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