[BiO BB] Please guide me

Andrius obj at obj.hopto.org
Fri Jan 30 07:53:13 EST 2004

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?

More information about the BBB mailing list