference-GSS123456-01-010-SG-2.json GSS123456-01-010-SG-2 Instance examples/GREGoR_example.fsh 147 - 168 +Group-cbtn-study-family.json FM-00C8Y7DG Instance examples/family.fsh 11 - 30 Group-cmg-research-study-bhcmg-consent-group-hmb-npu.json cmg-research-study-bhcmg-consent-group-hmb-npu Instance examples/ResearchStudy-BH-CMG.fsh 89 - 100 Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.json cmg-research-study-bhcmg-consent-group-irb-hmb-npu Instance examples/ResearchStudy-BH-CMG.fsh 135 - 146 -Group-kf-research-study-cbtn-participants.json kf-research-study-cbtn-participants Instance examples/ResearchStudy-CBTN.fsh 92 - 103 +Group-gregor-research-study-participants.json gregor-research-study-participants Instance examples/GREGoR_example.fsh 12 - 23 +Group-gregor-study-family.json GSS5555 Instance examples/GREGoR_example.fsh 91 - 106 +Group-kf-research-study-cbtn-participants.json kf-research-study-cbtn-participants Instance examples/CBTN_example.fsh 90 - 101 List-ncpi-research-collection-cmg.json ncpi-research-collection-cmg Instance examples/ResearchStudy-BH-CMG.fsh 163 - 175 -List-ncpi-research-collection-kfx01.json ncpi-research-collection-kfx01 Instance examples/ResearchStudy-CBTN.fsh 236 - 246 -List-ncpi-research-collection-pbta.json ncpi-research-collection-pbta Instance examples/ResearchStudy-CBTN.fsh 222 - 234 -Observation-BAM-CRAM-example.json BAM-CRAM-example Instance examples/file-metadata.fsh 29 - 58 -Observation-FASTQ-example.json FASTQ-example Instance examples/file-metadata.fsh 1 - 26 -Observation-PT-006SP660-condition.json PT-006SP660-condition Instance examples/condition.fsh 2 - 34 -Observation-VCF-example.json VCF-example Instance examples/file-metadata.fsh 60 - 89 -Observation-cbtn-family-relationship-mother.json cbtn-family-relationship-mother Instance examples/family.fsh 33 - 41 -Observation-cbtn-family-relationship-son.json cbtn-family-relationship-son Instance examples/family.fsh 48 - 56 -Organization-kf-research-study-organization-chop.json kf-research-study-organization-chop Instance examples/ResearchStudy-CBTN.fsh 4 - 11 -Patient-6812345.json 6812345 Instance examples/participant.fsh 222 - 255 -Patient-PT-005B7CZ4.json PT-005B7CZ4 Instance examples/participant.fsh 132 - 164 -Patient-PT-KZG2CZ95.json PT-KZG2CZ95 Instance examples/participant.fsh 15 - 54 -Person-cbtn-example-person.json cbtn-example-person Instance examples/participant.fsh 77 - 86 -Person-emerge-example-person.json emerge-example-person Instance examples/participant.fsh 257 - 266 -Person-pcgc-example-person.json pcgc-example-person Instance examples/participant.fsh 167 - 176 -PractitionerRole-kf-research-study-personnel-role-op-lead.json kf-research-study-personnel-role-op-lead Instance examples/ResearchStudy-CBTN.fsh 29 - 35 -PractitionerRole-kf-research-study-personnel-role-pi-x01.json kf-research-study-personnel-role-pi-x01 Instance examples/ResearchStudy-CBTN.fsh 13 - 19 -PractitionerRole-kf-research-study-personnel-role-pi.json kf-research-study-personnel-role-pi Instance examples/ResearchStudy-CBTN.fsh 21 - 27 -ResearchStudy-SD-BHJXBDQK.json SD-BHJXBDQK Instance examples/participant.fsh 103 - 116 -ResearchStudy-SD-PREASA7S.json SD-PREASA7S Instance examples/participant.fsh 193 - 206 +List-ncpi-research-collection-kfx01.json ncpi-research-collection-kfx01 Instance examples/CBTN_example.fsh 234 - 244 +List-ncpi-research-collection-pbta.json ncpi-research-collection-pbta Instance examples/CBTN_example.fsh 220 - 232 +Observation-FASTQ-example.json FASTQ-example Instance examples/CBTN_example.fsh 366 - 388 +Observation-GSS123456-condition.json GSS123456-condition Instance examples/GREGoR_example.fsh 119 - 133 +Observation-PT-006SP660-condition.json PT-006SP660-condition Instance examples/CBTN_example.fsh 276 - 308 +Observation-cbtn-family-relationship-mother.json cbtn-family-relationship-mother Instance examples/family.fsh 32 - 40 +Observation-cbtn-family-relationship-son.json cbtn-family-relationship-son Instance examples/family.fsh 47 - 55 +Observation-gregor-example-metadata.json gregor-example-metadata Instance examples/GREGoR_example.fsh 171 - 197 +Observation-gregor-family-relationship-mother.json gregor-family-relationship-mother Instance examples/GREGoR_example.fsh 108 - 116 +Organization-kf-research-study-organization-chop.json kf-research-study-organization-chop Instance examples/CBTN_example.fsh 2 - 9 +Patient-GSS123456.json GSS123456 Instance examples/GREGoR_example.fsh 50 - 66 +Patient-GSS654321.json GSS654321 Instance examples/GREGoR_example.fsh 40 - 48 +Patient-PT-006SP660.json PT-006SP660 Instance examples/CBTN_example.fsh 247 - 271 +Person-gregor-example-person.json gregor-example-person Instance examples/GREGoR_example.fsh 68 - 77 +PractitionerRole-kf-research-study-personnel-role-op-lead.json kf-research-study-personnel-role-op-lead Instance examples/CBTN_example.fsh 27 - 33 +PractitionerRole-kf-research-study-personnel-role-pi-x01.json kf-research-study-personnel-role-pi-x01 Instance examples/CBTN_example.fsh 11 - 17 +PractitionerRole-kf-research-study-personnel-role-pi.json kf-research-study-personnel-role-pi Instance examples/CBTN_example.fsh 19 - 25 ResearchStudy-cmg-research-study-bhcmg.json cmg-research-study-bhcmg Instance examples/ResearchStudy-BH-CMG.fsh 16 - 67 ResearchStudy-cmg-research-study-subject-cmg-hmb-npu.json cmg-research-study-subject-cmg-hmb-npu Instance examples/ResearchStudy-BH-CMG.fsh 102 - 115 ResearchStudy-cmg-research-study-subject-cmg-irb-hmb-npu.json cmg-research-study-subject-cmg-irb-hmb-npu Instance examples/ResearchStudy-BH-CMG.fsh 148 - 161 -ResearchStudy-kf-research-study-cbtn.json kf-research-study-cbtn Instance examples/ResearchStudy-CBTN.fsh 37 - 88 -ResearchStudy-kf-research-study-subject-gru-dac.json kf-research-study-subject-gru-dac Instance examples/ResearchStudy-CBTN.fsh 120 - 133 -ResearchStudy-kf-research-study-subject-gru-dbgap.json kf-research-study-subject-gru-dbgap Instance