From 773910938e647a37e923aafa693e70a60e88cbd1 Mon Sep 17 00:00:00 2001 From: Eric Torstenson Date: Tue, 30 Jul 2024 14:45:34 -0500 Subject: [PATCH] Participant (#21) * Actual products of the sushi run * Participant initial pass * Additional clarity for profile 'info' * Refinement of the above * Added key Aliases for OMB, NCIT and UCUM * Fixed a few lingering errors * Removed draft to strip out extraneous warning/error in QA * Fixed some issues with broken links * Largely functional participant profile(s) and first example * Clearer wording and proper format of link * First example for patient * :see_no_evil: Ignore temp vim files * :memo: Initial repo contributors guide * :sparkles: Add versioning, release, emoji commits, and emoji PRs * :recycle: Add link to contrib guide on readme * :recycle: Incorporate PR comments * :recycle: Clean up and make sdlc steps more clear * Added extension relating to sex at birth * Beginnings of the technical writing as example for IG Contributors. * Fixed some broken links due to case * Add the Person and StudyParticipant profiles to the Participant module (#28) * :sparkles: Add Person and Study Participant Modules --------- Co-authored-by: Natasha Singh Co-authored-by: brendagutman <77469967+brendagutman@users.noreply.github.com> --- .gitignore | 3 +- README.md | 10 + fsh-generated/fsh-index.json | 642 +++++++++++++ fsh-generated/fsh-index.txt | 81 ++ fsh-generated/includes/fsh-link-references.md | 80 ++ fsh-generated/includes/menu.xml | 164 ++++ .../resources/CodeSystem-collection-type.json | 27 + fsh-generated/resources/CodeSystem-ncpi.json | 88 ++ .../CodeSystem-research-data-access-code.json | 55 ++ .../CodeSystem-research-data-access-type.json | 35 + ...em-research-data-date-of-birth-method.json | 35 + .../resources/CodeSystem-study-name-type.json | 35 + .../CodeSystem-study-personnel-role.json | 27 + fsh-generated/resources/Consent-GRU.json | 68 ++ fsh-generated/resources/Consent-HMB.json | 68 ++ .../Consent-hmb-irb-npu-consent.json | 78 ++ .../resources/Consent-hmb-npu-consent.json | 73 ++ .../resources/Consent-kf-gru-dac-consent.json | 68 ++ .../Consent-kf-gru-dbgap-consent.json | 68 ++ .../Consent-kf-gsr-allowed-access.json | 58 ++ .../Consent-kf-registered-allowed-access.json | 58 ++ ...rch-study-bhcmg-consent-group-hmb-npu.json | 19 + ...study-bhcmg-consent-group-irb-hmb-npu.json | 19 + ...p-kf-research-study-cbtn-participants.json | 19 + ...ide-ncpi-fhir-implementation-guide-v2.json | 844 ++++++++++++++++++ .../List-ncpi-research-collection-cmg.json | 59 ++ .../List-ncpi-research-collection-kfx01.json | 39 + .../List-ncpi-research-collection-pbta.json | 59 ++ ...n-kf-research-study-organization-chop.json | 13 + fsh-generated/resources/Patient-6812345.json | 98 ++ .../resources/Patient-PT-005B7CZ4.json | 91 ++ .../resources/Patient-PT-KZG2CZ95.json | 107 +++ .../resources/Person-cbtn-example-person.json | 22 + .../Person-emerge-example-person.json | 22 + .../resources/Person-pcgc-example-person.json | 22 + ...research-study-personnel-role-op-lead.json | 17 + ...-research-study-personnel-role-pi-x01.json | 17 + ...e-kf-research-study-personnel-role-pi.json | 17 + .../resources/ResearchStudy-SD-BHJXBDQK.json | 36 + .../resources/ResearchStudy-SD-PREASA7S.json | 36 + ...esearchStudy-cmg-research-study-bhcmg.json | 136 +++ ...mg-research-study-subject-cmg-hmb-npu.json | 36 + ...esearch-study-subject-cmg-irb-hmb-npu.json | 36 + .../ResearchStudy-kf-research-study-cbtn.json | 154 ++++ ...udy-kf-research-study-subject-gru-dac.json | 36 + ...y-kf-research-study-subject-gru-dbgap.json | 36 + ...kf-research-study-subject-gsr-allowed.json | 36 + ...-kf-research-study-subject-registered.json | 36 + .../ResearchStudy-phv00407460.v2.json | 36 + ...Subject-cbtn-example-participantstudy.json | 19 + ...bject-emerge-example-participantstudy.json | 19 + ...Subject-pcgc-example-participantstudy.json | 19 + ...ctureDefinition-SharedDataModelPerson.json | 54 ++ ...ion-SharedDataModelResearchCollection.json | 94 ++ ...aredDataModelResearchDataAccessPolicy.json | 68 ++ ...on-SharedDataModelResearchParticipant.json | 155 ++++ ...finition-SharedDataModelResearchStudy.json | 345 +++++++ ...ition-SharedDataModelStudyParticipant.json | 73 ++ ...eDefinition-access-policy-description.json | 52 ++ .../StructureDefinition-access-policy.json | 54 ++ .../StructureDefinition-access-type.json | 54 ++ .../StructureDefinition-label-extension.json | 101 +++ ...tureDefinition-ncpi-Study-Participant.json | 68 ++ .../StructureDefinition-ncpi-participant.json | 151 ++++ .../StructureDefinition-ncpi-person.json | 39 + ...efinition-ncpi-research-access-policy.json | 147 +++ ...reDefinition-ncpi-research-collection.json | 92 ++ ...ructureDefinition-ncpi-research-study.json | 140 +++ ...ion-research-age-at-last-vital-status.json | 51 ++ ...inition-research-date-of-birth-method.json | 54 ++ ...ition-research-disease-use-limitation.json | 54 ++ ...ructureDefinition-research-population.json | 50 ++ ...nition-research-study-acknowledgement.json | 52 ++ ...ition-research-study-associated-party.json | 197 ++++ ...ctureDefinition-research-study-design.json | 54 ++ ...uctureDefinition-research-study-group.json | 60 ++ ...ctureDefinition-research-study-result.json | 70 ++ ...nition-research-study-subject-consent.json | 53 ++ ...tureDefinition-research-study-subject.json | 46 + ...StructureDefinition-research-web-Link.json | 73 ++ .../ValueSet-collection-type-vs.json | 17 + .../resources/ValueSet-mesh-terms.json | 18 + ...ValueSet-research-data-access-code-vs.json | 17 + ...ValueSet-research-data-access-type-vs.json | 17 + ...research-data-date-of-birth-method-vs.json | 16 + .../ValueSet-study-name-type-vs.json | 17 + .../ValueSet-study-personnel-role-vs.json | 17 + input/fsh/Alias.fsh | 12 +- input/fsh/examples/ResearchStudy-CBTN.fsh | 3 +- input/fsh/examples/participant.fsh | 293 ++++++ input/fsh/modules/participant.fsh | 145 +++ input/fsh/modules/research-accesss-policy.fsh | 1 - ...haredDataModelResearchParticipant-intro.md | 11 + ...uctureDefinition-ncpi-participant-intro.md | 33 + ...uctureDefinition-ncpi-participant-notes.md | 16 + .../StructureDefinition-ncpi-person-intro.md | 18 + .../StructureDefinition-ncpi-person-notes.md | 1 + ...ureDefinition-ncpi-research-study-intro.md | 3 +- ...Definition-ncpi-study-participant-intro.md | 18 + ...Definition-ncpi-study-participant-notes.md | 1 + ...tructureDefinition-research-study-intro.md | 1 - 101 files changed, 7144 insertions(+), 8 deletions(-) create mode 100644 fsh-generated/fsh-index.json create mode 100644 fsh-generated/fsh-index.txt create mode 100644 fsh-generated/includes/fsh-link-references.md create mode 100644 fsh-generated/includes/menu.xml create mode 100644 fsh-generated/resources/CodeSystem-collection-type.json create mode 100644 fsh-generated/resources/CodeSystem-ncpi.json create mode 100644 fsh-generated/resources/CodeSystem-research-data-access-code.json create mode 100644 fsh-generated/resources/CodeSystem-research-data-access-type.json create mode 100644 fsh-generated/resources/CodeSystem-research-data-date-of-birth-method.json create mode 100644 fsh-generated/resources/CodeSystem-study-name-type.json create mode 100644 fsh-generated/resources/CodeSystem-study-personnel-role.json create mode 100644 fsh-generated/resources/Consent-GRU.json create mode 100644 fsh-generated/resources/Consent-HMB.json create mode 100644 fsh-generated/resources/Consent-hmb-irb-npu-consent.json create mode 100644 fsh-generated/resources/Consent-hmb-npu-consent.json create mode 100644 fsh-generated/resources/Consent-kf-gru-dac-consent.json create mode 100644 fsh-generated/resources/Consent-kf-gru-dbgap-consent.json create mode 100644 fsh-generated/resources/Consent-kf-gsr-allowed-access.json create mode 100644 fsh-generated/resources/Consent-kf-registered-allowed-access.json create mode 100644 fsh-generated/resources/Group-cmg-research-study-bhcmg-consent-group-hmb-npu.json create mode 100644 fsh-generated/resources/Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.json create mode 100644 fsh-generated/resources/Group-kf-research-study-cbtn-participants.json create mode 100644 fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json create mode 100644 fsh-generated/resources/List-ncpi-research-collection-cmg.json create mode 100644 fsh-generated/resources/List-ncpi-research-collection-kfx01.json create mode 100644 fsh-generated/resources/List-ncpi-research-collection-pbta.json create mode 100644 fsh-generated/resources/Organization-kf-research-study-organization-chop.json create mode 100644 fsh-generated/resources/Patient-6812345.json create mode 100644 fsh-generated/resources/Patient-PT-005B7CZ4.json create mode 100644 fsh-generated/resources/Patient-PT-KZG2CZ95.json create mode 100644 fsh-generated/resources/Person-cbtn-example-person.json create mode 100644 fsh-generated/resources/Person-emerge-example-person.json create mode 100644 fsh-generated/resources/Person-pcgc-example-person.json create mode 100644 fsh-generated/resources/PractitionerRole-kf-research-study-personnel-role-op-lead.json create mode 100644 fsh-generated/resources/PractitionerRole-kf-research-study-personnel-role-pi-x01.json create mode 100644 fsh-generated/resources/PractitionerRole-kf-research-study-personnel-role-pi.json create mode 100644 fsh-generated/resources/ResearchStudy-SD-BHJXBDQK.json create mode 100644 fsh-generated/resources/ResearchStudy-SD-PREASA7S.json create mode 100644 fsh-generated/resources/ResearchStudy-cmg-research-study-bhcmg.json create mode 100644 fsh-generated/resources/ResearchStudy-cmg-research-study-subject-cmg-hmb-npu.json create mode 100644 fsh-generated/resources/ResearchStudy-cmg-research-study-subject-cmg-irb-hmb-npu.json create mode 100644 fsh-generated/resources/ResearchStudy-kf-research-study-cbtn.json create mode 100644 fsh-generated/resources/ResearchStudy-kf-research-study-subject-gru-dac.json create mode 100644 fsh-generated/resources/ResearchStudy-kf-research-study-subject-gru-dbgap.json create mode 100644 fsh-generated/resources/ResearchStudy-kf-research-study-subject-gsr-allowed.json create mode 100644 fsh-generated/resources/ResearchStudy-kf-research-study-subject-registered.json create mode 100644 fsh-generated/resources/ResearchStudy-phv00407460.v2.json create mode 100644 fsh-generated/resources/ResearchSubject-cbtn-example-participantstudy.json create mode 100644 fsh-generated/resources/ResearchSubject-emerge-example-participantstudy.json create mode 100644 fsh-generated/resources/ResearchSubject-pcgc-example-participantstudy.json create mode 100644 fsh-generated/resources/StructureDefinition-SharedDataModelPerson.json create mode 100644 fsh-generated/resources/StructureDefinition-SharedDataModelResearchCollection.json create mode 100644 fsh-generated/resources/StructureDefinition-SharedDataModelResearchDataAccessPolicy.json create mode 100644 fsh-generated/resources/StructureDefinition-SharedDataModelResearchParticipant.json create mode 100644 fsh-generated/resources/StructureDefinition-SharedDataModelResearchStudy.json create mode 100644 fsh-generated/resources/StructureDefinition-SharedDataModelStudyParticipant.json create mode 100644 fsh-generated/resources/StructureDefinition-access-policy-description.json create mode 100644 fsh-generated/resources/StructureDefinition-access-policy.json create mode 100644 fsh-generated/resources/StructureDefinition-access-type.json create mode 100644 fsh-generated/resources/StructureDefinition-label-extension.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-Study-Participant.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-participant.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-person.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-research-access-policy.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-research-collection.json create mode 100644 fsh-generated/resources/StructureDefinition-ncpi-research-study.json create mode 100644 fsh-generated/resources/StructureDefinition-research-age-at-last-vital-status.json create mode 100644 fsh-generated/resources/StructureDefinition-research-date-of-birth-method.json create mode 100644 fsh-generated/resources/StructureDefinition-research-disease-use-limitation.json create mode 100644 fsh-generated/resources/StructureDefinition-research-population.json create mode 100644 fsh-generated/resources/StructureDefinition-research-study-acknowledgement.json create mode 100644 fsh-generated/resources/StructureDefinition-research-study-associated-party.json create mode 100644 fsh-generated/resources/StructureDefinition-research-study-design.json create mode 100644 fsh-generated/resources/StructureDefinition-research-study-group.json create mode 100644 fsh-generated/resources/StructureDefinition-research-study-result.json create mode 100644 fsh-generated/resources/StructureDefinition-research-study-subject-consent.json create mode 100644 fsh-generated/resources/StructureDefinition-research-study-subject.json create mode 100644 fsh-generated/resources/StructureDefinition-research-web-Link.json create mode 100644 fsh-generated/resources/ValueSet-collection-type-vs.json create mode 100644 fsh-generated/resources/ValueSet-mesh-terms.json create mode 100644 fsh-generated/resources/ValueSet-research-data-access-code-vs.json create mode 100644 fsh-generated/resources/ValueSet-research-data-access-type-vs.json create mode 100644 fsh-generated/resources/ValueSet-research-data-date-of-birth-method-vs.json create mode 100644 fsh-generated/resources/ValueSet-study-name-type-vs.json create mode 100644 fsh-generated/resources/ValueSet-study-personnel-role-vs.json create mode 100644 input/fsh/examples/participant.fsh create mode 100644 input/fsh/modules/participant.fsh create mode 100644 input/pagecontent/StructureDefinition-SharedDataModelResearchParticipant-intro.md create mode 100755 input/pagecontent/StructureDefinition-ncpi-participant-intro.md create mode 100755 input/pagecontent/StructureDefinition-ncpi-participant-notes.md create mode 100755 input/pagecontent/StructureDefinition-ncpi-person-intro.md create mode 100755 input/pagecontent/StructureDefinition-ncpi-person-notes.md create mode 100755 input/pagecontent/StructureDefinition-ncpi-study-participant-intro.md create mode 100755 input/pagecontent/StructureDefinition-ncpi-study-participant-notes.md diff --git a/.gitignore b/.gitignore index adbc6009..8358210e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,5 @@ .DS_Store Thumbs.db -/fsh-generated /input-cache /output /temp @@ -8,3 +7,5 @@ Thumbs.db *.swp *.swn *.swo +*.sh +*.bat diff --git a/README.md b/README.md index 71197f17..1c18e612 100644 --- a/README.md +++ b/README.md @@ -35,6 +35,14 @@ Defining examples for your IG components will eliminate warnings from your QA lo #### Technical Documentation for Profiles and Relationships - Artifact Intro and Notes For intro and notes content that will be merged into the relevant artifact page, the publisher application itself is very specific: The filename should match the resulting HTML file in Humpback notation minus the extension followed by either "-intro.md" or "-notes.md". The material inside -intro.md files will appear *before* the differential table. Material inside -note.md files will appear afterward inside the header, *Notes". These files will be written into the directory, input/pagecontent. +For profiles, we definitely should define: +* **Added Profile Restrictions** Where we list all properties as being **should**, **must**, etc. +* **Recommended Practices** - We should add bullets for each relevant property under headings of **recommended** and **optional**. + +Also, under **Recommended Practices** and guidance about any special cases such as we are doing with [Population Details](https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition-ncpi-research-study.html#population-details) + +**Notes** (sibling to the **Recommended Restrictions**) Should indicate any other general profile relationships that should be discussed. + > To determine the correct filename corresponding to the artifact of interest, please see the file, fsh-generated/includes/fsh-link-references.md where you can find the resulting HTML filename for each FSH based artifact. For each profile, there should always be a matching -info file that contains the following information: @@ -44,6 +52,8 @@ For each profile, there should always be a matching -info file that contains the The -notes.md file is optional and should be used to add clarification for unusual cases or other details that should be called out that don't naturally fit within the typical use cases. + + #### Example Overview Each module should have at least a single example page as part of the release. This should, at the very least, link each of the associated example profiles with an explanation of how they fit together if the example spans multiple profiles. To provide context within the example page itself, you can provide -info.md and -notes.md pages similarly to profiles, extensions, etc. diff --git a/fsh-generated/fsh-index.json b/fsh-generated/fsh-index.json new file mode 100644 index 00000000..c86a7c5a --- /dev/null +++ b/fsh-generated/fsh-index.json @@ -0,0 +1,642 @@ +[ + { + "outputFile": "CodeSystem-collection-type.json", + "fshName": "CollectionType", + "fshType": "CodeSystem", + "fshFile": "modules/research-collection.fsh", + "startLine": 2, + "endLine": 11 + }, + { + "outputFile": "CodeSystem-ncpi.json", + "fshName": "Ncpi", + "fshType": "CodeSystem", + "fshFile": "terminologies/ncpi.fsh", + "startLine": 6, + "endLine": 34 + }, + { + "outputFile": "CodeSystem-research-data-access-code.json", + "fshName": "ResearchDataAccessCode", + "fshType": "CodeSystem", + "fshFile": "modules/research-accesss-policy.fsh", + "startLine": 6, + "endLine": 22 + }, + { + "outputFile": "CodeSystem-research-data-access-type.json", + "fshName": "ResearchDataAccessType", + "fshType": "CodeSystem", + "fshFile": "modules/research-accesss-policy.fsh", + "startLine": 33, + "endLine": 44 + }, + { + "outputFile": "CodeSystem-research-data-date-of-birth-method.json", + "fshName": "ResearchDataDateOfBirthMethod", + "fshType": "CodeSystem", + "fshFile": "modules/participant.fsh", + "startLine": 18, + "endLine": 29 + }, + { + "outputFile": "CodeSystem-study-name-type.json", + "fshName": "StudyNameType", + "fshType": "CodeSystem", + "fshFile": "modules/research-study.fsh", + "startLine": 99, + "endLine": 110 + }, + { + "outputFile": "CodeSystem-study-personnel-role.json", + "fshName": "StudyPersonnelRole", + "fshType": "CodeSystem", + "fshFile": "modules/research-study.fsh", + "startLine": 120, + "endLine": 129 + }, + { + "outputFile": "Consent-GRU.json", + "fshName": "GRU", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 88, + "endLine": 101 + }, + { + "outputFile": "Consent-HMB.json", + "fshName": "HMB", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 178, + "endLine": 191 + }, + { + "outputFile": "Consent-hmb-irb-npu-consent.json", + "fshName": "hmb-irb-npu-consent", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-BH-CMG.fsh", + "startLine": 117, + "endLine": 133 + }, + { + "outputFile": "Consent-hmb-npu-consent.json", + "fshName": "hmb-npu-consent", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-BH-CMG.fsh", + "startLine": 71, + "endLine": 86 + }, + { + "outputFile": "Consent-kf-gru-dac-consent.json", + "fshName": "kf-gru-dac-consent", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-CBTN.fsh", + "startLine": 105, + "endLine": 118 + }, + { + "outputFile": "Consent-kf-gru-dbgap-consent.json", + "fshName": "kf-gru-dbgap-consent", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-CBTN.fsh", + "startLine": 135, + "endLine": 148 + }, + { + "outputFile": "Consent-kf-gsr-allowed-access.json", + "fshName": "kf-gsr-allowed-access", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-CBTN.fsh", + "startLine": 165, + "endLine": 176 + }, + { + "outputFile": "Consent-kf-registered-allowed-access.json", + "fshName": "kf-registered-allowed-access", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-CBTN.fsh", + "startLine": 193, + "endLine": 204 + }, + { + "outputFile": "Group-cmg-research-study-bhcmg-consent-group-hmb-npu.json", + "fshName": "cmg-research-study-bhcmg-consent-group-hmb-npu", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-BH-CMG.fsh", + "startLine": 89, + "endLine": 100 + }, + { + "outputFile": "Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.json", + "fshName": "cmg-research-study-bhcmg-consent-group-irb-hmb-npu", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-BH-CMG.fsh", + "startLine": 135, + "endLine": 146 + }, + { + "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 + }, + { + "outputFile": "List-ncpi-research-collection-cmg.json", + "fshName": "ncpi-research-collection-cmg", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-BH-CMG.fsh", + "startLine": 163, + "endLine": 175 + }, + { + "outputFile": "List-ncpi-research-collection-kfx01.json", + "fshName": "ncpi-research-collection-kfx01", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-CBTN.fsh", + "startLine": 