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Family update #49

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Sep 16, 2024
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606 changes: 343 additions & 263 deletions fsh-generated/fsh-index.json

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154 changes: 82 additions & 72 deletions fsh-generated/fsh-index.txt

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60 changes: 35 additions & 25 deletions fsh-generated/includes/fsh-link-references.md
Original file line number Diff line number Diff line change
@@ -2,13 +2,15 @@
[AccessPolicyDescription]: StructureDefinition-access-policy-description.html
[AccessType]: StructureDefinition-access-type.html
[AdaptorTrimmedCS]: CodeSystem-adaptor-trimmed-cs.html
[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
[cbtn-family-role-mother]: Group-cbtn-family-role-mother.html
[cbtn-family-role-son]: Group-cbtn-family-role-son.html
[AssayStrategyCS]: CodeSystem-assay-strategy-cs.html
[ConditionAssertionVS]: ValueSet-condition-assertion-vs.html
[ConditionAssertion]: CodeSystem-condition-assertion.html
[AliquotAvailability]: StructureDefinition-aliquot-availability.html
[NcpiBAMCRAM]: StructureDefinition-ncpi-bamcram.html
[cmg-research-study-bhcmg]: ResearchStudy-cmg-research-study-bhcmg.html
@@ -24,53 +26,58 @@
[CollectionTypeVS]: ValueSet-collection-type-vs.html
[CollectionType]: CodeSystem-collection-type.html
[AliquotConcentration]: StructureDefinition-aliquot-concentration.html
[ConditionCodeVS]: ValueSet-condition-code-vs.html
[Consanguinity]: StructureDefinition-consanguinity.html
[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
[ComponentElements]: CodeSystem-component-elements.html
[ResearchDataDateOfBirthMethodVS]: ValueSet-research-data-date-of-birth-method-vs.html
[ResearchDataDateOfBirthMethod]: CodeSystem-research-data-date-of-birth-method.html
[EDAMOntologyTerms]: ValueSet-edam-ontology-terms.html
[SA-000]: Specimen-SA-000.html
[PT-006SP660]: DocumentReference-PT-006SP660.html
[BAM-CRAM-example]: Observation-BAM-CRAM-example.html
[GSS123456-01-010]: Specimen-GSS123456-01-010.html
[PT-006SP660-condition]: Observation-PT-006SP660-condition.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
[NcpiFamilyRole]: StructureDefinition-ncpi-family-role.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
[LocationAccess]: StructureDefinition-location-access.html
[ncpi-research-collection-kfx01]: List-ncpi-research-collection-kfx01.html
[Label]: StructureDefinition-label-extension.html
[BiospecimenLaterality]: StructureDefinition-biospecimen-laterality.html
[ConditionLaterality]: StructureDefinition-condition-laterality.html
[LateralityQualifierVS]: ValueSet-condition-laterality-vs.html
[LibraryPrepCS]: CodeSystem-library-prep-cs.html
[LibrarySelectionCS]: CodeSystem-library-selection-cs.html
[NcpiSpecimenCollection]: StructureDefinition-ncpi-specimen-NcpiSpecimenCollection.html
[SpecimenCollection]: StructureDefinition-specimen-collection.html
[ConditionLocation]: StructureDefinition-condition-location.html
[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
[NcpiAnalysisFile]: StructureDefinition-ncpi-analysis-file.html
[NcpiAssayFile]: StructureDefinition-ncpi-assay-file.html
[NCPICollectedSample]: StructureDefinition-ncpi-collected-sample.html
[NCPINonCollectedSample]: StructureDefinition-ncpi-non-collected-sample.html
[NcpiCondition]: StructureDefinition-ncpi-condition.html
[NcpiFamilyTypes]: CodeSystem-ncpi-family-types.html
[NcpiFASTQ]: StructureDefinition-ncpi-fastq.html
[Ncpi]: CodeSystem-ncpi.html
@@ -79,21 +86,22 @@
[MetadataElements]: CodeSystem-metadata-elements.html
[NcpiParticipant]: StructureDefinition-ncpi-participant.html
[NcpiPerson]: StructureDefinition-ncpi-person.html
[NcpiReadsFile]: StructureDefinition-ncpi-reads-file.html
[NcpiResearchAccessPolicy]: StructureDefinition-ncpi-research-access-policy.html
[NcpiResearchCollection]: StructureDefinition-ncpi-research-collection.html
[NcpiResearchStudy]: StructureDefinition-ncpi-research-study.html
[ResearchStudyGroup]: StructureDefinition-research-study-group.html
[NcpiSequencingFile]: StructureDefinition-ncpi-sequencing-file.html
[NcpiStudyFamily]: StructureDefinition-ncpi-study-family.html
[NcpiStudyParticipant]: StructureDefinition-ncpi-Study-Participant.html
[cmg-research-study-bhcmg-consent-group-hmb-npu]: Group-cmg-research-study-bhcmg-consent-group-hmb-npu.html
[cmg-research-study-subject-cmg-hmb-npu]: ResearchStudy-cmg-research-study-subject-cmg-hmb-npu.html
[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
[NcpiProteomics]: StructureDefinition-ncpi-proteomics.html
[HashExtension]: StructureDefinition-hash-extension.html
[ReferenceGenomeCS]: CodeSystem-reference-genome-cs.html
[kf-registered-allowed-access]: Consent-kf-registered-allowed-access.html
@@ -115,6 +123,7 @@
[BiospecimenAvailability]: CodeSystem-biospecimen-availability.html
[CmdAliquot]: StructureDefinition-SharedDataModelAliquot.html
[CdmBiospecimenCollection]: StructureDefinition-SharedDataModelBiospecimenCollection.html
[CdmCondition]: StructureDefinition-SharedDataModelCondition.html
[CdmFamilyRelationship]: StructureDefinition-SharedDataModelFamilyRelationship.html
[CdmFamilyRole]: StructureDefinition-SharedDataModelFamilyRole.html
[CdmFile]: StructureDefinition-SharedDataModelFile.html
@@ -131,14 +140,15 @@
[Description]: StructureDefinition-description.html
[FamilyRole]: StructureDefinition-family-role.html
[StudyFamilyFocus]: StructureDefinition-study-family-focus.html
[StudyFamily]: StructureDefinition-study-family.html
[StudyNameTypeVS]: ValueSet-study-name-type-vs.html
[StudyNameType]: CodeSystem-study-name-type.html
[StudyPersonnelRoleVS]: ValueSet-study-personnel-role-vs.html
[StudyPersonnelRole]: CodeSystem-study-personnel-role.html
[ncpi-research-collection-cmg]: List-ncpi-research-collection-cmg.html
[FileFormat]: StructureDefinition-file-format.html
[FileSize]: StructureDefinition-file-size.html
[ConditionTypeVS]: ValueSet-condition-type-vs.html
[ConditionType]: CodeSystem-condition-type.html
[HashValue]: StructureDefinition-hash-value.html
[NcpiVCF]: StructureDefinition-ncpi-vcf.html
[ContentVersion]: StructureDefinition-content-version.html
19 changes: 2 additions & 17 deletions fsh-generated/includes/menu.xml
Original file line number Diff line number Diff line change
@@ -101,25 +101,10 @@
</a>
<ul class="dropdown-menu">
<li>
<a href="example_research_study.html">Research Study</a>
<a href="example_cbtn.html">CBTN Example</a>
</li>
<li>
<a href="example_participant.html">Participant-level Data</a>
</li>
<li>
<a href="example_phenotype_condition.html">Phenotype/Condition</a>
</li>
<li>
<a href="example_family.html">Family</a>
</li>
<li>
<a href="example_specimen.html">Specimen</a>
</li>
<li>
<a href="example_assays.html">Assays</a>
</li>
<li>
<a href="example_files.html">File Data</a>
<a href="example_gregor.html">GREGoR Example</a>
</li>
</ul>
</li>
6 changes: 5 additions & 1 deletion fsh-generated/resources/CodeSystem-adaptor-trimmed-cs.json
Original file line number Diff line number Diff line change
@@ -15,7 +15,11 @@
{
"code": "no",
"display": "No"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 2
"count": 3
}
6 changes: 5 additions & 1 deletion fsh-generated/resources/CodeSystem-assay-strategy-cs.json
Original file line number Diff line number Diff line change
@@ -11,7 +11,11 @@
{
"code": "WGS",
"display": "Whole Genome Sequencing"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 1
"count": 2
}
8 changes: 0 additions & 8 deletions fsh-generated/resources/CodeSystem-condition-codes.json

