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Note from an interloper (thanks)

Robert Stevens robert.stevens at
Wed Apr 10 12:41:50 PDT 2002

Bill suggests an effort called LOGO or logical GO. take a look at this is an experment in re-casting the GO 
into DAML+OIL, a Description Logic. We hope to be able to improve manage 
the development and delivery of GO (via consistency and reasoned 
classification), but still deliver GO to its annotatoers in a form they are 
happy to use. This work is being carried out in collaboration with elements 
of the GO consortium.



At 03:52 10/04/02 -0500, Bill Andersen wrote:
>On 4/9/02 15:04, "pdy951 at"
><pdy951 at> wrote:
> > Bill,
>I'm at a loss - I didn't get your name...
> > Don't worry, you didn't hurt my feelings. Thanks for leaving my name 
> out but
> > people can get that by following the thread back.
> >
> > Thanks for the critique, I'll keep it in mind. Are you aware that GO is 
> not an
> > ontology? I don't think that any of the computer scientists who is 
> involved in
> > GO think that it is a real ontology (subject of ISMB meeting last summer),
> > it's a hierarchy of processes, components and functions (not gene names)
> > ranging from general to quite specific. The name has already caught on so
> > changing it to Gene Nontology or G!O is proabably not going to happen.
>I don't want the GO crowd to give up on building an ontology.  I think that
>it's a really important thing to do, and not just because my company is in
>the ontology-based software business.
>I not GO, then what?  GO already has a tremendous amount of momentum behind
>it and a lot of smart people working on it.  The amount of data out there
>isn't shrinking, and some kind of organizing framework is going to prove
>essential - if it's built the right way.
>One thing that could be done is to do a parallel effort (call it LoGO, for
>logical GO, or something fun like that) to give as much logical and
>philosophical underpinning to GO as makes sense, given the fact that much of
>it represents a science that is in rapid flux.  Ontology geeks could, for
>example, take the existing GO as a starting place, go off in a corner and
>work on formalizing the low-hanging fruit, and then sanity check the result
>(in plain English) with the group at large.  Anything that is uncomfortable
>to the group could simply be shelved or rejected.
>I said something like this at a bioinformatics workshop at NAS two years ago
>in response to someone who told me "you can't put all those logical rules
>into a database - the data are too dirty".  Maybe so, but my response to him
>was "Are you telling me you don't know *anything* about your domain?  You
>aren't sure, for example, if molecules exist?  Or that a molecule is not a
>reaction?"  Well, that was an admittedly hyperbolic example, but it makes a
>point.  There is always much more than we think that is stable and can be
>formalized.  But a lot of this "bread-and-butter" stuff tends not to spring
>to mind (understandably so) for subject experts, who cached a lot of it away
>in the recesses of their minds before they entered grad school.
>The need to formalize this background theory becomes critical whenever you
>take humans even partially out the loop.  Computers have no idea what our
>natural language terms mean, but they're pretty good at keeping us honest in
>their use if we only tell them a little bit about how to constrain their
>possible interpretations.  Peter Karp's work is a good example of this - you
>can get a long way with a small amount of formalization, and even farther
>with more.  It's kind of an black art, given the present state of ontology
>and knowledge representation, to decide how much is enough, but it can be
>Correct me if I'm wrong, but from what I know about GO, it's an attempt to
>organize, as you say, terminology relating to gene function.  And GO seems
>to attack the problem directly at that level, without relying for example on
>having a theory of chemistry or molecular structure, etc., to build on.  I
>have a feeling that this lack of theoretical basis was at the core of Sydney
>Brenner's beef.
> > I was just as vague and opinionated as Sydney in my first post. I 
> apologize.
> > Sydney used the analogy of our names and how they don't really define 
> who we
> > are. We don't name the genes in GO we name the things they do based on
> > scientific evidence. So for Sydney, I have evidence that he is a molecular
> > biologist so I would call him that. Maybe if I had less evidence, I 
> would call
> > him a biologist or a scientist. Calling him Sydney Brenner doesn't say
> > anything about who he is but trying to chraracterize what he does based on
> > evidence has merit. From his analogy I didn't think he understood that 
> we were
> > not trying to name the genes.
>That could be.  Without more details from him on what motivated his critique
>it's hard to say.  There is a lot more to be said about this business of
>"self-naming" objects but it gets quickly into hairy philosophical and
>logical issues.  The upshot is that no such auto-naming scheme as Sydney
>suggests can be guaranteed to work - we will always have to rely on our folk
>use of plain old names, as GO does, to interpret what some of these concepts
>mean.  So, while his heart is, IMHO, in the right place, I think he has the
>details wrong.  If anyone is interested in why I think this is, please feel
>free to write, but since it's not central to GO and will be a diversion to
>anyone who doesn't like logic, perhaps it's best kept offline.
> > Maybe we all need to work on our reading comprehension. Anyways, I have
> > learned never to check my email on a weekend.
>  .bill
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