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♻️ reorganize menus, reconfigure example file structure
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,204 @@ | ||
| // NCPI Research Study | ||
| Instance: research-study-gregor | ||
| InstanceOf: NcpiResearchStudy | ||
| Title: "Example study from GREGoR" | ||
| Usage: #example | ||
| Description: "Example study from GREGoR" | ||
| * identifier[0] | ||
| * value = "AnVIL_GREGoR_GSS_U08_GRU" | ||
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| * status = #completed | ||
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| Instance: gregor-research-study-participants | ||
| InstanceOf: ResearchStudyGroup | ||
| Title: "Participants from the CBTN research study" | ||
| Usage: #example | ||
| Description: "Participants from the CBTN research study" | ||
| * identifier[0] | ||
| * system = "https://anvil.terra.bio/" | ||
| * value = "GREGoR Participants" | ||
| * name = "Participants from the GREGoR research study GSS U08 GRU" | ||
| * quantity = 555 | ||
| * actual = true | ||
| * type = #person | ||
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| Instance: gregor-gru-consent | ||
| InstanceOf: NcpiResearchAccessPolicy | ||
| Title: "GREGoR General Research Use (GRU) Consent" | ||
| Usage: #example | ||
| Description: "General Research Use (GRU)" | ||
| * status = #draft | ||
| * scope = http://terminology.hl7.org/CodeSystem/consentscope#research | ||
| * category.coding = http://terminology.hl7.org/CodeSystem/consentcategorycodes#research | ||
| * policyRule = http://terminology.hl7.org/CodeSystem/consentpolicycodes#cric | ||
| * provision.type = http://hl7.org/fhir/consent-provision-type#permit | ||
| * provision.purpose[+] = $ncpi-data-access-code#GRU "General Research Use" | ||
| * extension[description].valueMarkdown = "Use of the data is limited only by the terms of the model Data Use Certification." | ||
| * extension[accessType].valueCodeableConcept = $ncpi-data-access-type#controlled | ||
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| // NCPI Participant | ||
| Instance: GSS654321 | ||
| InstanceOf: NcpiParticipant | ||
| Title: "Example family member based on data from GREGoR" | ||
| Usage: #example | ||
| Description: "Example family member based on data from GREGoR." | ||
| // Notice that we can use the DbGaP study ID for easier searching | ||
| * identifier[0] | ||
| * system = "https://anvil.terra.bio/" | ||
| * value = "GSS654321" | ||
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| Instance: GSS123456 | ||
| InstanceOf: NcpiParticipant | ||
| Title: "Example patients based on data from GREGoR" | ||
| Usage: #example | ||
| Description: "Example patients based on data from GREGoR." | ||
| // Notice that we can use the DbGaP study ID for easier searching | ||
| * identifier[0] | ||
| * system = "https://anvil.terra.bio/" | ||
| * value = "GSS123456" | ||
| * extension[us-core-birth-sex].valueCode = #M "Male" | ||
| * extension[us-core-race] | ||
| * extension[ombCategory].valueCoding = $omb-race-eth#2106-3 "White" | ||
| * extension[text].valueString = "White" | ||
| * extension[us-core-ethnicity] | ||
| * extension[ombCategory].valueCoding = $omb-race-eth#2186-5 "Not Hispanic or Latino" | ||
| * extension[text].valueString = "Not Hispanic or Latino" | ||
| * extension[population].valueString = "English|Scottish" | ||
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| Instance: gregor-example-person | ||
| InstanceOf: NcpiPerson | ||
| Title: "Example patients based on data from GREGoR" | ||
| Usage: #example | ||
| Description: "Example patients based on data from GREGoR" | ||
| * identifier | ||
| * system = "https://anvil.terra.bio" | ||
| * value = "PS_000" | ||
| * link | ||
| * target = Reference(GSS123456) | ||
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| Instance: gregor-example-participantstudy | ||
| InstanceOf: NcpiStudyParticipant | ||
| Title: "Example mappings based on data from GREGoR" | ||
| Usage: #example | ||
| Description: "Example mappings based on data from GREGoR" | ||
| * individual = Reference(GSS123456) | ||
| * study = Reference(research-study-gregor) | ||
| * status = #candidate | ||
| * consent = Reference(gregor-gru-consent) | ||
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| // NCPI Family | ||
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| Instance: GSS5555 | ||
| InstanceOf: NcpiStudyFamily | ||
| Title: "Example patients based on data from GREGoR" | ||
| Usage: #example | ||
| Description: "Example patients based on data from GREGoR." | ||
| * id = "gregor-study-family" | ||
| * identifier[0] | ||
| * system = "https://anvil.terra.bio/" | ||
| * value = "GSS5555" | ||
| * type = #person // Required by Group with required VS | ||
| * actual = true // Required by Group | ||
