[Biopython-dev] BioSQL questions

Yves Bastide Yves.Bastide at irisa.fr
Fri Nov 22 05:23:46 EST 2002

Bioentries are retrieved via two classes, DBSeqRecord and DBInternalSeq. 

I'm asking because it seems sound, but I don't understand why which data 
is retrieved by which class, e.g. sequence name by DBInternalSeq.

Concerning the sequence name: a bioentry contains four ids:

* bioentry_id, the internal id

* display_id, called "name" by SeqRecord

* accession, called "id"

* identifier, not retrieved.

In Genbank parlance, display_id == LOCUS, accession == ACCESSION (duh!) 
and identifier == GI.

Obviously, the GI should be retrieved; and I think "id" should be 
renamed to "accession".



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