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[protege-owl] Question about OWL representation of synonyms in OBO ontologies
andrea.splendiani at univ-rennes1.fr
Fri May 23 03:21:19 PDT 2008
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-
In the specifics, in GO-OWL synonyms are represented as:
<rdfs:label xml:lang="en">enolase complex</rdfs:label>
As opposed to the representation in other OBO ontologies, such as SO:
<rdfs:label xml:lang="en">U5 3' long terminal repeat region</
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 ?
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
what's the reason behind this ?
post-doc, bootstrep project (www.bootstrep.eu)
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