From 75146438c8e432a31803d2f89f972d7a6b16d0b9 Mon Sep 17 00:00:00 2001 From: Ann Holmes Date: Mon, 16 Feb 2026 18:22:42 -0500 Subject: [PATCH 1/2] :wrench: updates to code systems to align with linkml v5 enums --- ...CodeSystem-clinical-data-source-types.json | 4 + .../resources/CodeSystem-data-categories.json | 8 +- .../resources/CodeSystem-research-domain.json | 75 +++++++++++++++++++ .../resources/CodeSystem-study-design.json | 20 +++++ .../CodeSystem-ClinicalDataSourceTypes.fsh | 3 +- .../codesystems/CodeSystem-DataCategories.fsh | 4 +- .../codesystems/CodeSystem-ResearchDomain.fsh | 25 +++++++ .../codesystems/CodeSystem-StudyDesign.fsh | 5 ++ 8 files changed, 137 insertions(+), 7 deletions(-) create mode 100644 fsh-generated/resources/CodeSystem-research-domain.json create mode 100644 input/fsh/codesystems/CodeSystem-ResearchDomain.fsh diff --git a/fsh-generated/resources/CodeSystem-clinical-data-source-types.json b/fsh-generated/resources/CodeSystem-clinical-data-source-types.json index bbd2a3f..92b46d1 100644 --- a/fsh-generated/resources/CodeSystem-clinical-data-source-types.json +++ b/fsh-generated/resources/CodeSystem-clinical-data-source-types.json @@ -27,6 +27,10 @@ { "code": "unknown", "display": "Unknown" + }, + { + "code": "wearable", + "display": "Wearable" } ], "version": "0.1.0", diff --git a/fsh-generated/resources/CodeSystem-data-categories.json b/fsh-generated/resources/CodeSystem-data-categories.json index 8e15845..3a50258 100644 --- a/fsh-generated/resources/CodeSystem-data-categories.json +++ b/fsh-generated/resources/CodeSystem-data-categories.json @@ -13,8 +13,8 @@ "display": "Unharmonized Demographic/Clinical Data" }, { - "code": "harmonized_demographic_clinical_data", - "display": "Harmonized Demographic/Clinical Data" + "code": "demographic_clinical_data", + "display": "Demographic/Clinical Data" }, { "code": "Clinical", @@ -69,8 +69,8 @@ "display": "Other" }, { - "code": "sleep_study", - "display": "Sleep Study" + "code": "sleep", + "display": "Sleep" } ], "version": "0.1.0", diff --git a/fsh-generated/resources/CodeSystem-research-domain.json b/fsh-generated/resources/CodeSystem-research-domain.json new file mode 100644 index 0000000..037ed84 --- /dev/null +++ b/fsh-generated/resources/CodeSystem-research-domain.json @@ -0,0 +1,75 @@ +{ + "resourceType": "CodeSystem", + "status": "active", + "content": "fragment", + "name": "ResearchDomain", + "id": "research-domain", + "title": "Research Domain", + "description": "Research Domains Used in INCLUDE Clinical Trials Data", + "url": "https://includedcc.org/fhir/code-systems/research_domain", + "concept": [ + { + "code": "auditory_perception", + "display": "Auditory Perception" + }, + { + "code": "behavior_and_behavior_mechanisims", + "display": "Behavior and Behavior Mechanisms" + }, + { + "code": "congenital_heart_defects", + "display": "Congenital Heart Defects" + }, + { + "code": "embryonic_and_fetal_development", + "display": "Embryonic and Fetal Development" + }, + { + "code": "immune_system_diseases", + "display": "Immune System Diseases" + }, + { + "code": "hematologic_diseases", + "display": "Hematologic Diseases" + }, + { + "code": "neurodevelopment", + "display": "Neurodevelopment" + }, + { + "code": "nutritional_and_metabolic_diseases", + "display": "Nutritional and Metabolic Diseases" + }, + { + "code": "sleep_wake_disorders", + "display": "Sleep-Wake Disorders" + }, + { + "code": "all_co_occuring_conditions", + "display": "All Co-Occurring Conditions" + }, + { + "code": "physical_fitness", + "display": "Physical Fitness" + }, + { + "code": "psychiatric_disorders", + "display": "Psychiatric Disorders" + }, + { + "code": "respiratory_tract_diseases", + "display": "Respiratory Tract Diseases" + }, + { + "code": "social_determinints_of_health", + "display": "Social Determinants of Health" + }, + { + "code": "other", + "display": "Other" + } + ], + "version": "0.1.0", + "experimental": false, + "publisher": "NCPI FHIR Works" +} diff --git a/fsh-generated/resources/CodeSystem-study-design.json b/fsh-generated/resources/CodeSystem-study-design.json index d5ccd2f..36d7cdd 100644 --- a/fsh-generated/resources/CodeSystem-study-design.json +++ b/fsh-generated/resources/CodeSystem-study-design.json @@ -40,6 +40,26 @@ "code": "longitudinal", "display": "Longitudinal" }, + { + "code": "observational", + "display": "Observational" + }, + { + "code": "registry", + "display": "Registry" + }, + { + "code": "expanded_access", + "display": "Expanded Access" + }, + { + "code": "technology_development", + "display": "Technology Development" + }, + { + "code": "trial_readiness_study", + "display": "Trial Readiness Study" + }, { "code": "tumor_vs_matched_normal", "display": "Tumor