[BioSQL-l] GO dbxrefs in swissprot

[Hilmar Lapp]

On Thursday, July 1, 2004, at 06:29  AM, Andreas Henschel wrote:

> Strange enough, its not that all GO dbxrefs get ignored: the 
> bioseqdb.dbxref table contains more then 9000 GO entries. The 
> swissprot flatfile contains more than 52000, though (tested with > grep).

How many unique entries are these though? Keep in mind that the dbxref 
table is normalized.

When you say the GO dbxrefs did not appear, how do you mean? Are you 
referring to dbxrefs present in the source file but absent as 
association rows in bioentry_dbxref?

If you have a swissprot entry that has GO dbxrefs in the source file 
but fails to have those associated in bioentry_dbxref, check whether 
the Bio::Seq object that's coming from the parser has them as 
annotation. It would sound strange if some entries get the associations 
whereas others don't.

	-hilmar

-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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