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[protege-owl] Question about OWL representation of synonyms in OBO ontologies

Andrea Splendiani andrea.splendiani at univ-rennes1.fr
Fri May 23 03:21:19 PDT 2008


Hi,

I'm writing this email to this mailing list as I could not find a more  
specific one. Apologies if this is off-topic and please tell me which  
is the appropriate ml, if you know.

I have question about synonyms representation in the OWL version of  
GO, as I'm having problems in handling their representation in the XML- 
RDF serialization.

In the specifics, in GO-OWL synonyms are represented as:

     <owl:Class rdf:about="GO#GO_0000015">
      ...
         <oboInOwl:hasExactSynonym rdf:datatype="&rdfs;Literal"
             >http://purl.org/obo/owl/#genid42</ 
oboInOwl:hasExactSynonym>
      ...
     </owl:Class>

and :

<rdf:Description rdf:about="#genid42"/>
     <oboInOwl:Synonym>
         <rdfs:label xml:lang="en">enolase complex</rdfs:label>
     </oboInOwl:Synonym>

As opposed to the representation in other OBO ontologies, such as SO:

<owl:Class rdf:about="http://purl.org/obo/owl/SO#SO_0000432">
...
     <oboInOwl:hasExactSynonym>
       <oboInOwl:Synonym>
         <rdfs:label xml:lang="en">U5 3' long terminal repeat region</ 
rdfs:label>
       </oboInOwl:Synonym>
     </oboInOwl:hasExactSynonym>
   </owl:Class>

I understand the second representation, I have problems in  
understanding the first.

In particular, is this a way to represent a literal, as a resource ?  
You are saying that something has type literal, but that something is  
actually not a literal but a resource.
And in the description, where is the association between the URI and  
the synonym ? (the Description tag seems to be closed too early).

I cannot handle the first representation in Jena, there is some type  
problem around literals. And cannot query with SPARQL (through Jena).

In protegégé individuals of synonyms have an "empty" icon in the go  
representation instead of a "full" one as in SO.

Any hint ?

best,
Andrea Splendiani


P.S.: also, this is related to CHEBI in OWL, but some of you may be  
knowledgeable about this, in chebi-owl I find the following types of  
URI:

         <oboInOwl:hasDbXref>
           <oboInOwl:DbXref>
             <rdfs:label>ChEBI:NULL</rdfs:label>
             <oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyU
RI">http://purl.org/obo/owl/ChEBI#ChEBI_NULL</oboInOwl:hasURI>
           </oboInOwl:DbXref>
         </oboInOwl:hasDbXref>

what's the reason behind this ?


-----------
Andrea Splendiani
post-doc, bootstrep project (www.bootstrep.eu)

UPRES-EA 3888 - Laboratoire d'Informatique Médicale
CHU de Pontchaillou
2, rue Henri Le Guilloux
35033 Rennes - France
Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.)
Fax : +33 2 99 28 41 60

48° 07.275N
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