[BiO BB] Please guide me
dmb at mrc-dunn.cam.ac.uk
Fri Jan 30 07:30:14 EST 2004
PERL = Protein Engineering Research Language ;)
> Michael Gruenberger wrote:
>>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?
> when i was mentioning common schema i wasn't considering database schema
> (structure). such global database
> schema won't make sense since everyone may have different requirements. i meant
> common schema as a common communication
> protocol. yes, it's not a right word, it came from web services, xml schema, etc.
> and yes, new bioinformatics language would make
> lot more for community. indeed, i see some confusion about why should every
> bioinformatician use perl (well, perl comes first when you ask google)... nor
> it's designed for it, nor it make learning path easier (time to come and do
> research). i think the new language should be developed, language which makes good
> string processing as perl does and introduces constructs/objects which are
> familiar for people with
> biological background.
>>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?
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