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6 changes: 5 additions & 1 deletion fsh-generated/resources/CodeSystem-library-prep-cs.json
Original file line number Diff line number Diff line change
@@ -11,7 +11,11 @@
{
"code": "polyA",
"display": "polyA"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 1
"count": 2
}
6 changes: 5 additions & 1 deletion fsh-generated/resources/CodeSystem-library-selection-cs.json
Original file line number Diff line number Diff line change
@@ -11,7 +11,11 @@
{
"code": "PolyTEnrichment",
"display": "Poly-T Enrichment"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 1
"count": 2
}
Original file line number Diff line number Diff line change
@@ -11,7 +11,11 @@
{
"code": "IlluminaHiSeq2000",
"display": "Illumina HiSeq2000"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 1
"count": 2
}
16 changes: 14 additions & 2 deletions fsh-generated/resources/CodeSystem-reference-genome-cs.json
Original file line number Diff line number Diff line change
@@ -14,8 +14,20 @@
},
{
"code": "GRCh38",
"display": "GRCh38"
"display": "CRCh38"
},
{
"code": "GRCh38p13",
"display": "GRCh38.p13"
},
{
"code": "GRCh38p14",
"display": "GRCh38.p14"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 2
"count": 5
}
6 changes: 5 additions & 1 deletion fsh-generated/resources/CodeSystem-strandedness-cs.json
Original file line number Diff line number Diff line change
@@ -15,7 +15,11 @@
{
"code": "unstranded",
"display": "Unstranded"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 2
"count": 3
}
6 changes: 5 additions & 1 deletion fsh-generated/resources/CodeSystem-workflow-tool-cs.json
Original file line number Diff line number Diff line change
@@ -15,7 +15,11 @@
{
"code": "GATKHaplotypeCaller",
"display": "GATK-Haplotype Caller"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 2
"count": 3
}
6 changes: 5 additions & 1 deletion fsh-generated/resources/CodeSystem-workflow-type-cs.json
Original file line number Diff line number Diff line change
@@ -15,7 +15,11 @@
{
"code": "somatic",
"display": "Somatic"
},
{
"code": "unknown",
"display": "Unknown"
}
],
"count": 2
"count": 3
}
68 changes: 0 additions & 68 deletions fsh-generated/resources/Consent-GRU.json