236, + "endLine": 246 + }, + { + "outputFile": "List-ncpi-research-collection-pbta.json", + "fshName": "ncpi-research-collection-pbta", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-CBTN.fsh", + "startLine": 222, + "endLine": 234 + }, + { + "outputFile": "Organization-kf-research-study-organization-chop.json", + "fshName": "kf-research-study-organization-chop", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-CBTN.fsh", + "startLine": 4, + "endLine": 11 + }, + { + "outputFile": "Patient-6812345.json", + "fshName": "6812345", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 222, + "endLine": 255 + }, + { + "outputFile": "Patient-PT-005B7CZ4.json", + "fshName": "PT-005B7CZ4", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 132, + "endLine": 164 + }, + { + "outputFile": "Patient-PT-KZG2CZ95.json", + "fshName": "PT-KZG2CZ95", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 15, + "endLine": 54 + }, + { + "outputFile": "Person-cbtn-example-person.json", + "fshName": "cbtn-example-person", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 77, + "endLine": 86 + }, + { + "outputFile": "Person-emerge-example-person.json", + "fshName": "emerge-example-person", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 257, + "endLine": 266 + }, + { + "outputFile": "Person-pcgc-example-person.json", + "fshName": "pcgc-example-person", + "fshType": "Instance", + "fshFile": "examples/participant.fsh", + "startLine": 167, + "endLine": 176 + }, + { + "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 + }, + { + "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 + }, + { + "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 + }, + { + "outputFile": "ResearchStudy-cmg-research-study-bhcmg.json", + "fshName": "cmg-research-study-bhcmg", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-BH-CMG.fsh", + "startLine": 16, + "endLine": 67 + }, + { + "outputFile": "ResearchStudy-cmg-research-study-subject-cmg-hmb-npu.json", + "fshName": "cmg-research-study-subject-cmg-hmb-npu", + "fshType": "Instance", + "fshFile": "examples/ResearchStudy-BH-CMG.fsh", + "startLine": 102, + "endLine": 115 + }, + { + "outputFile": "ResearchStudy-cmg-research-study-subject-cmg-irb-hmb-npu.json", + "fshName": "cmg-research-study-subject-cmg-irb-hmb-npu", + "fshType": 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00000000..8c02b25a --- /dev/null +++ b/fsh-generated/fsh-index.txt @@ -0,0 +1,81 @@ +Output File Name Type FSH File Lines +CodeSystem-collection-type.json CollectionType CodeSystem modules/research-collection.fsh 2 - 11 +CodeSystem-ncpi.json Ncpi CodeSystem terminologies/ncpi.fsh 6 - 34 +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-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 +Consent-GRU.json GRU Instance examples/participant.fsh 88 - 101 +Consent-HMB.json HMB Instance examples/participant.fsh 178 - 191 +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 +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 +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 +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 +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 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+StructureDefinition-research-study-associated-party.json ResearchStudyAssociatedParty Extension modules/research-study.fsh 31 - 57 +StructureDefinition-research-study-design.json ResearchStudyDesign Extension modules/research-study.fsh 7 - 13 +StructureDefinition-research-study-group.json ResearchStudyGroup Profile modules/research-study-group.fsh 1 - 12 +StructureDefinition-research-study-result.json ResearchStudyResult Extension modules/research-study.fsh 15 - 20 +StructureDefinition-research-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 +ValueSet-collection-type-vs.json CollectionTypeVS ValueSet modules/research-collection.fsh 13 - 18 +ValueSet-mesh-terms.json MeshTerms ValueSet modules/research-accesss-policy.fsh 54 - 60 +ValueSet-research-data-access-code-vs.json ResearchDataAccessCodeVS ValueSet modules/research-accesss-policy.fsh 25 - 30 +ValueSet-research-data-access-type-vs.json ResearchDataAccessTypeVS ValueSet modules/research-accesss-policy.fsh 47 - 52 +ValueSet-research-data-date-of-birth-method-vs.json ResearchDataDateOfBirthMethodVS ValueSet modules/participant.fsh 31 - 35 +ValueSet-study-name-type-vs.json StudyNameTypeVS ValueSet modules/research-study.fsh 113 - 118 +ValueSet-study-personnel-role-vs.json StudyPersonnelRoleVS ValueSet modules/research-study.fsh 131 - 136 \ No newline at end of file diff --git a/fsh-generated/includes/fsh-link-references.md b/fsh-generated/includes/fsh-link-references.md new file mode 100644 index 00000000..f80277d7 --- /dev/null +++ b/fsh-generated/includes/fsh-link-references.md @@ -0,0 +1,80 @@ +[AccessPolicy]: StructureDefinition-access-policy.html +[AccessPolicyDescription]: 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b/fsh-generated/resources/CodeSystem-ncpi.json @@ -0,0 +1,88 @@ +{ + "resourceType": "CodeSystem", + "status": "active", + "content": "fragment", + "name": "Ncpi", + "id": "ncpi", + "title": "NCPI FHIR Codes", + "description": "Codes that would apply to NCPI projects", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/ncpi", + "concept": [ + { + "code": "Consortium", + "display": "Study Consortium" + }, + { + "code": "StudyCohort", + "display": "Study Cohort" + }, + { + "code": "ConsentGroup", + "display": "Study Consent Group" + }, + { + "code": "Summary", + "display": "Summary Data" + }, + { + "code": "CohortCount", + "display": "Number of cohorts that are part of this study" + }, + { + "code": "SubStudyCount", + "display": "Number of sub-studies that are part of this study" + }, + { + "code": "SampleCount", + "display": "Number of samples that are part of this study" + }, + { + "code": "Participant", + "display": "Number of participants that are part of this study" + }, 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"Enumerations for how DOB was constructed", + "description": "Enumerations for how DOB was constructed", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method", + "concept": [ + { + "code": "exact", + "display": "Exact" + }, + { + "code": "year-only", + "display": "Year Only" + }, + { + "code": "shifted", + "display": "Shifted" + }, + { + "code": "decade-only", + "display": "Decade Only" + }, + { + "code": "other", + "display": "Other" + } + ], + "experimental": false, + "caseSensitive": true, + "count": 5 +} diff --git a/fsh-generated/resources/CodeSystem-study-name-type.json b/fsh-generated/resources/CodeSystem-study-name-type.json new file mode 100644 index 00000000..e60fba82 --- /dev/null +++ b/fsh-generated/resources/CodeSystem-study-name-type.json @@ -0,0 +1,35 @@ +{ + "resourceType": "CodeSystem", + "status": "draft", + "content": "complete", + "name": "StudyNameType", + "id": "study-name-type", + "title": "Study Name Type", + "description": "Some common types of study 'names'.", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/study-name-type", + "concept": [ + { + "code": "formal-title", + "display": "Formal Title" + }, + { + "code": "internal-name", + "display": "Internal Name" + }, + { + "code": "familiar-ame", + "display": "Familiar Name (Nickname)" + }, + { + "code": "acronym", + "display": "Acronym" + }, + { + "code": "alternative-name", + "display": "Alternative Name" + } + ], + "experimental": false, + "caseSensitive": true, + "count": 5 +} diff --git a/fsh-generated/resources/CodeSystem-study-personnel-role.json b/fsh-generated/resources/CodeSystem-study-personnel-role.json new file mode 100644 index 00000000..232efb50 --- /dev/null +++ b/fsh-generated/resources/CodeSystem-study-personnel-role.json @@ -0,0 +1,27 @@ +{ + "resourceType": "CodeSystem", + "status": "draft", + "content": "complete", + "name": "StudyPersonnelRole", + "id": "study-personnel-role", + "title": "Study Personnel 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+ "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/Consent-hmb-irb-npu-consent.json b/fsh-generated/resources/Consent-hmb-irb-npu-consent.json new file mode 100644 index 00000000..bd0e8056 --- /dev/null +++ b/fsh-generated/resources/Consent-hmb-irb-npu-consent.json @@ -0,0 +1,78 @@ +{ + "resourceType": "Consent", + "id": "hmb-irb-npu-consent", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + ] + }, + "category": [ + { + "coding": [ + { + "code": "research", + "system": "http://terminology.hl7.org/CodeSystem/consentcategorycodes", + "display": "Research Information Access" + } + ] + } + ], + "provision": { + "purpose": [ + { + "code": "HMB", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code", + "display": "Health/Medical/Biomedical" + }, + { + "code": "IRB", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code", + "display": "IRB approval required" + }, + { + "code": "NPU", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code", + "display": "Not-for-profit use only" + } + ], + "type": "permit" + }, + "extension": [ + { + "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" + } + ] + } + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description", + "valueMarkdown": "Health/Medical/Biomedical, IRB Approval Required, Not for profit use" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link", + "valueUrl": "https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=DUC&view_pdf&stacc=phs000711.v7.p2" + } + ], + "status": "draft", + "scope": { + "coding": [ + { + "code": "research", + "system": 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"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-kf-gru-dbgap-consent.json b/fsh-generated/resources/Consent-kf-gru-dbgap-consent.json new file mode 100644 index 00000000..e3a14ef9 --- /dev/null +++ b/fsh-generated/resources/Consent-kf-gru-dbgap-consent.json @@ -0,0 +1,68 @@ +{ + "resourceType": "Consent", + "id": "kf-gru-dbgap-consent", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + ] + }, + "category": [ + { + "coding": [ + { + "code": "research", + "system": "http://terminology.hl7.org/CodeSystem/consentcategorycodes", + "display": "Research Information Access" + } + ] + } + ], + "provision": { + "purpose": [ + { + "code": "GRU", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code", + "display": "General Research Use" + } + ], + "type": "permit" + }, + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description", + "valueMarkdown": "Use of the data is limited only by the terms of the model Data Use Certification." + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/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/Consent-kf-gsr-allowed-access.json b/fsh-generated/resources/Consent-kf-gsr-allowed-access.json new file mode 100644 index 00000000..fcd70314 --- /dev/null +++ b/fsh-generated/resources/Consent-kf-gsr-allowed-access.json @@ -0,0 +1,58 @@ +{ + "resourceType": "Consent", + "id": "kf-gsr-allowed-access", + "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" + } + ] + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description", + "valueMarkdown": "Public Posting of Genomic Summary Results - Allowed." + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link", + "valueUrl": "https://www.genome.gov/about-nhgri/Policies-Guidance/Data-Sharing-Policies-and-Expectations/GSR-update-FAQs" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-type", + "valueCodeableConcept": { + "coding": [ + { + "code": "gsr-allowed", + "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-kf-registered-allowed-access.json b/fsh-generated/resources/Consent-kf-registered-allowed-access.json new file mode 100644 index 00000000..9abd3bc5 --- /dev/null +++ b/fsh-generated/resources/Consent-kf-registered-allowed-access.json @@ -0,0 +1,58 @@ +{ + "resourceType": "Consent", + "id": "kf-registered-allowed-access", + "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" + } + ] + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description", + "valueMarkdown": "Spans clinical data, expression data, somatic mutations, etc" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link", + "valueUrl": "https://kidsfirstdrc.org/portal/portal-features/#dataAccess" + }, + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-type", + "valueCodeableConcept": { + "coding": [ + { + "code": "registered", + "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/Group-cmg-research-study-bhcmg-consent-group-hmb-npu.json b/fsh-generated/resources/Group-cmg-research-study-bhcmg-consent-group-hmb-npu.json new file mode 100644 index 00000000..08918234 --- /dev/null +++ b/fsh-generated/resources/Group-cmg-research-study-bhcmg-consent-group-hmb-npu.json @@ -0,0 +1,19 @@ +{ + "resourceType": "Group", + "id": "cmg-research-study-bhcmg-consent-group-hmb-npu", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" + ] + }, + "identifier": [ + { + "system": "http://mendelian.org/fhir/Group", + "value": "HMB-NPU-Participants" + } + ], + "type": "person", + "actual": true, + "name": "BM-CMG Study HMB-NPU Participants", + "quantity": 1665 +} diff --git a/fsh-generated/resources/Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.json b/fsh-generated/resources/Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.json new file mode 100644 index 00000000..691dd9ea --- /dev/null +++ b/fsh-generated/resources/Group-cmg-research-study-bhcmg-consent-group-irb-hmb-npu.json @@ -0,0 +1,19 @@ +{ + "resourceType": "Group", + "id": "cmg-research-study-bhcmg-consent-group-irb-hmb-npu", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" + ] + }, + "identifier": [ + { + "system": "http://mendelian.org/fhir/Group", + "value": "IRB-HMB-NPU-Participants" + } + ], + "type": "person", + "actual": true, + "name": "BM-CMG Study IRB-HMB-NPU Participants", + "quantity": 1665 +} diff --git a/fsh-generated/resources/Group-kf-research-study-cbtn-participants.json b/fsh-generated/resources/Group-kf-research-study-cbtn-participants.json new file mode 100644 index 00000000..f1c4db3c --- /dev/null +++ b/fsh-generated/resources/Group-kf-research-study-cbtn-participants.json @@ -0,0 +1,19 @@ +{ + "resourceType": "Group", + "id": "kf-research-study-cbtn-participants", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" + ] + }, + "identifier": [ + { + "system": "https://cbtn.org/", + "value": "CBTN-Participants" + } + ], + "type": "person", + "actual": true, + "name": "Participants from the CBTN research study", + "quantity": 6667 +} diff --git a/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json b/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json new file mode 100644 index 00000000..7ede8185 --- /dev/null +++ b/fsh-generated/resources/ImplementationGuide-ncpi-fhir-implementation-guide-v2.json @@ -0,0 +1,844 @@ +{ + "resourceType": "ImplementationGuide", + "id": "ncpi-fhir-implementation-guide-v2", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ImplementationGuide/ncpi-fhir-implementation-guide-v2", + "version": "0.1.0", + "name": "NCPIFHIRIGv2", + "title": "NCPI FHIR Implementation Guide v2", + "status": "draft", + "publisher": "NCPI FHIR Working Group", + "contact": [ + { + "name": "NCPI FHIR Working Group", + "telecom": [ + { + "system": "url", + "value": "http://example.org/example-publisher" + }, + { + "system": "email", + "value": "ncpi-fhir-ig@googlegroups.com" + } + ] + } + ], + "description": "FHIR Implementation Guide for the NIH Cloud Platform Interoperability Effort (NCPI).", + "packageId": "ncpi-fhir-implementation-guide-v2", + "fhirVersion": [ + "4.3.0" + ], + "dependsOn": [ + { + "packageId": "hl7.fhir.us.core", + "version": "3.1.1", + "uri": "http://hl7.org/fhir/us/core/ImplementationGuide/hl7.fhir.us.core", + "id": "hl7_fhir_us_core" + } + ], + "definition": { + "resource": [ + { + "reference": { + "reference": "StructureDefinition/access-policy" + }, + "name": "Access policy", + "description": "Access Policy Extension", + "exampleBoolean": false + }, + { + "reference": { + "reference": "StructureDefinition/access-policy-description" + }, + "name": "Access Policy Description", + "description": "Descriptive text summarizing the policy restrictions and other details associated with this access provision.", + "exampleBoolean": false + }, + { + "reference": { + "reference": "StructureDefinition/access-type" + }, + "name": "Access Type", + "description": "Access type code associated with downloads affected by this Access Policy ( open | registered | controlled )", + "exampleBoolean": false + }, + { + "reference": { + "reference": "StructureDefinition/research-age-at-last-vital-status" + }, + "name": "Age at Last Vital Status Extension", + "description": "Age at Last Vital Status Extension", + "exampleBoolean": false + }, + { + "reference": { + "reference": "ResearchStudy/cmg-research-study-bhcmg" + }, + "name": "Baylor Hopkins Center for Mendelian Genomics (BH CMG)", + "description": "The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-study" + }, + { + "reference": { + "reference": "Consent/kf-gru-dac-consent" + }, + "name": "CBTN General Research Use (GRU) Consent DAC", + "description": "General Research Use (GRU)", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + }, + { + "reference": { + "reference": "Consent/kf-gru-dbgap-consent" + }, + "name": "CBTN General Research Use (GRU) Consent dbGaP", + "description": "General Research Use (GRU)", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + }, + { + "reference": { + "reference": "ResearchStudy/kf-research-study-subject-gsr-allowed" + }, + "name": "CBTN Genomic Summary Results (GSR) Allowed Access", + "description": "Genomic Summary Results (GSR) Allowed Access", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" + }, + { + "reference": { + "reference": "ResearchStudy/kf-research-study-subject-gru-dac" + }, + "name": "CBTN GRU data access via DAC", + "description": "GRU data access via DAC", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" + }, + { + "reference": { + "reference": "ResearchStudy/kf-research-study-subject-gru-dbgap" + }, + "name": "CBTN GRU data access via dbGaP", + "description": "GRU data access via dbGaP", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" + }, + { + "reference": { + "reference": "PractitionerRole/kf-research-study-personnel-role-op-lead" + }, + "name": "CBTN Operations Lead", + "description": "CBTN Operations Lead", + "exampleBoolean": true + }, + { + "reference": { + "reference": "ResearchStudy/kf-research-study-subject-registered" + }, + "name": "CBTN Registered Tier Access", + "description": "CBTN Registered Tier Access", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" + }, + { + "reference": { + "reference": "ResearchStudy/kf-research-study-cbtn" + }, + "name": "Children's Brain Tumor Network (CBTN)", + "description": "Brain tumors are the most common form of cancer in children aged 0-19 in the United States, and are the largest cause of cancer-related deaths. The estimated number of new cases in 2019 is nearly 3,800 and thus brain tumors are a rare disease. Despite their relative rarity, the years of potential life lost due to brain tumors in 2009 was estimated at 47,631 years for children and adolescents aged 0-19 in the United States; this is a disproportionate amount of life lost compared to adult cancers and represents an unrecognized societal threat. There is an urgent need to improve therapies for these children. Most of the high-grade glial and embryonal brain cancers still remain largely incurable despite decades of clinical and laboratory research. Existing non-targeted chemotherapies and radiation, while at times effective, often represent pyrrhic victories, leaving behind life-long health burdens and causing a significant risk of secondary malignancies. NIH funded pediatric brain tumor cohort-based genomic dataset generation efforts have lagged behind other histologies and have yet to be included as part of large-scale sequencing efforts. However, consortia-based initiatives like those supported by the Children's Brain Tumor Network (CBTN) have demonstrated the early potential for clinically annotated genomic cohorts and their utility and interest by both the pediatric cancer and structural birth defect community with more than 130 data access requests for a non-embargoed cohort of tumor/normal whole genomes and paired tumor RNAseq. Indeed more than one quarter of this 800-subject initial sequencing cohort were identified to have birth-defect-associated clinical annotations in their clinical records, however, to our knowledge limited to no trio-based genomics cohort studies exist for any one pediatric brain tumor histology. The project's proposed sequencing cohort defines the largest, clinically annotated pediatric brain tumor cohort study to date and seeks to define the intersection of germline and somatic underpinnings of pediatric brain tumors across a shared developmental context of cancer and structural birth defects.", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-study" + }, + { + "reference": { + "reference": "Organization/kf-research-study-organization-chop" + }, + "name": "Children's Hospital of