manually removed 'types' to resolve 'ValueError: Conflicting URIs (https://w3id.org/biolink/bican-biolink-schema, https://w3id.org/linkml/types) for item: string'

Author: puja-trivedi

linkml-schema/bican_biolink.yaml

@@ -445,375 +445,7 @@ subsets:
     definition_uri: https://w3id.org/biolink/vocab/Testing
     description: TBD
     from_schema: https://w3id.org/biolink/biolink-model
-types:
-  chemical formula value:
-    name: chemical formula value
-    definition_uri: https://w3id.org/biolink/vocab/ChemicalFormulaValue
-    description: A chemical formula
-    notes:
-    - Should be implemented as a stronger type
-    from_schema: https://w3id.org/biolink/biolink-model
-    base: str
-    uri: xsd:string
-  iri type:
-    name: iri type
-    definition_uri: https://w3id.org/biolink/vocab/IriType
-    description: An IRI
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: uriorcurie
-    base: URIorCURIE
-    uri: xsd:string
-    repr: str
-  label type:
-    name: label type
-    definition_uri: https://w3id.org/biolink/vocab/LabelType
-    description: A string that provides a human-readable name for an entity
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: string
-    base: str
-    uri: xsd:string
-  predicate type:
-    name: predicate type
-    definition_uri: https://w3id.org/biolink/vocab/PredicateType
-    description: A CURIE from the biolink related_to hierarchy. For example, biolink:related_to,
-      biolink:causes, biolink:treats.
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: uriorcurie
-    base: URIorCURIE
-    uri: xsd:string
-    repr: str
-  narrative text:
-    name: narrative text
-    definition_uri: https://w3id.org/biolink/vocab/NarrativeText
-    description: A string that provides a human-readable description of something
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: string
-    base: str
-    uri: xsd:string
-  symbol type:
-    name: symbol type
-    definition_uri: https://w3id.org/biolink/vocab/SymbolType
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: string
-    base: str
-    uri: xsd:string
-  frequency value:
-    name: frequency value
-    definition_uri: https://w3id.org/biolink/vocab/FrequencyValue
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: string
-    base: str
-    uri: UO:0000105
-  percentage frequency value:
-    name: percentage frequency value
-    definition_uri: https://w3id.org/biolink/vocab/PercentageFrequencyValue
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: double
-    base: float
-    uri: UO:0000187
-  quotient:
-    name: quotient
-    definition_uri: https://w3id.org/biolink/vocab/Quotient
-    from_schema: https://w3id.org/biolink/biolink-model
-    aliases:
-    - ratio
-    typeof: double
-    base: float
-    uri: UO:0010006
-  unit:
-    name: unit
-    id_prefixes:
-    - UO
-    definition_uri: https://w3id.org/biolink/vocab/Unit
-    from_schema: https://w3id.org/biolink/biolink-model
-    exact_mappings:
-    - qud:Unit
-    typeof: string
-    base: str
-    uri: UO:0000000
-  time type:
-    name: time type
-    definition_uri: https://w3id.org/biolink/vocab/TimeType
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: time
-    base: XSDTime
-    uri: xsd:string
-    repr: str
-  biological sequence:
-    name: biological sequence
-    definition_uri: https://w3id.org/biolink/vocab/BiologicalSequence
-    from_schema: https://w3id.org/biolink/biolink-model
-    typeof: string
-    base: str
-    uri: xsd:string
-  string:
-    name: string
-    definition_uri: https://w3id.org/linkml/String
-    description: A character string
-    notes:
-    - In RDF serializations, a slot with range of string is treated as a literal or
-      type xsd:string.   If you are authoring schemas in LinkML YAML, the type is
-      referenced with the lower case "string".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    exact_mappings:
-    - schema:Text
-    base: str
-    uri: xsd:string
-  integer:
-    name: integer
-    definition_uri: https://w3id.org/linkml/Integer
-    description: An integer
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "integer".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    exact_mappings:
-    - schema:Integer
-    base: int
-    uri: xsd:integer
-  boolean:
-    name: boolean
-    definition_uri: https://w3id.org/linkml/Boolean
-    description: A binary (true or false) value
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "boolean".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    exact_mappings:
-    - schema:Boolean
-    base: Bool
-    uri: xsd:boolean
-    repr: bool
-  float:
-    name: float
-    definition_uri: https://w3id.org/linkml/Float
-    description: A real number that conforms to the xsd:float specification
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "float".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    exact_mappings:
-    - schema:Float
-    base: float
-    uri: xsd:float
-  double:
-    name: double
-    definition_uri: https://w3id.org/linkml/Double
-    description: A real number that conforms to the xsd:double specification
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "double".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    close_mappings:
-    - schema:Float
-    base: float
-    uri: xsd:double
-  decimal:
-    name: decimal
-    definition_uri: https://w3id.org/linkml/Decimal
-    description: A real number with arbitrary precision that conforms to the xsd:decimal
-      specification
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "decimal".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    broad_mappings:
-    - schema:Number
-    base: Decimal
-    uri: xsd:decimal
-  time:
-    name: time
-    definition_uri: https://w3id.org/linkml/Time
