Merge pull request #269 from include-dcc/PL-2025-05-15

Pl 2025 05 15

Author: lopierra

src/linkml/include_schema.yaml

@@ -56,6 +56,8 @@ classes:
     - guidMapped
     - acknowledgments
     - citationStatement
+    - doi
+    - doiCitation
     slot_usage:
       dataCategory:
         description: Categories of data expected to be collected in this study
@@ -92,6 +94,8 @@ classes:
     - otherAccessAuthority
     - isHarmonized
     - datasetManifestLocation
+    - doi
+    - doiCitation
     slot_usage:
       dataCategory:
         description: General category of data in Dataset; pipe-separated if multiple
@@ -151,8 +155,8 @@ classes:
     - race
     - ethnicity
     - downSyndromeStatus
-    - ageAtFirstPatientEngagement
-    - firstPatientEngagementEvent
+    - ageAtFirstParticipantEngagement
+    - firstParticipantEngagementEvent
     - outcomesVitalStatus
     - ageAtLastVitalStatus
     slot_usage:
@@ -264,13 +268,14 @@ classes:
         range: Participant
       sampleGlobalId:
         range: Biospecimen
+
 ####################################################################################################
 # Slot Usage Overview
 # ====================
 # This section outlines the use of various slots (fields) across different entity classes,
 # including how slots can be customized or referenced within specific classes.
 # Slot usage enables fine-grained control over how each slot behaves within the context of each class.
-
+#
 # Slot Usage: Directly Assigned to Entity Classes
 # -------------------------------------------------------
 # These slots are associated with specific classes, defining essential attributes for each entity.
@@ -283,7 +288,7 @@ classes:
 # - experimentalStrategy: Used in DataFile, Dataset
 # - studyCode: Used in Participant
 # - participantExternalId: Used in Participant
-
+#
 # Referential Slot Usage: Cross-Class References
 # ------------------------------------------------
 # These slots are used in multiple classes to establish relationships and link data across entities.
@@ -295,8 +300,8 @@ classes:
 # - sampleGlobalId: Referenced in DataFile, DatasetManifest
 # - fileGlobalId: Referenced in DatasetManifest
 # - datasetGlobalId: (Usage not fully defined, consider adding specific references)
-
 ####################################################################################################
+
 slots:
   studyCode:
     definition_uri: include:studyCode
@@ -447,6 +452,18 @@ slots:
     title: Citation Statement
     range: string
     multivalued: true
+  doi:
+    definition_uri: include:doi
+    description: Unique Digital Object Identifier for each Study and Dataset, minted by the DCC using DataCite 
+    title: DOI
+    range: uri
+    required: false #change to true after pilot
+  doiCitation:
+    definition_uri: include:doiCitation
+    description: Bibliographic citation for DOI, generated by DataCite
+    title: DOI Citation
+    range: string
+    required: false #change to true after pilot
   datasetName:
     definition_uri: include:datasetName
     description: Full name of the dataset, provided by contributor
@@ -596,18 +613,18 @@ slots:
     title: Down Syndrome Status
     range: enum_downSyndromeStatus
     required: true
-  ageAtFirstPatientEngagement:
-    definition_uri: include:ageAtFirstPatientEngagement
+  ageAtFirstParticipantEngagement:
+    definition_uri: include:ageAtFirstParticipantEngagement
     description: Age in days of Participant at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available.
-    title: Age at First Patient Engagement
+    title: Age at First Participant Engagement
     range: integer
     minimum_value: 0
     maximum_value: 33000
     required: true
-  firstPatientEngagementEvent:
-    definition_uri: include:firstPatientEngagementEvent
-    description: Event for which Age at First Patient Engagement is given (e.g. enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available.
-    title: First Patient Engagement Event
+  firstParticipantEngagementEvent:
+    definition_uri: include:firstParticipantEngagementEvent
+    description: Event for which Age at First Participant Engagement is given (e.g. enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available.
+    title: First Participant Engagement Event
     required: true
     range: string
   outcomesVitalStatus:
@@ -946,6 +963,8 @@ enums:
         title: DS-COG-AML
       ds_determined:
         title: DS-DETERMINED
+      ds_home:
+        title: DS-HOME
       ds_hsat:
         title: DS-HSAT
       ds_isp:
@@ -972,17 +991,24 @@ enums:
         title: EXcEEDS
       htp:
         title: HTP
+      ibis-ds:
+        title: IBIS-DS
+      jaki_ds:
+        title: JAKi-DS
       optimal:
         title: OPTimal
       team_ds:
         title: TEAM-DS
+      tomi:
+        title: TOMI
       trc_ds:
         title: TRC-DS
       x01_desmith:
         title: X01-deSmith
       x01_hakonarson:
         title: X01-Hakonarson
   enum_researchDomain:
+    #TODO: replace/add NIH internal categories from Huiqing
     definition_uri: include:enum_researchDomain
     permissible_values:
       behavior_and_behavior_mechanisms:
@@ -997,6 +1023,9 @@ enums:
       hematologic_diseases:
         title: Hematologic Diseases
         meaning: mesh:D006402
+      neurodevelopment:
+        title: Neurodevelopment
+        meaning: 
       sleep_wake_disorders:
         title: Sleep Wake Disorders
         meaning: mesh:D012893
@@ -1058,6 +1087,7 @@ enums:
         description: Data obtained from survey, questionnaire, etc. filled out by participant or caregiver
       other:
         title: Other
+        description: Data obtained from other source, such as tissue bank
       unknown:
         title: Unknown
   enum_dataCategory: