Linkml v5 updates

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",

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",

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"
+}

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"

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

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"
+* #unknown "Unknown"
+* #wearable "Wearable"

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"

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"

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"