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RE: using OBO in owl format to describe data

From: Nigam Shah <nigam@stanford.edu>
Date: Thu, 12 Oct 2006 10:23:23 -0700
To: "'Xiaoshu Wang'" <wangxiao@musc.edu>, "'Joanne Luciano'" <jluciano@genetics.med.harvard.edu>
Cc: "'Mary Montoya'" <mhm@ncgr.org>, <semantic-web@w3.org>, <public-semweb-lifesci@w3.org>
Message-ID: <002901c6ee23$1f74c450$8119fea9@stanford.edu>

> I am not familiar with the OBO, from what I just read from the
> OBO spec, I think OBO does have term like "intersection_of",
> "union_of", "disjoint_from". From I can see now, the
> translation should be syntactic for most, but not all,
> concepts. For those concepts that there is any OWL equivalent,
> for instance, is_cyclic, you probably need to invent some OWL
> construct for yourself. 

Hi All,

The latest updates on the OBO to OWL translation are at:


For those interested in details, there is a google spreadsheet which
tells you exactly what maps to what (with a rationale) this is at:


> But now goes back to Mary's question, I do think obo:Term is
> for the same concept of "resource" in RDF.  There is no need for the
> obo:Term. 

Yes and there is no obo:Term in the mapping.

> The OBO prefix should be turned into a namespace URI, then the
> obo:id can be concatenated to form the URI for each specific
> term.

That's whats is done.

> However, regarding how to assign the namespace URI, you
> should consult the OBO administration about the policy because
> dereferening any URI should lead to soemthing but not a 404.

Well, techincally not all URI are URLs ... And a 404 only applies to

> So, assigning the namespace URI also means the responsibility of
> maintaining the document. 

We are hoping to do this with
www.bioontology.org/ontologyname#termname, please see the mapping if
you are interested in the details.

Received on Thursday, 12 October 2006 17:26:13 UTC

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