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[bioontology-support] Strange handling of ontology identifiers

Natasha F. Noy noy at stanford.edu
Tue Jul 27 13:29:23 PDT 2010


Dear Camille,

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#"


So, it is really up to the OWL API whether or not to attach such a  
prefix when displaying a "short" id. We definitely don't add anything  
on our own.

We know that we should actually display more clearly what the prefix  
stands for -- it's on our feature request list.

Best,

Natasha


On Jul 22, 2010, at 10:05 AM, Camille Laibe wrote:

> Dear BioPortal Support,
>
> I have a question related to the handling of term identifiers in  
> BioPortal.
> If I take the example of terms from the Ontology of Physics for  
> Biology (OPB), you display the identifiers in the following way:  
> "OPB:OPB_00464". However, if I download the OWL file of the  
> ontology, the identifiers look like "OPB_00464".
> Why did you add "OPB:" in the front of these identifiers?
>
> I know that the OBO foundry ontologies usually have an identifier  
> pattern like <acronym>:<digits>, but this is not a rule (they just  
> recommend to have identifiers which do not carry any meaning) and it  
> seems to me that OPB decided to use a "_" instead of a ":" (which is  
> actually a pretty good idea considering the issues with ":" in OWL  
> files).
>
> I'm looking forward to hearing from you.
>
> -- 
> Camille Laibe
> BioModels.net Coordinator
> European Bioinformatics Institute, Cambridge (UK)
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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