-    description: A time object represents a (local) time of day, independent of any
-      particular day
-    notes:
-    - URI is dateTime because OWL reasoners do not work with straight date or time
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "time".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    exact_mappings:
-    - schema:Time
-    base: XSDTime
-    uri: xsd:time
-    repr: str
-  date:
-    name: date
-    definition_uri: https://w3id.org/linkml/Date
-    description: a date (year, month and day) in an idealized calendar
-    notes:
-    - URI is dateTime because OWL reasoners don't work with straight date or time
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "date".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    exact_mappings:
-    - schema:Date
-    base: XSDDate
-    uri: xsd:date
-    repr: str
-  datetime:
-    name: datetime
-    definition_uri: https://w3id.org/linkml/Datetime
-    description: The combination of a date and time
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "datetime".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    exact_mappings:
-    - schema:DateTime
-    base: XSDDateTime
-    uri: xsd:dateTime
-    repr: str
-  date_or_datetime:
-    name: date_or_datetime
-    definition_uri: https://w3id.org/linkml/DateOrDatetime
-    description: Either a date or a datetime
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "date_or_datetime".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: str
-    uri: linkml:DateOrDatetime
-    repr: str
-  uriorcurie:
-    name: uriorcurie
-    definition_uri: https://w3id.org/linkml/Uriorcurie
-    description: a URI or a CURIE
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "uriorcurie".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: URIorCURIE
-    uri: xsd:anyURI
-    repr: str
-  curie:
-    name: curie
-    definition_uri: https://w3id.org/linkml/Curie
-    conforms_to: https://www.w3.org/TR/curie/
-    description: a compact URI
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "curie".
-    comments:
-    - in RDF serializations this MUST be expanded to a URI
-    - in non-RDF serializations MAY be serialized as the compact representation
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: Curie
-    uri: xsd:string
-    repr: str
-  uri:
-    name: uri
-    definition_uri: https://w3id.org/linkml/Uri
-    conforms_to: https://www.ietf.org/rfc/rfc3987.txt
-    description: a complete URI
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "uri".
-    comments:
-    - in RDF serializations a slot with range of uri is treated as a literal or type
-      xsd:anyURI unless it is an identifier or a reference to an identifier, in which
-      case it is translated directly to a node
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    close_mappings:
-    - schema:URL
-    base: URI
-    uri: xsd:anyURI
-    repr: str
-  ncname:
-    name: ncname
-    definition_uri: https://w3id.org/linkml/Ncname
-    description: Prefix part of CURIE
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "ncname".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: NCName
-    uri: xsd:string
-    repr: str
-  objectidentifier:
-    name: objectidentifier
-    definition_uri: https://w3id.org/linkml/Objectidentifier
-    description: A URI or CURIE that represents an object in the model.
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "objectidentifier".
-    comments:
-    - Used for inheritance and type checking
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: ElementIdentifier
-    uri: shex:iri
-    repr: str
-  nodeidentifier:
-    name: nodeidentifier
-    definition_uri: https://w3id.org/linkml/Nodeidentifier
-    description: A URI, CURIE or BNODE that represents a node in a model.
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "nodeidentifier".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: NodeIdentifier
-    uri: shex:nonLiteral
-    repr: str
-  jsonpointer:
-    name: jsonpointer
-    definition_uri: https://w3id.org/linkml/Jsonpointer
-    conforms_to: https://datatracker.ietf.org/doc/html/rfc6901
-    description: A string encoding a JSON Pointer. The value of the string MUST conform
-      to JSON Point syntax and SHOULD dereference to a valid object within the current
-      instance document when encoded in tree form.
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "jsonpointer".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: str
-    uri: xsd:string
-    repr: str
-  jsonpath:
-    name: jsonpath
-    definition_uri: https://w3id.org/linkml/Jsonpath
-    conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html
-    description: A string encoding a JSON Path. The value of the string MUST conform
-      to JSON Point syntax and SHOULD dereference to zero or more valid objects within
-      the current instance document when encoded in tree form.
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "jsonpath".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: str
-    uri: xsd:string
-    repr: str
-  sparqlpath:
-    name: sparqlpath
-    definition_uri: https://w3id.org/linkml/Sparqlpath
-    conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths
-    description: A string encoding a SPARQL Property Path. The value of the string
-      MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects
-      within the current instance document when encoded as RDF.
-    notes:
-    - If you are authoring schemas in LinkML YAML, the type is referenced with the
-      lower case "sparqlpath".
-    from_schema: https://w3id.org/linkml/types
-    imported_from: linkml:types
-    base: str
-    uri: xsd:string
-    repr: str
+
 slots:
   node property:
     name: node property