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Re: How to align ontology terms that are similar but are set to potentially incompatible domain?

From: François Scharffe <francois.scharffe@lirmm.fr>
Date: Fri, 10 Feb 2012 14:37:03 +0100
Message-ID: <4F351D7F.2040006@lirmm.fr>
To: Peter DeVries <pete.devries@gmail.com>
CC: public-lod@w3.org
Hi Pete,

This is an interesting use case showing the complexity of aligning 
ontologies, and the lack of a standard way to represent alignments.

I couldn't access http://lod.taxonconcept.org/ so I'll give you an 
examples using the Biological Taxonomy Vocabulary (biol) the Wildlife 
Ontology (wo) and GeoSpecies (gs).

The easiest case is term equivalence, as it seems to be between
and biol:name
You can use owl:equivalentProperty between them.

It becomes more complex if the terms are not fullly equivalent:

on one side gs:hasScientificName
has domain gs:SpeciesConcept
which is subclass of gs:TaxonConcept

on the other side wo:scientificName
has domain wo:TaxonName which is related to wo:TaxonRank through the 
wo:name object property, and wo:Species is subclass of wo:TaxonRank

so it seems that gs:hasScientificName
applies to a narrower domain.

You can thus use skos:narrower to indicate this relation.
It is more precise than skos:closeMatch but still quite vague.

So it would be better to specify the exact relation between the two 
properties, by specifying the type of the wo instances should be wo:Species.
Forall ?x ?y  ( gs:hasScientificName(?x ?y) :- and( wo:scientificName(?x 
?y) rdf:type(?x, wo:Species) ) )

Now the problems:
- The skos approach raise problems given the semantics of the skos terms,
the properties aligned using skos:closeMatch or skos:narrower become 
skos Concepts. This might lead to some unwanted effects when using a 
- The RIF rule does not completely do its job as it is only an 
implication. I don't think it can be written in the other direction (RIF 
expert needed here).
- three different vocabs are needed to represent three correspondences.

An alternative solution is to use EDOAL [1] which is made for alignment 
representation and allows export to skos, owl or rif through the 
Alignment API [2].
Here are the above three correspondences in EDOAL (rdf/n3):
:1 a align:Cell;
  align:entity1 wo:scientificName;
  align:entity2 biol:name;
align:relation "=".

:2 a align:Cell;
  align:entity1 gs:hasScientificName;
  align:entity2 wo:scientificName;
  align:relation "<".

:3 a align:Cell;
  align:entity1 gs:hasScientificName;
  align:entity2 [
   edoal:and wo:scientificName;
edoal:and [
    a eodal:PropertyDomainRestriction;
    edoal:class wo:Species.

Hope this helps !


[1] http://alignapi.gforge.inria.fr/edoal.html
[2] http://alignapi.gforge.inria.fr/

is that they are equivalent but only for the part where

Le 09/02/12 21:18, Peter DeVries a écrit :
>  I was wondering what the best way to align similar ontology terms are 
> not exactly equivalent either because they have a specific domain or
>  because there are slight differences in how they are used. For 
> instance some uses of Scientific Name include form with authority and 
> others
>  have a separate term for the scientific name with authority.
>  Here are the terms that I am most concerned about, but similar issues 
> apply to genus, family etc.
> <!-- http://lod.taxonconcept.org/ontology/txn.owl#scientificName -->
> <owl:DatatypeProperty 
> rdf:about="http://lod.taxonconcept.org/ontology/txn.owl#scientificName">
> <rdfs:label>scientificName</rdfs:label>
> <vs:term_status>testing</vs:term_status>
> <owl:equivalentProperty 
> rdf:resource="http://lod.taxonconcept.org/ontology/txn.owl#hasScientificName"/>
> <skos:closeMatch rdf:resource="http://purl.org/NET/biol/ns#name"/>
> <skos:closeMatch 
> rdf:resource="http://www.uniprot.org/core/scientificName"/>
> <skos:closeMatch 
> rdf:resource="http://rdf.geospecies.org/ont/geospecies#hasScientificName"/>
> <skos:closeMatch 
> rdf:resource="http://rs.tdwg.org/dwc/terms/scientificName"/>
> <skos:closeMatch 
> rdf:resource="http://purl.org/ontology/wo/scientificName"/>
> <rdfs:isDefinedBy 
> rdf:resource="http://lod.taxonconcept.org/ontology/txn.owl"/>
> <rdfs:subPropertyOf 
> rdf:resource="http://www.w3.org/2004/02/skos/core#prefLabel"/>
> </owl:DatatypeProperty>
> <!-- http://lod.taxonconcept.org/ontology/txn.owl#commonName -->
> <owl:DatatypeProperty 
> rdf:about="http://lod.taxonconcept.org/ontology/txn.owl#commonName">
> <rdfs:label>commonName</rdfs:label>
> <vs:term_status>testing</vs:term_status>
> <rdfs:isDefinedBy 
> rdf:resource="http://lod.taxonconcept.org/ontology/txn.owl"/>
> <skos:closeMatch rdf:resource="http://purl.org/NET/biol/ns#commonName"/>
> <skos:closeMatch 
> rdf:resource="http://rs.tdwg.org/dwc/terms/vernacularName"/>
> <skos:closeMatch 
> rdf:resource="http://rdf.geospecies.org/ont/geospecies#hasVernacularName"/>
> <skos:closeMatch rdf:resource="http://purl.org/ontology/wo/commonName"/>
> <rdfs:subPropertyOf 
> rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/>
> </owl:DatatypeProperty>
> <!-- http://lod.taxonconcept.org/ontology/txn.owl#authority -->
> <owl:DatatypeProperty 
> rdf:about="http://lod.taxonconcept.org/ontology/txn.owl#authority">
> <rdfs:label>authority</rdfs:label>
> <rdfs:comment>The author and year of the species description 
> publication i.e (Baker, 1899)</rdfs:comment>
> <vs:term_status>testing</vs:term_status>
> <rdfs:isDefinedBy 
> rdf:resource="http://lod.taxonconcept.org/ontology/txn.owl"/>
> <skos:closeMatch 
>  rdf:resource="http://lod.taxonconcept.org/ontology/txn.owl#scientificNameAuthorship"/>
> <skos:closeMatch  rdf:resource="http://purl.org/NET/biol/ns#authority"/>
> <skos:closeMatch 
>  rdf:resource="http://rs.tdwg.org/dwc/terms/scientificNameAuthorship"/>
> <skos:closeMatch 
>  rdf:resource="http://rdf.geospecies.org/ont/geospecies#hasScientificNameAuthorship"/>
> </owl:DatatypeProperty>
> Respectfully,
> - Pete
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries@wisc.edu <mailto:pdevries@wisc.edu>
> TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies 
> <http://about.geospecies.org/> Knowledge Bases
> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
> --------------------------------------------------------------------------------------
Received on Friday, 10 February 2012 13:37:36 UTC

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