NIH-NCPI · torstees · May 31, 2023 · May 31, 2023 · May 31, 2023 · Jun 9, 2023
diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
@@ -8,7 +8,7 @@ on:
 jobs:
   validate:
     name: Validate Implementation Guide
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         node-version: [10, 12]
@@ -19,7 +19,7 @@ jobs:
       - name: Set up OpenJDK
         uses: actions/setup-java@v1
         with:
-          java-version: 8
+          java-version: 11
 
       - name: Set up Jekyll
         run: |
@@ -34,7 +34,7 @@ jobs:
 
       - name: Install SUSHI and add FSH definitions
         run: |
-          npm install -g fsh-sushi
+          npm install -g fsh-sushi@^2.10.2
           sushi .
 
       - name: Update IG publisher

diff --git a/.github/workflows/deploy_preview.yml b/.github/workflows/deploy_preview.yml
@@ -7,15 +7,15 @@ on:
 jobs:
   publish:
     name: 📝 Preview Implementation Guide
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: 👩‍💻 Checkout code
         uses: actions/checkout@v3
 
       - name: 🛠 Set up OpenJDK
         uses: actions/setup-java@v1
         with:
-          java-version: 8
+          java-version: 11
 
       - name: 🛠 Set up Jekyll
         run: |
@@ -30,7 +30,7 @@ jobs:
 
       - name: 🛠 Install SUSHI and add FSH definitions
         run: |
-          npm install -g fsh-sushi
+          npm install -g fsh-sushi@^2.10.2
           sushi .
 
       - name: ⬆️ Update IG publisher

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -10,7 +10,7 @@ on:
 jobs:
   publish:
     name: Publish Implementation Guide
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         node-version: [10, 12]
@@ -21,7 +21,7 @@ jobs:
       - name: Set up OpenJDK
         uses: actions/setup-java@v1
         with:
-          java-version: 8
+          java-version: 11
 
       - name: Set up Jekyll
         run: |
@@ -36,7 +36,7 @@ jobs:
 
       - name: Install SUSHI and add FSH definitions
         run: |
-          npm install -g fsh-sushi
+          npm install -g fsh-sushi@^2.10.2
           sushi .
 
       - name: Update IG publisher

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -10,7 +10,7 @@ on:
 jobs:
   release:
     if: github.event.pull_request.merged && contains(github.event.pull_request.labels.*.name, 'release')
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Manual workaround for Github not having a runtime macro to check for the default branch
         id: gatekeeper

diff --git a/input/fsh/Alias.fsh b/input/fsh/Alias.fsh
@@ -36,6 +36,8 @@ Alias: $observation-category = http://terminology.hl7.org/CodeSystem/observation
 Alias: $refseq = http://www.ncbi.nlm.nih.gov/refseq
 Alias: $varnomen = http://varnomen.hgvs.org
 Alias: $umls = https://uts.nlm.nih.gov/uts/umls
+Alias: $nihcc = https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/nih-consent
+Alias: $studydesign = https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/ResearchStudy-StudyDesign
 
 // ValueSet
 Alias: $v3-FamilyMember = http://terminology.hl7.org/ValueSet/v3-FamilyMember
@@ -58,6 +60,8 @@ Alias: $hpo = http://purl.obolibrary.org/obo/hp.owl
 Alias: $omim = https://omim.org/
 Alias: $mondo = http://purl.obolibrary.org/obo/mondo.owl
 
