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

Re: ontology specs for self-publishing experiment

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Mon, 10 Jul 2006 11:25:49 +0100
To: chris mungall <cjm@fruitfly.org>
Cc: w3c semweb hcls <public-semweb-lifesci@w3.org>
Message-ID: <upsgdwyc2.fsf@newcastle.ac.uk>

>>>>> "cm" == chris mungall <cjm@fruitfly.org> writes:

  >> Converting between one syntax and another is fairly simple, and
  >> there are some reasonably tools for it. XSLT would work for
  >> converting XML into RDF. I wouldn't like to use it for converting
  >> the other way (actually I wouldn't like to use it at all, but
  >> this is personal prejudice!).
  >> This is assuming, however, that the semantics of the two
  >> representations are compatible. To give an example, syntactically
  >> it is possible to convert between the GO DAG and an OWL
  >> representation of GO. However, the GO part-of relationship
  >> doesn't distinguish universal and existential, while OWL forces
  >> you to make this distinction; you can't sit on the fence.

  cm> Hi Phillip

  cm> Actually GO uses the definition of part_of from the OBO relation
  cm> ontology
  cm> http://obo.sourceforge.net/relationship/#OBO_REL:part_of

  cm> You can see from the definition that the use of this relation
  cm> suggests an existential relation. The GO OWL transform encodes
  cm> this, so you don't need to sit on the fence, the decision has
  cm> been made for you.


My apologies. You are, of course, correct in saying that GO defines
an existential relationship, and I'm rather out of date in saying that
it doesn't (didn't!). 

  cm> There are definitely some issues here in using the
  cm> defined OBO relations (which involve time) to OWL (which has no
  cm> explicit account of time)

Yeah, this is true. Time is a difficult one to model anyway, and OWL
doesn't help here. 

Received on Monday, 10 July 2006 10:26:11 UTC

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