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[bioontology-support] Strange handling of ontology identifiers

Camille Laibe camille.laibe at ebi.ac.uk
Wed Jul 28 09:30:14 PDT 2010


Dear Natasha,

Thank you for your answer, but please read below.

> Actually, the OWL file does define an "OPB" prefix for the base namespace"
>
> <rdf:RDF xmlns="http://bhi.washington.edu/OPB#"
> xml:base="http://bhi.washington.edu/OPB"
> ......
> xmlns:OPB="http://bhi.washington.edu/OPB#"

I agree with you, however:
There is an "OPB" namespace which is defined 
(xmlns:OPB="http://bhi.washington.edu/OPB#") but it is unused (there is 
no tag prefixed with "OPB:" in the OWL file).
There is also a default namespace declared 
(xmlns="http://bhi.washington.edu/OPB#"), but it should be unused as 
well as all tags in the OWL file are prefixed (with 'owl:', 'rdfs:', 
'rdf:', ...).
Finally there is the xml:base declaration 
(xml:base="http://bhi.washington.edu/OPB"), that, I guess, you use for 
the generation of your "Full Id" field, which interestingly provides a 
correct value: http://bhi.washington.edu/OPB#OPB_00464 (no addition of 
"OPB:" in the middle).
Therefore, I am still puzzled by this weird display of "OPB:OPB_00464", 
and I would like to know if there is something wrong in the OWL file 
itself or if there is a bug in the library that you use to parse the OWL 
file.

Which library do you use to parse the OWL files?
The OWL files you provide for download, are they the same as the ones 
which were submitted to you or do you process them in any way?

Best regards.

-- 
Camille Laibe
BioModels.net Coordinator
European Bioinformatics Institute, Cambridge (UK)



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