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[bioontology-support] Feedback

Ray Fergerson ray.fergerson at stanford.edu
Tue Jun 14 14:11:32 PDT 2011


Barry,

The NIFSTD owl ontology imports owl versions of both GO and SO (along with
a large number of other ontologies). The SO ontology version being
imported does have a unique term defined for kinetoplast which is distinct
from the one in GO. The details from the original files are given below.

(Big thanks to Tania for digging this out of the files.) 

Ray

------------------

ID: http://purl.org/obo/owl/GO#GO_0020023
Location: 
http://ontology.neuinfo.org/NIF/BiomaterialEntities/cellular_component.owl

Declaration:

<owl:Class rdf:about="http://purl.org/obo/owl/GO#GO_0020023">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >kinetoplast</rdfs:label>
....

--------------------

ID: http://purl.org/obo/owl/SO#SO_0000741
Location: http://ontology.neuinfo.org/NIF/BiomaterialEntities/sequence.owl

Declaration:

<owl:Class rdf:about="http://purl.org/obo/owl/SO#SO_0000741">
<oboInOwl:hasAlternativeId 
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >SO:0000826</oboInOwl:hasAlternativeId>
<oboInOwl:hasExactSynonym>
<oboInOwl:Synonym>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >kinetoplast_chromosome</rdfs:label>
</oboInOwl:Synonym>
</oboInOwl:hasExactSynonym>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >kinetoplast</rdfs:label>
....


> -----Original Message-----
> From: Barry Smith [mailto:phismith at buffalo.edu]
> Sent: Saturday, June 04, 2011 5:20 AM
> To: Ray Fergerson
> Cc: support at bioontology.org; karen.eilbeck at genetics.utah.edu
> Subject: Re: [bioontology-support] Feedback
> 
> Ray
> It seems that there is something wrong with the way SO is being
> imported into Bioportal. There are no SO terms with GO ideas.
> 
> >> Name : Barry Smith
> >> Comment:
> >> In Sequence Types and Features the term 'kinetoplast' occurs twice;
> >
> 
> On Fri, Jun 3, 2011 at 7:58 PM, Ray Fergerson
> <ray.fergerson at stanford.edu> wrote:
> > Barry,
> >
> > The duplicate terms show up because there are in fact two terms with
> > distinct identifiers with the same label in NIFSTD. One has id:
> > so:SO_0000741 and the other go:GO_0020023.
> >
> > Ray
> >



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