[BioSQL-l] RE: gene ontology questions (bug)

[Marc Colosimo]

On Tue, 3 Jun 2003, Hilmar Lapp wrote:
> > bioseqdb=# select term_id, name, identifier from term where name = 
> > 'caspase activity';
> >  term_id |       name       | identifier 
> > ---------+------------------+------------
> >      681 | caspase activity | GO:0004199
> > (1 row)
> > 
> > As you see, caspase activity was entered with a different identifier.
> 
> I suspected that, but normally the error message gives better hints at
> that. This is almost certainly a problem of either
> 
> 	a) the input file, in that it mentions the term twice with
> different identifiers,

Here is what is in the file that I got from geneontology:

grep 'caspase activity' function.ontology 
       %caspase activity ; GO:0030693
   %caspase activity ; GO:0004199 ; EC:3.4.22.36
   %effector caspase activity ; GO:0004207 ; EC:3.4.22.-
   %signaling (initiator) caspase activity ; GO:0004200 ; EC:3.4.22.-


> 
> Or
> 
> 	b) the bioperl ontology dagflat parser.
> 
> Could you please check whether a) is true. If it's not (i.e., term
> 'caspase activity' only occurs with one and the same identifier), send
> me the file so that I can debug the parser.

You can get the file from <http://www.geneontology.org/#ontologies> 
Molecular Function was the one I grabbed.

-marc