BioPortal Mappings

BioPortal Mapping Notes

This page documents mapping sources and common relationships in the NCBO BioPortal, with examples of different mappings that already exist in BioPortal. We welcome comments on the mapping processes and relations; please send email to support@bioontology.org.

Related Mapping Documents

• BioPortal Mappings: the BioPortal mapping service

Mapping Sources

• The National Center for Biomedical Ontology (NCBO)
  • NCBO lexical mapping (loom): Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-space and punctuation from labels. Any labels with no more than 3 characters are excluded. These mappings are represented by the mapping relationship skos:closeMatch.
  • NCBO Identical URI (loom): Mapping for terms with the same URI from different ontologies. These mappings are represented by the mapping relationship skos:exactMatch.

• Unified Medical Language System (UMLS)
  • NLM UMLS (CUI): Mappings between terms from different ontologies that were created automatically, linking terms with the same UMLS concept unique identifier (CUI). The CUIs are assigned to terms in the UMLS by editors at the NLM. These mappings are represented by the mapping relationship skos:closeMatch.
  • NLM UMLS (MRMAP): Mappings between terms from the UMLS MRMAP.RRF data. These mappings are represented by the mapping relationship skos:closeMatch.

• The Open Biological and Biomedical Ontologies (OBO)
  • OBO xref: Mappings between ontology terms related by an OBO xref property. These mappings are represented by the mapping relationship skos:relatedMatch.
  • See also, OBO mappings

Mapping Relationships

There are mappings of the following types in BioPortal:

• identical, the same : owl:sameAs
  • Definition (from OWL): owl:sameAs is used to state that two URI references refer to the same individual

• related (but not necessarily similar): rdfs:seeAlso
  • Definition (from RDFS): The property rdfs:seeAlso specifies a resource that might provide additional information about the subject resource.

• related match: skos:relatedMatch
  • Definition: (from SKOS-REFERENCE): The property skos:relatedMatch is used to state an associative mapping link between two concepts; skos:relatedMatch is a sub-property of skos:mappingRelation.
  • Symmetry: skos:relatedMatch is an instance of owl:SymmetricProperty; for bidirectional mappings between <conceptA> and <conceptB> that are rdf:type skos:Concept:

   <conceptA> skos:relatedMatch <conceptB> .
   <conceptB> skos:relatedMatch <conceptA> .

• close match: skos:closeMatch
  • Definition (from SKOS-REFERENCE): The property skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property. The skos:closeMatch is a sub-property of skos:mappingRelation.
  • Symmetry: skos:closeMatch is an instance of owl:SymmetricProperty; for bidirectional mappings between <conceptA> and <conceptB> that are rdf:type skos:Concept:

   <conceptA> skos:closeMatch <conceptB> .
   <conceptB> skos:closeMatch <conceptA> .

• exact match: skos:exactMatch
  • Definition (from SKOS-REFERENCE): The property skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The skos:exactMatch it is a sub-property of skos:closeMatch and, in addition, it is an instance of owl:TransitiveProperty. Also, skos:exactMatch is disjoint with each of the properties skos:relatedMatch, skos:broadMatch and skos:narrowMatch.
  • Symmetry: skos:exactMatch is an instance of owl:SymmetricProperty; for bidirectional mappings between <conceptA> and <conceptB> that are rdf:type skos:Concept:

   <conceptA> skos:exactMatch <conceptB> .
   <conceptB> skos:exactMatch <conceptA> .