W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > October 2006

RE: using OBO in owl format to describe data

From: Xiaoshu Wang <wangxiao@musc.edu>
Date: Thu, 12 Oct 2006 12:34:06 -0400
To: "'Joanne Luciano'" <jluciano@genetics.med.harvard.edu>
Cc: "'Mary Montoya'" <mhm@ncgr.org>, <semantic-web@w3.org>, <public-semweb-lifesci@w3.org>
Message-ID: <000601c6ee1c$3c11c3d0$4a741780@bioxiao>

--Joanne,

> Having had many surprises in learning how the open world 
> works and how OWL works
> I'm curious to know how this is handled.  I have not yet taken on   
> the task to learn
> OBO as I hope not have to. I would like to feel confident 
> that I can convert a file into OWL and use it, however I 
> can't see how an automated translator, without some user 
> interaction or settings can know, for example, that a set of 
> subclasses must be disjoint, for example.  Is the translation 
> primarily syntactic?

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. 

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. 

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

Other OBO terms should be easily mapped to rdfs/owl or dubline core as well,
like

obo:name ==> rdfs:label
obo:comment ==> rdfs:comment
definition => dc:description 
...

If there isn't any equivalent term, create one.  Just be sure to publish the
mapping and hopefully everyone can adopt your convention.

That's my 2c.

Xiaoshu
Received on Thursday, 12 October 2006 16:34:47 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:45 GMT