Re: [oor-dev] OOR Sandbox - SKOS, and FOAF

["Benjamin Dai" <benjamin.dai@xxxxxxxxxxxx>]

Hi Mike,

 

The NCBO and Protégé team has further sleuthing and have identified the source of the SKOS issue in OOR.  Basically, Protégé 3.4 back-end doesn’t fully support all of OWL-FULL/RDF (e.g., guessing at un-typed resource).  The good news is that we will be doing a patch to BioPortal to handle SKOS. 

 

Cheers.

 

Benjamin Dai
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Center for Biomedical Informatics Research

benjamin.dai@xxxxxxxxxxxx

http://www.bioontology.org

W:  650-725-2508

 

 

From: Benjamin Dai [mailto:benjamin.dai@xxxxxxxxxxxx]
Sent: Friday, February 20, 2009 12:07 PM
To: 'Mike Dean'
Cc: musen@xxxxxxxxxxxx; 'mmontegut@xxxxxxxxxxxx'; 'Timothy Redmond'; noy@xxxxxxxxxxxx; 'Tania Tudorache'; 'Peter Yim'
Subject: OOR Sandbox - SKOS, and FOAF

 

Hi Mike,

 

FYI, I just reviewed SKOS and FOAF in OOR and noticed that that they are not fully navigable.  Here’s the status on the two bugs:

 

1) FOAF – This bug has been resolved, but has not yet been pushed to BioPortal Production.  The push should occur over the next few weeks.  Once the push occurs, we’ll also roll it out on the OOR Sandbox.  Note that the bug related to any concept that had an ID that is a URL (i.e., starts with http://).   It will be resolved in the next BioPortal Production push.

 

2) SKOS – This one is a bit more tricky.  This is an OWL-API bug which affect ontologies that are edited with Protege-4 or the OWL-API which use the axiom annotation feature (SKOS being one of them).    The bug breaks the backwards compatibility to any OWL 1.0 tool which includes Protégé 3.4 (and Jena) which we currently use in our BioPortal back-end.  The OWL-API fix is trivial and will probably show up soon.  Once the fix has been delivered, we’ll attempt to incorporate it into a BioPortal release.

 

Just thought you’d like to get a heads-up on these two issues.

 

Cheers.

 

Benjamin Dai

Chief Software Architect

The National Center for Biomedical Ontology

Stanford Center for Biomedical Informatics Research

benjamin.dai@xxxxxxxxxxxx

http://www.bioontology.org

W:  650-725-2508

 

 

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