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

Tania Tudorache tudorache at stanford.edu
Fri May 23 15:47:32 PDT 2008


Hi Andrea,

Here are some references to the OBO-to-OWL conversion:

http://bioinformatics.oxfordjournals.org/cgi/content/full/23/14/1868

http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page


This conversion is used by the OBOConverter plugin that is available in Protege:

http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter

You can also contact the author, Dilvan Moreira, for more information on the mappings.

The empty icons in the IndividualsTab denote anonymous individuals. These are individuals that do not have a URI that identifies them for the outside world. They do have an internal ID that can be used to identify them in the document where they are defined. We have added this capability in the Protege UI, at the request of our users (the ones dealing with OBO). This is a thread that might be of interest [1].

Cheers,
Tania


[1]: https://mailman.stanford.edu/pipermail/protege-owl/2006-November/000634.html



Andrea Splendiani wrote:
> 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)
>
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