[BiO BB] Please guide me

Jeremy Semeiks jrs at denny.farviolet.com
Thu Jan 29 17:13:12 EST 2004

On Wed, Jan 28, 2004 at 01:59:19AM -0800, BORN II CODE wrote:

> Hi ! i am a still new to bioinformatics.currently i am working on
> developing a database with the intergration of xml.as far as i
> understand, most of the databanks has its own data(heterogenous
> format).what are the fields that i must know in order to develop a
> database?how can i retrieve biological data from these databanks.i
> only know things at the surface level.many of the articles are very
> confusing.as far as i am concern there are things like protein
> sequence and DNA sequence.where can i get a sample database table
> containing field for such entity??

There are a few unified biological schemas out there: BioSQL, Chado,
GUS, and Ensembl. You might be able to adapt one of these pre-made
schemas; the relevant factors are what biological data you need to
store, exactly, and what you're interested in doing with them. At the
moment, I don't think there's any single comprehensive solution.

You can use Bioperl to parse most of the standard flat-text databanks.

Good luck,

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