+Alias: $mesh = urn:oid:2.16.840.1.113883.6.177
+
 // ValueSet
 Alias: $disease-codes = http://fhir.ncpi-project-forge.io/ValueSet/disease-codes
 Alias: $phenotype-codes = http://fhir.ncpi-project-forge.io/ValueSet/phenotype-codes
@@ -67,4 +71,5 @@ Alias: $condition-interitanc-codes = http://fhir.ncpi-project-forge.io/ValueSet/
 // NCPI Observations
 Alias: $ncpi = https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/ncpi
 Alias: $ncpi_datatypes = https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/ncpi-data-types
+Alias: $ncpi-study-types = https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/ncpi-study-types
 Alias: $ucum = http://unitsofmeasure.org
diff --git a/input/fsh/CodeSystem-DbGAPStudyDesign.fsh b/input/fsh/CodeSystem-DbGAPStudyDesign.fsh
@@ -0,0 +1,25 @@
+CodeSystem: DbGapStudyDesign
+Id: dbgap-study-design
+Title: "dbGaP Study Design"
+Description: "StudyDesign codes from dbGaP FHIR Service pulled Aug 2023."
+* ^url = $studydesign
+* ^status = #draft
+* ^experimental = false
+* ^caseSensitive = true
+* ^content = #fragment
+* ^count = 15
+* #Case-Set "Case Set"
+* #Case-Control "Case-Control"
+* #Clinical-Genetic-Testing "Clinical Genetic Testing"
+* #Clinical-Trial "Clinical Trial"
+* #Collection "Collection"
+* #Control-Set "Control Set"
+* #Cross-Sectional "Cross-Sectional"
+* #Family/Twin/Trios "Family/Twin/Trios"
+* #Interventional "Interventional"
+* #Mendelian "Mendelian"
+* #Metagenomics "Metagenomics"
+* #Methods "Methods"
+* #Prospective-Longitudinal-Cohort "Prospective Longitudinal Cohort"
+* #Tumor-vs-Matched-Normal "Tumor vs. Matched-Normal"
+* #Xenograft "Xenograft"
diff --git a/input/fsh/CodeSystem-HPO.fsh b/input/fsh/CodeSystem-HPO.fsh
@@ -1913,3 +1913,5 @@ Description: "The Human Phenotype Ontology (HPO) provides a standardized vocabul
 * #HP:0006808 "Cerebral hypomyelination"
 * #HP:0002926 "Abnormality of thyroid physiology"
 * #HP:0007970 "Congenital ptosis"
+* #HP:0030853 "Heterotaxy"
+* #HP:0010772 "Anomalous pulmonary venous return"
diff --git a/input/fsh/CodeSystem-LoincAnswers.fsh b/input/fsh/CodeSystem-LoincAnswers.fsh
@@ -2,7 +2,7 @@ CodeSystem: LoincAnswers
 Id: loinc-answers
 Title: "LOINC Answers"
 Description: "LOINC ANSWERS used by NCPI resources"
-* ^url = "ncpi:loinc-answers"
+* ^url = "https://nih-ncpi.github.io/ncpi-fhir-ig/CodeSystem/loinc-answers"
 * ^status = #draft
 * ^experimental = false
 * ^caseSensitive = true

