BioPortal Mappings

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This page defines common mappings types in the NCBO BioPortal and provides examples of different mappings that already exist in BioPortal. We welcome comments on this set of mapping relations. Please send email to support@bioontology.org.

BioPortal Mapping Types

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
  • exact match: skos:exactMatch
    • Definition (from SKOS): 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. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
  • close match: skos:closeMatch
    • Definition (from SKOS): 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.
  • 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.
  • homologous to (for anatomical terms): not defined yet
    • Definition: The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).

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";

rdfs:seeAlso 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"

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