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two questions: DAML+OIL, mapping to KEGG 'orthology'

Jean-Luc Delatre jld at club-internet.fr
Mon May 20 22:31:14 PDT 2002


Hi Chris and Paul,

I am happy to see that the gofriends list is sometimes alive!

As I already proposed in some of my previous messages, I will be happy 
to give a hand to anyone having to deal with *practical* problems of
ontology merging and consistency.

I am no biologist or whatever of that kind, only a software consultant,
but I am specially interested in GO and GO like ontologies because
these are the fields where some *real* work is ongoing, not just
philosophical discussions.

I have already suggested a few directions in the SUO forum:

   http://suo.ieee.org/email/msg08372.html

But the folks there are more interested in "metaphysics" than in results.
The focus should be on *usefullness*, and this is no less complicated 
than "philosophy", as Chris rightly remarked:

> Actually the biggest barrier to the use of DAML+OIL and similar DL based 
> ontologies is the added complexity they introduce.

Then, may be, while waiting for the GONG project to reach maturity 
(or anything similar using one kind or another of "heavy machinery"), 
to help with *today* requirements some "lightweight" solutions could be 
in order .

My purpose in offering this free help is to investigate a "live" case 
and further my acquaintance with *dynamically changing* ontologies.

So, if any of you is struggling with ontology merging I will be interested
in participating, I can help (most likely), and I mean it!

Cheers.

-- Jean-Luc Delatre
--------------------------------------------------------------------------
"If AI has made little obvious progress it may be because we are too busy
 trying to produce useful systems before we know how they should  work."
 - Marcel Schoppers (1983!)
At http://groups.google.com/groups?selm=4187%40uiucdcs.UUCP&oe=ISO-8859-1
--------------------------------------------------------------------------
 http://perso.club-internet.fr/jld/  -- GSM: +33 6 11 24 06 29

>Objet: 
>        Re: two questions: DAML+OIL, mapping to KEGG 'orthology'
>    Date: 
>        Fri, 17 May 2002 09:56:02 +0100
>     De: 
>        Chris Wroe <cwroe at cs.man.ac.uk>
>      A: 
>        Paul Shannon <pshannon at systemsbiology.org>
> Copies à: 
>        go-friends at genome.Stanford.EDU
>
> Paul,
> 
> At 15:19 15/05/2002 -0700, you wrote:
> 
> > On the recommendation of Midori Harris, I wish to ask
> > a couple of questions:
> >
> > First:  I have seen some mention of presenting the GO ontologies
> > in DAML+OIL.  Has this been done?  If so, are you pleased with
> > the expressiveness of this approach, and would you recommend it?
> 
> I'm involved in the Gene Ontology Next Generation (GONG) Project whose major aim is to evaluate
> whether the expressiveness and reasoning capabilities of DAML+OIL will support the future
> development, maintenance and use of GO.
> 
> There is a minimal web page at http://img.cs.man.ac.uk/gong
> 
> We have translated GO RDF to DAML+OIL but this is purely a syntactic transformation.
> The next step is to 'dissect' the definitions of a sample of the GO terms into a property based
> DAML+OIL description.
> 
> So for example:
> 
> GO:0004054 arginine kinase may be (for sake of argument) be described as
>         enzyme which [catalyses and only catalyses] (phosphorylation which [acts_on and only
> acts_on] L-arginine)
> 
> GO:0019202 amino acid kinase defined as
>         enzyme which [catalyses and only catalyses] (phosphorylation which [acts_on and only
> acts_on] amino acid)
> 
> (These aren't complete definitions as they don't talk about the other substrate and product but
> anyway I can send you the DAML+OIL for this example.)
> 
> When we have a classification of small molecules including amino acids the DAML+OIL reasoner will
> be able to infer arginine kinase is-a amino acid kinase. It will flag as inconsistent an attempt
> to manually assert fructokinase is-a amino acid kinase. Finally, it opens up the possibility of
> dynamically composing concepts as required (analogous to GO cross products) formally constraining
> what is reasonable to assemble together.
> 
> It is early days in the GONG project. DAML+OIL does limit its expressiveness to allow decidable
> reasoning. However, as long as you limit the use of DAML+OIL to terminological information (for
> which it was intended) then it is fine. I am actually used to using a less expressive DL based
> ontology language (GRAIL).
> 
> Actually the biggest barrier to the use of DAML+OIL and similar DL based ontologies is the added
> complexity they introduce. A major focus of the GONG project is to build an environment to make
> migration to the added expressiveness of DAML+OIL as simple as possible and to simplify the
> deployment of the resulting DAML+OIL ontology.
> 
> Chris
> 
> > Second: Do you know of any attempt to map between (or even
> > unify) the GO ontologies, and the 'orthology' used by KEGG?
> > Here at the Institute of Systems Biology, our biologists are
> > very fond of KEGG; I -- as a programmer -- am naturally
> > drawn to clean design of GO, which I have used for the last year.
> >
> > I want to make both KEGG and GO functional classifications
> > available here, and I want to use data structures and
> > ontology representations which make the most sense.  If you
> > have any advice for me, I'd love to hear it.
> >
> > Many thanks,
> >
> >   - Paul Shannon
> >
> > --
> > This message is from the GOFriends moderated mailing list.  A list of public
> > announcements and discussion of the Gene Ontology (GO) project.
> > Problems with the list?           E-mail: owner-gofriends at geneontology.org
> > Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
> > Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
> > Web:          http://www.geneontology.org/
> 
> Dr Chris Wroe
> Clinical Research Fellow
> Department of Computer Science
> University of Manchester

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