[BiO BB] Please guide me

Andrius obj at obj.hopto.org
Thu Jan 29 19:56:00 EST 2004

Jeremy Semeiks wrote:

>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.
Won't it be a good idea to develop one. It seems that tools for doing 
bioinformatics are still maturing and
one of the things to make them mature are common schemas and standards. 
I think there's a nice potential
for developers in this direction.

>You can use Bioperl to parse most of the standard flat-text databanks.
>Good luck,
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org

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