Philadelphia", + "description": "Represents the Organization for which CHOP PIs are affiliated", + "exampleBoolean": true + }, + { + "reference": { + "reference": "ValueSet/collection-type-vs" + }, + "name": "Collection Type", + "description": "Enumerated list of Collection types", + "exampleBoolean": false + }, + { + "reference": { + "reference": "CodeSystem/collection-type" + }, + "name": "Collection Type", + "description": "Enumerated list of collection types", + "exampleBoolean": false + }, + { + "reference": { + "reference": "PractitionerRole/kf-research-study-personnel-role-pi" + }, + "name": "dbGaP PI", + "description": "dbGaP PI", + "exampleBoolean": true + }, + { + "reference": { + "reference": "PractitionerRole/kf-research-study-personnel-role-pi-x01" + }, + "name": "dbGaP PI, X01 FY 2021", + "description": "dbGaP PI, X01 FY 2021", + "exampleBoolean": true + }, + { + "reference": { + "reference": "ValueSet/research-data-date-of-birth-method-vs" + }, + "name": "Enumerations for how DOB was constructed", + "description": "Enumerations for how DOB was constructed", + "exampleBoolean": false + }, + { + "reference": { + "reference": "CodeSystem/research-data-date-of-birth-method" + }, + "name": "Enumerations for how DOB was constructed", + "description": "Enumerations for how DOB was constructed", + "exampleBoolean": false + }, + { + "reference": { + "reference": "ResearchSubject/cbtn-example-participantstudy" + }, + "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" + }, + { + "reference": { + "reference": "ResearchSubject/emerge-example-participantstudy" + }, + "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" + }, + { + "reference": { + "reference": "ResearchSubject/pcgc-example-participantstudy" + }, + "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" + }, + { + "reference": { + "reference": "Patient/PT-KZG2CZ95" + }, + "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-participant" + }, + { + "reference": { + "reference": "Person/cbtn-example-person" + }, + "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" + }, + { + "reference": { + "reference": "Patient/6812345" + }, + "name": "Example patients based on data from eMERGE", + "description": "Example patients based on data from eMERGE", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + }, + { + "reference": { + "reference": "Person/emerge-example-person" + }, + "name": "Example patients based on data from eMERGE", + "description": "Example patients based on data from eMERGE", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person" + }, + { + "reference": { + "reference": "Patient/PT-005B7CZ4" + }, + "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" + }, + { + "reference": { + "reference": "Person/pcgc-example-person" + }, + "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" + }, + { + "reference": { + "reference": "Consent/kf-gsr-allowed-access" + }, + "name": "Genomic Summary Results (GSR) Allowed Access", + "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/hmb-irb-npu-consent" + }, + "name": "HMB-IRB-NPU Consent", + "description": "Consented with Health/Medical/Biomedical + IRB Required + Not for profit use", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + }, + { + "reference": { + "reference": "Consent/hmb-npu-consent" + }, + "name": "HMB-NPU Consent", + "description": "Consented with Health/Medical/Biomedical + Not for profit use", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + }, + { + "reference": { + "reference": "List/ncpi-research-collection-kfx01" + }, + "name": "Kids First X01s", + "description": "Kids First X01s", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-collection" + }, + { + "reference": { + "reference": "StructureDefinition/label-extension" + }, + "name": "Label", + "description": "A text label accompanied by a code indicating the label type (such as Acronym, subtitle, etc)", + "exampleBoolean": false + }, + { + "reference": { + "reference": "ValueSet/mesh-terms" + }, + "name": "MeSH Terms", + "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": 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"name": "Participants consented under HMB-NPU", + "description": "BH-CMG study's population consented under Health/Medical/Biomedical + Not for profit use", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" + }, + { + "reference": { + "reference": "ResearchStudy/cmg-research-study-subject-cmg-hmb-npu" + }, + "name": "Participants consented under HMB-NPU", + "description": "CMG Consent Group, Health/Medical/Biomedical + Not for profit use", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" + }, + { + "reference": { + "reference": "Group/cmg-research-study-bhcmg-consent-group-irb-hmb-npu" + }, + "name": "Participants consented under IRB-HMB-NPU", + "description": "BH-CMG study's population consented under Health/Medical/Biomedical + IRB Required + Not for profit use", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group" + }, + { + "reference": { + "reference": "ResearchStudy/cmg-research-study-subject-cmg-irb-hmb-npu" + }, + "name": "Participants consented under IRB-HMB-NPU", + "description": "BH-CMG Consent Group, Health/Medical/Biomedical + IRB Required + Not for profit use", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" + }, + { + "reference": { + "reference": "Group/kf-research-study-cbtn-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" + }, + "name": "Pediatric Brain Tumor Atlas", + "description": "Pediatric Brain Tumor Atlas", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-collection" + }, + { + "reference": { + "reference": "Consent/kf-registered-allowed-access" + }, + "name": "Registered Tier Access", + "description": "Registered Tier Access", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + }, + { + "reference": { + "reference": "ValueSet/research-data-access-code-vs" + }, + "name": "Research Data Access Codes", + "description": "Enumerated list of access codes such as dbGaP consent codes among others.", + "exampleBoolean": false + }, + { + "reference": { + "reference": "CodeSystem/research-data-access-code" + }, + "name": "Research Data Access Codes", + "description": "Enumerated list of access codes such as dbGaP consent codes among others.", + "exampleBoolean": false + }, + { + "reference": { + "reference": "ValueSet/research-data-access-type-vs" + }, + "name": "Research Data Access Type Codes", + "description": "Enumerated list of access type codes such as 'Open Access', 'Registered Access' and 'Controlled Access'", + 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"description": "Some common types of study 'names'.", + "exampleBoolean": false + }, + { + "reference": { + "reference": "CodeSystem/study-name-type" + }, + "name": "Study Name Type", + "description": "Some common types of study 'names'.", + "exampleBoolean": false + }, + { + "reference": { + "reference": "ValueSet/study-personnel-role-vs" + }, + "name": "Study Personnel Role", + "description": "Roles associated with study personnel.", + "exampleBoolean": false + }, + { + "reference": { + "reference": "CodeSystem/study-personnel-role" + }, + "name": "Study Personnel Role", + "description": "Roles associated with study personnel.", + "exampleBoolean": false + }, + { + "reference": { + "reference": "List/ncpi-research-collection-cmg" + }, + "name": "The Centers for Medelian Genetics", + "description": "The Centers for Medelian Genetics", + "exampleCanonical": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-collection" + } + ], + "page": { + "nameUrl": 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"generation": "markdown" + }, + { + "nameUrl": "example_phenotype_condition.html", + "title": "Example Phenotype Condition", + "generation": "markdown" + }, + { + "nameUrl": "example_research_study.html", + "title": "Example Research Study", + "generation": "markdown" + }, + { + "nameUrl": "example_specimen.html", + "title": "Example Specimen", + "generation": "markdown" + }, + { + "nameUrl": "FHIR_Basics.html", + "title": "FHIR Basics", + "generation": "markdown" + }, + { + "nameUrl": "fhir_version.html", + "title": "Fhir Version", + "generation": "markdown" + }, + { + "nameUrl": "IG_Versioning.html", + "title": "IG Versioning", + "generation": "markdown" + }, + { + "nameUrl": "module_assays.html", + "title": "Module Assays", + "generation": "markdown" + }, + { + "nameUrl": "module_family.html", + "title": "Module Family", + "generation": "markdown" + }, + { + "nameUrl": "module_files.html", + "title": "Module Files", + "generation": "markdown" + }, + { + "nameUrl": 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"use_case_tbd.html", + "title": "Use Case Tbd", + "generation": "markdown" + } + ] + }, + "parameter": [ + { + "code": "copyrightyear", + "value": "2023+" + }, + { + "code": "releaselabel", + "value": "ci-build" + } + ] + } +} diff --git a/fsh-generated/resources/List-ncpi-research-collection-cmg.json b/fsh-generated/resources/List-ncpi-research-collection-cmg.json new file mode 100644 index 00000000..948e403a --- /dev/null +++ b/fsh-generated/resources/List-ncpi-research-collection-cmg.json @@ -0,0 +1,59 @@ +{ + "resourceType": "List", + "id": "ncpi-research-collection-cmg", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-collection" + ] + }, + "note": [ + { + "text": "The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments." + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link", + "valueUrl": "https://mendeliangenomics.org/" + }, + { + "extension": [ + { + "url": "type", + "valueCodeableConcept": { + "coding": [ + { + "code": "acronym", + "system": "http://terminology.hl7.org/CodeSystem/title-type" + } + ] + } + }, + { + "url": "label", + "valueString": "CMG" + } + ], + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/label-extension" + } + ], + "entry": [ + { + "item": { + "reference": "ResearchStudy/cmg-research-study-bhcmg" + } + } + ], + "title": "The Centers for Medelian Genetics", + "code": { + "coding": [ + { + "code": "consortium", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/collection-type", + "display": "Consortium" + } + ] + }, + "status": "current", + "mode": "snapshot" +} diff --git a/fsh-generated/resources/List-ncpi-research-collection-kfx01.json b/fsh-generated/resources/List-ncpi-research-collection-kfx01.json new file mode 100644 index 00000000..848fa346 --- /dev/null +++ b/fsh-generated/resources/List-ncpi-research-collection-kfx01.json @@ -0,0 +1,39 @@ +{ + "resourceType": "List", + "id": "ncpi-research-collection-kfx01", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-collection" + ] + }, + "note": [ + { + "text": "Through its Data Resource Center and NIH X01 grant mechanism, Kids First supports data generation and data sharing in the cloud. To date, the program has supported the public release of data from 30 projects and made available nearly 30,000 genomes, representing structural birth defects and childhood cancer patients and families through the Kids First Data Resource Portal" + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link", + "valueUrl": "https://cbtn.org/pediatric-brain-tumor-atlas" + } + ], + "entry": [ + { + "item": { + "reference": "ResearchStudy/kf-research-study-cbtn" + } + } + ], + "title": "Kids First X01s", + "code": { + "coding": [ + { + "code": "program", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/collection-type", + "display": "Program" + } + ] + }, + "status": "current", + "mode": "snapshot" +} diff --git a/fsh-generated/resources/List-ncpi-research-collection-pbta.json b/fsh-generated/resources/List-ncpi-research-collection-pbta.json new file mode 100644 index 00000000..71cb3709 --- /dev/null +++ b/fsh-generated/resources/List-ncpi-research-collection-pbta.json @@ -0,0 +1,59 @@ +{ + "resourceType": "List", + "id": "ncpi-research-collection-pbta", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-collection" + ] + }, + "note": [ + { + "text": "The Pediatric Brain Tumor Atlas (PBTA) is a collaborative effort to accelerate discoveries for therapeutic intervention for children diagnosed with a brain tumor. The first PBTA dataset release occurred in September of 2018 and includes data from tumor types including matched tumor/normal, whole genome data (WGS), RNAseq, proteomics, longitudinal clinical data, imaging data including MRIs and radiology reports, histology slide images and pathology reports. Funding for this initiative was provided by more than 50 foundation sponsors" + } + ], + "extension": [ + { + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link", + "valueUrl": "https://cbtn.org/pediatric-brain-tumor-atlas" + }, + { + "extension": [ + { + "url": "type", + "valueCodeableConcept": { + "coding": [ + { + "code": "acronym", + "system": "http://terminology.hl7.org/CodeSystem/title-type" + } + ] + } + }, + { + "url": "label", + "valueString": "PBTA" + } + ], + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/label-extension" + } + ], + "entry": [ + { + "item": { + "reference": "ResearchStudy/kf-research-study-cbtn" + } + } + ], + "title": "Pediatric Brain Tumor Atlas", + "code": { + "coding": [ + { + "code": "consortium", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/collection-type", + "display": "Consortium" + } + ] + }, + "status": "current", + "mode": "snapshot" +} diff --git 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The dataset(s) used for the analyses described in this manuscript was obtained from the database of Genotype and Phenotype (dbGaP) found at http://www.ncbi.nlm.nih.gov/gap through dbGaP accession number phs000711.v7.p2." + }, + { + "type": "citation", + "label": "Publication", + "citation": "Gonzaga-Jauregui C, Lupski JR, Gibbs RA\nHuman genome sequencing in health and disease.\nAnnu Rev Med. 2012; 63:35-61.\nPMID: 22248320" + }, + { + "type": "citation", + "label": "Publication", + "citation": "Bamshad MJ, Shendure JA, Valle D, Hamosh A, Lupski JR, Gibbs RA, Boerwinkle E, Lifton RP, Gerstein M, Gunel M, Mane S, Nickerson DA, Centers for Mendelian Genomics\nThe Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions.\nAm J Med Genet A. 2012 Jul; 158A(7):1523-5.\nPMID: 22628075" + }, + { + "type": "citation", + "label": "Publication", + "citation": "Boone PM, Campbell IM, Baggett BC, Soens ZT, Rao MM, Hixson PM, Patel A, Bi W, Cheung SW, Lalani SR, Beaudet AL, Stankiewicz P, Shaw CA, Lupski JR\nDeletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles.\nGenome Res. 2013 Sep; 23(9):1383-94.\nPMID: 23685542" + }, + { + "type": "citation", + "label": "Publication", + "citation": "Cheung YH, Gayden T, Campeau PM, LeDuc CA, Russo D, Nguyen VH, Guo J, Qi M, Guan Y, Albrecht S, Moroz B, Eldin KW, Lu JT, Schwartzentruber J, Malkin D, Berghuis AM, Emil S, Gibbs RA, Burk DL, Vanstone M, Lee BH, Orchard D, Boycott KM, Chung WK, Jabado N\nA recurrent PDGFRB mutation causes familial infantile myofibromatosis.\nAm J Hum Genet. 2013 Jun 06; 92(6):996-1000.\nPMID: 23731537" + }, + { + "type": "citation", + "label": "Publication", + "citation": "Campeau PM, Kasperaviciute D, Lu JT, Burrage LC, Kim C, Hori M, Powell BR, Stewart F, Félix TM, van den Ende J, Wisniewska M, Kayserili H, Rump P, Nampoothiri S, Aftimos S, Mey A, Nair LD, Begleiter ML, De Bie I, Meenakshi G, Murray ML, Repetto GM, Golabi M, Blair E, Male A, Giuliano F, Kariminejad A, Newman WG, Bhaskar SS, Dickerson JE, Kerr B, Banka S, Giltay JC, Wieczorek D, Tostevin A, Wiszniewska J, Cheung SW, Hennekam RC, Gibbs RA, Lee BH, Sisodiya SM\nThe genetic basis of DOORS syndrome: an exome-sequencing study.\nLancet Neurol. 2014 Jan; 13(1):44-58.\nPMID: 24291220" + }, + { + "type": "documentation", + "label": "AdditionalDocumentation", + "url": "https://app.terra.bio/#workspaces/anvil-datastorage/AnVIL_CMG_BaylorHopkins_HMB-IRB-NPU_WES" + }, + { + "type": "documentation", + "label": "Grant", + "display": "1U54HG006542. 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Additionally, use the following statement to acknowledge the submitter(s) of this study:\n\n\nThe data from this study phs002517 was made available pre-publication without embargo to support rapid and collaborative research in pediatric cancer via the NCI's Cancer Research Data Commons (https://datacommons.cancer.gov). This availability is made possible with the support of NCI's Childhood Cancer Data Initiative (grant No. 3P30CA082103-21S9) and Gabriella Miller Kids First Pediatric Research Program (X01 CA267587). Initial data generation efforts and coordination costs were supported by a number of philanthropic and industry partners with further details at cbtn.org.\n\n\n\nSuggested Acknowledgement Statement for secondary users: The results analyzed and here are based in whole or in part analyzing the study phs002517 and were accessed from the NCI's Cancer Research Data Commons (https://datacommons.cancer.gov)." + }, + { + "extension": [ + { + "url": "name", + "valueString": "Adam C. Resnick" + }, + { + "url": "role", + "valueCodeableConcept": { + "coding": [ + { + "code": "primary-investigator", + "system": "http://hl7.org/fhir/research-study-party-role" + } + ] + } + }, + { + "url": "party", + "valueReference": { + "reference": "PractitionerRole/kf-research-study-personnel-role-pi-x01" + } + } + ], + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-associated-party" + }, + { + "extension": [ + { + "url": "name", + "valueString": "Allison P. Heath" + }, + { + "url": "role", + "valueCodeableConcept": { + "coding": [ + { + "code": "primary-investigator", + "system": "http://hl7.org/fhir/research-study-party-role" + } + ] + } + }, + { + "url": "party", + "valueReference": { + "reference": "PractitionerRole/kf-research-study-personnel-role-pi" + } + } + ], + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-associated-party" + }, + { + "extension": [ + { + "url": "name", + "valueString": "Jennifer Mason" + }, + { + "url": "role", + "valueCodeableConcept": { + "coding": [ + { + "code": "study-director", + "system": "http://hl7.org/fhir/research-study-party-role" + } + ] + } + }, + { + "url": "party", + "valueReference": { + "reference": "PractitionerRole/kf-research-study-personnel-role-op-lead" + } + } + ], + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-associated-party" + } + ], + "title": "Children's Brain Tumor Network (CBTN)", + "description": "Brain tumors are the most common form of cancer in children aged 0-19 in the United States, and are the largest cause of cancer-related deaths. The estimated number of new cases in 2019 is nearly 3,800 and thus brain tumors are a rare disease. Despite their relative rarity, the years of potential life lost due to brain tumors in 2009 was estimated at 47,631 years for children and adolescents aged 0-19 in the United States; this is a disproportionate amount of life lost compared to adult cancers and represents an unrecognized societal threat. There is an urgent need to improve therapies for these children. Most of the high-grade glial and embryonal brain cancers still remain largely incurable despite decades of clinical and laboratory research. Existing non-targeted chemotherapies and radiation, while at times effective, often represent pyrrhic victories, leaving behind life-long health burdens and causing a significant risk of secondary malignancies. NIH funded pediatric brain tumor cohort-based genomic dataset generation efforts have lagged behind other histologies and have yet to be included as part of large-scale sequencing efforts. However, consortia-based initiatives like those supported by the Children's Brain Tumor Network (CBTN) have demonstrated the early potential for clinically annotated genomic cohorts and their utility and interest by both the pediatric cancer and structural birth defect community with more than 130 data access requests for a non-embargoed cohort of tumor/normal whole genomes and paired tumor RNAseq. Indeed more than one quarter of this 800-subject initial sequencing cohort were identified to have birth-defect-associated clinical annotations in their clinical records, however, to our knowledge limited to no trio-based genomics cohort studies exist for any one pediatric brain tumor histology. The project's proposed sequencing cohort defines the largest, clinically annotated pediatric brain tumor cohort study to date and seeks to define the intersection of germline and somatic underpinnings of pediatric brain tumors across a shared developmental context of cancer and structural birth defects.", + "status": "completed" +} diff --git a/fsh-generated/resources/ResearchStudy-kf-research-study-subject-gru-dac.json b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-gru-dac.json new file mode 100644 index 00000000..daf1a3e7 --- /dev/null +++ b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-gru-dac.json @@ -0,0 +1,36 @@ +{ + "resourceType": "ResearchStudy", + "id": "kf-research-study-subject-gru-dac", + "meta": { + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject" + ] + }, + "identifier": [ + { + "system": "https://cbtn.org/", + "value": "GRU-DAC" + } + ], + "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-kf-research-study-subject-gru-dbgap.json b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-gru-dbgap.json new file mode 100644 index 00000000..0119cca7 --- /dev/null +++ b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-gru-dbgap.json @@ -0,0 +1,36 @@ +{ + "resourceType": "ResearchStudy", + "id": "kf-research-study-subject-gru-dbgap", + "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-kf-research-study-subject-gsr-allowed.json b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-gsr-allowed.json new file mode 100644 index 00000000..54d85b15 --- /dev/null +++ b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-gsr-allowed.json @@ -0,0 +1,36 @@ +{ + "resourceType": "ResearchStudy", + "id": "kf-research-study-subject-gsr-allowed", + "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/ResearchStudy-kf-research-study-subject-registered.json b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-registered.json new file mode 100644 index 00000000..c1db7284 --- /dev/null +++ b/fsh-generated/resources/ResearchStudy-kf-research-study-subject-registered.json @@ -0,0 +1,36 @@ +{ + "resourceType": "ResearchStudy", + "id": "kf-research-study-subject-registered", + "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": "CBTN Registered Tier Access", + "status": "completed" +} diff --git a/fsh-generated/resources/ResearchStudy-phv00407460.v2.json b/fsh-generated/resources/ResearchStudy-phv00407460.v2.json new file mode 100644 index 00000000..419475f9 --- /dev/null +++ b/fsh-generated/resources/ResearchStudy-phv00407460.v2.json @@ -0,0 +1,36 @@ +{ + "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 new file mode 100644 index 00000000..6edf25de --- /dev/null +++ b/fsh-generated/resources/ResearchSubject-cbtn-example-participantstudy.json @@ -0,0 +1,19 @@ +{ + "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 new file mode 100644 index 00000000..1bf34524 --- /dev/null +++ b/fsh-generated/resources/ResearchSubject-emerge-example-participantstudy.json @@ -0,0 +1,19 @@ +{ + "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 new file mode 100644 index 00000000..f331e552 --- /dev/null +++ b/fsh-generated/resources/ResearchSubject-pcgc-example-participantstudy.json @@ -0,0 +1,19 @@ +{ + "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/StructureDefinition-SharedDataModelPerson.json b/fsh-generated/resources/StructureDefinition-SharedDataModelPerson.json new file mode 100644 index 00000000..33895f7c --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelPerson.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "SharedDataModelPerson", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelPerson", + "name": "CdmPerson", + "title": "Shared Data Model for Research Persons", + "status": "draft", + "description": "The **Shared data model for Person**", + "fhirVersion": "4.3.0", + "kind": "logical", + "abstract": false, + "type": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelPerson", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Base", + "derivation": "specialization", + "differential": { + "element": [ + { + "id": "SharedDataModelPerson", + "path": "SharedDataModelPerson", + "short": "Shared Data Model for Research Persons", + "definition": "The **Shared data model for Person**" + }, + { + "id": "SharedDataModelPerson.identifier", + "path": "SharedDataModelPerson.identifier", + "short": "Unique Person identifier.", + "definition": "Unique Person identifier.", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelPerson.participant", + "path": "SharedDataModelPerson.participant", + "short": "The participant we are describing", + "definition": "The participant we are describing", + "min": 1, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "http://hl7.org/fhir/StructureDefinition/valueset-reference" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-SharedDataModelResearchCollection.json b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchCollection.json new file mode 100644 index 00000000..c736865a --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchCollection.json @@ -0,0 +1,94 @@ +{ + "resourceType": "StructureDefinition", + "id": "SharedDataModelResearchCollection", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchCollection", + "name": "CdmResearchCollection", + "title": "Shared Data Model for Research Collection", + "status": "draft", + "description": "The **Shared Data Model for Research Collection** represent various collections of research data including, but not limited, to Consortia, Programs, adhoc collections of Studies and datasets among other types of collections.", + "fhirVersion": "4.3.0", + "kind": "logical", + "abstract": false, + "type": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchCollection", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Base", + "derivation": "specialization", + "differential": { + "element": [ + { + "id": "SharedDataModelResearchCollection", + "path": "SharedDataModelResearchCollection", + "short": "Shared Data Model for Research Collection", + "definition": "The **Shared Data Model for Research Collection** represent various collections of research data including, but not limited, to Consortia, Programs, adhoc collections of Studies and datasets among other types of collections." + }, + { + "id": "SharedDataModelResearchCollection.name", + "path": "SharedDataModelResearchCollection.name", + "short": "The title of the collection.", + "definition": "The title of the collection.", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchCollection.description", + "path": "SharedDataModelResearchCollection.description", + "short": "The description of the collection.", + "definition": "The description of the collection.", + "min": 0, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchCollection.type", + "path": "SharedDataModelResearchCollection.type", + "short": "The type of collection being described.", + "definition": "The type of collection being described.", + "min": 1, + "max": "1", + "type": [ + { + "code": "code" + } + ], + "binding": { + "strength": "extensible", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/collection-type-vs" + } + }, + { + "id": "SharedDataModelResearchCollection.website", + "path": "SharedDataModelResearchCollection.website", + "short": "A URL for a website, document, or other reference that provides more information as an authoritative source of information about the collection.", + "definition": "A URL for a website, document, or other reference that provides more information as an authoritative source of information about the collection.", + "min": 0, + "max": "1", + "type": [ + { + "code": "url" + } + ] + }, + { + "id": "SharedDataModelResearchCollection.items", + "path": "SharedDataModelResearchCollection.items", + "short": "List of references to items included in the list. These can be studies, datasets, etc.", + "definition": "List of references to items included in the list. These can be studies, datasets, etc.", + "min": 1, + "max": "*", + "type": [ + { + "code": "Reference" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-SharedDataModelResearchDataAccessPolicy.json b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchDataAccessPolicy.json new file mode 100644 index 00000000..5110747a --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchDataAccessPolicy.json @@ -0,0 +1,68 @@ +{ + "resourceType": "StructureDefinition", + "id": "SharedDataModelResearchDataAccessPolicy", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchDataAccessPolicy", + "name": "CdmResearchDataAccessPolicy", + "title": "Shared Data Model for Research Data Access Policy", + "status": "draft", + "description": "The **Shared Data Model for Research Data Access Policy** represent the various Data Use Agreements that govern a researcher's access and use of research data.", + "fhirVersion": "4.3.0", + "kind": "logical", + "abstract": false, + "type": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchDataAccessPolicy", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Base", + "derivation": "specialization", + "differential": { + "element": [ + { + "id": "SharedDataModelResearchDataAccessPolicy", + "path": "SharedDataModelResearchDataAccessPolicy", + "short": "Shared Data Model for Research Data Access Policy", + "definition": "The **Shared Data Model for Research Data Access Policy** represent the various Data Use Agreements that govern a researcher's access and use of research data." + }, + { + "id": "SharedDataModelResearchDataAccessPolicy.policyCode", + "path": "SharedDataModelResearchDataAccessPolicy.policyCode", + "short": "Enumerated values that describe the policy including: dbGaP consent codes, DUO Terms among others. The bindings to these terms should enable groups to create their own codes.", + "definition": "Enumerated values that describe the policy including: dbGaP consent codes, DUO Terms among others. The bindings to these terms should enable groups to create their own codes.", + "min": 1, + "max": "*", + "type": [ + { + "code": "code" + } + ], + "binding": { + "strength": "required", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/research-data-access-code-vs" + } + }, + { + "id": "SharedDataModelResearchDataAccessPolicy.description", + "path": "SharedDataModelResearchDataAccessPolicy.description", + "short": "Free text further describing the policy, including description of necessary steps for gaining access to data", + "definition": "Free text further describing the policy, including description of necessary steps for gaining access to data", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchDataAccessPolicy.website", + "path": "SharedDataModelResearchDataAccessPolicy.website", + "short": "TBD", + "definition": "TBD", + "min": 0, + "max": "1", + "type": [ + { + "code": "url" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-SharedDataModelResearchParticipant.json b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchParticipant.json new file mode 100644 index 00000000..21d85e6d --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchParticipant.json @@ -0,0 +1,155 @@ +{ + "resourceType": "StructureDefinition", + "id": "SharedDataModelResearchParticipant", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchParticipant", + "name": "CdmResearchParticipant", + "title": "Shared Data Model for Research Participants", + "status": "draft", + "description": "The **Shared Data Model for Research Participants**", + "fhirVersion": "4.3.0", + "kind": "logical", + "abstract": false, + "type": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchParticipant", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Base", + "derivation": "specialization", + "differential": { + "element": [ + { + "id": "SharedDataModelResearchParticipant", + "path": "SharedDataModelResearchParticipant", + "short": "Shared Data Model for Research Participants", + "definition": "The **Shared Data Model for Research Participants**" + }, + { + "id": "SharedDataModelResearchParticipant.participantID", + "path": "SharedDataModelResearchParticipant.participantID", + "short": "Unique participant identifier. System identifier used for internal references.", + "definition": "Unique participant identifier. System identifier used for internal references.", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.externalID", + "path": "SharedDataModelResearchParticipant.externalID", + "short": "Unique participant identifier. System identifier used for internal references.", + "definition": "Unique participant identifier. System identifier used for internal references.", + "min": 0, + "max": "*", + "type": [ + { + "code": "code" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.population", + "path": "SharedDataModelResearchParticipant.population", + "short": "Population, Race, and/or Ethnicity information.", + "definition": "Population, Race, and/or Ethnicity information.", + "min": 0, + "max": "*", + "type": [ + { + "code": "code" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.ombRace", + "path": "SharedDataModelResearchParticipant.ombRace", + "short": "OMB coded Race for backwards compatibility", + "definition": "OMB coded Race for backwards compatibility", + "min": 0, + "max": "*", + "type": [ + { + "code": "code" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.ombEth", + "path": "SharedDataModelResearchParticipant.ombEth", + "short": "OMB coded Ethnicity for backwards compatibility", + "definition": "OMB coded Ethnicity for backwards compatibility", + "min": 0, + "max": "*", + "type": [ + { + "code": "code" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.sex", + "path": "SharedDataModelResearchParticipant.sex", + "short": "Sex assigned at birth (or pre-natal observed sex)", + "definition": "Sex assigned at birth (or pre-natal observed sex)", + "min": 1, + "max": "1", + "type": [ + { + "code": "code" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.dateOfBirth", + "path": "SharedDataModelResearchParticipant.dateOfBirth", + "short": "Date of Birth of the participant. Details of privacy method should be included in DOBMethod", + "definition": "Date of Birth of the participant. Details of privacy method should be included in DOBMethod", + "min": 0, + "max": "1", + "type": [ + { + "code": "date" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.dobMethod", + "path": "SharedDataModelResearchParticipant.dobMethod", + "short": "Specifies method used to alter DOB for research sharing. Details should be available in the study protocols.", + "definition": "Specifies method used to alter DOB for research sharing. Details should be available in the study protocols.", + "min": 0, + "max": "1", + "type": [ + { + "code": "code" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.ageAtLastVitalStatus", + "path": "SharedDataModelResearchParticipant.ageAtLastVitalStatus", + "short": "Age at last vital status", + "definition": "Age at last vital status", + "min": 0, + "max": "1", + "type": [ + { + "code": "date" + } + ] + }, + { + "id": "SharedDataModelResearchParticipant.vitalStatus", + "path": "SharedDataModelResearchParticipant.vitalStatus", + "short": "Vital Status", + "definition": "Vital Status", + "min": 0, + "max": "1", + "type": [ + { + "code": "code" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-SharedDataModelResearchStudy.json b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchStudy.json new file mode 100644 index 00000000..0423ed95 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelResearchStudy.json @@ -0,0 +1,345 @@ +{ + "resourceType": "StructureDefinition", + "id": "SharedDataModelResearchStudy", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchStudy", + "name": "CdmResearchStudy", + "title": "Shared Data Model for Research Study", + "status": "draft", + "description": "The **Shared Data Model for Research Study** represents the understanding of what a Research Study is from the context of users and authors of the NCPI FHIR IG.", + "fhirVersion": "4.3.0", + "kind": "logical", + "abstract": false, + "type": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchStudy", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Base", + "derivation": "specialization", + "differential": { + "element": [ + { + "id": "SharedDataModelResearchStudy", + "path": "SharedDataModelResearchStudy", + "short": "Shared Data Model for Research Study", + "definition": "The **Shared Data Model for Research Study** represents the understanding of what a Research Study is from the context of users and authors of the NCPI FHIR IG." + }, + { + "id": "SharedDataModelResearchStudy.persistentIdentifier", + "path": "SharedDataModelResearchStudy.persistentIdentifier", + "short": "External facing, globally unique identifier.", + "definition": "External facing, globally unique identifier.", + "min": 0, + "max": "*", + "type": [ + { + "code": "Identifier" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.parentStudy", + "path": "SharedDataModelResearchStudy.parentStudy", + "short": "Parent study, required only for substudies.", + "definition": "Parent study, required only for substudies.", + "min": 0, + "max": "1", + "type": [ + { + "code": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelResearchStudy" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.name", + "path": "SharedDataModelResearchStudy.name", + "short": "Name is a repeatable object that consists of sets of two fields. All ResearchStudy records must have at least one Name object with Name.Type=”formal title”.", + "definition": "Name is a repeatable object that consists of sets of two fields. All ResearchStudy records must have at least one Name object with Name.Type=”formal title”.", + "min": 1, + "max": "*", + "type": [ + { + "code": "BackboneElement" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.name.text", + "path": "SharedDataModelResearchStudy.name.text", + "short": "The study's name", + "definition": "The study's name", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.name.type", + "path": "SharedDataModelResearchStudy.name.type", + "short": "Type of name or title this name relates to (formal-title, internale-name, familiar-name, etc)", + "definition": "Type of name or title this name relates to (formal-title, internale-name, familiar-name, etc)", + "min": 0, + "max": "1", + "type": [ + { + "code": "code" + } + ], + "binding": { + "strength": "extensible", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/study-name-type-vs" + } + }, + { + "id": "SharedDataModelResearchStudy.description", + "path": "SharedDataModelResearchStudy.description", + "short": "short summary of relevant and important information about the study.", + "definition": "short summary of relevant and important information about the study.", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.website", + "path": "SharedDataModelResearchStudy.website", + "short": "A URL for a website that provides information about the research effort as a whole.", + "definition": "A URL for a website that provides information about the research effort as a whole.", + "min": 0, + "max": "*", + "type": [ + { + "code": "url" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.totalParticipants", + "path": "SharedDataModelResearchStudy.totalParticipants", + "short": "Number of total participants represented by the data in this study.", + "definition": "Number of total participants represented by the data in this study.", + "min": 0, + "max": "1", + "type": [ + { + "code": "integer" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.studyFocus", + "path": "SharedDataModelResearchStudy.studyFocus", + "short": "The primary focus(es) of the study. This can include terms related to disease area, intervention, drug, device, or other focus. MeSH terms are preferred.", + "definition": "The primary focus(es) of the study. This can include terms related to disease area, intervention, drug, device, or other focus. MeSH terms are preferred.", + "min": 0, + "max": "*", + "type": [ + { + "code": "BackboneElement" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.studyFocus.term", + "path": "SharedDataModelResearchStudy.studyFocus.term", + "short": "The term used to describe the focus of the study. A valid MeSH is preferred.", + "definition": "The term used to describe the focus of the study. A valid MeSH is preferred.", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.studyFocus.termSource", + "path": "SharedDataModelResearchStudy.studyFocus.termSource", + "short": "The source ontology or vocabulary for subjectFocus.Term (optional if term uses curie).", + "definition": "The source ontology or vocabulary for subjectFocus.Term (optional if term uses curie).", + "min": 0, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.enrollmentCriteria", + "path": "SharedDataModelResearchStudy.enrollmentCriteria", + "short": "EnrollmentCriteria describes the inclusion and exclusion criteria used to enroll participants in this study. This can be provided as a free text description, but may also be structured using bullets, tables, or other organizational methods.", + "definition": "EnrollmentCriteria describes the inclusion and exclusion criteria used to enroll participants in this study. This can be provided as a free text description, but may also be structured using bullets, tables, or other organizational methods.", + "min": 0, + "max": "1", + "type": [ + { + "code": "markdown" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.population", + "path": "SharedDataModelResearchStudy.population", + "short": "Population is a repeatable object that consists of sets of two fields. Population provides an overall description of the general population enrolled in the study, including basic demographics at a minimum and other useful population descriptors as appropriate.", + "definition": "Population is a repeatable object that consists of sets of two fields. Population provides an overall description of the general population enrolled in the study, including basic demographics at a minimum and other useful population descriptors as appropriate.", + "min": 0, + "max": "*", + "type": [ + { + "code": "BackboneElement" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.population.type", + "path": "SharedDataModelResearchStudy.population.type", + "short": "A term that specifies the population being described.", + "definition": "A term that specifies the population being described.", + "min": 1, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.population.description", + "path": "SharedDataModelResearchStudy.population.description", + "short": "A free text field that provides more information about the population specified in PopulationType within the context of this researchStudy.", + "definition": "A free text field that provides more information about the population specified in PopulationType within the context of this researchStudy.", + "min": 0, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.citation", + "path": "SharedDataModelResearchStudy.citation", + "short": "Provide any relevant information regarding how to cite this study. This can be as specific as including a full citation or as simple as a DOI.", + "definition": "Provide any relevant information regarding how to cite this study. This can be as specific as including a full citation or as simple as a DOI.", + "min": 0, + "max": "*", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.publications", + "path": "SharedDataModelResearchStudy.publications", + "short": "Provide a list of publications that use this data. This may be updated to include new publications as they are created.", + "definition": "Provide a list of publications that use this data. This may be updated to include new publications as they are created.", + "min": 0, + "max": "*", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.additionalDocumentation", + "path": "SharedDataModelResearchStudy.additionalDocumentation", + "short": "AdditionalDocumentation should be used to provide URLs, citations, or other appropriate references to technical documentation that is important for understanding the data included in this study. This can include data dictionaries, methods descriptions, github repositories, case report forms (CRFs), or any other relevant documentation.", + "definition": "AdditionalDocumentation should be used to provide URLs, citations, or other appropriate references to technical documentation that is important for understanding the data included in this study. This can include data dictionaries, methods descriptions, github repositories, case report forms (CRFs), or any other relevant documentation.", + "min": 0, + "max": "*", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.consortium", + "path": "SharedDataModelResearchStudy.consortium", + "short": "If the data in this study was gathered as part of a consortial effort, list the consortium here.", + "definition": "If the data in this study was gathered as part of a consortial effort, list the consortium here.", + "min": 0, + "max": "1", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.acknowledgements", + "path": "SharedDataModelResearchStudy.acknowledgements", + "short": "Acknowledgements describes any attribution or acknowledgements relevant to the study. This can include but is not limited to funding sources, organizational affiliations or sponsors.", + "definition": "Acknowledgements describes any attribution or acknowledgements relevant to the study. This can include but is not limited to funding sources, organizational affiliations or sponsors.", + "min": 0, + "max": "*", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.personnel", + "path": "SharedDataModelResearchStudy.personnel", + "short": "Every study must have at least one Primary Contact defined. Additional personnel such as Primary Investigator(s), Administrator(s), Collaborator(s) or other roles may also be included. If there are no appropriate individuals who can serve as primary contact for a study, an organization may be provided.", + "definition": "Every study must have at least one Primary Contact defined. Additional personnel such as Primary Investigator(s), Administrator(s), Collaborator(s) or other roles may also be included. If there are no appropriate individuals who can serve as primary contact for a study, an organization may be provided.", + "min": 0, + "max": "*", + "type": [ + { + "code": "BackboneElement" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.personnel.name", + "path": "SharedDataModelResearchStudy.personnel.name", + "short": "The name of the person being described.", + "definition": "The name of the person being described.", + "min": 1, + "max": "1", + "type": [ + { + "code": "HumanName" + } + ] + }, + { + "id": "SharedDataModelResearchStudy.personnel.role", + "path": "SharedDataModelResearchStudy.personnel.role", + "short": "The role of the person being described.", + "definition": "The role of the person being described.", + "min": 1, + "max": "1", + "type": [ + { + "code": "code" + } + ], + "binding": { + "strength": "extensible", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/study-personnel-role-vs" + } + }, + { + "id": "SharedDataModelResearchStudy.personnel.organization", + "path": "SharedDataModelResearchStudy.personnel.organization", + "short": "The organizational affiliation of the person being described.", + "definition": "The organizational affiliation of the person being described.", + "min": 0, + "max": "1", + "type": [ + { + "code": "string" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-SharedDataModelStudyParticipant.json b/fsh-generated/resources/StructureDefinition-SharedDataModelStudyParticipant.json new file mode 100644 index 00000000..0ab0a73f --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-SharedDataModelStudyParticipant.json @@ -0,0 +1,73 @@ +{ + "resourceType": "StructureDefinition", + "id": "SharedDataModelStudyParticipant", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelStudyParticipant", + "name": "CdmStudyParticipant", + "title": "Shared Data Model for Research Participant and Study Mapping", + "status": "draft", + "description": "The **Shared data model for StudyParticipant**", + "fhirVersion": "4.3.0", + "kind": "logical", + "abstract": false, + "type": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelStudyParticipant", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Base", + "derivation": "specialization", + "differential": { + "element": [ + { + "id": "SharedDataModelStudyParticipant", + "path": "SharedDataModelStudyParticipant", + "short": "Shared Data Model for Research Participant and Study Mapping", + "definition": "The **Shared data model for StudyParticipant**" + }, + { + "id": "SharedDataModelStudyParticipant.participant", + "path": "SharedDataModelStudyParticipant.participant", + "short": "The participant we are describing", + "definition": "The participant we are describing", + "min": 1, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "http://hl7.org/fhir/StructureDefinition/valueset-reference" + ] + } + ] + }, + { + "id": "SharedDataModelStudyParticipant.researchStudy", + "path": "SharedDataModelStudyParticipant.researchStudy", + "short": "The Research Study this participant has a relationship with", + "definition": "The Research Study this participant has a relationship with", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "http://hl7.org/fhir/StructureDefinition/valueset-reference" + ] + } + ] + }, + { + "id": "SharedDataModelStudyParticipant.accessPolicy", + "path": "SharedDataModelStudyParticipant.accessPolicy", + "short": "The Access Policy that may apply to this participant's data from this study. Not canonical, ie, one must rely on the row level AP.", + "definition": "The Access Policy that may apply to this participant's data from this study. Not canonical, ie, one must rely on the row level AP.", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "http://hl7.org/fhir/StructureDefinition/valueset-reference" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-access-policy-description.json b/fsh-generated/resources/StructureDefinition-access-policy-description.json new file mode 100644 index 00000000..a2371157 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-access-policy-description.json @@ -0,0 +1,52 @@ +{ + "resourceType": "StructureDefinition", + "id": "access-policy-description", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description", + "name": "AccessPolicyDescription", + "title": "Access Policy Description", + "status": "draft", + "description": "Descriptive text summarizing the policy restrictions and other details associated with this access provision.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Consent" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Access Policy Description", + "definition": "Descriptive text summarizing the policy restrictions and other details associated with this access provision." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "short": "Descriptive text summarizing the policy restrictions and other details associated with this access provision.", + "min": 1, + "type": [ + { + "code": "markdown" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-access-policy.json b/fsh-generated/resources/StructureDefinition-access-policy.json new file mode 100644 index 00000000..39137edf --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-access-policy.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "access-policy", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy", + "name": "AccessPolicy", + "title": "Access policy", + "status": "draft", + "description": "Access Policy Extension", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "ResearchSubject" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Access policy", + "definition": "Access Policy Extension" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "min": 1, + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-access-type.json b/fsh-generated/resources/StructureDefinition-access-type.json new file mode 100644 index 00000000..e16553c2 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-access-type.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "access-type", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-type", + "name": "AccessType", + "title": "Access Type", + "status": "draft", + "description": "Access type code associated with downloads affected by this Access Policy ( open | registered | controlled )", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Consent" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Access Type", + "definition": "Access type code associated with downloads affected by this Access Policy ( open | registered | controlled )" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-type" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ], + "binding": { + "strength": "required", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/research-data-access-type-vs" + } + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-label-extension.json b/fsh-generated/resources/StructureDefinition-label-extension.json new file mode 100644 index 00000000..1ef7809e --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-label-extension.json @@ -0,0 +1,101 @@ +{ + "resourceType": "StructureDefinition", + "id": "label-extension", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/label-extension", + "name": "Label", + "title": "Label", + "status": "draft", + "description": "A text label accompanied by a code indicating the label type (such as Acronym, subtitle, etc)", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "List" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Label", + "definition": "A text label accompanied by a code indicating the label type (such as Acronym, subtitle, etc)" + }, + { + "id": "Extension.extension:type", + "path": "Extension.extension", + "sliceName": "type", + "short": "primary|official|scientific|plain-language|subtitle|acronym|earlier-title|language|autotranslated|human-use|machine-use|duplicate-uid", + "min": 0, + "max": "1", + "mustSupport": true + }, + { + "id": "Extension.extension:type.extension", + "path": "Extension.extension.extension", + "max": "0" + }, + { + "id": "Extension.extension:type.url", + "path": "Extension.extension.url", + "fixedUri": "type" + }, + { + "id": "Extension.extension:type.value[x]", + "path": "Extension.extension.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ], + "binding": { + "strength": "required", + "valueSet": "http://hl7.org/fhir/ValueSet/title-type" + } + }, + { + "id": "Extension.extension:label", + "path": "Extension.extension", + "sliceName": "label", + "short": "The name", + "min": 0, + "max": "1", + "mustSupport": true + }, + { + "id": "Extension.extension:label.extension", + "path": "Extension.extension.extension", + "max": "0" + }, + { + "id": "Extension.extension:label.url", + "path": "Extension.extension.url", + "fixedUri": "label" + }, + { + "id": "Extension.extension:label.value[x]", + "path": "Extension.extension.value[x]", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/label-extension" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "max": "0" + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-Study-Participant.json b/fsh-generated/resources/StructureDefinition-ncpi-Study-Participant.json new file mode 100644 index 00000000..31208051 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-Study-Participant.json @@ -0,0 +1,68 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-Study-Participant", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-Study-Participant", + "version": "0.1.0", + "name": "NcpiStudyParticipant", + "title": "NCPI Study Participant", + "status": "draft", + "description": "Research Study", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "ResearchSubject", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/ResearchSubject", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "ResearchSubject.extension", + "path": "ResearchSubject.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "ResearchSubject.extension:access-policy", + "path": "ResearchSubject.extension", + "sliceName": "access-policy", + "short": "The Access Policy that may apply to this participant's data from this study. Not canonical, ie, one must rely on the row level AP.", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy" + ] + } + ] + }, + { + "id": "ResearchSubject.study", + "path": "ResearchSubject.study", + "short": "The Research Study this participant has a relationship with" + }, + { + "id": "ResearchSubject.individual", + "path": "ResearchSubject.individual", + "short": "The participant we are describing", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-participant.json b/fsh-generated/resources/StructureDefinition-ncpi-participant.json new file mode 100644 index 00000000..eaea461c --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-participant.json @@ -0,0 +1,151 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-participant", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant", + "version": "0.1.0", + "name": "NcpiParticipant", + "title": "NCPI Participant", + "status": "draft", + "description": "Research oriented patient", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Patient", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Patient", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Patient.id", + "path": "Patient.id", + "short": "ParticipantID - Unique participant identifier. System identifier used for internal references.", + "min": 1 + }, + { + "id": "Patient.extension", + "path": "Patient.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Patient.extension:us-core-birth-sex", + "path": "Patient.extension", + "sliceName": "us-core-birth-sex", + "short": "Sex assigned at birth (or pre-natal observed sex)", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex" + ] + } + ] + }, + { + "id": "Patient.extension:us-core-race", + "path": "Patient.extension", + "sliceName": "us-core-race", + "short": "US Core Race", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race" + ] + } + ] + }, + { + "id": "Patient.extension:us-core-ethnicity", + "path": "Patient.extension", + "sliceName": "us-core-ethnicity", + "short": "US Core Ethnicity", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity" + ] + } + ] + }, + { + "id": "Patient.extension:population", + "path": "Patient.extension", + "sliceName": "population", + "short": "Population, Race, and/or Ethnicity information.", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-population" + ] + } + ] + }, + { + "id": "Patient.extension:dob-method", + "path": "Patient.extension", + "sliceName": "dob-method", + "short": "Specifies method used to alter DOB for research sharing. Details should be available in the study protocols.", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-date-of-birth-method" + ] + } + ] + }, + { + "id": "Patient.extension:age-at-last-vital-status", + "path": "Patient.extension", + "sliceName": "age-at-last-vital-status", + "short": "Age or date of last vital status", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-age-at-last-vital-status" + ] + } + ] + }, + { + "id": "Patient.identifier", + "path": "Patient.identifier", + "short": "External IDs for this participant. Requires scoping." + }, + { + "id": "Patient.birthDate", + "path": "Patient.birthDate", + "short": "Date of Birth of the participant. Details of privacy method should be included in DOBMethod" + }, + { + "id": "Patient.deceased[x]", + "path": "Patient.deceased[x]", + "short": "Implementers can provide relativeDateTime or actual date or T/F, depending on data available." + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-person.json b/fsh-generated/resources/StructureDefinition-ncpi-person.json new file mode 100644 index 00000000..babcb70c --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-person.json @@ -0,0 +1,39 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-person", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-person", + "version": "0.1.0", + "name": "NcpiPerson", + "title": "NCPI Person", + "status": "draft", + "description": "Person", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Person", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Person", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Person.id", + "path": "Person.id", + "short": "Unique participant identifier", + "min": 1 + }, + { + "id": "Person.link.target", + "path": "Person.link.target", + "short": "The participant we are describing", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-participant" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-research-access-policy.json b/fsh-generated/resources/StructureDefinition-ncpi-research-access-policy.json new file mode 100644 index 00000000..e36c4466 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-research-access-policy.json @@ -0,0 +1,147 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-research-access-policy", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy", + "version": "0.1.0", + "name": "NcpiResearchAccessPolicy", + "title": "NCPI Research Access Policy", + "status": "draft", + "description": "Limitations and/or requirements that define how a user may gain access to a particular set of data.", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Consent", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Consent", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Consent", + "path": "Consent", + "constraint": [ + { + "key": "completed-consent-code", + "severity": "error", + "human": "If category is DS then there must be a ResearchConsentDiseaseAbbreviation", + "expression": "provision.purpose.where(code = 'DS').empty() or provision.extension.where(url='https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/research-disease-use-limitation').exists()", + "source": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + } + ] + }, + { + "id": "Consent.extension", + "path": "Consent.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + }, + "min": 1 + }, + { + "id": "Consent.extension:description", + "path": "Consent.extension", + "sliceName": "description", + "short": "Descriptive text summarizing the policy restrictions and other details associated with this access provision.", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-policy-description" + ] + } + ] + }, + { + "id": "Consent.extension:accessType", + "path": "Consent.extension", + "sliceName": "accessType", + "short": "Type of access restrictions on file downloads ( open | registered | controlled )", + "min": 1, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/access-type" + ] + } + ] + }, + { + "id": "Consent.extension:website", + "path": "Consent.extension", + "sliceName": "website", + "short": "URL describing the policy restrictions in detail.", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link" + ] + } + ] + }, + { + "id": "Consent.category", + "path": "Consent.category", + "patternCodeableConcept": { + "coding": [ + { + "code": "research", + "system": "http://terminology.hl7.org/CodeSystem/consentcategorycodes", + "display": "Research Information Access" + } + ] + } + }, + { + "id": "Consent.provision.extension", + "path": "Consent.provision.