Difference between revisions of "BioPortal Mappings"

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= BioPortal Mapping Notes =
 
= BioPortal Mapping Notes =
  
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This page documents mapping processes and common mapping types in the [http://bioportal.bioontology.org 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 [mailto:support@bioontology.org support@bioontology.org].
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This page documents mapping sources and common relationships in the [http://bioportal.bioontology.org 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 [mailto:support@bioontology.org support@bioontology.org].
  
 
== Related Mapping Documents ==
 
== Related Mapping Documents ==
  
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* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service REST Service for Mappings]
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* [http://bioportal.bioontology.org/mappings BioPortal Mappings]: the BioPortal mapping service
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* [http://bioportal.bioontology.org/mappings BioPortal Mappings]
 
  
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= Mapping Sources =
  
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= Mapping Processes =
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* [http://www.bioontology.org/ The National Center for Biomedical Ontology (NCBO)]
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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. These mappings are represented by the mapping relationship '''skos:closeMatch'''.
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** '''NCBO Identical URI (loom)''': Mapping for terms with the same URI from different ontologies. These mappings are represented by the mapping relationship '''skos:exactMatch'''.
  
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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.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. These mappings are represented by the mapping relationship '''skos:closeMatch'''.
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** '''NLM UMLS (MRMAP)''': Mappings between terms from the UMLS MRMAP.RRF data. These mappings are represented by the mapping relationship '''skos:closeMatch'''.
  
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* '''NCBO (Identical URI)''': Mapping for terms with the same URI from different ontologies.
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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. These mappings are represented by the mapping relationship '''skos:relatedMatch'''.
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** See also, [http://obofoundry.org/index.cgi?show=mappings OBO mappings]
  
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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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= Mapping Relationships =
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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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= BioPortal Mapping Types =
 
  
 
There are mappings of the following types in BioPortal:
 
There are mappings of the following types in BioPortal:
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     <conceptA> skos:exactMatch <conceptB> .
 
     <conceptA> skos:exactMatch <conceptB> .
 
     <conceptB> skos:exactMatch <conceptA> .
 
     <conceptB> skos:exactMatch <conceptA> .
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* '''broad match''': [http://www.w3.org/2004/02/skos/core#broadMatch skos:broadMatch]
 
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** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:broadMatch</tt> and <tt>skos:narrowMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:broadMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.
 
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** '''Symmetry''': <tt>skos:broadMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:narrowMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:
 
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    <conceptA> skos:broadMatch <conceptB> .
 
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    <conceptB> skos:narrowMatch <conceptA> .
 
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* '''narrow match''': [http://www.w3.org/2004/02/skos/core#narrowMatch skos:narrowMatch]
 
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** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS-REFERENCE]): The properties <tt>skos:narrowMatch</tt> and <tt>skos:broadMatch</tt> are used to state a hierarchical mapping link between two concepts; <tt>skos:narrowMatch</tt> is a sub-property of <tt>skos:mappingRelation</tt>.
 
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** '''Symmetry''': <tt>skos:narrowMatch</tt> is <tt>owl:inverseOf</tt> <tt>skos:broadMatch</tt>; for bidirectional mappings between <tt><conceptA></tt> and <tt><conceptB></tt> that are <tt>rdf:type skos:Concept</tt>:
 
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    <conceptA> skos:narrowMatch <conceptB> .
 
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    <conceptB> skos:broadMatch <conceptA> .
 
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* '''homologous to''' (for anatomical terms): ''not defined yet''
 
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** '''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).
 
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= Survey of BioPortal Mappings =
 
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The table below presents the statistics and examples of BioPortal mappings as of July 2010.
 
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{| border="1" cellpadding="2"
 
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| align="center" style="background:#f0f0f0;"|'''relationship'''
 
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| width="125" align="center" style="background:#f0f0f0;"|'''basis'''
 
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| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''
 
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| align="center" style="background:#f0f0f0;"|'''Source'''
 
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| align="center" style="background:#f0f0f0;"|'''Total mappings'''
 
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|  width="1025" align="center" style="background:#f0f0f0;"|'''Notes'''
 
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|-
 
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| 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
 
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<tt>select * from mappings where map_source = "LEXEVS_UMLS_MAPPER";</tt>
 
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|-
 
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| 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
 
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<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "lexical similarity";</tt>
 
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|-
 
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| 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
 
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<tt>select * from mappings where map_source = "exact match or synonym match";</tt>
 
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|-
 
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| 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
 
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<tt>select * from mappings where (destination_ont=1131 or source_ont=1131) and map_type="Manual";</tt>
 
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|-
 
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| owl:sameAs||shared id||Manual||||271,000||Mappings between the terms that share the same ID
 
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<tt>select * from mappings where map_source = "<a href=\"http://www.bioontology.org/wiki/index.php/LOOM\">LOOM</a>" and relationship_type = "direct reference";</tt>
 
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|-
 
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| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms
 
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<tt>select * from mappings where map_source = "OBO xref";</tt>
 
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|-
 
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| 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
 
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<tt>select * from mappings where map_source = "DbXref";</tt>
 
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|-
 
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| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO
 
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<tt>select * from mappings where map_source = "Upload";  </tt>
 
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|-
 
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| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings
 
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<tt>select * from mappings where map_source = "<a href=\"http://umlsks.nlm.nih.gov/\" target=\"_blank\">UMLS</a>";</tt>
 
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|-
 
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| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface
 
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<tt>select * from mappings where map_source = "BioPortal UI"</tt>
 
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|-
 
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| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT
 
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<tt>select * from mappings where map_source = "NCICB"</tt>
 
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|-
 
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| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity
 
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<tt>select * from mappings where map_source = "<a href=\"http://www.ebi.ac.uk/efo\">EFO</a>"</tt>
 
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|-
 
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| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT
 
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<tt>select * from mappings where map_source = "NLM"</tt>
 
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|}
 

Latest revision as of 17:42, 23 January 2017

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. 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.

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> .
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