| * extension[family-type].valueCodeableConcept = $ncpi-family-types#Duo "Duo" | ||
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| 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 | ||
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| Instance: gregor-family-relationship-mother | ||
| InstanceOf: NcpiFamilyRelationship | ||
| Title: "An example family relationship based on data from CBTN" | ||
| Usage: #example | ||
| Description: "An example family relationship based on data from CBTN." | ||
| * subject = Reference(GSS123456) | ||
| * focus = Reference(GSS654321) | ||
| * code = $family-role-code#CHILD "child" | ||
| * status = #registered | ||
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| // NCPI Condition | ||
| Instance: GSS123456-condition | ||
| InstanceOf: NcpiCondition | ||
| Title: "Example condition using data from GREGoR" | ||
| Usage: #example | ||
| Description: "Example condition using data from GREGoR" | ||
| * status = #final | ||
| * subject = Reference(GSS123456) | ||
| * code.coding = $hpo#HP:0006951 /* condition code */ | ||
| * code.text = "retrocerebellar cyst" /* condition text */ | ||
| * valueCodeableConcept = $condition-assertion#Present /* assertion */ | ||
| * category = $condition-type#Disease /* condition type */ | ||
| * component.code = #ageAtOnset | ||
| * component[ageAtOnset].valueCodeableConcept = $hpo#HP:0011463 /* age at onset */ | ||
| * component.code = #otherModifiers | ||
| * component[otherModifiers].valueCodeableConcept = $hpo#HP:0012832 | ||
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| //NCPI Biospecimen | ||
| Instance: GSS123456-01-010 /*Collection Event ID can't have underscores*/ | ||
| InstanceOf: NCPICollectedSample | ||
| Title: "Example biospecimen based on data from GREGoR" | ||
| Usage: #example | ||
| Description: "Example biospecimen based on data from GREGoR" | ||
| * identifier.value = "GSS123456-s1" /*Sample ID*/ | ||
| * subject = Reference(GSS123456) /*Participant ID*/ | ||
| * type.text = "DNA" /*Sample Type*/ | ||
| * collection.method.text = "DNA" | ||
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| // NCPI File | ||
| Instance: GSS123456-01-010-SG-2 | ||
| InstanceOf: NcpiFile | ||
| Title: "Example file based on CBTN" | ||
| Usage: #example | ||
| Description: "Use case of file information from CBTN" | ||
| * identifier.value = "GSS123456-01-010-SG-2" | ||
| * subject = Reference(GSS123456) | ||
| * description = "Aligned DNA short read" | ||
| * type = $edam#operation_3198 "Read mapping" | ||
| * extension[content-version].valueString = "V1" | ||
| * status = #current | ||
| * content[+] | ||
| * attachment.url = "gs://fc-secure-a1f0e28d-c9d9-43bb-b4ba-5e0h81784fb1/GSS123456/SR_GS/GSS123456.bam" | ||
| * extension[location-access].valueReference = Reference(kf-gru-dac-consent) | ||
| * extension[file-format].valueCodeableConcept.coding = $edam#format_2572 "BAM" | ||
| * extension[file-size] | ||
| * valueQuantity | ||
| * value = 1044770380 | ||
| * unit = "bytes" | ||
| * extension[hash] | ||
| * extension[hash-value].valueString = "9c2460c4647fdc57261f040042863fa0" | ||
| * extension[hash-type].valueCode = #md5 | ||
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| // NCPI File Metadata | ||
| Instance: gregor-example-metadata | ||
| InstanceOf: NcpiBAMCRAM | ||
| Title: "Example file metadata for a BAM-CRAM file from GREGoR" | ||
| Usage: #example | ||
| Description: "Example file metadata for a BAM-CRAM file from GREGoR" | ||
| * focus = Reference(GSS123456) | ||
| * status = #final | ||
| * code = $edam#format_2572 /*for a BAM file | $edam#format_3462 for CRAM*/ | ||
| * specimen = Reference(GSS123456-01-010) /*using specimen is a placeholder for using a slice of component for related samples*/ | ||
| * component.code = #AssayStrategy | ||
| * component[assay_strategy].valueCodeableConcept = #unknown | ||
| * component.code = #PlatformInstrument | ||
| * component[platform_instrument].valueCodeableConcept = #unknown | ||
| * component.code = #LibraryPrep | ||
| * component[library_prep].valueCodeableConcept = #unknown | ||
| * component.code = #LibrarySelection | ||
| * component[library_selection].valueCodeableConcept = #unknown | ||
| * component.code = #Strandedness | ||
| * component[strandedness].valueCodeableConcept = #unknown | ||
| * component.code = #ReferenceGenome | ||
| * component[reference_genome].valueCodeableConcept = #GRCh38 | ||
| * component.code = #IsPairedEnd | ||
| * component[is_paired_end].valueBoolean = false | ||
| * component.code = #WorkflowTool | ||
| * component[workflow_tool].valueCodeableConcept = #unknown | ||
| * component.code = #WorkflowType | ||
| * component[workflow_type].valueCodeableConcept = #alignment |
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