Difference between revisions of "BioPortal Mappings"

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(→‎Mapping Sources: Adding links to web sites for NCBO, UMLS, and OBO foundry.)
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= Mapping Sources =
 
= Mapping Sources =
  
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* '''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.
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* [http://www.bioontology.org/ The National Center for Biomedical Ontology (NCBO)]
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* '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.
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** '''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.
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* '''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.
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** '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.
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* '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data.
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* '''OBO xref''': Mappings between ontology terms related by an OBO xref.
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* [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS)]
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** '''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.
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** '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data.
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* [http://obofoundry.org/ The Open Biological and Biomedical Ontologies (OBO)]
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** '''OBO xref''': Mappings between ontology terms related by an OBO xref property.
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** See also, [http://obofoundry.org/index.cgi?show=mappings OBO mappings]
  
 
= Mapping Relationships =
 
= Mapping Relationships =

Revision as of 07:40, 31 May 2012

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

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.
    • NCBO (Identical URI): Mapping for terms with the same URI from different ontologies.
  • 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.
    • NLM UMLS (MRMAP): Mappings between terms from the UMLS MRMAP.RRF data.

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> .
  • broad match: skos:broadMatch
    • Definition (from SKOS-REFERENCE): The properties skos:broadMatch and skos:narrowMatch are used to state a hierarchical mapping link between two concepts; skos:broadMatch is a sub-property of skos:mappingRelation.
    • Symmetry: skos:broadMatch is owl:inverseOf skos:narrowMatch; for bidirectional mappings between <conceptA> and <conceptB> that are rdf:type skos:Concept:
   <conceptA> skos:broadMatch <conceptB> .
   <conceptB> skos:narrowMatch <conceptA> .
  • narrow match: skos:narrowMatch
    • Definition (from SKOS-REFERENCE): The properties skos:narrowMatch and skos:broadMatch are used to state a hierarchical mapping link between two concepts; skos:narrowMatch is a sub-property of skos:mappingRelation.
    • Symmetry: skos:narrowMatch is owl:inverseOf skos:broadMatch; for bidirectional mappings between <conceptA> and <conceptB> that are rdf:type skos:Concept:
   <conceptA> skos:narrowMatch <conceptB> .
   <conceptB> skos:broadMatch <conceptA> .
  • 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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