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Consent.provision.extension:diseaseUseLimitation", + "path": "Consent.provision.extension", + "sliceName": "diseaseUseLimitation", + "short": "Consent Code Disease Abbreviation", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-disease-use-limitation" + ] + } + ] + }, + { + "id": "Consent.provision.purpose", + "path": "Consent.provision.purpose", + "binding": { + "strength": "extensible", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/research-data-access-code-vs" + } + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-research-collection.json b/fsh-generated/resources/StructureDefinition-ncpi-research-collection.json new file mode 100644 index 00000000..fa2a395a --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-research-collection.json @@ -0,0 +1,92 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-research-collection", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-collection", + "name": "NcpiResearchCollection", + "title": "NCPI Research Collection", + "status": "draft", + "description": "Collections of research data including, but not limited, to Consortia, Programs, adhoc collections of Studies and datasets among other types of collections.", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "List", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/List", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "List.extension", + "path": "List.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "List.extension:website", + "path": "List.extension", + "sliceName": "website", + "short": "URL describing the research collection, this can include a formal website, such as the Consortium or Program's website, or to an online document describing the collection.", + "min": 0, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link" + ] + } + ] + }, + { + "id": "List.extension:label", + "path": "List.extension", + "sliceName": "label", + "short": "Alias such as acronym and alternate names.", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/label-extension" + ] + } + ] + }, + { + "id": "List.title", + "path": "List.title", + "short": "The collection's title.", + "min": 1 + }, + { + "id": "List.code", + "path": "List.code", + "short": "The type of collection being described.", + "min": 1, + "binding": { + "strength": "extensible", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/collection-type-vs" + } + }, + { + "id": "List.note", + "path": "List.note", + "short": "The description of the collection." + }, + { + "id": "List.entry", + "path": "List.entry", + "short": "List of references to items included in the list.", + "min": 1 + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-ncpi-research-study.json b/fsh-generated/resources/StructureDefinition-ncpi-research-study.json new file mode 100644 index 00000000..782b623f --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-ncpi-research-study.json @@ -0,0 +1,140 @@ +{ + "resourceType": "StructureDefinition", + "id": "ncpi-research-study", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-study", + "version": "0.0.1", + "name": "NcpiResearchStudy", + "title": "NCPI Research Study", + "status": "draft", + "description": "The NCPI Research Study FHIR resource represents an individual research effort and acts as a grouper or “container” for that effort’s study participants and their related data files.", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "ResearchStudy", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/ResearchStudy", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "ResearchStudy.extension", + "path": "ResearchStudy.extension", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "url" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "ResearchStudy.extension:studyDesign", + "path": "ResearchStudy.extension", + "sliceName": "studyDesign", + "short": "Study Design and Study Type", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-design" + ] + } + ] + }, + { + "id": "ResearchStudy.extension:result", + "path": "ResearchStudy.extension", + "sliceName": "result", + "short": "Link to results generated during the study.", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-result" + ] + } + ] + }, + { + "id": "ResearchStudy.extension:associatedParty", + "path": "ResearchStudy.extension", + "sliceName": "associatedParty", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-associated-party" + ] + } + ] + }, + { + "id": "ResearchStudy.extension:acknowledgement", + "path": "ResearchStudy.extension", + "sliceName": "acknowledgement", + "short": "URL describing the policy restrictions in detail.", + "min": 0, + "max": "*", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-acknowledgement" + ] + } + ] + }, + { + "id": "ResearchStudy.identifier", + "path": "ResearchStudy.identifier", + "short": "External facing, globally unique identifiers. When providing more than one identifier, researchers should indicate the 'official' identifier by assigning 'official' to that identifier's use property.", + "min": 1 + }, + { + "id": "ResearchStudy.title", + "path": "ResearchStudy.title", + "short": "Study's formal title." + }, + { + "id": "ResearchStudy.category.coding", + "path": "ResearchStudy.category.coding", + "short": "Indicate this is an NCPI Research Study", + "patternCoding": { + "code": "StudyCohort", + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/ncpi", + "display": "Study Cohort" + } + }, + { + "id": "ResearchStudy.focus", + "path": "ResearchStudy.focus", + "short": "The primary, non-disease focus(es) of the study. This can include terms related to intervention, drug, device, or other focus.", + "comment": "Researcher specified foci that are not specific to disease/phenotype codes." + }, + { + "id": "ResearchStudy.condition", + "path": "ResearchStudy.condition", + "short": "The primary focus(es) of the study. This is specific to the disease. MeSH terms are preferred.", + "comment": "Disease and phenotype codes identified in the CDM study's 'focus'." + }, + { + "id": "ResearchStudy.relatedArtifact", + "path": "ResearchStudy.relatedArtifact", + "short": "Attribution, Study Weblinks, Citation, Study Documents, etc." + }, + { + "id": "ResearchStudy.description", + "path": "ResearchStudy.description", + "short": "Study Description (Recommended)" + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-age-at-last-vital-status.json b/fsh-generated/resources/StructureDefinition-research-age-at-last-vital-status.json new file mode 100644 index 00000000..0ecae71a --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-age-at-last-vital-status.json @@ -0,0 +1,51 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-age-at-last-vital-status", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-age-at-last-vital-status", + "name": "AgeAtLastVitalStatus", + "title": "Age at Last Vital Status Extension", + "status": "draft", + "description": "Age at Last Vital Status Extension", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Patient" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Age at Last Vital Status Extension", + "definition": "Age at Last Vital Status Extension" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-age-at-last-vital-status" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "short": "Indicate age via relative date time extension or official date of when last vital status was assessed.", + "type": [ + { + "code": "Quantity" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-date-of-birth-method.json b/fsh-generated/resources/StructureDefinition-research-date-of-birth-method.json new file mode 100644 index 00000000..dc4c292d --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-date-of-birth-method.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-date-of-birth-method", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-date-of-birth-method", + "name": "ResearchDateOfBirthMethod", + "title": "Research Date of Birth Method", + "status": "draft", + "description": "Code indicating method of the DOB construction", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Patient" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Date of Birth Method", + "definition": "Code indicating method of the DOB construction" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-date-of-birth-method" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "Coding" + } + ], + "binding": { + "strength": "extensible", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/research-data-date-of-birth-method-vs" + } + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-disease-use-limitation.json b/fsh-generated/resources/StructureDefinition-research-disease-use-limitation.json new file mode 100644 index 00000000..6299fb2b --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-disease-use-limitation.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-disease-use-limitation", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-disease-use-limitation", + "name": "ResearchDiseaseUseLimitation", + "title": "Research Usage Limitation Disease Code", + "status": "draft", + "description": "Coding associated with limitation on what research can be performed this data.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Consent.provision" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Usage Limitation Disease Code", + "definition": "Coding associated with limitation on what research can be performed this data." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-disease-use-limitation" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ], + "binding": { + "strength": "example", + "valueSet": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/mesh-terms" + } + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-population.json b/fsh-generated/resources/StructureDefinition-research-population.json new file mode 100644 index 00000000..fe824605 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-population.json @@ -0,0 +1,50 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-population", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-population", + "name": "ResearchPopulation", + "title": "Research Population", + "status": "draft", + "description": "Code describing the population (CDC)", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Patient" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Population", + "definition": "Code describing the population (CDC)" + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-population" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-study-acknowledgement.json b/fsh-generated/resources/StructureDefinition-research-study-acknowledgement.json new file mode 100644 index 00000000..5d535161 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-study-acknowledgement.json @@ -0,0 +1,52 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-study-acknowledgement", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-acknowledgement", + "name": "ResearchStudyAcknowledgement", + "title": "Research Study Acknowledgement", + "status": "draft", + "description": "Provides an informative description of acknowledgement expectations for those using data from the research study.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "ResearchStudy" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Study Acknowledgement", + "definition": "Provides an informative description of acknowledgement expectations for those using data from the research study." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-acknowledgement" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "short": "Details about acknowledgement requirements for derivative publications.", + "min": 1, + "type": [ + { + "code": "markdown" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-study-associated-party.json b/fsh-generated/resources/StructureDefinition-research-study-associated-party.json new file mode 100644 index 00000000..319d3068 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-study-associated-party.json @@ -0,0 +1,197 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-study-associated-party", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-associated-party", + "name": "ResearchStudyAssociatedParty", + "title": "Research Study Associated Party", + "status": "draft", + "description": "Sponsors, collaborators, and other parties affiliated with a research study.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "ResearchStudy" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Study Associated Party", + "definition": "Sponsors, collaborators, and other parties affiliated with a research study." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "min": 1 + }, + { + "id": "Extension.extension:name", + "path": "Extension.extension", + "sliceName": "name", + "short": "Name of associated party", + "min": 1, + "max": "1", + "mustSupport": true + }, + { + "id": "Extension.extension:name.extension", + "path": "Extension.extension.extension", + "max": "0" + }, + { + "id": "Extension.extension:name.url", + "path": "Extension.extension.url", + "fixedUri": "name" + }, + { + "id": "Extension.extension:name.value[x]", + "path": "Extension.extension.value[x]", + "type": [ + { + "code": "string" + } + ] + }, + { + "id": "Extension.extension:role", + "path": "Extension.extension", + "sliceName": "role", + "short": "sponsor | lead-sponsor | sponsor-investigator | primary-investigator | collaborator | funding-source | general-contact | recruitment-contact | sub-investigator | study-director | study-chair\nBinding: Research Study Party Role (Extensible)", + "min": 0, + "max": "1", + "mustSupport": true + }, + { + "id": "Extension.extension:role.extension", + "path": "Extension.extension.extension", + "max": "0" + }, + { + "id": "Extension.extension:role.url", + "path": "Extension.extension.url", + "fixedUri": "role" + }, + { + "id": "Extension.extension:role.value[x]", + "path": "Extension.extension.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ], + "binding": { + "strength": "required", + "valueSet": "https://hl7.org/fhir/valueset-research-study-party-role.html" + } + }, + { + "id": "Extension.extension:period", + "path": "Extension.extension", + "sliceName": "period", + "short": "When active in the role", + "min": 0, + "max": "*" + }, + { + "id": "Extension.extension:period.extension", + "path": "Extension.extension.extension", + "max": "0" + }, + { + "id": "Extension.extension:period.url", + "path": "Extension.extension.url", + "fixedUri": "period" + }, + { + "id": "Extension.extension:period.value[x]", + "path": "Extension.extension.value[x]", + "type": [ + { + "code": "Period" + } + ] + }, + { + "id": "Extension.extension:classifier", + "path": "Extension.extension", + "sliceName": "classifier", + "short": "nih | fda | government | nonprofit | academic | industry\nBinding: Research Study Party Organization Type (Example)", + "min": 0, + "max": "*" + }, + { + "id": "Extension.extension:classifier.extension", + "path": "Extension.extension.extension", + "max": "0" + }, + { + "id": "Extension.extension:classifier.url", + "path": "Extension.extension.url", + "fixedUri": "classifier" + }, + { + "id": "Extension.extension:classifier.value[x]", + "path": "Extension.extension.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ], + "binding": { + "strength": "required", + "valueSet": "https://hl7.org/fhir/valueset-research-study-party-organization-type.html" + } + }, + { + "id": "Extension.extension:party", + "path": "Extension.extension", + "sliceName": "party", + "short": "Individual or organization associated with study (use practitionerRole to specify their organisation)", + "min": 0, + "max": "1", + "mustSupport": true + }, + { + "id": "Extension.extension:party.extension", + "path": "Extension.extension.extension", + "max": "0" + }, + { + "id": "Extension.extension:party.url", + "path": "Extension.extension.url", + "fixedUri": "party" + }, + { + "id": "Extension.extension:party.value[x]", + "path": "Extension.extension.value[x]", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Practitioner", + "http://hl7.org/fhir/StructureDefinition/PractitionerRole", + "http://hl7.org/fhir/StructureDefinition/Organization" + ] + } + ] + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-associated-party" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "max": "0" + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-study-design.json b/fsh-generated/resources/StructureDefinition-research-study-design.json new file mode 100644 index 00000000..4abb6701 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-study-design.json @@ -0,0 +1,54 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-study-design", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-design", + "name": "ResearchStudyDesign", + "title": "Research Study Design", + "status": "draft", + "description": "Codes categorizing the type of study such as investigational vs. observational, type of blinding, type of randomization, safety vs. efficacy, etc.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "ResearchStudy" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Study Design", + "definition": "Codes categorizing the type of study such as investigational vs. observational, type of blinding, type of randomization, safety vs. efficacy, etc." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-design" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "CodeableConcept" + } + ], + "binding": { + "strength": "example", + "valueSet": "https://hl7.org/fhir/valueset-study-design.html" + } + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-study-group.json b/fsh-generated/resources/StructureDefinition-research-study-group.json new file mode 100644 index 00000000..302cdf6c --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-study-group.json @@ -0,0 +1,60 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-study-group", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-group", + "version": "0.0.1", + "name": "ResearchStudyGroup", + "title": "NCPI Research Study Group", + "status": "draft", + "description": "Grouping subject participation within a research study is helpful to provide definitive lists of participants that fit a specific criteria such as *All Participants* or *Participants From a Particular Consent Group*, etc. ", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "Group", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Group", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Group.type", + "path": "Group.type", + "patternCode": "person" + }, + { + "id": "Group.actual", + "path": "Group.actual", + "patternBoolean": true + }, + { + "id": "Group.code", + "path": "Group.code", + "patternCodeableConcept": { + "coding": [ + { + "code": "C142710", + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "display": "Study Participant" + } + ] + } + }, + { + "id": "Group.quantity", + "path": "Group.quantity", + "min": 1 + }, + { + "id": "Group.member.entity", + "path": "Group.member.entity", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Patient" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-study-result.json b/fsh-generated/resources/StructureDefinition-research-study-result.json new file mode 100644 index 00000000..11c757ea --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-study-result.json @@ -0,0 +1,70 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-study-result", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-result", + "name": "ResearchStudyResult", + "title": "Research Study Result", + "status": "draft", + "description": "Link to citations associated with the study's publications.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "ResearchStudy" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Study Result", + "definition": "Link to citations associated with the study's publications." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-result" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "slicing": { + "discriminator": [ + { + "type": "type", + "path": "$this" + } + ], + "ordered": false, + "rules": "open" + } + }, + { + "id": "Extension.value[x]:valueReference", + "path": "Extension.value[x]", + "sliceName": "valueReference", + "min": 0, + "max": "1", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.org/fhir/StructureDefinition/Citation" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-study-subject-consent.json b/fsh-generated/resources/StructureDefinition-research-study-subject-consent.json new file mode 100644 index 00000000..44e177ad --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-study-subject-consent.json @@ -0,0 +1,53 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-study-subject-consent", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject-consent", + "name": "ResearchStudySubjectConsent", + "title": "Research Study Subject Consent", + "status": "draft", + "description": "ResearchStudySubjectConsent provides link to a consent through which participants were enrolled.