GO identifiers being mis-parsed? Was Re: [Bioperl-l] Building biosql database errors

Sean Davis sdavis2 at mail.nih.gov
Tue Feb 10 18:21:58 EST 2004

I thank Andreas for pointing out the obvious and the email list points this
out as an ongoing problem, solved for the meantime by installing GO with
--nodelete.  However, there was another set of errors that remained after
fixing this and seemingly related to terms such as:


When I changed the ':' to '-' globally in the GO flat files, I got rid of
the exceptions (Any ideas?).  I continued to have issues with installing,
though, in that the name column often contains the GO:xxxxxxx number rather
than the name.  I assume that the identifier column is supposed to contain
the GO:xxxxxxx numbers, instead.  It seems that any values in the flat file
that contain a ':' are being treated as GO identifiers, as when I change all
things like "metacyc:xxxx" or "EC:xxxx" to use '-' instead of ':', the
output is as expected.  I don't know enough about methods code to find where
that parsing occurs, but just wanted to bring it up as an issue for me.  Is
this a problem specific to me or have others found similar issues?

I am using bioperl-1.4 with bioperl-db installed from cvs this morning on
macos 10.3.2. 


On 2/10/04 3:35 PM, "Andreas Bernauer" <andreas.bernauer at gmx.de> wrote:

> Sean Davis wrote: I am trying to build a biosql database on a mysql database.
> I have mysql and biosql schema running and can successfully load some data,
> but for a proportion of the data when loading ontology or locuslink, I get the
> following (many times).  Am I doing something wrong, or is this to be
> expected? 
>> -------------------- WARNING --------------------- MSG: insert in
>> Bio::DB::BioSQL::TermAdaptor (driver) failed, values were
>> ("GO:0042597","periplasmic space","The region between the inner (cytoplasmic)
>> and outer membrane (Gram-negative bacteria) or inner membrane and cell wall
>> (fungi).","") FKs (84) Duplicate entry 'periplasmic space-84' for key 2 ^ |
>> +-------------------------+ | I don't know, but maybe this + means something?
>> I guess, the db can't handle duplicate keys.
> Andreas. _______________________________________________ Bioperl-l mailing
> list Bioperl-l at portal.open-bio.org
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