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68 changes: 0 additions & 68 deletions fsh-generated/resources/Consent-HMB.json

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81 changes: 0 additions & 81 deletions fsh-generated/resources/DocumentReference-PT-006SP660.json

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38 changes: 0 additions & 38 deletions fsh-generated/resources/Group-cbtn-family-role-mother.json

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38 changes: 0 additions & 38 deletions fsh-generated/resources/Group-cbtn-family-role-son.json

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40 changes: 40 additions & 0 deletions fsh-generated/resources/Group-cbtn-study-family.json
Original file line number Diff line number Diff line change
@@ -38,6 +38,46 @@
}
}
],
"member": [
{
"entity": {
"extension": [
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/family-role",
"valueCodeableConcept": {
"coding": [
{
"code": "MTH",
"system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode",
"display": "mother"
}
]
}
}
],
"reference": "PT-KZG2CZ95"
}
},
{
"entity": {
"extension": [
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/family-role",
"valueCodeableConcept": {
"coding": [
{
"code": "SON",
"system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode",
"display": "natural son"
}
]
}
}
],
"reference": "PT-005B7CZ4"
}
}
],
"type": "person",
"actual": true
}

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184 changes: 0 additions & 184 deletions fsh-generated/resources/Observation-BAM-CRAM-example.json

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11 changes: 10 additions & 1 deletion fsh-generated/resources/Observation-FASTQ-example.json
Original file line number Diff line number Diff line change
@@ -8,7 +8,7 @@
},
"focus": [
{
"reference": "PT_006SP660"
"reference": "DocumentReference/GF-6BAD9S7D"
}
],
"component": [
@@ -120,6 +120,15 @@
]
},
"valueBoolean": true
},
{
"code": {
"coding": [
{
"code": "TargetRegion"
}
]
}
}
],
"status": "final",
175 changes: 0 additions & 175 deletions fsh-generated/resources/Observation-VCF-example.json

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Original file line number Diff line number Diff line change
@@ -8,11 +8,11 @@
},
"focus": [
{
"reference": "Patient/PT-005B7CZ4"
"reference": "PT-005B7CZ4"
}
],
"subject": {
"reference": "Patient/PT-KZG2CZ95"
"reference": "PT-KZG2CZ95"
},
"code": {
"coding": [
Original file line number Diff line number Diff line change
@@ -8,11 +8,11 @@
},
"focus": [
{
"reference": "Patient/PT-KZG2CZ95"
"reference": "PT-KZG2CZ95"
}
],
"subject": {
"reference": "Patient/PT-005B7CZ4"
"reference": "PT-005B7CZ4"
},
"code": {
"coding": [
98 changes: 0 additions & 98 deletions fsh-generated/resources/Patient-6812345.json

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91 changes: 0 additions & 91 deletions fsh-generated/resources/Patient-PT-005B7CZ4.json

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107 changes: 0 additions & 107 deletions fsh-generated/resources/Patient-PT-KZG2CZ95.json

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22 changes: 0 additions & 22 deletions fsh-generated/resources/Person-cbtn-example-person.json

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22 changes: 0 additions & 22 deletions fsh-generated/resources/Person-emerge-example-person.json

