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

[Hilmar Lapp]

On Monday, June 2, 2003, at 02:16  PM, Marc Colosimo wrote:

> I got the latest
> (todays) cvs version and dropped the old one. Do I need the
> accelerators and views?
>

No. (I believe right now only Biojava takes advantage of them.)

> accession numbers with associated terms.

This would go into bioentry_qualifier_value (with value being empty).

> So, I loaded in the first
> part and I wanted to link the terms to their descriptions. Also,
> they have a protein domain ontology. What would that correspond to?
>

I don't know what it precisely, but Generally speaking you'd put the 
domain ontology into the term table.

>>
>>>
>>> Second, I tried to load in stuff (function.ontology) from
>>> geneontology.org
>>> using the script load_ontology.pl.
>
> [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.

> 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?

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).

You can also specify --safe in which case the upload will continue 
after the failure.

	-hilmar

-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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