vs Matched Normal" diff --git a/input/fsh/codesystems/CodeSystem-ClinicalDataSourceTypes.fsh b/input/fsh/codesystems/CodeSystem-ClinicalDataSourceTypes.fsh index fcfa117..aea3184 100644 --- a/input/fsh/codesystems/CodeSystem-ClinicalDataSourceTypes.fsh +++ b/input/fsh/codesystems/CodeSystem-ClinicalDataSourceTypes.fsh @@ -12,4 +12,5 @@ Description: "Clinical Data Source Types" * #investigator-assessment "Investigator Assessment" * #participant-or-caregiver-report "Participant or Caregiver Report" * #other "Other" -* #unknown "Unknown" \ No newline at end of file +* #unknown "Unknown" +* #wearable "Wearable" \ No newline at end of file diff --git a/input/fsh/codesystems/CodeSystem-DataCategories.fsh b/input/fsh/codesystems/CodeSystem-DataCategories.fsh index bf5a49b..92bcfa2 100644 --- a/input/fsh/codesystems/CodeSystem-DataCategories.fsh +++ b/input/fsh/codesystems/CodeSystem-DataCategories.fsh @@ -9,7 +9,7 @@ Description: "Data Categories Used in INCLUDE Datasets" * ^publisher = "NCPI FHIR Works" * ^content = #fragment * #unharmonized_demographic_clinical_data "Unharmonized Demographic/Clinical Data" -* #harmonized_demographic_clinical_data "Harmonized Demographic/Clinical Data" +* #demographic_clinical_data "Demographic/Clinical Data" * #Clinical "Clinical" * #Genomics "Genomics" * #Transcriptomics "Transcriptomics" @@ -23,4 +23,4 @@ Description: "Data Categories Used in INCLUDE Datasets" * #fitness "Fitness" * #physical_activity "Physical Activity" * #other "Other" -* #sleep_study "Sleep Study" +* #sleep "Sleep" diff --git a/input/fsh/codesystems/CodeSystem-ResearchDomain.fsh b/input/fsh/codesystems/CodeSystem-ResearchDomain.fsh new file mode 100644 index 0000000..f2ee21d --- /dev/null +++ b/input/fsh/codesystems/CodeSystem-ResearchDomain.fsh @@ -0,0 +1,25 @@ +CodeSystem: ResearchDomain +Id: research-domain +Title: "Research Domain" +Description: "Research Domains Used in INCLUDE Clinical Trials Data" +* ^url = $research_domain +* ^version = "0.1.0" +* ^status = #active +* ^experimental = false +* ^publisher = "NCPI FHIR Works" +* ^content = #fragment +* #auditory_perception "Auditory Perception" +* #behavior_and_behavior_mechanisims "Behavior and Behavior Mechanisms" +* #congenital_heart_defects "Congenital Heart Defects" +* #embryonic_and_fetal_development "Embryonic and Fetal Development" +* #immune_system_diseases "Immune System Diseases" +* #hematologic_diseases "Hematologic Diseases" +* #neurodevelopment "Neurodevelopment" +* #nutritional_and_metabolic_diseases "Nutritional and Metabolic Diseases" +* #sleep_wake_disorders "Sleep-Wake Disorders" +* #all_co_occuring_conditions "All Co-Occurring Conditions" +* #physical_fitness "Physical Fitness" +* #psychiatric_disorders "Psychiatric Disorders" +* #respiratory_tract_diseases "Respiratory Tract Diseases" +* #social_determinints_of_health "Social Determinants of Health" +* #other "Other" \ No newline at end of file diff --git a/input/fsh/codesystems/CodeSystem-StudyDesign.fsh b/input/fsh/codesystems/CodeSystem-StudyDesign.fsh index 6bdb538..e867eb3 100644 --- a/input/fsh/codesystems/CodeSystem-StudyDesign.fsh +++ b/input/fsh/codesystems/CodeSystem-StudyDesign.fsh @@ -16,4 +16,9 @@ Description: "Study Designs Used in INCLUDE Datasets" * #family_twins_trios "Family/Twins/Trios" * #interventional "Interventional" * #longitudinal "Longitudinal" +* #observational "Observational" +* #registry "Registry" +* #expanded_access "Expanded Access" +* #technology_development "Technology Development" +* #trial_readiness_study "Trial Readiness Study" * #tumor_vs_matched_normal "Tumor vs Matched Normal" \ No newline at end of file From cde143c31bee04317bcc9a09bc4e2e271d0b6743 Mon Sep 17 00:00:00 2001 From: Ann Holmes Date: Wed, 18 Feb 2026 11:13:14 -0500 Subject: [PATCH 2/2] :wrench: update alias file with research domains --- input/fsh/Alias.fsh | 1 + 1 file changed, 1 insertion(+) diff --git a/input/fsh/Alias.fsh b/input/fsh/Alias.fsh index 883f9ec..6fcab2c 100755 --- a/input/fsh/Alias.fsh +++ b/input/fsh/Alias.fsh @@ -55,6 +55,7 @@ Alias: $arm_allocation = https://includedcc.org/fhir/code-systems/arm_allocation Alias: $intervention_assignment_strategy = https://includedcc.org/fhir/code-systems/intervention_assignment_strategy Alias: $intervention_types = https://includedcc.org/fhir/code-systems/intervention_types Alias: $trial_phase = https://includedcc.org/fhir/code-systems/trial_phase +Alias: $research_domain = https://includedcc.org/fhir/code-systems/research_domain // ValueSet Alias: $v3-FamilyMember = http://terminology.hl7.org/ValueSet/v3-FamilyMember Alias: $measurement_codes = http://includedcc.org/fhir/code-systems/measurement_codes