Vocabulary tables

src/common_access_model/schema/common_access_model.yaml

@@ -388,12 +388,59 @@ classes:
     title: Concept
     description: A standardized concept with display information.
     slots:
-    - concept_curie
-    - display
+      - concept_curie
+      - concept_id
+      - vocabulary_prefix
+      - concept_code
+      - display
+      - definition
     slot_usage:
       concept_curie:
         required: true
         identifier: true
+        range: uriorcurie
+  Synonym:
+    title: Concept Synonym
+    description: Alternate display names for concepts.
+    slots:
+      - concept_curie
+      - display
+      - display_type
+      - language
+  DeprecatedConcept:
+    title: Deprecated Concept
+    description: Identifies concepts that are not currently valid.
+    slots:
+      - concept_curie
+      - deprecation_type
+      - replacement_curie
+  Vocabulary:
+    description: Flat table containing each of the ontologies used for dataset annotations
+    slots:
+      - vocabulary_prefix
+      - name
+      - vocabulary_uri
+      - vocabulary_id
+      - fhir_system
+      - description
+      - version
+      - vocabulary_source 
+    slot_usage:
+      vocabulary_prefix:
+        identifier: true
+        range: string
+        pattern: "^[A-Za-z][A-Za-z0-9_\\-\\.]*$"
+        comments:
+          - "Must start with a letter; thereafter allows letters, digits, underscores, hyphens, and dots to accommodate OLS/UMLS source variability."
+          - "RISK: In order for all of our data to correctly join, the format of the prefix must always align with the prefix used in this table."
+        todos:
+          - "Ensure that MapDragon and TermWeaver both rely on the same rules for prefixes"
+  ConceptRelationship:
+    description: Relationships between two terms.
+    slots:
+      - concept_curie
+      - target_concept_curie
+      - relationship_curie
   Sample:
     title: Sample
     description: A functionally equivalent specimen taken from a participant or processed from such a sample.
@@ -969,6 +1016,71 @@ slots:
     title: Display String
     description: The friendly display string of the coded term.
     range: string
+  display_type:
+    title: Display Type
+    description: The type of display name, eg, "Preferred".
+    range: string
+  deprecation_type:
+    title: Deprecation Type
+    description: The type of or reason for deprecation, if known.
+    range: string
+  replacement_curie:
+    title: Replacement CURIE
+    description: A replacement curie for this deprecated concept, if applicable.
+    range: string
+  language:
+    title: Language
+    description: The ISO 639 language code of this entity.
+    range: string
+  concept_code:
+    title: Concept Code
+    description: Identifier as it is defined within the ontology
+    required: true
+    range: string
+  concept_id:
+    title: OMOP Concept ID
+    description: The OMOP Concept ID for the term, if applicable
+    range: integer
+  definition:
+    title: Definition
+    description: Detailed definition or description for the term
+    range: string
+  vocabulary_id:
+    title: OMOP Vocabulary ID
+    description: The OMOP Vocabulary ID associated with the vocabulary, if applicable
+    range: string
+  vocabulary_uri:
+    title: Vocabulary URI
+    description: Official URI associated with the vocabulary
+    required: true
+    range: uri
+  fhir_system:
+    title: FHIR System
+    description: System used within FHIR valuesets and codings
+    required: true
+    range: uri
+  vocabulary_prefix:
+    title: Canonical Curie Prefix
+    description: The authoritative namespace prefix allocated to the vocabulary. Used to resolve compact identifiers (CURIEs) to their full semantic URIs or FHIR system URLs.
+    range: Vocabulary
+  version:
+    title: Version
+    description: Version associated with the current vocabulary content
+    range: string
+  vocabulary_source:
+    title: Vocabulary data source
+    description: Source used for accessing the vocabulary's content
+    range: string
+    comments:
+      - "This is currently poorly defined because we haven't fully defined the nature of the data pulls. Most likely it will end up as a filename (.owl, .obo, etc) or another tool, etc"
+  target_concept_curie:
+    title: Target Concept ID
+    description: The concept to which this term relates
+    range: Concept
+  relationship_curie:
+    title: Mapping Relationship
+    description: The relationship between the subject (this term) and the object (target_concept_id).
+    range: uriorcurie
   concept_source:
     title: Concept Source Text
     description: The source text yielding the standardized concept.

tests/data/valid/Concept-000.yaml

@@ -1,2 +1,4 @@
 concept_curie: test_concept:000
-display: Test
+display: Test
+vocabulary_prefix: test
+concept_code: '000'

tests/data/valid/Vocabulary-000.yaml

@@ -0,0 +1,6 @@
+vocabulary_prefix: test_concept
+name: Test Vocabulary
+vocabulary_uri: https://github.com/include-dcc/common-access-model/blob/main/tests/data/valid/Vocabulary-000.yaml
+fhir_system: https://github.com/include-dcc/common-access-model/blob/main/tests/data/valid/Vocabulary-000.yaml
+version: '0.1'
+vocabulary_source: https://github.com/include-dcc/common-access-model/blob/main/tests/data/valid/Vocabulary-000.yaml