diff --git a/input/fsh/CodeSystem-Mondo.fsh b/input/fsh/CodeSystem-Mondo.fsh
@@ -11,3 +11,7 @@ Description: "The Mondo Disease Ontology (Mondo) aims to harmonize disease defin
 * #MONDO:0005072 "neuroblastoma"
 * #MONDO:0002749 "extracranial neuroblastoma"
 * #MONDO:0008542 "tetralogy of fallot"
+* #MONDO:0016054 "cerebral malformation"
+* #MONDO:0016033 "Cornelia de Lange syndrome"
+* #MONDO:0007130 "congenital total pulmonary venous return anomaly"
+* #MONDO:0017705 "congenital pulmonary venous return anomaly"
diff --git a/input/fsh/CodeSystem-NCIt.fsh b/input/fsh/CodeSystem-NCIt.fsh
@@ -11,3 +11,4 @@ Description: "NCI Thesaurus (NCIt) provides reference terminology for many NCI a
 * #C3270 "Neuroblastoma"
 * #C5437 "Extracranial Neuroblastoma"
 * #C84505 "Tetralogy of Fallot"
+* #C142710 "Study Participant"
diff --git a/input/fsh/CodeSystem-NcpiStudyTypes.fsh b/input/fsh/CodeSystem-NcpiStudyTypes.fsh
@@ -0,0 +1,21 @@
+CodeSystem: NcpiStudyType
+Id: ncpi-study-type
+Title: "NCPI Study Type"
+Description: "Enumerated List of Research Study Types used in NCPI Funded studies."
+* ^url = $ncpi-study-types
+* ^version = "0.1.0"
+* ^status = #active
+* ^experimental = false
+* ^publisher = "NCPI FHIR Works"
+* ^content = #fragment 
+* #Family "Family"
+* #Cohort "Cohort"
+* #Mixed "Mixed"
+* #Repository "Repository"
+* #RNA-Sequencing "RNA Sequencing"
+* #Parent-Offspring-Trios "Parent-Offspring Trios"
+* #Cross-Sectional "Cross-Sectional"
+* #Control-Set "Control Set"
+* #Tumor-vs-Matched-Normal "Tumor vs. Matched-Normal"
+* #Observational "Observational"
+* #Longitudinal "Longitudinal"
diff --git a/input/fsh/CodeSystem-NihConsentCodes.fsh b/input/fsh/CodeSystem-NihConsentCodes.fsh
@@ -0,0 +1,16 @@
+CodeSystem: NihConsentCodes
+Id: nih-consent
+Title: "NIH Consent Codes"
+Description: "A set of terms describing the data use limitations associated with a given consent group."
+* ^version = "0.1.0"
+* ^status = #active
+* ^url = $nihcc
+* #GRU "General Research Use"
+* #HMB "Health/Medical/Biomedical"
+* #DS "Disease-Specific (Disease/Trait/Exposure)"
+* #IRB "IRB approval required"
+* #PUB "Publication required"
+* #COL "Collaboration Required"
+* #NPU "Not-for-profit use only"
+* #MDS "Methods"
+* #GSO "Genetic studies only"
diff --git a/input/fsh/Example-CMG-ResearchStudy.fsh b/input/fsh/Example-CMG-ResearchStudy.fsh
@@ -0,0 +1,162 @@
+// We'll use the Baylor Hopkins CMG DbGAP resources to build this example 
+// which will conform to the current NCPI Research Study model. 
+//
+// https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000711.v7.p2
+// 
+// This particular study has sufficient complexity to show the most 
+// important aspects of the current model's design without being too cumbersome
+// to fully represent. 
+
+// The Consortium resource provides a single point of reference to link 
+// together research studies that exist under the single umbrella. 
+Instance: cmg-research-consortium
+InstanceOf: ResearchConsortium
+Title: "The Center for Mendelian Genomics Consortium (CMG) Consortium"
+Usage: #example
+Description: "The Center for Mendelian Genomics Consortium."
+* name = "Center for Mendelian Genomics Consortium"
+* alias[0] = "CMG"
+* telecom 
+  * system = #url
+  * value = "http://mendelian.org/"
+
+Instance: cmg-research-study-bhcmg
+InstanceOf: NcpiResearchStudy
+Title: "Baylor Hopkins Center for Mendelian Genomics (BH CMG)"
+Usage: #example
+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."
+// Notice that we can use the DbGaP study ID for easier searching
+* identifier[0]
+  * system = "http://mendelian.org/fhir"
+  * value = "BH-CMG"
+* identifier[1]
+  * system = "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id="
+  * value = "phs000711"
+* title = "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."
+* status = #completed
+* sponsor = Reference(cmg-research-consortium)
+* category 
+  * coding 
+    * system = $ncpi
+    * code = #StudyCohort 
+    * display = "Study Cohort"
+* focus[+] = $mondo#MONDO:0016054 "cerebral malformation"
+* focus[+].coding[0] = $hpo#HP:0030853 "Heterotaxy"
+* focus[=].coding[1] = $mesh#D059446 "Heterotaxy Syndrome"
+* focus[+].coding[0] = $mondo#MONDO:0016033 "Cornelia de Lange syndrome"
+* focus[=].coding[1] = $mesh#D003635 "De Lange Syndrome"
+// This particular study doesn't have a specific 
+* relatedArtifact[0]
+  * type = #derived-from
+  * label = "DbGaP"
+  * display = "phs000711"
+  * url = "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000711"
+* relatedArtifact[+]
+  * type = #documentation
+  * label = "Citation"
+  * citation = "Gonzaga-Jauregui C, Lupski JR, Gibbs RA. Human genome sequencing in health and disease. Annu Rev Med. 2012;63:35-61. doi: 10.1146/annurev-med-051010-162644. PMID: 22248320; PMCID: PMC3656720."
