[BioSQL-l] Swissprot Problems

[Raphael A. Bauer]

Hi,

just an interesting thing from Swiss-Prot:
If we want to load the latest Swiss-Prot flatfile with
load_seqdatabase.pl we get the following error (normally our
load_seqdatabase.pl works fine):

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values
were
("",""A multicenter comparison of methods for typing strains of Pseudomonas
aeruginosa predominantly from patients with cystic fibrosis."","J. Infect.
Dis. 169:134-142(1994).","CRC-237261AF859664D3","","") FKs (613823)
ERROR:  null value in column "authors" violates not-null constraint
---------------------------------------------------
Could not store Q53391:
------------- EXCEPTION  -------------
...

And that is what I would expect, because Q53391 has no RA line.
The Swiss-Prot manual says:

RG	Reference group	Once or more (Optional if RA line)	
RA	Reference authors	Once or more (Optional if RG line)
...
...
so I don't know how one can deal with this, because it is a clear
violation of the Swiss-Prot manual statements and therefore a violation
of the BioSQL schema definition (authors NOT NULL)...

We will remove the NOT NULL statements from the authors line in the
BioSQL schema to deal with this..

Any better ideas?

Raphael....