[BiO BB] Please guide me

Michael Gruenberger mgruenb at gmx.net
Fri Jan 30 05:29:16 EST 2004

I can see why the idea of a common language is a good idea, but I don't
understand how a schema would achieve that? 

If you want databases to talk to each other in a common language then
you need a common network transport (e.g. web services, XML, SOAP,
BioMoby) and a common set of terms or ontologies (e.g. GO, EMAP, MA,
MPATH, see http://obo.sourceforge.net/ or http://www.geneontology.org). 

This would basically allow your databases to talk to each other and I'm
sure a common schema would make life easier, but it would be a lot of
additional work to integrate this 'global schema' into existing
databases. And some if not most of it would be redundant, at least for
our database, because we don't for example store information about
genes, but simply store the gene name + GO id and then link to other
database which have more detailed information.

Hmmm... I'd really like to understand your idea though! Could you give
an example of how this would work?



Michael Gruenberger
Database developer, Pathbase, http://www.pathbase.net
PGP-Public Key ID: 278E1DFF

On Fri, 2004-01-30 at 09:34, Dan Bolser wrote:
> ++ 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.
> Ta,
> Dan.
> >>I guess people can add more.
> > _______________________________________________
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