+  * document.url = "https://pubmed.ncbi.nlm.nih.gov/22248320/"
+* relatedArtifact[+]
+  * type = #documentation
+  * label = "Website"
+  * document.url = "https://mendeliangenomics.org/"
+* enrollment = Reference(cmg-research-study-bhcmg-group)
+* extension[studyDesign].valueCodeableConcept.coding[0] = $studydesign#Mendelian "Mendelian"
+* extension[studyDesign].valueCodeableConcept.coding[1] = $ncpi-study-types#Mixed "Mixed"
+
+Instance: cmg-research-study-bhcmg-group
+InstanceOf: StudyGroup
+Title: "BH CMG Study Participants"
+Usage: #example
+Description: "BH-CMG study's entire population"
+* name = "BH-CMG Study Participants"
+* quantity = 2445
+* actual = true
+* type = #person
+
+Instance: hmb-npu-consent
+InstanceOf: ResearchStudyConsent
+Title: "HMB-NPU Consent"
+Usage: #example
+Description: "Consented with Health/Medical/Biomedical + Not for profit use"
+* status = #draft
+* scope = #research
+* category.coding = http://terminology.hl7.org/CodeSystem/consentcategorycodes#research
+* provision.type = http://hl7.org/fhir/consent-provision-type#permit
+* provision.purpose[+] = $nihcc#HMB "Health/Medical/Biomedical"
+* provision.purpose[+] = $nihcc#NPU "Not-for-profit use only"
+//* category.text = "HMB-NPU"
+
+Instance: cmg-research-study-subject-cmg-hmb-npu
+InstanceOf: ResearchStudySubject
+Title: "Participants consented under HMB-NPU"
+Usage: #example
+Description: "CMG Consent Group, Health/Medical/Biomedical + Not for profit use"
+* identifier[0]
+  * system = "http://mendelian.org/fhir"
+  * value = "BH-CMG-HMB-NPU"
+* title = "BH-CMG HMB-NPU Consent Study Subject"
+* description = "CMG Consent Group, Health/Medical/Biomedical + Not for profit use"
+* status = #completed
+* partOf = Reference(cmg-research-study-bhcmg)
+* extension[consent].valueReference = Reference(hmb-npu-consent)
+* enrollment = Reference(cmg-research-study-bhcmg-consent-group-hmb-npu)
+// Do we want to link these back to the consortium?
+* sponsor = Reference(cmg-research-consortium)
+
+Instance: cmg-research-study-bhcmg-consent-group-hmb-npu
+InstanceOf: StudyGroup
+Title: "Participants consented under HMB-NPU"
+Usage: #example
+Description: "BH-CMG study's population consented under Health/Medical/Biomedical + Not for profit use"
+* identifier[0]
+  * system = "http://mendelian.org/fhir/Group"
+  * value = "HMB-NPU-Participants"
+* name = "BM-CMG Study HMB-NPU Participants"
+* quantity = 1665
+* actual = true
+* type = #person
+
+Instance: hmb-irb-npu-consent
+InstanceOf: ResearchStudyConsent
+Title: "HMB-IRB-NPU Consent"
+Usage: #example
+Description: "Consented with Health/Medical/Biomedical + IRB Required + Not for profit use"
+* status = #draft
+* scope = #research
+* category.coding = http://terminology.hl7.org/CodeSystem/consentcategorycodes#research
+* provision.type = http://hl7.org/fhir/consent-provision-type#permit
+* provision.purpose[+] = $nihcc#HMB "Health/Medical/Biomedical"
+* provision.purpose[+] = $nihcc#IRB "IRB approval required"
+* provision.purpose[+] = $nihcc#NPU "Not-for-profit use only"
+//* category.text = "HMB-IRB-NPU"
+
+Instance: cmg-research-study-subject-cmg-hmb-irb-npu
+InstanceOf: ResearchStudySubject
+Title: "Participants consented under HMB-IRB-NPU"
+Usage: #example
+Description: "CMG Consent Group, HMB-IRB-NPU"
+* identifier[0]
+  * system = "http://mendelian.org/fhir"
+  * value = "BH-CMG-HMB-IRB-NPU"
+* title = "BH-CMG HMB-IRB-NPU Consent Study Subject"
+* status = #completed
+* partOf = Reference(cmg-research-study-bhcmg)
+* extension[consent].valueReference = Reference(hmb-irb-npu-consent)
+* enrollment = Reference(cmg-research-study-bhcmg-group-hmb-irb-npu)
+
+Instance: cmg-research-study-bhcmg-consent-group-hmb-irb-npu
+InstanceOf: StudyGroup
+Title: "Participants consented under HMB-IRB-NPU"
+Usage: #example
+Description: "BH-CMG study's population consented under Health/Medical/Biomedical + IRB Approval Required + Not for profit use"
+* identifier[0]
+  * system = "http://mendelian.org/fhir/Group"
+  * value = "HMB-IRB-NPU-Participants"
+* name = "BM-CMG Study HMB-IRB-NPU Participants"
+* quantity = 780
+* actual = true
+* type = #person
+
+
diff --git a/input/fsh/Example-ConceptMap-DataDictionary.fsh b/input/fsh/Example-ConceptMap-DataDictionary.fsh
@@ -24,8 +24,8 @@ The codes used below were chosen purely for example's sake and are in no way an
 * $loinc#LP35925-4 "Body mass index (BMI)"
 * $umls#C0872128 "case control"
 * $hpo#HP:0010772 "Anomalous pulmonary venous return"
-* $mondo#0017705 "congenital pulmonary venous return anomaly"
-* $mondo#0007130 "congenital total pulmonary venous return anomaly"
+* $mondo#MONDO:0017705 "congenital pulmonary venous return anomaly"
+* $mondo#MONDO:0007130 "congenital total pulmonary venous return anomaly"
 
 Instance: example-study-data-dictionary-conceptmap-1
 InstanceOf: StudyDataDictionaryHarmony