examples/ResearchStudy-CBTN.fsh 150 - 163 -ResearchStudy-kf-research-study-subject-gsr-allowed.json kf-research-study-subject-gsr-allowed Instance examples/ResearchStudy-CBTN.fsh 178 - 191 -ResearchStudy-kf-research-study-subject-registered.json kf-research-study-subject-registered Instance examples/ResearchStudy-CBTN.fsh 206 - 219 -ResearchStudy-phv00407460.v2.json phv00407460.v2 Instance examples/participant.fsh 270 - 283 -ResearchSubject-cbtn-example-participantstudy.json cbtn-example-participantstudy Instance examples/participant.fsh 118 - 126 -ResearchSubject-emerge-example-participantstudy.json emerge-example-participantstudy Instance examples/participant.fsh 285 - 293 -ResearchSubject-pcgc-example-participantstudy.json pcgc-example-participantstudy Instance examples/participant.fsh 208 - 216 -Specimen-SA-000.json SA-000 Instance examples/biospecimen.fsh 3 - 31 +ResearchStudy-kf-research-study-cbtn.json kf-research-study-cbtn Instance examples/CBTN_example.fsh 35 - 86 +ResearchStudy-kf-research-study-subject-gru-dac.json kf-research-study-subject-gru-dac Instance examples/CBTN_example.fsh 118 - 131 +ResearchStudy-kf-research-study-subject-gru-dbgap.json kf-research-study-subject-gru-dbgap Instance examples/CBTN_example.fsh 148 - 161 +ResearchStudy-kf-research-study-subject-gsr-allowed.json kf-research-study-subject-gsr-allowed Instance examples/CBTN_example.fsh 176 - 189 +ResearchStudy-kf-research-study-subject-registered.json kf-research-study-subject-registered Instance examples/CBTN_example.fsh 204 - 217 +ResearchStudy-research-study-gregor.json research-study-gregor Instance examples/GREGoR_example.fsh 2 - 10 +ResearchSubject-gregor-example-participantstudy.json gregor-example-participantstudy Instance examples/GREGoR_example.fsh 79 - 87 +Specimen-GSS123456-01-010.json GSS123456-01-010 Instance examples/GREGoR_example.fsh 136 - 144 +Specimen-SA-000.json SA-000 Instance examples/CBTN_example.fsh 311 - 339 StructureDefinition-SharedDataModelAliquot.json CmdAliquot Logical modules/biospecimen.fsh 62 - 70 StructureDefinition-SharedDataModelBiospecimenCollection.json CdmBiospecimenCollection Logical modules/biospecimen.fsh 3 - 13 StructureDefinition-SharedDataModelCondition.json CdmCondition Logical modules/condition.fsh 3 - 21 -StructureDefinition-SharedDataModelFamilyRelationship.json CdmFamilyRelationship Logical modules/family.fsh 149 - 155 +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-SharedDataModelPerson.json CdmPerson Logical modules/participant.fsh 93 - 98 @@ -108,26 +106,26 @@ StructureDefinition-hash-value.json HashValue StructureDefinition-label-extension.json Label Extension extensions/Label.fsh 1 - 13 StructureDefinition-location-access.json LocationAccess Extension modules/files.fsh 64 - 70 StructureDefinition-ncpi-Study-Participant.json NcpiStudyParticipant Profile modules/participant.fsh 133 - 145 -StructureDefinition-ncpi-bamcram.json NcpiBAMCRAM Profile modules/file-metadata.fsh 153 - 200 +StructureDefinition-ncpi-bamcram.json NcpiBAMCRAM Profile modules/file-metadata.fsh 162 - 209 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-family-relationship.json NcpiFamilyRelationship Profile modules/family.fsh 157 - 171 -StructureDefinition-ncpi-fastq.json NcpiFASTQ Profile modules/file-metadata.fsh 104 - 151 -StructureDefinition-ncpi-file-metadata.json NcpiFileMetadata Profile modules/file-metadata.fsh 79 - 86 +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 300 - 347 -StructureDefinition-ncpi-maf.json NcpiMAF Profile modules/file-metadata.fsh 251 - 298 +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-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 349 - 396 +StructureDefinition-ncpi-proteomics.json NcpiProteomics Profile modules/file-metadata.fsh 358 - 405 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 88 - 94 +StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.json NcpiSpecimenCollection Profile modules/file-metadata.fsh 97 - 103 StructureDefinition-ncpi-study-family.json NcpiStudyFamily Profile modules/family.fsh 108 - 131 -StructureDefinition-ncpi-vcf.json NcpiVCF Profile modules/file-metadata.fsh 202 - 249 +StructureDefinition-ncpi-vcf.json NcpiVCF Profile modules/file-metadata.fsh 211 - 258 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 @@ -140,7 +138,7 @@ StructureDefinition-research-study-result.json ResearchStudyR StructureDefinition-research-study-subject-consent.json ResearchStudySubjectConsent Extension modules/research-study-subject.fsh 1 - 5 StructureDefinition-research-study-subject.json ResearchStudySubject Profile modules/research-study-subject.fsh 7 - 15 StructureDefinition-research-web-Link.json ResearchWebLink Extension extensions/ResearchWebLink.fsh 2 - 9 -StructureDefinition-specimen-collection.json SpecimenCollection Extension modules/file-metadata.fsh 96 - 102 +StructureDefinition-specimen-collection.json SpecimenCollection Extension modules/file-metadata.fsh 105 - 111 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 diff --git a/fsh-generated/includes/fsh-link-references.md b/fsh-generated/includes/fsh-link-references.md index 4744fa522..fd259941f 100644 --- a/fsh-generated/includes/fsh-link-references.md +++ b/fsh-generated/includes/fsh-link-references.md @@ -5,6 +5,7 @@ [AgeAtAssertion]: StructureDefinition-age-at-assertion.html [AgeAtLastVitalStatus]: StructureDefinition-research-age-at-last-vital-status.html [HashType]: StructureDefinition-hash-type.html +[gregor-family-relationship-mother]: Observation-gregor-family-relationship-mother.html [cbtn-family-relationship-mother]: Observation-cbtn-family-relationship-mother.html [cbtn-family-relationship-son]: Observation-cbtn-family-relationship-son.html [AssayStrategyCS]: CodeSystem-assay-strategy-cs.html @@ -35,27 +36,28 @@ [ResearchDataDateOfBirthMethod]: CodeSystem-research-data-date-of-birth-method.html [EDAMOntologyTerms]: ValueSet-edam-ontology-terms.html [SA-000]: Specimen-SA-000.html +[GSS123456-01-010]: Specimen-GSS123456-01-010.html [PT-006SP660-condition]: Observation-PT-006SP660-condition.html -[PT-006SP660]: DocumentReference-PT-006SP660.html -[BAM-CRAM-example]: Observation-BAM-CRAM-example.html +[GSS123456-condition]: Observation-GSS123456-condition.html +[GSS654321]: Patient-GSS654321.html +[GF-6BAD9S7D]: DocumentReference-GF-6BAD9S7D.html +[GSS123456-01-010-SG-2]: DocumentReference-GSS123456-01-010-SG-2.html +[gregor-example-metadata]: Observation-gregor-example-metadata.html [FASTQ-example]: Observation-FASTQ-example.html -[VCF-example]: Observation-VCF-example.html -[cbtn-example-participantstudy]: ResearchSubject-cbtn-example-participantstudy.html -[emerge-example-participantstudy]: ResearchSubject-emerge-example-participantstudy.html -[pcgc-example-participantstudy]: ResearchSubject-pcgc-example-participantstudy.html +[gregor-example-participantstudy]: ResearchSubject-gregor-example-participantstudy.html +[PT-006SP660]: Patient-PT-006SP660.html [cbtn-study-family]: Group-cbtn-study-family.html -[PT-KZG2CZ95]: Patient-PT-KZG2CZ95.html -[cbtn-example-person]: Person-cbtn-example-person.html -[6812345]: Patient-6812345.html -[emerge-example-person]: Person-emerge-example-person.html -[PT-005B7CZ4]: Patient-PT-005B7CZ4.html -[pcgc-example-person]: Person-pcgc-example-person.html +[GSS123456]: Patient-GSS123456.html +[gregor-example-person]: Person-gregor-example-person.html +[gregor-study-family]: Group-gregor-study-family.html +[research-study-gregor]: ResearchStudy-research-study-gregor.html [NcpiFamilyRelationship]: StructureDefinition-ncpi-family-relationship.html [FamilyType]: StructureDefinition-family-type.html [NcpiFamilyTypesVS]: ValueSet-ncpi-family-types-vs.html [NCPISample]: StructureDefinition-ncpi-sample.html [NcpiGeneFusionOrExpression]: StructureDefinition-ncpi-gene-fusion-expression.html [kf-gsr-allowed-access]: Consent-kf-gsr-allowed-access.html +[gregor-gru-consent]: Consent-gregor-gru-consent.html [HashTypeCS]: CodeSystem-example-hash-type-code-system.html [hmb-irb-npu-consent]: Consent-hmb-irb-npu-consent.html [hmb-npu-consent]: Consent-hmb-npu-consent.html @@ -73,11 +75,6 @@ [BodyLocationQualifierVS]: ValueSet-condition-location-vs.html [NcpiMAF]: StructureDefinition-ncpi-maf.html [MeshTerms]: ValueSet-mesh-terms.html -[GRU]: Consent-GRU.html -[HMB]: Consent-HMB.html -[SD-BHJXBDQK]: ResearchStudy-SD-BHJXBDQK.html -[SD-PREASA7S]: ResearchStudy-SD-PREASA7S.html -[phv00407460.v2]: ResearchStudy-phv00407460.v2.html [NCPICollectedSample]: StructureDefinition-ncpi-collected-sample.html [NCPINonCollectedSample]: StructureDefinition-ncpi-non-collected-sample.html [NcpiCondition]: StructureDefinition-ncpi-condition.html @@ -100,6 +97,7 @@ [cmg-research-study-bhcmg-consent-group-irb-hmb-npu]: Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.html [cmg-research-study-subject-cmg-irb-hmb-npu]: ResearchStudy-cmg-research-study-subject-cmg-irb-hmb-npu.html [kf-research-study-cbtn-participants]: Group-kf-research-study-cbtn-participants.html +[gregor-research-study-participants]: Group-gregor-research-study-participants.html [ncpi-research-collection-pbta]: List-ncpi-research-collection-pbta.html [ConditionAsserter]: StructureDefinition-condition-asserter.html [PlatformInstrumentCS]: CodeSystem-platform-instrument-cs.html diff --git a/fsh-generated/includes/menu.xml b/fsh-generated/includes/menu.xml index 31e168483..297040aab 100644 --- a/fsh-generated/includes/menu.xml +++ b/fsh-generated/includes/menu.xml @@ -101,25 +101,10 @@ diff --git a/fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json b/fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json index d6f022a3d..cd0b1c0c3 100644 --- a/fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json +++ b/fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json @@ -15,7 +15,11 @@ { "code": "no", "display": "No" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 2 + "count": 3 } diff --git a/fsh-generated/resources/CodeSystem-assay-strategy-cs.json b/fsh-generated/resources/CodeSystem-assay-strategy-cs.json index 9bcdef13d..2ee05a0b9 100644 --- a/fsh-generated/resources/CodeSystem-assay-strategy-cs.json +++ b/fsh-generated/resources/CodeSystem-assay-strategy-cs.json @@ -11,7 +11,11 @@ { "code": "WGS", "display": "Whole Genome Sequencing" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 1 + "count": 2 } diff --git a/fsh-generated/resources/CodeSystem-library-prep-cs.json b/fsh-generated/resources/CodeSystem-library-prep-cs.json index 111905071..3bd9bfd6d 100644 --- a/fsh-generated/resources/CodeSystem-library-prep-cs.json +++ b/fsh-generated/resources/CodeSystem-library-prep-cs.json @@ -11,7 +11,11 @@ { "code": "polyA", "display": "polyA" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 1 + "count": 2 } diff --git a/fsh-generated/resources/CodeSystem-library-selection-cs.json b/fsh-generated/resources/CodeSystem-library-selection-cs.json index 147cdb329..277974578 100644 --- a/fsh-generated/resources/CodeSystem-library-selection-cs.json +++ b/fsh-generated/resources/CodeSystem-library-selection-cs.json @@ -11,7 +11,11 @@ { "code": "PolyTEnrichment", "display": "Poly-T Enrichment" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 1 + "count": 2 } diff --git a/fsh-generated/resources/CodeSystem-platform-instrument-cs.json b/fsh-generated/resources/CodeSystem-platform-instrument-cs.json index b84dd5c31..85ea70b48 100644 --- a/fsh-generated/resources/CodeSystem-platform-instrument-cs.json +++ b/fsh-generated/resources/CodeSystem-platform-instrument-cs.json @@ -11,7 +11,11 @@ { "code": "IlluminaHiSeq2000", "display": "Illumina HiSeq2000" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 1 + "count": 2 } diff --git a/fsh-generated/resources/CodeSystem-reference-genome-cs.json b/fsh-generated/resources/CodeSystem-reference-genome-cs.json index 83cef0073..feb097286 100644 --- a/fsh-generated/resources/CodeSystem-reference-genome-cs.json +++ b/fsh-generated/resources/CodeSystem-reference-genome-cs.json @@ -23,7 +23,11 @@ { "code": "GRCh38p14", "display": "GRCh38.p14" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 4 + "count": 5 } diff --git a/fsh-generated/resources/CodeSystem-strandedness-cs.json b/fsh-generated/resources/CodeSystem-strandedness-cs.json index ba9f282db..54ba2b7f6 100644 --- a/fsh-generated/resources/CodeSystem-strandedness-cs.json +++ b/fsh-generated/resources/CodeSystem-strandedness-cs.json @@ -15,7 +15,11 @@ { "code": "unstranded", "display": "Unstranded" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 2 + "count": 3 } diff --git a/fsh-generated/resources/CodeSystem-workflow-tool-cs.json b/fsh-generated/resources/CodeSystem-workflow-tool-cs.json index 8f20a02de..abb7c15e4 100644 --- a/fsh-generated/resources/CodeSystem-workflow-tool-cs.json +++ b/fsh-generated/resources/CodeSystem-workflow-tool-cs.json @@ -15,7 +15,11 @@ { "code": "GATKHaplotypeCaller", "display": "GATK-Haplotype Caller" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 2 + "count": 3 } diff --git a/fsh-generated/resources/CodeSystem-workflow-type-cs.json b/fsh-generated/resources/CodeSystem-workflow-type-cs.json index af7087a31..8db83d9a6 100644 --- a/fsh-generated/resources/CodeSystem-workflow-type-cs.json +++ b/fsh-generated/resources/CodeSystem-workflow-type-cs.json @@ -15,7 +15,11 @@ { "code": "somatic", "display": "Somatic" + }, + { + "code": "unknown", + "display": "Unknown" } ], - "count": 2 + "count": 3 } diff --git a/fsh-generated/resources/Consent-GRU.json b/fsh-generated/resources/Consent-GRU.json deleted file mode 100644 index a391297c3..000000000 --- a/fsh-generated/resources/Consent-GRU.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "resourceType": "Consent", - "id": "GRU", - "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/research-web-Link", - "valueUrl": "https://redcap.chop.edu/surveys/?s=A7M873HMN8" - }, - { - "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/Consent-HMB.json b/fsh-generated/resources/Consent-HMB.json deleted file mode 100644 index 4f96bb77c..000000000 --- a/fsh-generated/resources/Consent-HMB.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "resourceType": "Consent", - "id": "HMB", - "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/research-web-Link", - "valueUrl": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002517" - }, - { - "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-PT-006SP660.json b/fsh-generated/resources/DocumentReference-PT-006SP660.json deleted file mode 100644 index ebde4eaa9..000000000 --- a/fsh-generated/resources/DocumentReference-PT-006SP660.json +++ /dev/null @@ -1,81 +0,0 @@ -{ - "resourceType": "DocumentReference", - "id": "PT-006SP660", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file" - ] - }, - "identifier": [ - { - "value": "PT_006SP660" - } - ], - "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": "GF_6BAD9S7D" - }, - "description": "Annotated Variant Call", - "type": { - "coding": [ - { - "code": "operation_3227", - "system": "http://edamontology.org", - "display": "Variant calling" - } - ] - }, - "status": "current" -} diff --git a/fsh-generated/resources/Group-cbtn-study-family.json b/fsh-generated/resources/Group-cbtn-study-family.json index b0202b9bd..7bc2830a0 100644 --- a/fsh-generated/resources/Group-cbtn-study-family.json +++ b/fsh-generated/resources/Group-cbtn-study-family.json @@ -55,7 +55,7 @@ } } ], - "reference": "Patient/PT-KZG2CZ95" + "reference": "PT-KZG2CZ95" } }, { @@ -74,7 +74,7 @@ } } ], - "reference": "Patient/PT-005B7CZ4" + "reference": "PT-005B7CZ4" } } ], 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 4add3de5b..9cdb98ccd 100644 --- a/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json +++ b/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json @@ -93,6 +93,14 @@ "description": "Algorithm used to calculate the hash (and size, where applicable)", "exampleBoolean": false }, + { + "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.", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-family-relationship" + }, { "reference": { "reference": "Observation/cbtn-family-relationship-mother" @@ -334,79 +342,79 @@ }, { "reference": { - "reference": "Observation/PT-006SP660-condition" + "reference": "Specimen/GSS123456-01-010" }, - "name": "Example condition using data from Kids First", - "description": "Example condition using data from Kids First.", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-condition" + "name": "Example biospecimen based on data from GREGoR", + "description": "Example biospecimen based on data from GREGoR", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-collected-sample" }, { "reference": { - "reference": "DocumentReference/PT-006SP660" + "reference": "Observation/PT-006SP660-condition" }, - "name": "Example file based on CBTN", - "description": "Use case of file information from CBTN", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file" + "name": "Example condition using data from CBTN", + "description": "Example condition using data from CBTN.", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-condition" }, { "reference": { - "reference": "Observation/BAM-CRAM-example" + "reference": "Observation/GSS123456-condition" }, - "name": "Example file metadata for a BAM-CRAM file", - "description": "Example file metadata for a BAM-CRAM file", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram" + "name": "Example condition using data from GREGoR", + "description": "Example condition using data from GREGoR", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-condition" }, { "reference": { - "reference": "Observation/FASTQ-example" + "reference": "Patient/GSS654321" }, - "name": "Example file metadata for a FASTQ file", - "description": "Example file metadata for a FASTQ file", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-fastq" + "name": "Example family member based on data from GREGoR", + "description": "Example