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

• REST Service for Mappings
• BioPortal Mappings

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> .

Survey of BioPortal Mappings

The table below presents the statistics and examples of BioPortal mappings as of July 2010.

relationship	basis	Manual/Automatic	Source	Total mappings	Notes
skos:closeMatch	identical UMLS CUIs	Manual	LEXEVS_UMLS_MAPPER	2,028,186	Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";
skos:closeMatch	lexical similarity	Automatic	LOOM	1,449,303	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 select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";
skos:closeMatch	lexical similarity	Automatic		2,562	Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings select * from mappings where map_source = "exact match or synonym match";
skos:closeMatch	lexical similarity	Manual		628	Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";
owl:sameAs	shared id	Manual		271,000	Mappings between the terms that share the same ID select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";
skos:relatedMatch	OBO xref	Manual		17,776	Mappings based on OBO xref mappings, which indicate related terms select * from mappings where map_source = "OBO xref";
skos:exactMatch	Dbxref	Manual		7,028	Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs select * from mappings where map_source = "DbXref";
skos:exactMatch		Manual		68	Mappings generated manually by a user; all involve terms from NEMO select * from mappings where map_source = "Upload";
skos:closeMatch	identical UMLS CUIs	Manual		902	Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";
skos:closeMatch		Manual	BioPortal UI	117	Mappings created by users through the BioPortal user interface select * from mappings where map_source = "BioPortal UI"
skos:closeMatch		Manual	NCICB	3078	Manual mappings between Mouse anatomy and NCIT select * from mappings where map_source = "NCICB"
skos:closeMatch	lexical similarity	Automatic	EFO	673	Mappings generated automatically based on lexical similarity select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"
skos:closeMatch		Manual	NLM	2,662	Manual mappings between Mouse anatomy and NCIT select * from mappings where map_source = "NLM"