[BiO BB] Please guide me

Austin Tanney Austin.Tanney at arragen.com
Fri Jan 30 05:26:41 EST 2004

I agree completely Dan,

For example, within the field of genetics, gene names themselves are non-descriptive, and indeed many genes have many different synonyms. This has, of course, led to the development of gene ontology's for use in computer applications to aid the identification of genes computationally. The more we can standardise the methods by which we communicate information, both between ourselves and, more importantly between ourselves and machines, the less time we waste reinventing the wheel.


-----Original Message-----
From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk]
Sent: 30 January 2004 09:35
To: bio_bulletin_board at bioinformatics.org
Cc: B.A.T.Svensson at lumc.nl
Subject: RE: [BiO BB] Please guide me

++ HKG--
>>> What would the benefits of a common schema be?
>>interoperability, foundation of the field, common development
>>environment, growth
> A common schem wont help one to achive that.

Not directly no - but it would be a big help!

Maybe this is a big prejudice of mine, but I am actually quite passionate about this
idea. After all, when one mathematician talks to another, they have a common formal
language with which to do so - chemists too and the same with comp-sci. Now, while
every biologist damn well knows he has a common language to communicate with his
peers, this language is not easily formalized. The previous examples are able to
work by defining primitives and association rules, but in biology the primitives are
already high level concepts, and the association rules are often the results of
ongoing research activities. Thus these 'fundamentals' are not easy to agree - this
is why we must develop a formal framework within which precise definitions and
relationships can emerge pragmatically, in effect leading to a global schema. From
the viewpoint of the philosophy of science I think this is how it works in the
brains of biologists (I could be wrong), the difficulty is getting something similar
to happen in a computer friendly way. I am 100% confident (maybe you see my
prejudice) that this will happen someday.


>>I guess people can add more.
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