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22 changes: 0 additions & 22 deletions fsh-generated/resources/Person-pcgc-example-person.json

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36 changes: 0 additions & 36 deletions fsh-generated/resources/ResearchStudy-SD-BHJXBDQK.json

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36 changes: 0 additions & 36 deletions fsh-generated/resources/ResearchStudy-SD-PREASA7S.json

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36 changes: 0 additions & 36 deletions fsh-generated/resources/ResearchStudy-phv00407460.v2.json

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4 changes: 2 additions & 2 deletions fsh-generated/resources/Specimen-SA-000.json
Original file line number Diff line number Diff line change
@@ -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"
}
}
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
"name": "CdmCondition",
"title": "Shared Data Model for Condition",
"status": "draft",
"description": "The **Shared Data Model for Condition**",
"description": "The Shared Data Model for **Condition**",
"fhirVersion": "4.3.0",
"kind": "logical",
"abstract": false,
@@ -18,11 +18,11 @@
"id": "SharedDataModelCondition",
"path": "SharedDataModelCondition",
"short": "Shared Data Model for Condition",
"definition": "The **Shared Data Model for Condition**"
"definition": "The Shared Data Model for **Condition**"
},
{
"id": "SharedDataModelCondition.participantID",
"path": "SharedDataModelCondition.participantID",
"id": "SharedDataModelCondition.participant",
"path": "SharedDataModelCondition.participant",
"short": "The participant we are describing",
"definition": "The participant we are describing",
"min": 1,
@@ -65,13 +65,13 @@
{
"id": "SharedDataModelCondition.ageAtAssertion",
"path": "SharedDataModelCondition.ageAtAssertion",
"short": "The date or age at which this condition is being asserted. ",
"definition": "The date or age at which this condition is being asserted. ",
"short": "The date or age at which this condition is being asserted.",
"definition": "The date or age at which this condition is being asserted.",
"min": 0,
"max": "1",
"type": [
{
"code": "date"
"code": "Quantity"
}
]
},
@@ -166,6 +166,32 @@
}
]
},
{
"id": "SharedDataModelCondition.locationQualifier",
"path": "SharedDataModelCondition.locationQualifier",
"short": "Any spatial/location qualifiers",
"definition": "Any spatial/location qualifiers",
"min": 0,
"max": "1",
"type": [
{
"code": "code"
}
]
},
{
"id": "SharedDataModelCondition.lateralityQualifier",
"path": "SharedDataModelCondition.lateralityQualifier",
"short": "Any laterality qualifiers",
"definition": "Any laterality qualifiers",
"min": 0,
"max": "1",
"type": [
{
"code": "code"
}
]
},
{
"id": "SharedDataModelCondition.assertionSource",
"path": "SharedDataModelCondition.assertionSource",
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@
"context": [
{
"type": "element",
"expression": "Element"
"expression": "Group.content.extension"
}
],
"type": "Extension",
128 changes: 0 additions & 128 deletions fsh-generated/resources/StructureDefinition-ncpi-analysis-file.json

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90 changes: 0 additions & 90 deletions fsh-generated/resources/StructureDefinition-ncpi-assay-file.json

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213 changes: 208 additions & 5 deletions fsh-generated/resources/StructureDefinition-ncpi-bamcram.json
Original file line number Diff line number Diff line change
@@ -11,14 +11,217 @@
"kind": "resource",
"abstract": false,
"type": "Observation",
"baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-reads-file",
"baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata",
"derivation": "constraint",
"differential": {
"element": [
{
"id": "Observation.extension",
"path": "Observation.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
}
},
{
"id": "Observation.extension:specimen-collection",
"path": "Observation.extension",
"sliceName": "specimen-collection",
"short": "Linkage for related samples",
"min": 0,
"max": "*",
"type": [
{
"code": "Extension",
"profile": [
"https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection"
]
}
]
},
{
"id": "Observation.component",
"path": "Observation.component",
"min": 7
"slicing": {
"discriminator": [
{
"type": "value",
"path": "code"
}
],
"rules": "open",
"ordered": false,
"description": "Slice pattern for component.code"
},
"min": 9
},
{
"id": "Observation.component:assay_strategy",
"path": "Observation.component",
"sliceName": "assay_strategy",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:assay_strategy.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "AssayStrategy"
}
]
}
},
{
"id": "Observation.component:assay_strategy.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:platform_instrument",
"path": "Observation.component",
"sliceName": "platform_instrument",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:platform_instrument.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "PlatformInstrument"
}
]
}
},
{
"id": "Observation.component:platform_instrument.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:library_prep",
"path": "Observation.component",
"sliceName": "library_prep",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:library_prep.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "LibraryPrep"
}
]
}
},
{
"id": "Observation.component:library_prep.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:library_selection",
"path": "Observation.component",
"sliceName": "library_selection",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:library_selection.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "LibrarySelection"
}
]
}
},
{
"id": "Observation.component:library_selection.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:strandedness",
"path": "Observation.component",
"sliceName": "strandedness",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:strandedness.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "Strandedness"
}
]
}
},
{
"id": "Observation.component:strandedness.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:target_region",
"path": "Observation.component",
"sliceName": "target_region",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:target_region.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "TargetRegion"
}
]
}
},
{
"id": "Observation.component:target_region.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:is_paired_end",
@@ -54,7 +257,7 @@
"id": "Observation.component:adaptor_trimmed",
"path": "Observation.component",
"sliceName": "adaptor_trimmed",
"min": 1,
"min": 0,
"max": "1"
},
{
@@ -111,7 +314,7 @@
"id": "Observation.component:workflow_type",
"path": "Observation.component",
"sliceName": "workflow_type",
"min": 0,
"min": 1,
"max": "1"
},
{
@@ -138,7 +341,7 @@
"id": "Observation.component:workflow_tool",
"path": "Observation.component",
"sliceName": "workflow_tool",
"min": 0,
"min": 1,
"max": "1"
},
{
140 changes: 0 additions & 140 deletions fsh-generated/resources/StructureDefinition-ncpi-conditon.json