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "Element" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Study Subject Consent", + "definition": "ResearchStudySubjectConsent provides link to a consent through which participants were enrolled." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject-consent" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-access-policy" + ] + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-study-subject.json b/fsh-generated/resources/StructureDefinition-research-study-subject.json new file mode 100644 index 00000000..e1db584d --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-study-subject.json @@ -0,0 +1,46 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-study-subject", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject", + "version": "0.1.0", + "name": "ResearchStudySubject", + "title": "Research Study Subject", + "status": "draft", + "description": "A ResearchStudySubject is representative of a group of participants whose consent and data use is governed by the same restrictions. This profile is an R4 proxy for the more flexible R5 ResearchSubject.", + "fhirVersion": "4.3.0", + "kind": "resource", + "abstract": false, + "type": "ResearchStudy", + "baseDefinition": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-research-study", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "ResearchStudy.extension", + "path": "ResearchStudy.extension", + "min": 1 + }, + { + "id": "ResearchStudy.extension:consent", + "path": "ResearchStudy.extension", + "sliceName": "consent", + "min": 1, + "max": "1", + "type": [ + { + "code": "Extension", + "profile": [ + "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-study-subject-consent" + ] + } + ] + }, + { + "id": "ResearchStudy.partOf", + "path": "ResearchStudy.partOf", + "min": 1, + "max": "1" + } + ] + } +} diff --git a/fsh-generated/resources/StructureDefinition-research-web-Link.json b/fsh-generated/resources/StructureDefinition-research-web-Link.json new file mode 100644 index 00000000..736763c9 --- /dev/null +++ b/fsh-generated/resources/StructureDefinition-research-web-Link.json @@ -0,0 +1,73 @@ +{ + "resourceType": "StructureDefinition", + "id": "research-web-Link", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link", + "name": "ResearchWebLink", + "title": "Research Web Link", + "status": "draft", + "description": "A URL pointing to a either a research study's website, an online document or other research related site or document.", + "fhirVersion": "4.3.0", + "kind": "complex-type", + "abstract": false, + "context": [ + { + "type": "element", + "expression": "List" + }, + { + "type": "element", + "expression": "Consent" + } + ], + "type": "Extension", + "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Extension", + "path": "Extension", + "short": "Research Web Link", + "definition": "A URL pointing to a either a research study's website, an online document or other research related site or document." + }, + { + "id": "Extension.extension", + "path": "Extension.extension", + "max": "0" + }, + { + "id": "Extension.url", + "path": "Extension.url", + "fixedUri": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/research-web-Link" + }, + { + "id": "Extension.value[x]", + "path": "Extension.value[x]", + "slicing": { + "discriminator": [ + { + "type": "type", + "path": "$this" + } + ], + "ordered": false, + "rules": "open" + }, + "min": 1 + }, + { + "id": "Extension.value[x]:valueUrl", + "path": "Extension.value[x]", + "sliceName": "valueUrl", + "short": "The URL associated with the document or related website.", + "min": 1, + "max": "1", + "type": [ + { + "code": "url" + } + ] + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-collection-type-vs.json b/fsh-generated/resources/ValueSet-collection-type-vs.json new file mode 100644 index 00000000..37d913e8 --- /dev/null +++ b/fsh-generated/resources/ValueSet-collection-type-vs.json @@ -0,0 +1,17 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "CollectionTypeVS", + "id": "collection-type-vs", + "title": "Collection Type", + "description": "Enumerated list of Collection types", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/collection-type-vs", + "experimental": false, + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/collection-type" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-mesh-terms.json b/fsh-generated/resources/ValueSet-mesh-terms.json new file mode 100644 index 00000000..5ba16f56 --- /dev/null +++ b/fsh-generated/resources/ValueSet-mesh-terms.json @@ -0,0 +1,18 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "MeshTerms", + "id": "mesh-terms", + "title": "MeSH Terms", + "description": "Example terms from Medical Subject Headings (MeSH) Ontology", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/mesh-terms", + "version": "0.1.0", + "experimental": false, + "compose": { + "include": [ + { + "system": "urn:oid:2.16.840.1.113883.6.177" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-research-data-access-code-vs.json b/fsh-generated/resources/ValueSet-research-data-access-code-vs.json new file mode 100644 index 00000000..cc89ad69 --- /dev/null +++ b/fsh-generated/resources/ValueSet-research-data-access-code-vs.json @@ -0,0 +1,17 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "ResearchDataAccessCodeVS", + "id": "research-data-access-code-vs", + "title": "Research Data Access Codes", + "description": "Enumerated list of access codes such as dbGaP consent codes among others.", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/research-data-access-code-vs", + "experimental": false, + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-research-data-access-type-vs.json b/fsh-generated/resources/ValueSet-research-data-access-type-vs.json new file mode 100644 index 00000000..917b8cab --- /dev/null +++ b/fsh-generated/resources/ValueSet-research-data-access-type-vs.json @@ -0,0 +1,17 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "ResearchDataAccessTypeVS", + "id": "research-data-access-type-vs", + "title": "Research Data Access Type Codes", + "description": "Enumerated list of access type codes such as 'Open Access', 'Registered Access' and 'Controlled Access'", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/research-data-access-type-vs", + "experimental": false, + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-research-data-date-of-birth-method-vs.json b/fsh-generated/resources/ValueSet-research-data-date-of-birth-method-vs.json new file mode 100644 index 00000000..a0d11f3e --- /dev/null +++ b/fsh-generated/resources/ValueSet-research-data-date-of-birth-method-vs.json @@ -0,0 +1,16 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "ResearchDataDateOfBirthMethodVS", + "id": "research-data-date-of-birth-method-vs", + "title": "Enumerations for how DOB was constructed", + "description": "Enumerations for how DOB was constructed", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/research-data-date-of-birth-method-vs", + "compose": { + "include": [ + { + "system": "http://terminology.hl7.org/CodeSystem/title-type" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-study-name-type-vs.json b/fsh-generated/resources/ValueSet-study-name-type-vs.json new file mode 100644 index 00000000..be151b4a --- /dev/null +++ b/fsh-generated/resources/ValueSet-study-name-type-vs.json @@ -0,0 +1,17 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "StudyNameTypeVS", + "id": "study-name-type-vs", + "title": "Study Name Type", + "description": "Some common types of study 'names'.", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/study-name-type-vs", + "experimental": false, + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/study-name-type" + } + ] + } +} diff --git a/fsh-generated/resources/ValueSet-study-personnel-role-vs.json b/fsh-generated/resources/ValueSet-study-personnel-role-vs.json new file mode 100644 index 00000000..2bda2214 --- /dev/null +++ b/fsh-generated/resources/ValueSet-study-personnel-role-vs.json @@ -0,0 +1,17 @@ +{ + "resourceType": "ValueSet", + "status": "draft", + "name": "StudyPersonnelRoleVS", + "id": "study-personnel-role-vs", + "title": "Study Personnel Role", + "description": "Roles associated with study personnel.", + "url": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/ValueSet/study-personnel-role-vs", + "experimental": false, + "compose": { + "include": [ + { + "system": "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/study-personnel-role" + } + ] + } +} diff --git a/input/fsh/Alias.fsh b/input/fsh/Alias.fsh index d16519f2..168e4063 100644 --- a/input/fsh/Alias.fsh +++ b/input/fsh/Alias.fsh @@ -1,4 +1,12 @@ +// US Core Extensions +Alias: $us-core-race = http://hl7.org/fhir/us/core/StructureDefinition/us-core-race +Alias: $us-core-ethnicity = http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity +Alias: $cqf-relativeDateTime = http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime + +Alias: $omb-race-eth = urn:oid:2.16.840.1.113883.6.238 // Race & Ethnicity - CDC +Alias: $admin-gender = http://hl7.org/fhir/administrative-gender + Alias: $ncpi = https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/ncpi Alias: $study-name-type = https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/study-name-type Alias: $ncpi-collection-type = https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/collection-type @@ -6,5 +14,7 @@ Alias: $ncpi-data-access-code = https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSy Alias: $ncpi-data-access-type = https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type Alias: $title-type = http://terminology.hl7.org/CodeSystem/title-type Alias: $mesh = urn:oid:2.16.840.1.113883.6.177 +Alias: $ncpi-dob-method = https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method -Alias: $ncit = http://purl.obolibrary.org/obo/ncit.owl \ No newline at end of file +Alias: $ncit = http://purl.obolibrary.org/obo/ncit.owl +Alias: $ucum = http://unitsofmeasure.org \ No newline at end of file diff --git a/input/fsh/examples/ResearchStudy-CBTN.fsh b/input/fsh/examples/ResearchStudy-CBTN.fsh index 69d21d55..bb3aa0da 100644 --- a/input/fsh/examples/ResearchStudy-CBTN.fsh +++ b/input/fsh/examples/ResearchStudy-CBTN.fsh @@ -73,7 +73,7 @@ Description: "Brain tumors are the most common form of cancer in children aged 0 * label = "Publication" * url = "https://cbtn.org/publications" * status = #completed -* extension[acknowledgement].valueMarkdown = "Please cite/reference the use of dbGaP data by including the dbGaP accession phs002517.v2.p2. Additionally, use the following statement to acknowledge the submitter(s) of this study:\n\n\nThe data from this study phs002517 was made available pre-publication without embargo to support rapid and collaborative research in pediatric cancer via the NCI's Cancer Research Data Commons (https://datacommons.cancer.gov). This availability is made possible with the support of NCI's Childhood Cancer Data Initiative (grant No. 3P30CA082103-21S9) and Gabriella Miller Kids First Pediatric Research Program (X01 CA267587). Initial data generation efforts and coordination costs were supported by a number of philanthropic and industry partners with further details at cbtn.org.\n\n\n\nSuggested Acknowledgement Statement for secondary users: The results analyzed and here are based in whole or in part analyzing the study phs002517 and were accessed from the NCI's Cancer Research Data Commons (https://datacommons.cancer.gov)." +* extension[acknowledgement].valueMarkdown = """Please cite/reference the use of dbGaP data by including the dbGaP accession phs002517.v2.p2. Additionally, use the following statement to acknowledge the submitter(s) of this study:\n\n\nThe data from this study phs002517 was made available pre-publication without embargo to support rapid and collaborative research in pediatric cancer via the NCI's Cancer Research Data Commons (https://datacommons.cancer.gov). This availability is made possible with the support of NCI's Childhood Cancer Data Initiative (grant No. 3P30CA082103-21S9) and Gabriella Miller Kids First Pediatric Research Program (X01 CA267587). Initial data generation efforts and coordination costs were supported by a number of philanthropic and industry partners with further details at cbtn.org.\n\n\n\nSuggested Acknowledgement Statement for secondary users: The results analyzed and here are based in whole or in part analyzing the study phs002517 and were accessed from the NCI's Cancer Research Data Commons (https://datacommons.cancer.gov).""" * extension[research-study-associated-party][+] * extension[name].valueString = "Adam C. Resnick" * extension[role].valueCodeableConcept = http://hl7.org/fhir/research-study-party-role#primary-investigator @@ -84,7 +84,6 @@ Description: "Brain tumors are the most common form of cancer in children aged 0 * extension[party].valueReference = Reference(kf-research-study-personnel-role-pi) * extension[research-study-associated-party][+] * extension[name].valueString = "Jennifer Mason" -* extension[research-study-associated-party][+] * extension[role].valueCodeableConcept = http://hl7.org/fhir/research-study-party-role#study-director * extension[party].valueReference = Reference(kf-research-study-personnel-role-op-lead) diff --git a/input/fsh/examples/participant.fsh b/input/fsh/examples/participant.fsh new file mode 100644 index 00000000..44c9598f --- /dev/null +++ b/input/fsh/examples/participant.fsh @@ -0,0 +1,293 @@ +/* + +CBTN, PCGC, and eMERGE examples for: +* NcpiParticipant +* NcpiPerson +* stub AccessPolicy +* stub ResearchStudy +* NcpiParticipantStudy + +*/ + + +// Example 1 + +Instance: PT-KZG2CZ95 +InstanceOf: NcpiParticipant +Title: "Example patients based on data from CBTN" +Usage: #example +Description: "Example patients based on data from CBTN." +// Notice that we can use the DbGaP study ID for easier searching +* identifier[0] + * system = "https://cbtn.org/" + * value = "C21156" +* identifier[1] + * system = "https://data.kidsfirstdrc.org" + * value = "PT_KZG2CZ95" +* birthDate.extension[+] + * url = $cqf-relativeDateTime + * extension[+] + * url = "target" + * valueReference = Reference(PT-KZG2CZ95) + * extension[+] + * url = "targetPath" + * valueString = "birthDate" + * extension[+] + * url = "relationship" + * valueCode = #after + * extension[+] + * url = "offset" + * valueDuration = 2006 'days' + * valueDuration.unit = "d" +* extension[us-core-birth-sex].valueCode = #F "Female" +* 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[dob-method].valueCoding = $ncpi-dob-method#year-only +* extension[age-at-last-vital-status].valueQuantity + * value = 6314 + * unit = "days" + * system = $ucum + * code = #d "days" +/* + +* extension[age-at-last-vital-status].valueDate = 1991-01-23 + * extension[+] + * url = $cqf-relativeDateTime + * extension[+] + * url = "target" + * valueReference = Reference(PT-KZG2CZ95) + * extension[+] + * url = "targetPath" + * valueString = "birthDate" + * extension[+] + * url = "relationship" + * valueCode = #after + * extension[+] + * url = "offset" + * valueDuration = 6314 'days' + * valueDuration.unit = "d" + + +*/ + +Instance: cbtn-example-person +InstanceOf: NcpiPerson +Title: "Example patients based on data from CBTN" +Usage: #example +Description: "Example patients based on data from CBTN" +* identifier + * system = "https://data.kidsfirstdrc.org" + * value = "PS_123" +* link + * target = Reference(PT-KZG2CZ95) + +Instance: GRU +InstanceOf: NcpiResearchAccessPolicy +Title: "Mock consent based on kf-gru-dac-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[website].valueUrl = "https://redcap.chop.edu/surveys/?s=A7M873HMN8" +* extension[accessType].valueCodeableConcept = $ncpi-data-access-type#controlled + +Instance: SD-BHJXBDQK +InstanceOf: ResearchStudySubject +Title: "Mock study based on kf-research-study-subject-gru-dac" +Usage: #example +Description: "GRU data access via DAC" +* identifier[0] + * system = "https://cbtn.org/" + * value = "SD-BHJXBDQK" +* title = "GRU-DAC Study Subject" +* description = "General Research Use data access via DAC" +* status = #completed +* partOf = Reference(kf-research-study-cbtn) +* extension[consent].valueReference = Reference(kf-gru-dac-consent) +* enrollment = Reference(kf-research-study-cbtn-participants) + +Instance: cbtn-example-participantstudy +InstanceOf: NcpiStudyParticipant +Title: "Example mappings based on data from CBTN" +Usage: #example +Description: "Example mappings based on data from CBTN" +* individual = Reference(PT-KZG2CZ95) +* study = Reference(SD-BHJXBDQK) +* status = #candidate +* consent = Reference(GRU) + + + +// Example 2 + +Instance: PT-005B7CZ4 +InstanceOf: NcpiParticipant +Title: "Example patients based on data from PCGC" +Usage: #example +Description: "Example patients based on data from PCGC." +* identifier[0] + * system = "http://chdgenes.org/" + * value = "20757" +* identifier[1] + * system = "http://chdgenes.org/" + * value = "PT_005B7CZ4" +* birthDate.extension[+] + * url = $cqf-relativeDateTime + * extension[+] + * url = "target" + * valueReference = Reference(PT-005B7CZ4) + * extension[+] + * url = "targetPath" + * valueString = "birthDate" + * extension[+] + * url = "relationship" + * valueCode = #after + * extension[+] + * url = "offset" + * valueDuration = 2006 'days' + * valueDuration.unit = "d" +* extension[us-core-birth-sex].valueCode = #F "Female" +* 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#2135-2 "Hispanic or Latino" + * extension[text].valueString = "Hispanic or Latino" + + +Instance: pcgc-example-person +InstanceOf: NcpiPerson +Title: "Example patients based on data from PCGC" +Usage: #example +Description: "Example patients based on data from PCGC" +* identifier + * system = "http://chdgenes.org/" + * value = "PS_123" +* link + * target = Reference(PT-005B7CZ4) + +Instance: HMB +InstanceOf: NcpiResearchAccessPolicy +Title: "Mock consent based on kf-gru-dbgap-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[website].valueUrl = "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002517" +* extension[accessType].valueCodeableConcept = $ncpi-data-access-type#controlled + +Instance: SD-PREASA7S +InstanceOf: ResearchStudySubject +Title: "Mock Study based on kf-research-study-subject-gru-dbgap" +Usage: #example +Description: "GRU data access via dbGaP" +* identifier[0] + * system = "https://cbtn.org/" + * value = "GRU-dbGaP" +* title = "GRU-dbGaP Study Subject" +* description = "General Research Use data access via dbGaP" +* status = #completed +* partOf = Reference(kf-research-study-cbtn) +* extension[consent].valueReference = Reference(kf-gru-dbgap-consent) +* enrollment = Reference(kf-research-study-cbtn-participants) + +Instance: pcgc-example-participantstudy +InstanceOf: NcpiStudyParticipant +Title: "Example mappings based on data from PCGC" +Usage: #example +Description: "Example mappings based on data from PCGC" +* individual = Reference(PT-005B7CZ4) +* study = Reference(SD-PREASA7S) +* status = #candidate +* consent = Reference(HMB) + + + +// Example 3 + +Instance: 6812345 +InstanceOf: NcpiParticipant +Title: "Example patients based on data from eMERGE" +Usage: #example +Description: "Example patients based on data from eMERGE" +* identifier[0] + * system = "https://emerge-network.org/" + * value = "12345" +* identifier[1] + * system = "https://emerge-network.org/" + * value = "6812345" +* birthDate.extension[+] + * url = $cqf-relativeDateTime + * extension[+] + * url = "target" + * valueReference = Reference(6812345) + * extension[+] + * url = "targetPath" + * valueString = "birthDate" + * extension[+] + * url = "relationship" + * valueCode = #after + * extension[+] + * url = "offset" + * valueDuration = 2006 'days' + * valueDuration.unit = "d" +* extension[us-core-birth-sex].valueCode = #F "Female" +* extension[us-core-race] + * extension[ombCategory].valueCoding = $omb-race-eth#1002-5 "American Indian or Alaska Native" + * extension[text].valueString = "American Indian or Alaska Native" +* extension[us-core-ethnicity] + * extension[ombCategory].valueCoding = $omb-race-eth#2186-5 "Not Hispanic or Latino" + * extension[text].valueString = "Not Hispanic or Latino" +* extension[dob-method].valueCoding = $ncpi-dob-method#decade-only + +Instance: emerge-example-person +InstanceOf: NcpiPerson +Title: "Example patients based on data from eMERGE" +Usage: #example +Description: "Example patients based on data from eMERGE" +* identifier + * system = "https://emerge-network.org/" + * value = "PS_321" +* link + * target = Reference(6812345) + +// Example uses GRU for consent seen in example 2 + +Instance: phv00407460.v2 +InstanceOf: ResearchStudySubject +Title: "Mock study based on kf-research-study-subject-gsr-allowed" +Usage: #example +Description: "Genomic Summary Results (GSR) Allowed Access" +* identifier[0] + * system = "https://cbtn.org/" + * value = "GSR-ALLOWED" +* title = "GSR-ALLOWED Study Subject" +* description = "Genomic Summary Results (GSR) Allowed Access" +* status = #completed +* partOf = Reference(kf-research-study-cbtn) +* extension[consent].valueReference = Reference(kf-gsr-allowed-access) +* enrollment = Reference(kf-research-study-cbtn-participants) + +Instance: emerge-example-participantstudy +InstanceOf: NcpiStudyParticipant +Title: "Example mappings based on data from eMERGE" +Usage: #example +Description: "Example mappings based on data from eMERGE" +* individual = Reference(6812345) +* study = Reference(phv00407460.v2) +* status = #candidate +* consent = Reference(GRU) diff --git a/input/fsh/modules/participant.fsh b/input/fsh/modules/participant.fsh new file mode 100644 index 00000000..c193ef9b --- /dev/null +++ b/input/fsh/modules/participant.fsh @@ -0,0 +1,145 @@ +// Participant Module + +Logical: CdmResearchParticipant +Id: SharedDataModelResearchParticipant +Title: "Shared Data Model for Research Participants" +Description: "The **Shared Data Model for Research Participants**" +* participantID 1..1 string "Unique participant identifier. System identifier used for internal references." +* externalID 0..