init public release

2026-09-08 10:59:05 +02:00
commit 9cdf012717
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+# BioCypher ODM Import Schema Configuration with BioLink Model Integration
+
+# Node types extracted from ODM generators mapped to BioLink classes
+study:
+  represented_as: node
+  preferred_id: oid
+  label_in_input: Study
+  is_a: biolink:ClinicalTrial
+  properties:
+    OID: str
+    Name: str
+    Description: str
+    Protocol: str
+    ModelID: str
+
+studyevent:
+  represented_as: node
+  preferred_id: oid
+  label_in_input: StudyEvent
+  is_a: biolink:ClinicalEntity
+  properties:
+    OID: str
+    Name: str
+    Type: str
+    StudyOID: str
+    ModelID: str
+
+form:
+  represented_as: node
+  preferred_id: oid
+  label_in_input: Form
+  is_a: biolink:InformationContentEntity
+  properties:
+    OID: str
+    Name: str
+    StudyOID: str
+    ModelID: str
+
+itemgroup:
+  represented_as: node
+  preferred_id: oid
+  label_in_input: ItemGroup
+  is_a: biolink:InformationContentEntity
+  properties:
+    OID: str
+    Name: str
+    StudyOID: str
+    ModelID: str
+
+item:
+  represented_as: node
+  preferred_id: oid
+  label_in_input: Item
+  is_a: biolink:ClinicalFinding
+  properties:
+    OID: str
+    Name: str
+    DataType: str
+    Question: str
+    StudyOID: str
+    ModelID: str
+
+alias:
+  represented_as: node
+  preferred_id: [context, name]
+  label_in_input: Alias
+  is_a: biolink:InformationContentEntity
+  properties:
+    Context: str
+    Name: str
+    ItemOID: str
+    StudyOID: str
+    ModelID: str
+
+measurementunit:
+  represented_as: node
+  preferred_id: oid
+  label_in_input: MeasurementUnit
+  is_a: biolink:Unit
+  properties:
+    OID: str
+    Name: str
+    Symbol: str
+
+basicdefinitions:
+  represented_as: node
+  preferred_id: [studyoid, modelid]
+  label_in_input: BasicDefinitions
+  is_a: biolink:InformationContentEntity
+  properties:
+    StudyOID: str
+    ModelID: str
+
+rangecheck:
+  represented_as: node
+  preferred_id: [comparator, constraint, checkvalue]
+  label_in_input: RangeCheck
+  is_a: biolink:ClinicalFinding
+  properties:
+    Comparator: str
+    Constraint: str
+    CheckValue: str
+
+codelist:
+  represented_as: node
+  preferred_id: oid
+  label_in_input: CodeList
+  is_a: biolink:InformationContentEntity
+  properties:
+    OID: str
+    Name: str
+    DataType: str
+    StudyOID: str
+    ModelID: str
+
+codelistitem:
+  represented_as: node
+  preferred_id: codedvalue
+  label_in_input: CodeListItem
+  is_a: biolink:ConceptualEntity
+  properties:
+    CodedValue: str
+    Decode: str
+
+# Edge types extracted from ODM generators mapped to BioLink predicates
+study_has_studyevent:
+  represented_as: edge
+  label_in_input: STUDY_HAS_STUDYEVENT
+  source: study
+  target: studyevent
+  is_a: biolink:related_to
+
+itemgroup_has_item:
+  represented_as: edge
+  label_in_input: ITEMGROUP_HAS_ITEM
+  source: itemgroup
+  target: item
+  is_a: biolink:has_part
+
+form_has_itemgroup:
+  represented_as: edge
+  label_in_input: FORM_HAS_ITEMGROUP
+  source: form
+  target: itemgroup
+  is_a: biolink:has_part
+
+studyevent_has_form:
+  represented_as: edge
+  label_in_input: STUDYEVENT_HAS_FORM
+  source: studyevent
+  target: form
+  is_a: biolink:has_part
+
+item_has_alias:
+  represented_as: edge
+  label_in_input: ITEM_HAS_ALIAS
+  source: item
+  target: alias
+  is_a: biolink:same_as
+
+itemgroup_has_alias:
+  represented_as: edge
+  label_in_input: ITEMGROUP_HAS_ALIAS
+  source: itemgroup
+  target: alias
+  is_a: biolink:same_as
+
+item_has_measurementunit:
+  represented_as: edge
+  label_in_input: ITEM_HAS_MEASUREMENTUNIT
+  source: item
+  target: measurementunit
+  is_a: biolink:has_attribute
+
+has_basedef:
+  represented_as: edge
+  label_in_input: HAS_BASEDEF
+  source: study
+  target: basicdefinitions
+  is_a: biolink:has_part
+
+basedef_has_measurementunit:
+  represented_as: edge
+  label_in_input: BASEDEF_HAS_MEASUREMENTUNIT
+  source: basicdefinitions
+  target: measurementunit
+  is_a: biolink:has_part
+
+item_has_rangecheck:
+  represented_as: edge
+  label_in_input: ITEM_HAS_RANGECHECK
+  source: item
+  target: rangecheck
+  is_a: biolink:has_attribute
+
+item_has_codelist:
+  represented_as: edge
+  label_in_input: ITEM_HAS_CODELIST
+  source: item
+  target: codelist
+  is_a: biolink:has_attribute
+
+codelist_has_codelistitem:
+  represented_as: edge
+  label_in_input: CODELIST_HAS_CODELISTITEM
+  source: codelist
+  target: codelistitem
+  is_a: biolink:has_part
+
+composite:
+  represented_as: edge
+  label_in_input: COMPOSITE
+  source: alias
+  target: alias
+  is_a: biolink:related_to