This file was deleted.

80 changes: 0 additions & 80 deletions fsh-generated/resources/StructureDefinition-ncpi-family-role.json

This file was deleted.

207 changes: 205 additions & 2 deletions fsh-generated/resources/StructureDefinition-ncpi-fastq.json
Original file line number Diff line number Diff line change
@@ -11,14 +11,217 @@
"kind": "resource",
"abstract": false,
"type": "Observation",
"baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-reads-file",
"baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata",
"derivation": "constraint",
"differential": {
"element": [
{
"id": "Observation.extension",
"path": "Observation.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
}
},
{
"id": "Observation.extension:specimen-collection",
"path": "Observation.extension",
"sliceName": "specimen-collection",
"short": "Linkage for related samples",
"min": 0,
"max": "*",
"type": [
{
"code": "Extension",
"profile": [
"https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection"
]
}
]
},
{
"id": "Observation.component",
"path": "Observation.component",
"min": 7
"slicing": {
"discriminator": [
{
"type": "value",
"path": "code"
}
],
"rules": "open",
"ordered": false,
"description": "Slice pattern for component.code"
},
"min": 8
},
{
"id": "Observation.component:assay_strategy",
"path": "Observation.component",
"sliceName": "assay_strategy",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:assay_strategy.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "AssayStrategy"
}
]
}
},
{
"id": "Observation.component:assay_strategy.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:platform_instrument",
"path": "Observation.component",
"sliceName": "platform_instrument",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:platform_instrument.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "PlatformInstrument"
}
]
}
},
{
"id": "Observation.component:platform_instrument.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:library_prep",
"path": "Observation.component",
"sliceName": "library_prep",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:library_prep.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "LibraryPrep"
}
]
}
},
{
"id": "Observation.component:library_prep.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:library_selection",
"path": "Observation.component",
"sliceName": "library_selection",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:library_selection.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "LibrarySelection"
}
]
}
},
{
"id": "Observation.component:library_selection.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:strandedness",
"path": "Observation.component",
"sliceName": "strandedness",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:strandedness.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "Strandedness"
}
]
}
},
{
"id": "Observation.component:strandedness.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:target_region",
"path": "Observation.component",
"sliceName": "target_region",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:target_region.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "TargetRegion"
}
]
}
},
{
"id": "Observation.component:target_region.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:is_paired_end",
133 changes: 0 additions & 133 deletions fsh-generated/resources/StructureDefinition-ncpi-reads-file.json

This file was deleted.

This file was deleted.