family member based on data from GREGoR.", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" }, { "reference": { - "reference": "Observation/VCF-example" + "reference": "DocumentReference/GF-6BAD9S7D" }, - "name": "Example file metadata for a VCF file", - "description": "Example file metadata for a VCF file", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-vcf" + "name": "Example file based on CBTN", + "description": "Use case of file information from CBTN", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file" }, { "reference": { - "reference": "ResearchSubject/cbtn-example-participantstudy" + "reference": "DocumentReference/GSS123456-01-010-SG-2" }, - "name": "Example mappings based on data from CBTN", - "description": "Example mappings based on data from CBTN", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" + "name": "Example file based on CBTN", + "description": "Use case of file information from CBTN", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file" }, { "reference": { - "reference": "ResearchSubject/emerge-example-participantstudy" + "reference": "Observation/gregor-example-metadata" }, - "name": "Example mappings based on data from eMERGE", - "description": "Example mappings based on data from eMERGE", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" + "name": "Example file metadata for a BAM-CRAM file from GREGoR", + "description": "Example file metadata for a BAM-CRAM file from GREGoR", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram" }, { "reference": { - "reference": "ResearchSubject/pcgc-example-participantstudy" + "reference": "Observation/FASTQ-example" }, - "name": "Example mappings based on data from PCGC", - "description": "Example mappings based on data from PCGC", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" + "name": "Example file metadata for a FASTQ file", + "description": "Example file metadata for a FASTQ file", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-fastq" }, { "reference": { - "reference": "Group/cbtn-study-family" + "reference": "ResearchSubject/gregor-example-participantstudy" }, - "name": "Example patients based on data from CBTN", - "description": "Example patients based on data from CBTN.", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-study-family" + "name": "Example mappings based on data from GREGoR", + "description": "Example mappings based on data from GREGoR", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" }, { "reference": { - "reference": "Patient/PT-KZG2CZ95" + "reference": "Patient/PT-006SP660" }, "name": "Example patients based on data from CBTN", "description": "Example patients based on data from CBTN.", @@ -414,43 +422,43 @@ }, { "reference": { - "reference": "Person/cbtn-example-person" + "reference": "Group/cbtn-study-family" }, "name": "Example patients based on data from CBTN", - "description": "Example patients based on data from CBTN", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" + "description": "Example patients based on data from CBTN.", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-study-family" }, { "reference": { - "reference": "Patient/6812345" + "reference": "Patient/GSS123456" }, - "name": "Example patients based on data from eMERGE", - "description": "Example patients based on data from eMERGE", + "name": "Example patients based on data from GREGoR", + "description": "Example patients based on data from GREGoR.", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" }, { "reference": { - "reference": "Person/emerge-example-person" + "reference": "Person/gregor-example-person" }, - "name": "Example patients based on data from eMERGE", - "description": "Example patients based on data from eMERGE", + "name": "Example patients based on data from GREGoR", + "description": "Example patients based on data from GREGoR", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" }, { "reference": { - "reference": "Patient/PT-005B7CZ4" + "reference": "Group/gregor-study-family" }, - "name": "Example patients based on data from PCGC", - "description": "Example patients based on data from PCGC.", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + "name": "Example patients based on data from GREGoR", + "description": "Example patients based on data from GREGoR.", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-study-family" }, { "reference": { - "reference": "Person/pcgc-example-person" + "reference": "ResearchStudy/research-study-gregor" }, - "name": "Example patients based on data from PCGC", - "description": "Example patients based on data from PCGC", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" + "name": "Example study from GREGoR", + "description": "Example study from GREGoR", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-study" }, { "reference": { @@ -500,6 +508,14 @@ "description": "Genomic Summary Results (GSR) Allowed Access", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" }, + { + "reference": { + "reference": "Consent/gregor-gru-consent" + }, + "name": "GREGoR General Research Use (GRU) Consent", + "description": "General Research Use (GRU)", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + }, { "reference": { "reference": "CodeSystem/example-hash-type-code-system" @@ -636,46 +652,6 @@ "description": "Example terms from Medical Subject Headings (MeSH) Ontology", "exampleBoolean": false }, - { - "reference": { - "reference": "Consent/GRU" - }, - "name": "Mock consent based on kf-gru-dac-consent", - "description": "General Research Use (GRU)", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" - }, - { - "reference": { - "reference": "Consent/HMB" - }, - "name": "Mock consent based on kf-gru-dbgap-consent", - "description": "General Research Use (GRU)", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" - }, - { - "reference": { - "reference": "ResearchStudy/SD-BHJXBDQK" - }, - "name": "Mock study based on kf-research-study-subject-gru-dac", - "description": "GRU data