* code "Unique participant identifier. System identifier used for internal references." +* population 0..* code "Population, Race, and/or Ethnicity information." +* ombRace 0..* code "OMB coded Race for backwards compatibility" +* ombEth 0..* code "OMB coded Ethnicity for backwards compatibility" +* sex 1..1 code "Sex assigned at birth (or pre-natal observed sex)" +* dateOfBirth 0..1 date "Date of Birth of the participant. Details of privacy method should be included in DOBMethod" +* dobMethod 0..1 code "Specifies method used to alter DOB for research sharing. Details should be available in the study protocols." +* ageAtLastVitalStatus 0..1 date "Age at last vital status" +* vitalStatus 0..1 code "Vital Status" + +CodeSystem: ResearchDataDateOfBirthMethod +Id: research-data-date-of-birth-method +Title: "Enumerations for how DOB was constructed" +Description: "Enumerations for how DOB was constructed" +* ^url = $ncpi-dob-method +* ^experimental = false +* ^caseSensitive = true +* #exact "Exact" +* #year-only "Year Only" +* #shifted "Shifted" +* #decade-only "Decade Only" +* #other "Other" + +ValueSet: ResearchDataDateOfBirthMethodVS +Id: research-data-date-of-birth-method-vs +Title: "Enumerations for how DOB was constructed" +Description: "Enumerations for how DOB was constructed" +* include codes from system $title-type + +Extension: ResearchPopulation +Id: research-population +Title: "Research Population" +Description: "Code describing the population (CDC)" +* insert SetContext(Patient) +* value[x] only CodeableConcept +// * valueCodeableConcept from research-population-vs + +Extension: ResearchDateOfBirthMethod +Id: research-date-of-birth-method +Title: "Research Date of Birth Method" +Description: "Code indicating method of the DOB construction" +* insert SetContext(Patient) +* value[x] only Coding +* valueCoding from research-data-date-of-birth-method-vs (extensible) + +Extension: AgeAtLastVitalStatus +Id: research-age-at-last-vital-status +Title: "Age at Last Vital Status Extension" +Description: "Age at Last Vital Status Extension" +* insert SetContext(Patient) +// * value[x] only date +* value[x] only Quantity +* valueQuantity ^short = "Indicate age via relative date time extension or official date of when last vital status was assessed." + +Profile: NcpiParticipant +Parent: Patient +Id: ncpi-participant +Title: "NCPI Participant" +Description: "Research oriented patient" +* ^version = "0.1.0" +* ^status = #draft +* id 1..1 +* id ^short = "ParticipantID - Unique participant identifier. System identifier used for internal references." +* identifier 0..* +* identifier ^short = "External IDs for this participant. Requires scoping." +* birthDate ^short = "Date of Birth of the participant. Details of privacy method should be included in DOBMethod" +* deceased[x] ^short = "Implementers can provide relativeDateTime or actual date or T/F, depending on data available." + +* extension contains USCoreBirthSexExtension named us-core-birth-sex 0..1 +* extension[us-core-birth-sex] ^short = "Sex assigned at birth (or pre-natal observed sex)" +* extension contains USCoreRaceExtension named us-core-race 0..1 +* extension[us-core-race] ^short = "US Core Race" +* extension contains USCoreEthnicityExtension named us-core-ethnicity 0..1 +* extension[us-core-ethnicity] ^short = "US Core Ethnicity" +* extension contains ResearchPopulation named population 0..1 +* extension[population] ^short = "Population, Race, and/or Ethnicity information." +* extension contains ResearchDateOfBirthMethod named dob-method 0..1 +* extension[dob-method] ^short = "Specifies method used to alter DOB for research sharing. Details should be available in the study protocols." +* extension contains AgeAtLastVitalStatus named age-at-last-vital-status 0..1 +* extension[age-at-last-vital-status] ^short = "Age or date of last vital status" + + + +// Person Module + +Logical: CdmPerson +Id: SharedDataModelPerson +Title: "Shared Data Model for Research Persons" +Description: "The **Shared data model for Person**" +* identifier 1..1 string "Unique Person identifier." +* participant 1..1 reference "The participant we are describing" + + +Profile: NcpiPerson +Parent: Person +Id: ncpi-person +Title: "NCPI Person" +Description: "Person" +* ^version = "0.1.0" +* ^status = #draft +* id 1..1 +* id ^short = "Unique participant identifier" +* link 1..* +* link.target only Reference(NcpiParticipant) +* link.target ^short = "The participant we are describing" + +// Study Participant Module + +Logical: CdmStudyParticipant +Id: SharedDataModelStudyParticipant +Title: "Shared Data Model for Research Participant and Study Mapping" +Description: "The **Shared data model for StudyParticipant**" +* participant 1..1 reference "The participant we are describing" +* researchStudy 0..1 reference "The Research Study this participant has a relationship with" +* accessPolicy 0..* reference "The Access Policy that may apply to this participant's data from this study. Not canonical, ie, one must rely on the row level AP." + +Extension: AccessPolicy +Id: access-policy +Title: "Access policy" +Description: "Access Policy Extension" +* insert SetContext(ResearchSubject) +* value[x] only Reference +* valueReference 1..1 +* valueReference only Reference(NcpiResearchAccessPolicy) + +Profile: NcpiStudyParticipant +Parent: ResearchSubject +Id: ncpi-Study-Participant +Title: "NCPI Study Participant" +Description: "Research Study" +* ^version = "0.1.0" +* ^status = #draft +* individual only Reference(NcpiParticipant) +* individual ^short = "The participant we are describing" +* study only Reference(ResearchStudy) +* study ^short = "The Research Study this participant has a relationship with" +* extension contains AccessPolicy named access-policy 0..* +* extension[access-policy] ^short = "The Access Policy that may apply to this participant's data from this study. Not canonical, ie, one must rely on the row level AP." diff --git a/input/fsh/modules/research-accesss-policy.fsh b/input/fsh/modules/research-accesss-policy.fsh index 5fc7b099..6f5bf0e8 100644 --- a/input/fsh/modules/research-accesss-policy.fsh +++ b/input/fsh/modules/research-accesss-policy.fsh @@ -56,7 +56,6 @@ Id: mesh-terms Title: "MeSH Terms" Description: "Example terms from Medical Subject Headings (MeSH) Ontology" * ^version = "0.1.0" -* ^status = #draft * ^experimental = false * include codes from system $mesh diff --git a/input/pagecontent/StructureDefinition-SharedDataModelResearchParticipant-intro.md b/input/pagecontent/StructureDefinition-SharedDataModelResearchParticipant-intro.md new file mode 100644 index 00000000..fa4c2d9c --- /dev/null +++ b/input/pagecontent/StructureDefinition-SharedDataModelResearchParticipant-intro.md @@ -0,0 +1,11 @@ +### NCPI Participant +#### Participant +Participants are a scoped entity that represents the anchor for all data for a specific real-world entity. Typically, this is a person involved in a research study and all of their data collected for that study (or set of studies). This entity has direct attributes (eg, demographics), so if two studies that share an identifier space present conflicting information, it may be necessary to have multiple participants. + +Participants (ie, data about an entity that is scope constrained) can be linked with a Person. +Participants can be associated with different substudies (and with different data sharing restrictions) via Study Participation. + +#### Person +In situations where a person participates in multiple studies that have participant data scoped in an exclusive way within one or more projects, we have a Person entity. It is functionally a “group” of Participants that are all describing one “actual” person. This is especially to support situations where access policies about that participant might be conflicting and cases where the data itself about the participant might conflict but cannot be adjudicated by the repository. +Study Participation +Study Participation (ResearchSubject) describes the relationship between a specific Participant and a Research Study that collects and is sharing data on that Participant. A single Participant may have this “Study Participation” relationship with multiple Research Studies, and each relationship may have a different sharing restriction. These relationships are primarily illustrative, as the Access Policy details of any given element are documented within that element. diff --git a/input/pagecontent/StructureDefinition-ncpi-participant-intro.md b/input/pagecontent/StructureDefinition-ncpi-participant-intro.md new file mode 100755 index 00000000..d4c16268 --- /dev/null +++ b/input/pagecontent/StructureDefinition-ncpi-participant-intro.md @@ -0,0 +1,33 @@ +#### Key Guidelines +The NCPI Participant profile is based on the standard resource type, [Patient](https://hl7.org/fhir/R4B/patient.html) and is intended to represent an individual participating in a specific research study. + +##### Added Profile Restrictions +In order to ensure that our resources are interoperable across studies, we have employed a number of restrictions that should make consuming Patient resources more consistent. + +* ID **should** be a globally unique identifier associated with the patient. This practice is intended to make constructing queries for the same patient compatible across different servers (such as QA vs PROD) but also to make the resource URLs more meaningful. +* identifier **should** have all appropriate Identifiers with a meaningful system/value pair. Such identifiers may include DbGAP accession IDs, global and external IDs, etc. +* race and ethnicity **must** be defined using OMB Categories using the relevant US Core extensions ([us-core-race extension](https://hl7.org/fhir/us/core/STU7/StructureDefinition-us-core-race.html) & [us-core-ethnicity](https://hl7.org/fhir/us/core/STU7/StructureDefinition-us-core-ethnicity.html)) +* Where birth date is known, the extension, [reseearch-date-of-birth-method](StructureDefinition-research-date-of-birth-method.html) **must** be provided to indicate the method used in the construction of that value. + +#### Recommended Practices +TDOD: Write Recommended Practices + +##### FHIR Mappings +The following fields from the shared data model are to be mapped into the NCPI Participant as shown below: + +| **Logical Model Property** | **Cardinality** | **NCPI Participant Mapping** |**Usage Guidance** | **Notes** | +[participantID](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.participantID)|1..1|id| Strongly recommended | It is strongly recommended for the Participant Resource ID to be a unique identifier with an appropriate system| +[externalID](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.externalID)|0..*|identifier|| +[population](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.population)|0..*|TBD|Strongly recommended || +[ombRace](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.ombRace)|0..*|extension|Required if available |Use the [us-core-race extension](https://hl7.org/fhir/us/core/STU7/StructureDefinition-us-core-race.html)| +[ombEth](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.ombEth)|0..*|extension|Required if available|Use the [us-core-ethnicity](https://hl7.org/fhir/us/core/STU7/StructureDefinition-us-core-ethnicity.html)| +[sex](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.sex)|1..1|extension|Required if avaialble|Use the [us-core-birthsex](https://hl7.org/fhir/us/core/STU7/StructureDefinition-us-core-birthsex.html) extension| +[dateOfBirth](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.dateOfBirth)|0..1|birthDate|Optional|| +[dobMethod](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.dobMethod)|0..1|extension [ResearchDateOfBirthMethod](StructureDefinition-research-date-of-birth-method.html)|Required if dateOfBirth is provided|| +[ageAtLastVitalStatus](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.ageAtLastVitalStatus)|0..1|extension [AgeAtLastVitalStatus](StructureDefinition-research-age-at-last-vital-status.html)|Recommended|| +[vitalStatus](StructureDefinition-SharedDataModelResearchParticipant-definitions.html#diff_SharedDataModelResearchParticipant.vitalStatus)|0..1|deceased|Recommended|| + +##### Study Participation +The conventional FHIR mechanism to link Patient resources to a ResearchStudy is through the use of a ResearchSubject resource. **TODO: Write up details regarding the TBD Profile, NCPI Person, and the NCPI ResearchStudy.** + +**TBD Write up details about linking a patient to the research study access policy (consent)** \ No newline at end of file diff --git a/input/pagecontent/StructureDefinition-ncpi-participant-notes.md b/input/pagecontent/StructureDefinition-ncpi-participant-notes.md new file mode 100755 index 00000000..b8a1e334 --- /dev/null +++ b/input/pagecontent/StructureDefinition-ncpi-participant-notes.md @@ -0,0 +1,16 @@ +#### US Core Race Values +The extension binds the following [ValueSet](https://cts.nlm.nih.gov/fhir/res/ValueSet/$expand?url=http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1021.24). Please note that, in order to view this, you must have logged into your browser using your API key (or provided the key using appriate flow specified by UMLS's docs) + +For those who don't have a key, or just want a quick reminder, the codes are listed below: + +ValueSet URL: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1021.24 + +| **Code** | **Display** | **System** | +| F | Female | http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender | +| M | Male | http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender | +| ASKU | asked but unknown | http://terminology.hl7.org/CodeSystem/v3-NullFlavor | +| OTH | other | http://terminology.hl7.org/CodeSystem/v3-NullFlavor | +| UNK | unknown | http://terminology.hl7.org/CodeSystem/v3-NullFlavor | +| asked-declined | Asked But Declined | http://terminology.hl7.org/CodeSystem/data-absent-reason | + +Please note that there are 3 different systems listed in the codes above. \ No newline at end of file diff --git a/input/pagecontent/StructureDefinition-ncpi-person-intro.md b/input/pagecontent/StructureDefinition-ncpi-person-intro.md new file mode 100755 index 00000000..942908e0 --- /dev/null +++ b/input/pagecontent/StructureDefinition-ncpi-person-intro.md @@ -0,0 +1,18 @@ +#### Key Guidelines +In situations where a person participates in multiple studies that have participant data scoped in an exclusive way within one or more projects, we have a Person entity. It is functionally a “group” of Participants that are all describing one “actual” person. This is especially to support situations where access policies about that participant might be conflicting and cases where the data itself about the participant might conflict but cannot be adjudicated by the repository. + +##### Added Profile Restrictions +In order to ensure that our resources are interoperable across studies, we have employed a number of restrictions that should make consuming Patient resources more consistent. + +* ID **should** be a globally unique identifier associated with the person. This practice is intended to make constructing queries for the same person compatible across different servers (such as QA vs PROD) but also to make the resource URLs more meaningful. + + +#### Recommended Practices +TODO: Write Recommended Practices + +##### FHIR Mappings +The following fields from the shared data model are to be mapped into the NCPI Participant as shown below: + +| **Logical Model Property** | **Cardinality** | **NCPI Person Mapping** |**Usage Guidance** | **Notes** | +Person|1..1|id| Required | It is strongly recommended for the Person ID to be a unique identifier with an appropriate system| +Participant|0..1|Reference|Required|It is strongly recommended for the Participant ID to be a unique identifier with an appropriate system| diff --git a/input/pagecontent/StructureDefinition-ncpi-person-notes.md b/input/pagecontent/StructureDefinition-ncpi-person-notes.md new file mode 100755 index 00000000..18866290 --- /dev/null +++ b/input/pagecontent/StructureDefinition-ncpi-person-notes.md @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/input/pagecontent/StructureDefinition-ncpi-research-study-intro.md b/input/pagecontent/StructureDefinition-ncpi-research-study-intro.md index 78151b85..15bf906b 100644 --- a/input/pagecontent/StructureDefinition-ncpi-research-study-intro.md +++ b/input/pagecontent/StructureDefinition-ncpi-research-study-intro.md @@ -42,7 +42,6 @@ Additional Study Groups may be included to describe various aspects of the study **Usage:** * Derived from this Resource Profile: [Research Study Subject](StructureDefinition-research-study-subject.html) -* Refer to this Resource Profile: [Study Summary](StructureDefinition-study-summary.html) and [Study Variable Summary](StructureDefinition-study-variable-summary.html) * Examples for this Resource Profile: [ResearchStudy/cmg-research-study-bhcmg](ResearchStudy-cmg-research-study-bhcmg.html) @@ -68,7 +67,7 @@ For those identifiers that have been defined by the investigators and collaborat ##### Utilize 'use' Property The [Identifier datatype](https://hl7.org/fhir/datatypes.html#Identifier) provides a **use** property which is used to indicate which identifier is **official** and **secondary** [(among others)](https://hl7.org/fhir/valueset-identifier-use.html) and should be used where appropriate. It is **strongly recommended** that the most visible external identifier be marked as **official**. -#### Common Data Model Mappings +### Common Data Model Mappings The following represents the mapping from the Logical Research Study model to this NCPI Research Study FHIR profile. | NCPI Shared Data Elements | FHIR Resource Mapping | Note | diff --git a/input/pagecontent/StructureDefinition-ncpi-study-participant-intro.md b/input/pagecontent/StructureDefinition-ncpi-study-participant-intro.md new file mode 100755 index 00000000..676cf319 --- /dev/null +++ b/input/pagecontent/StructureDefinition-ncpi-study-participant-intro.md @@ -0,0 +1,18 @@ +#### Key Guidelines +Study Participation (ResearchSubject) describes the relationship between a specific Participant and a Research Study that collects and is sharing data on that Participant. A single Participant may have this “Study Participation” relationship with multiple Research Studies, and each relationship may have a different sharing restriction. These relationships are primarily illustrative, as the Access Policy details of any given element are documented within that element. + +##### Added Profile Restrictions + + +#### Recommended Practices +TODO: Write Recommended Practices + +##### FHIR Mappings +The following fields from the shared data model are to be mapped into the NCPI Participant as shown below: + + +| **Logical Model Property** | **Cardinality** | **NCPI Participant Mapping** |**Usage Guidance** | **Notes** | +Participant|1..1|reference|Required|| +ResearchStudy|1..1|reference|Required|| +AccessPolicy|0..*|reference|Required if available|| + diff --git a/input/pagecontent/StructureDefinition-ncpi-study-participant-notes.md b/input/pagecontent/StructureDefinition-ncpi-study-participant-notes.md new file mode 100755 index 00000000..18866290 --- /dev/null +++ b/input/pagecontent/StructureDefinition-ncpi-study-participant-notes.md @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/input/pagecontent/StructureDefinition-research-study-intro.md b/input/pagecontent/StructureDefinition-research-study-intro.md index 4cf3b614..e5b18cb3 100644 --- a/input/pagecontent/StructureDefinition-research-study-intro.md +++ b/input/pagecontent/StructureDefinition-research-study-intro.md @@ -135,7 +135,6 @@ Additional Study Groups may be included to describe various aspects of the study * Derived from this Resource Profile: [Research Study Subject](structuredefinition-research-study-subject) -* Refer to this Resource Profile: [Study Summary](structuredefinition-study-summary) and [Study Variable Summary](structuredefinition-study-variable-summary) * Examples for this Resource Profile: [ResearchStudy/cmg-research-study-bhcmg](researchstudy-cmg-research-study-bhcmg) and [ResearchStudy/ncpi-research-study-01](researchstudy-ncpi-research-study-01)