34 changes: 34 additions & 0 deletions fsh-generated/resources/StructureDefinition-ncpi-study-family.json
Original file line number Diff line number Diff line change
@@ -103,6 +103,40 @@
"id": "Group.identifier",
"path": "Group.identifier",
"short": "External IDs for this participant. Requires scoping."
},
{
"id": "Group.member",
"path": "Group.member",
"min": 1
},
{
"id": "Group.member.entity",
"path": "Group.member.entity",
"short": "The participant we are describing.",
"type": [
{
"code": "Reference",
"targetProfile": [
"https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant"
]
}
]
},
{
"id": "Group.member.entity.extension:family-role",
"path": "Group.member.entity.extension",
"sliceName": "family-role",
"short": "The role this individual has in the family, specifically with respect to a proband or index participant",
"min": 0,
"max": "1",
"type": [
{
"code": "Extension",
"profile": [
"https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/family-role"
]
}
]
}
]
}
246 changes: 242 additions & 4 deletions fsh-generated/resources/StructureDefinition-ncpi-vcf.json
Original file line number Diff line number Diff line change
@@ -11,10 +11,218 @@
"kind": "resource",
"abstract": false,
"type": "Observation",
"baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-analysis-file",
"baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata",
"derivation": "constraint",
"differential": {
"element": [
{
"id": "Observation.extension",
"path": "Observation.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
}
},
{
"id": "Observation.extension:specimen-collection",
"path": "Observation.extension",
"sliceName": "specimen-collection",
"short": "Linkage for related samples",
"min": 0,
"max": "*",
"type": [
{
"code": "Extension",
"profile": [
"https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection"
]
}
]
},
{
"id": "Observation.component",
"path": "Observation.component",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "code"
}
],
"rules": "open",
"ordered": false,
"description": "Slice pattern for component.code"
},
"min": 6
},
{
"id": "Observation.component:assay_strategy",
"path": "Observation.component",
"sliceName": "assay_strategy",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:assay_strategy.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "AssayStrategy"
}
]
}
},
{
"id": "Observation.component:assay_strategy.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:platform_instrument",
"path": "Observation.component",
"sliceName": "platform_instrument",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:platform_instrument.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "PlatformInstrument"
}
]
}
},
{
"id": "Observation.component:platform_instrument.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:library_prep",
"path": "Observation.component",
"sliceName": "library_prep",
"min": 0,
"max": "1"
},
{
"id": "Observation.component:library_prep.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "LibraryPrep"
}
]
}
},
{
"id": "Observation.component:library_prep.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:library_selection",
"path": "Observation.component",
"sliceName": "library_selection",
"min": 0,
"max": "1"
},
{
"id": "Observation.component:library_selection.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "LibrarySelection"
}
]
}
},
{
"id": "Observation.component:library_selection.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:strandedness",
"path": "Observation.component",
"sliceName": "strandedness",
"min": 0,
"max": "1"
},
{
"id": "Observation.component:strandedness.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "Strandedness"
}
]
}
},
{
"id": "Observation.component:strandedness.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:target_region",
"path": "Observation.component",
"sliceName": "target_region",
"min": 1,
"max": "1"
},
{
"id": "Observation.component:target_region.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "TargetRegion"
}
]
}
},
{
"id": "Observation.component:target_region.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Observation.component:is_paired_end",
"path": "Observation.component",
@@ -45,11 +253,41 @@
}
]
},
{
"id": "Observation.component:adaptor_trimmed",
"path": "Observation.component",
"sliceName": "adaptor_trimmed",
"min": 0,
"max": "1"
},
{
"id": "Observation.component:adaptor_trimmed.code",
"path": "Observation.component.code",
"patternCodeableConcept": {
"coding": [
{
"code": "AdaptorTrimmed"
}
]
}
},
{
"id": "Observation.component:adaptor_trimmed.value[x]",
"path": "Observation.component.value[x]",
"type": [
{
"code": "CodeableConcept"
},
{
"code": "boolean"
}
]
},
{
"id": "Observation.component:reference_genome",
"path": "Observation.component",
"sliceName": "reference_genome",
"min": 0,
"min": 1,
"max": "1"
},
{
@@ -76,7 +314,7 @@
"id": "Observation.component:workflow_type",
"path": "Observation.component",
"sliceName": "workflow_type",
"min": 0,
"min": 1,
"max": "1"
},
{
@@ -103,7 +341,7 @@
"id": "Observation.component:workflow_tool",
"path": "Observation.component",
"sliceName": "workflow_tool",
"min": 0,
"min": 1,
"max": "1"
},
{
Original file line number Diff line number Diff line change
@@ -40,6 +40,9 @@
"id": "Extension.value[x]",
"path": "Extension.value[x]",
"type": [
{
"code": "string"
},
{
"code": "CodeableConcept"
}
54 changes: 0 additions & 54 deletions fsh-generated/resources/StructureDefinition-study-family.json

This file was deleted.

