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Panned by Brenner

Chris Mungall cjm at bdgp.lbl.gov
Sat Apr 6 15:42:39 PST 2002


Well, it was pretty cheeky and opinionated - but then it was an opinion
piece wasn't it?

The bit about "if you have time to waste..." stung.

On first reading he does seem to have missed the point, eliding all
mention of the utility of GO.

But then, maybe he isn't so concerned with that. So perhaps compiling a
compendium of GO success stories wouldn't be so useful in refuting him.
I don't really think the utility of GO is up for debate, there's no
question there.

I actually think he makes a good point, although the point is as old as
ontologies themselves. syntax vs semantics, sense vs referent, theory of
names, philosophers have been battling this one out for years. Let's leave
this one for them.

It is worth mentioning that the GO "names" are very well grounded to
"molish", to use Brenner's terms. I think this is something that everyone
working with GO intuitively understands, but we could perhaps be more
forthright about. I think a number of people share Brenner's views.

GO's use of definitions anchors the terms through the shared knowledge of
many biologists, and the large number of instances anchors the terms via
actual experiments, interpro2go grounds terms to "molish" further. Some
ontologists would say that GO needs richer structure to actually impart
'meaning'. That's another debate entirely. That work is happening anyway,
e.g. the GK project and others.

Pointless philosophical conundrum - if we ran GO through babelfish and
translated it into French, would that refute the argument?

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