[Biophp-dev] Parser-to-SQL scripts

Greg Tyrelle biophp-dev@bioinformatics.org
Mon, 9 Jun 2003 12:47:56 +1000

*** Serge Gregorio wrote: 
  |Yes.  Initially, the code would write to some pre-designed set of
  |tables.  Later, we can let the user design his own database for, say,
  |holding GenBank DNAs or PDB/mmCIF protein records.  Something like:

If your looking for a relation schema for sequences then I would
recommend supporting BioSQL [1]. A physical model of the schema can be
found here [2]. Bioperl, Biopython and Biojava include support for BioSQL.

For more information see the associated website [3] and mailing list [4].


[1] http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/?cvsroot=biosql
[2] http://www.animorphics.net/lifesci/biosql.html
[3] http://obda.open-bio.org/
[4] http://obda.open-bio.org/mailman/listinfo/biosql-l

Greg Tyrelle  (http://www.kinglab.unsw.edu.au/~greg)

"Logic only gives man what he needs, 
 magic gives man what he wants" - Tom Robbins