4 changes: 2 additions & 2 deletions fsh-generated/resources/ValueSet-condition-code-vs.json
Original file line number Diff line number Diff line change
@@ -3,13 +3,13 @@
"status": "draft",
"name": "ConditionCodeVS",
"id": "condition-code-vs",
"title": "Condiiton Codes",
"title": "Conditon Codes",
"description": "Includes all codes from **HPO** and **MONDO**",
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/condition-code-vs",
"compose": {
"include": [
{
"system": "http://purl.obolibrary.org/obo/hp.owl"
"system": "http://human-phenotype-ontology.org"
},
{
"system": "http://purl.obolibrary.org/obo/mondo.owl"
17 changes: 5 additions & 12 deletions input/fsh/examples/GREGoR_example.fsh
Original file line number Diff line number Diff line change
@@ -100,17 +100,10 @@ Description: "Example patients based on data from GREGoR."
* type = #person // Required by Group with required VS
* actual = true // Required by Group
* extension[family-type].valueCodeableConcept = $ncpi-family-types#Duo "Duo"

Instance: gregor-family-role-child
InstanceOf: NcpiFamilyRole
Title: "An example family role based on data from CBTN"
Usage: #example
Description: "An example family role based on data from CBTN."
* member.entity = Reference(GSS123456)
//* extension[study-family].valueReference = Reference(GSS5555)
//* extension[family-role].valueCodeableConcept = $family-role-code#CHILD "child"
* type = #person // Required by Group with required VS
* actual = true // Required by Group
* member[0].entity = Reference(GSS123456)
* member[0].entity.extension[family-role].valueCodeableConcept = $family-role-code#CHILD "child"
* member[1].entity = Reference(GSS654321)
* member[1].entity.extension[family-role].valueCodeableConcept = $family-role-code#MTH "mother"

Instance: gregor-family-relationship-mother
InstanceOf: NcpiFamilyRelationship
@@ -201,4 +194,4 @@ Description: "Example file metadata for a BAM-CRAM file from GREGoR"
* component.code = #WorkflowTool
* component[workflow_tool].valueCodeableConcept = #unknown
* component.code = #WorkflowType
* component[workflow_type].valueCodeableConcept = #alignment
* component[workflow_type].valueCodeableConcept = #alignment
32 changes: 6 additions & 26 deletions input/fsh/examples/family.fsh
Original file line number Diff line number Diff line change
@@ -2,14 +2,12 @@
Examples for:
* NcpiStudyFamily
* NcpiFamilyRole
* NcpiFamilyRelationship
*/


// Example 1
/*
Instance: FM-00C8Y7DG
InstanceOf: NcpiStudyFamily
Title: "Example patients based on data from CBTN"
@@ -23,20 +21,13 @@ Description: "Example patients based on data from CBTN."
* actual = true // Required by Group

* extension[family-type].valueCodeableConcept = $ncpi-family-types#Trio "Trio"
// * extension[desctiption].valueMarkdown = "Potential inheritance details"
// * extension[description].valueMarkdown = "Potential inheritance details"
// * extension[consanguinity].valueCodeableConcept = $snomedct_us#261665006 "Unknown"
* extension[study-family-focus].valueCodeableConcept = $mondo#0004992 "Cancer"
Instance: cbtn-family-role-mother
InstanceOf: NcpiFamilyRole
Title: "An example family role based on data from CBTN"
Usage: #example
Description: "An example family role based on data from CBTN."
* member.entity = Reference(PT-KZG2CZ95)
* extension[study-family].valueReference = Reference(FM-00C8Y7DG)
* extension[family-role].valueCodeableConcept = $family-role-code#MTH "mother"
* type = #person // Required by Group with required VS
* actual = true // Required by Group
* member[0].entity = Reference(PT-KZG2CZ95)
* member[0].entity.extension[family-role].valueCodeableConcept = $family-role-code#MTH "mother"
* member[1].entity = Reference(PT-005B7CZ4)
* member[1].entity.extension[family-role].valueCodeableConcept = $family-role-code#SON "natural son"

Instance: cbtn-family-relationship-mother
InstanceOf: NcpiFamilyRelationship
@@ -51,18 +42,7 @@ Description: "An example family relationship based on data from CBTN."

// Example 2

// This example uses the Study Family defined above.

Instance: cbtn-family-role-son
InstanceOf: NcpiFamilyRole
Title: "An example family role based on data from CBTN"
Usage: #example
Description: "An example family role based on data from CBTN."
* member.entity = Reference(PT-005B7CZ4)
* extension[study-family].valueReference = Reference(FM-00C8Y7DG)
* extension[family-role].valueCodeableConcept = $family-role-code#SON "natural son"
* type = #person // Required by Group with required VS
* actual = true // Required by Group

Instance: cbtn-family-relationship-son
InstanceOf: NcpiFamilyRelationship
@@ -72,4 +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 */
* status = #registered
61 changes: 28 additions & 33 deletions input/fsh/modules/family.fsh
Original file line number Diff line number Diff line change
@@ -3,7 +3,6 @@ Family Module
Logical models, profiles, extensions and valuesets for:
* NcpiStudyFamily
* NcpiFamilyRole
* NcpiFamilyRelationship
*/
@@ -21,6 +20,27 @@ Description: "The **Shared Data Model for Study Family**"
* consanguinity 0..1 code "Is there known or suspected consanguinity in this study family?"
* studyFamilyFocus 0..1 code "What is this study family investigating? EG, a specific condition"

