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

[Marc Colosimo]

On Mon, 2 Jun 2003, Hilmar Lapp wrote:
> > [snip]
> >
> >>
> >> You need to upgrade to the latest schema version. Ontology_term was
> >> renamed to term in the Singapore-version (which is essentially the CVS
> >> head).
> >
> > Got todays cvs for bioperl
> 
> also bioperl-db? I fixed a couple of issues there too a week or so ago.

yep!

> 
> > and  tried one more time to load it. It still
> > dies, but much later. I don't know if this is a real bug in 
> > load_ontology
> > or in the GO file.
> >
> > perl load_ontology.pl --dbname bioseqdb --dbuser mcolosim --driver Pg
> > ~/Affymetrix/function.ontology
> > Parsing input ...
> > Loading ontology Gene Ontology:
> >         ... terms
> > Could not store GO:0030693 (caspase activity):
> >
> > ------------- EXCEPTION  -------------
> 
> This is pretty strange. Is this the first term in the input file?
> 
> The strange thing is that normally the message about the preceding root 
> cause is printed. Did you turn off DBI PrintErrors? (Even if you did 
> there should be a message.) Are you sure you didn't trim off some 
> preceding message?

I didn't touch the script and that was the whole out put. 
> 
> You can check by GO_ID whether you actually have the respective term in 
> the database (and if so, whether it has the same name).

There is a bug! But whose does it belong to, I don't know. 

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.

bioseqdb=# \d term
[snip]
Indexes: term_pkey primary key btree (term_id),
         term_identifier_key unique btree (identifier),
         term_name_key unique btree (name, ontology_id),
         term_ont btree (ontology_id)

And I think the name needs to be unique! D'oh!

Marc