access via DAC", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" - }, - { - "reference": { - "reference": "ResearchStudy/SD-PREASA7S" - }, - "name": "Mock Study based on kf-research-study-subject-gru-dbgap", - "description": "GRU data access via dbGaP", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" - }, - { - "reference": { - "reference": "ResearchStudy/phv00407460.v2" - }, - "name": "Mock study based on kf-research-study-subject-gsr-allowed", - "description": "Genomic Summary Results (GSR) Allowed Access", - "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" - }, { "reference": { "reference": "StructureDefinition/ncpi-collected-sample" @@ -852,6 +828,14 @@ "description": "Participants from the CBTN research study", "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" }, + { + "reference": { + "reference": "Group/gregor-research-study-participants" + }, + "name": "Participants from the CBTN research study", + "description": "Participants from the CBTN research study", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" + }, { "reference": { "reference": "List/ncpi-research-collection-pbta" @@ -1336,38 +1320,13 @@ "generation": "markdown" }, { - "nameUrl": "example_assays.html", - "title": "Example Assays", - "generation": "markdown" - }, - { - "nameUrl": "example_family.html", - "title": "Example Family", - "generation": "markdown" - }, - { - "nameUrl": "example_files.html", - "title": "Example Files", - "generation": "markdown" - }, - { - "nameUrl": "example_participant.html", - "title": "Example Participant", - "generation": "markdown" - }, - { - "nameUrl": "example_phenotype_condition.html", - "title": "Example Phenotype Condition", - "generation": "markdown" - }, - { - "nameUrl": "example_research_study.html", - "title": "Example Research Study", + "nameUrl": "example_cbtn.html", + "title": "Example Cbtn", "generation": "markdown" }, { - "nameUrl": "example_specimen.html", - "title": "Example Specimen", + "nameUrl": "example_gregor.html", + "title": "Example Gregor", "generation": "markdown" }, { diff --git a/fsh-generated/resources/Observation-BAM-CRAM-example.json b/fsh-generated/resources/Observation-BAM-CRAM-example.json deleted file mode 100644 index 746719172..000000000 --- a/fsh-generated/resources/Observation-BAM-CRAM-example.json +++ /dev/null @@ -1,184 +0,0 @@ -{ - "resourceType": "Observation", - "id": "BAM-CRAM-example", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram" - ] - }, - "focus": [ - { - "reference": "PT_006SP660" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "code": "WorkflowType" - } - ] - } - }, - { - "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" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "Strandedness" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "unstranded" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "ReferenceGenome" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "GRCh37" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "IsPairedEnd" - } - ] - }, - "valueBoolean": false - }, - { - "code": { - "coding": [ - { - "code": "WorkflowTool" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "bammem" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "WorkflowType" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "alignment" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "TargetRegion" - } - ] - } - } - ], - "status": "final", - "code": { - "coding": [ - { - "code": "format_2572", - "system": "http://edamontology.org" - } - ] - }, - "specimen": { - "reference": "Specimen/SA-000" - } -} diff --git a/fsh-generated/resources/Observation-FASTQ-example.json b/fsh-generated/resources/Observation-FASTQ-example.json index f6295fee2..a95d1d266 100644 --- a/fsh-generated/resources/Observation-FASTQ-example.json +++ b/fsh-generated/resources/Observation-FASTQ-example.json @@ -8,7 +8,7 @@ }, "focus": [ { - "reference": "PT_006SP660" + "reference": "DocumentReference/GF-6BAD9S7D" } ], "component": [ diff --git a/fsh-generated/resources/Observation-VCF-example.json b/fsh-generated/resources/Observation-VCF-example.json deleted file mode 100644 index af2f2dea6..000000000 --- a/fsh-generated/resources/Observation-VCF-example.json +++ /dev/null @@ -1,184 +0,0 @@ -{ - "resourceType": "Observation", - "id": "VCF-example", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-vcf" - ] - }, - "focus": [ - { - "reference": "PT_006SP660" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "code": "WorkflowType" - } - ] - } - }, - { - "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" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "Strandedness" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "unstranded" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "ReferenceGenome" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "GRCh38" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "IsPairedEnd" - } - ] - }, - "valueBoolean": false - }, - { - "code": { - "coding": [ - { - "code": "WorkflowTool" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "GATKHaplotypeCaller" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "WorkflowType" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "somatic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "code": "TargetRegion" - } - ] - } - } - ], - "status": "final", - "code": { - "coding": [ - { - "code": "format_3016", - "system": "http://edamontology.org" - } - ] - }, - "specimen": { - "reference": "Specimen/SA-000" - } -} diff --git a/fsh-generated/resources/Observation-cbtn-family-relationship-mother.json b/fsh-generated/resources/Observation-cbtn-family-relationship-mother.json index 4e8af42b1..dc3fb282c 100644 --- a/fsh-generated/resources/Observation-cbtn-family-relationship-mother.json +++ b/fsh-generated/resources/Observation-cbtn-family-relationship-mother.json @@ -8,11 +8,11 @@ }, "focus": [ { - "reference": "Patient/PT-005B7CZ4" + "reference": "PT-005B7CZ4" } ], "subject": { - "reference": "Patient/PT-KZG2CZ95" + "reference": "PT-KZG2CZ95" }, "code": { "coding": [ diff --git a/fsh-generated/resources/Observation-cbtn-family-relationship-son.json b/fsh-generated/resources/Observation-cbtn-family-relationship-son.json index 49dd7359f..95bdbd10b 100644 --- a/fsh-generated/resources/Observation-cbtn-family-relationship-son.json +++ b/fsh-generated/resources/Observation-cbtn-family-relationship-son.json @@ -8,11 +8,11 @@ }, "focus": [ { - "reference": "Patient/PT-KZG2CZ95" + "reference": "PT-KZG2CZ95" } ], "subject": { - "reference": "Patient/PT-005B7CZ4" + "reference": "PT-005B7CZ4" }, "code": { "coding": [ diff --git a/fsh-generated/resources/Patient-6812345.json b/fsh-generated/resources/Patient-6812345.json deleted file mode 100644 index fd64dd31e..000000000 --- a/fsh-generated/resources/Patient-6812345.json +++ /dev/null @@ -1,98 +0,0 @@ -{ - "resourceType": "Patient", - "id": "6812345", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" - ] - }, - "identifier": [ - { - "system": "https://emerge-network.org/", - "value": "12345" - }, - { - "system": "https://emerge-network.org/", - "value": "6812345" - } - ], - "extension": [ - { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", - "valueCode": "F" - }, - { - "extension": [ - { - "url": "ombCategory", - "valueCoding": { - "code": "1002-5", - "system": "urn:oid:2.16.840.1.113883.6.238", - "display": "American Indian or Alaska Native" - } - }, - { - "url": "text", - "valueString": "American Indian or Alaska Native" - } - ], - "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": "decade-only", - "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method" - } - } - ], - "_birthDate": { - "extension": [ - { - "extension": [ - { - "url": "target", - "valueReference": { - "reference": "Patient/6812345" - } - }, - { - "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/Patient-PT-005B7CZ4.json b/fsh-generated/resources/Patient-PT-005B7CZ4.json deleted file mode 100644 index 41e12cabb..000000000 --- a/fsh-generated/resources/Patient-PT-005B7CZ4.json +++ /dev/null @@ -1,91 +0,0 @@ -{ - "resourceType": "Patient", - "id": "PT-005B7CZ4", - "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-005B7CZ4" - } - }, - { - "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/Patient-PT-KZG2CZ95.json b/fsh-generated/resources/Patient-PT-KZG2CZ95.json deleted file mode 100644 index 125f2ce45..000000000 --- a/fsh-generated/resources/Patient-PT-KZG2CZ95.json +++ /dev/null @@ -1,107 +0,0 @@ -{ - "resourceType": "Patient", - "id": "PT-KZG2CZ95", - "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_KZG2CZ95" - } - ], - "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" - } - ], - "_birthDate": { - "extension": [ - { - "extension": [ - { - "url": "target", - "valueReference": { - "reference": "Patient/PT-KZG2CZ95" - } - }, - { - "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-cbtn-example-person.json b/fsh-generated/resources/Person-cbtn-example-person.json deleted file mode 100644 index c6be9a0ae..000000000 --- a/fsh-generated/resources/Person-cbtn-example-person.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "resourceType": "Person", - "id": "cbtn-example-person", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" - ] - }, - "identifier": [ - { - "system": "https://data.kidsfirstdrc.org", - "value": "PS_123" - } - ], - "link": [ - { - "target": { - "reference": "Patient/PT-KZG2CZ95" - } - } - ] -} diff --git a/fsh-generated/resources/Person-emerge-example-person.json b/fsh-generated/resources/Person-emerge-example-person.json deleted file mode 100644 index 4aa9ca547..000000000 --- a/fsh-generated/resources/Person-emerge-example-person.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "resourceType": "Person", - "id": "emerge-example-person", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" - ] - }, - "identifier": [ - { - "system": "https://emerge-network.org/", - "value": "PS_321" - } - ], - "link": [ - { - "target": { - "reference": "Patient/6812345" - } - } - ] -} diff --git a/fsh-generated/resources/Person-pcgc-example-person.json b/fsh-generated/resources/Person-pcgc-example-person.json deleted file mode 100644 index 23dfe6553..000000000 --- a/fsh-generated/resources/Person-pcgc-example-person.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "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-005B7CZ4" - } - } - ] -} diff --git a/fsh-generated/resources/ResearchStudy-SD-BHJXBDQK.json b/fsh-generated/resources/ResearchStudy-SD-BHJXBDQK.json deleted file mode 100644 index 44b814c77..000000000 --- a/fsh-generated/resources/ResearchStudy-SD-BHJXBDQK.json +++ /dev/null @@ -1,36 +0,0 @@ -{ - "resourceType": "ResearchStudy", - "id": "SD-BHJXBDQK", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" - ] - }, - "identifier": [ - { - "system": "https://cbtn.org/", - "value": "SD-BHJXBDQK" - } - ], - "partOf": [ - { - "reference": "ResearchStudy/kf-research-study-cbtn" - } - ], - "extension": [ - { - "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject-consent", - "valueReference": { - "reference": "Consent/kf-gru-dac-consent" - } - } - ], - "enrollment": [ - { - "reference": "Group/kf-research-study-cbtn-participants" - } - ], - "title": "GRU-DAC Study Subject", - "description": "General Research Use data access via DAC", - "status": "completed" -} diff --git a/fsh-generated/resources/ResearchStudy-SD-PREASA7S.json b/fsh-generated/resources/ResearchStudy-SD-PREASA7S.json deleted file mode 100644 index ed7fe063a..000000000 --- a/fsh-generated/resources/ResearchStudy-SD-PREASA7S.json +++ /dev/null @@ -1,36 +0,0 @@ -{ - "resourceType": "ResearchStudy", - "id": "SD-PREASA7S", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" - ] - }, - "identifier": [ - { - "system": "https://cbtn.org/", - "value": "GRU-dbGaP" - } - ], - "partOf": [ - { - "reference": "ResearchStudy/kf-research-study-cbtn" - } - ], - "extension": [ - { - "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject-consent", - "valueReference": { - "reference": "Consent/kf-gru-dbgap-consent" - } - } - ], - "enrollment": [ - { - "reference": "Group/kf-research-study-cbtn-participants" - } - ], - "title": "GRU-dbGaP Study Subject", - "description": "General Research Use data access via dbGaP", - "status": "completed" -} diff --git a/fsh-generated/resources/ResearchStudy-phv00407460.v2.json b/fsh-generated/resources/ResearchStudy-phv00407460.v2.json deleted file mode 100644 index 419475f9a..000000000 --- a/fsh-generated/resources/ResearchStudy-phv00407460.v2.json +++ /dev/null @@ -1,36 +0,0 @@ -{ - "resourceType": "ResearchStudy", - "id": "phv00407460.v2", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" - ] - }, - "identifier": [ - { - "system": "https://cbtn.org/", - "value": "GSR-ALLOWED" - } - ], - "partOf": [ - { - "reference": "ResearchStudy/kf-research-study-cbtn" - } - ], - "extension": [ - { - "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject-consent", - "valueReference": { - "reference": "Consent/kf-gsr-allowed-access" - } - } - ], - "enrollment": [ - { - "reference": "Group/kf-research-study-cbtn-participants" - } - ], - "title": "GSR-ALLOWED Study Subject", - "description": "Genomic Summary Results (GSR) Allowed Access", - "status": "completed" -} diff --git a/fsh-generated/resources/ResearchSubject-cbtn-example-participantstudy.json b/fsh-generated/resources/ResearchSubject-cbtn-example-participantstudy.json deleted file mode 100644 index 6edf25deb..000000000 --- a/fsh-generated/resources/ResearchSubject-cbtn-example-participantstudy.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "resourceType": "ResearchSubject", - "id": "cbtn-example-participantstudy", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" - ] - }, - "individual": { - "reference": "Patient/PT-KZG2CZ95" - }, - "study": { - "reference": "ResearchStudy/SD-BHJXBDQK" - }, - "status": "candidate", - "consent": { - "reference": "Consent/GRU" - } -} diff --git a/fsh-generated/resources/ResearchSubject-emerge-example-participantstudy.json b/fsh-generated/resources/ResearchSubject-emerge-example-participantstudy.json deleted file mode 100644 index 1bf345248..000000000 --- a/fsh-generated/resources/ResearchSubject-emerge-example-participantstudy.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "resourceType": "ResearchSubject", - "id": "emerge-example-participantstudy", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" - ] - }, - "individual": { - "reference": "Patient/6812345" - }, - "study": { - "reference": "ResearchStudy/phv00407460.v2" - }, - "status": "candidate", - "consent": { - "reference": "Consent/GRU" - } -} diff --git a/fsh-generated/resources/ResearchSubject-pcgc-example-participantstudy.json b/fsh-generated/resources/ResearchSubject-pcgc-example-participantstudy.json deleted file mode 100644 index f331e5526..000000000 --- a/fsh-generated/resources/ResearchSubject-pcgc-example-participantstudy.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "resourceType": "ResearchSubject", - "id": "pcgc-example-participantstudy", - "meta": { - "profile": [ - "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant" - ] - }, - "individual": { - "reference": "Patient/PT-005B7CZ4" - }, - "study": { - "reference": "ResearchStudy/SD-PREASA7S" - }, - "status": "candidate", - "consent": { - "reference": "Consent/HMB" - } -} diff --git a/fsh-generated/resources/Specimen-SA-000.json b/fsh-generated/resources/Specimen-SA-000.json index 43f1ce013..5dcd48297 100644 --- a/fsh-generated/resources/Specimen-SA-000.json +++ b/fsh-generated/resources/Specimen-SA-000.json @@ -31,7 +31,7 @@ { "url": "target", "valueReference": { - "reference": "PT_006SP660" + "reference": "Patient/PT-006SP660" } }, { @@ -67,6 +67,6 @@ } ], "subject": { - "reference": "PT_006SP660" + "reference": "Patient/PT-006SP660" } } diff --git a/fsh-generated/resources/StructureDefinition-research-population.json b/fsh-generated/resources/StructureDefinition-research-population.json index fe8246050..7ba9246a2 100644 --- a/fsh-generated/resources/StructureDefinition-research-population.json +++ b/fsh-generated/resources/StructureDefinition-research-population.json @@ -40,6 +40,9 @@ "id": "Extension.value[x]", "path": "Extension.value[x]", "type": [ + { + "code": "string" + }, { "code": "CodeableConcept" } diff --git a/input/fsh/examples/GREGoR_example.fsh b/input/fsh/examples/GREGoR_example.fsh index 735382186..323f70723 100644 --- a/input/fsh/examples/GREGoR_example.fsh +++ b/input/fsh/examples/GREGoR_example.fsh @@ -101,9 +101,9 @@ Description: "Example patients based on data from GREGoR." * actual = true // Required by Group * extension[family-type].valueCodeableConcept = $ncpi-family-types#Duo "Duo" * member[0].entity = Reference(GSS123456) -* member[0].entity.extension.extension[family-role].valueCodeableConcept = $family-role-code#CHILD "child" +* member[0].entity.extension[family-role].valueCodeableConcept = $family-role-code#CHILD "child" * member[1].entity = Reference(GSS654321) -* member[1].entity.extension.extension[family-role].valueCodeableConcept = $family-role-code#MTH "mother" +* member[1].entity.extension[family-role].valueCodeableConcept = $family-role-code#MTH "mother" Instance: gregor-family-relationship-mother InstanceOf: NcpiFamilyRelationship diff --git a/input/fsh/examples/family.fsh b/input/fsh/examples/family.fsh index b35deab51..f73cc034c 100644 --- a/input/fsh/examples/family.fsh +++ b/input/fsh/examples/family.fsh @@ -8,7 +8,6 @@ Examples for: // Example 1 -/* Instance: FM-00C8Y7DG InstanceOf: NcpiStudyFamily Title: "Example patients based on data from CBTN" @@ -53,4 +52,4 @@ Description: "An example family relationship based on data from CBTN." * subject = Reference(PT-005B7CZ4) * focus = Reference(PT-KZG2CZ95) * code = $family-role-code#SON "natural son" -* status = #registered */ \ No newline at end of file +* status = #registered \ No newline at end of file