[BioSQL-l] GO dbxrefs in swissprot

[Andreas Henschel]

Hi all,

We just installed swissprot as the first database in the bioseqdb scheme 
(using load_seqdatabase.pl) and apparently it looked succesful (using 
--safe). However, a lot of swissprot entries dont get the Gene ontology 
(GO) cross referencing at all, although they are contained in the 
original flatfile.  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).

We then tested a single swissprot entry (P53396, containing GO dbxrefs) 
to be loaded, which did not give any error message. But again, the 
GO-crossrefs did not appear (InterPro, EMBL etc. worked fine).
Any idea?

Cheers,
Andreas Henschel
PhD student,
BioTec Dresden