// Family Role

Logical: CdmFamilyRole
Id: SharedDataModelFamilyRole
Title: "Shared Data Model for Family Role"
Description: "The **Shared Data Model for Family Role**"
* participant 1..1 Reference "The participant we are describing"
* studyFamily 1..1 Reference "The study family this participant is part of"
* familyRole 0..1 code "The role this individual has in the family, specifically with respect to a proband or index participant"


Extension: FamilyRole
Id: family-role
Title: "Study Family Focus"
Description: "Extension containing Family Role"

* insert SetContext(Group.content.extension)
* value[x] only CodeableConcept
* valueCodeableConcept ^short = "The role this individual has in the family, specifically with respect to a proband or index participant"
* valueCodeableConcept from $ncpi-family-member (extensible)

CodeSystem: NcpiFamilyTypes
Id: ncpi-family-types
Title: "NCPI Family Types CodeSystem"
@@ -104,17 +124,14 @@ Description: "Study Family"
* extension[consanguinity] ^short = "Is there known or suspected consanguinity in this study family?"
* extension contains StudyFamilyFocus named study-family-focus 0..1
* extension[study-family-focus] ^short = "What is this study family investigating? EG, a specific condition"
* member 1..*
* member.entity only Reference(NcpiParticipant)
* member.entity ^short = "The participant we are describing."
* member.entity.extension contains FamilyRole named family-role 0..1
* member.entity.extension[family-role] ^short = "The role this individual has in the family, specifically with respect to a proband or index participant"

// Family Role

Logical: CdmFamilyRole
Id: SharedDataModelFamilyRole
Title: "Shared Data Model for Family Role"
Description: "The **Shared Data Model for Family Role**"
* participant 1..1 Reference "The participant we are describing"
* studyFamily 1..1 Reference "The study family this participant is part of"
* familyRole 0..1 code "The role this individual has in the family, specifically with respect to a proband or index participant"

/*
Extension: StudyFamily
Id: study-family
Title: "Study Family Reference"
@@ -123,29 +140,7 @@ Description: "Extension containing Study Family Reference"
* value[x] only Reference
* valueReference 1..1
* valueReference only Reference(NcpiStudyFamily)

Extension: FamilyRole
Id: family-role
Title: "Study Family Focus"
Description: "Extension containing Family Role"
* value[x] only CodeableConcept
* valueCodeableConcept ^short = "The role this individual has in the family, specifically with respect to a proband or index participant"
* valueCodeableConcept from $ncpi-family-member (extensible)

Profile: NcpiFamilyRole
Parent: Group
Id: ncpi-family-role
Title: "Family Role"
Description: "Family Role"
* ^version = "0.1.0"
* ^status = #draft
* member.entity 1..1
* member.entity only Reference(NcpiParticipant)
* member.entity ^short = "The participant we are describing."
* extension contains StudyFamily named study-family 0..1
* extension[study-family] ^short = "The study family this participant is part of"
* extension contains FamilyRole named family-role 0..1
* extension[family-role] ^short = "The role this individual has in the family, specifically with respect to a proband or index participant"
*/


// Family Relationship
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|Biospecimen Collection|[Shared Data Model for Biospecimen](StructureDefinition-SharedDataModelBiospecimenCollection.html)|[Biospecimen Profile](StructureDefinition-ncpi-sample.html)|
|Sample|[Shared Data Model for Sample](StructureDefinition-SharedDataModelSample.html)|[Sample Profile](StructureDefinition-ncpi-sample.html)|
|Family Relationship|[Shared Data Model for Family Relationship](StructureDefinition-SharedDataModelFamilyRelationship.html)|[Family Relationship Profile](StructureDefinition-ncpi-family-relationship.html)|
|Family Role|[Shared Data Model for Family Role](StructureDefinition-SharedDataModelFamilyRole.html)|[Family Role Profile](StructureDefinition-ncpi-family-role.html)|
|File|[Shared Data Model for File](StructureDefinition-SharedDataModelFile.html)|[File Profile](StructureDefinition-ncpi-file.html)|
|Participant|[Shared Data Model for Participant](StructureDefinition-SharedDataModelResearchParticipant.html)|[Participant Profile](StructureDefinition-ncpi-participant.html)|
|Person|[Shared Data Model for Person](StructureDefinition-SharedDataModelPerson.html)|[Person Profile](StructureDefinition-ncpi-person.html)|