[Bioperl-l] [BioSQL-l] Problem loading GO.

Chris Fields cjfields at uiuc.edu
Tue Apr 17 12:18:19 EDT 2007


On Apr 17, 2007, at 11:05 AM, Leighton Pritchard wrote:
...
>
>>> and so is something for the GO guys to fix, I guess.
>>
>> The lack of a database for certain xrefs surely is. If the escaped
>> comma does throw off the BioPerl parser then that part is for BioPerl
>> to fix.
>
> I thinkk the problems are now all in the data I downloaded from
> http://www.geneontology.org/GO.downloads.shtml - I believe the BioPerl
> parser to be innocent of these charges ;)  I've submitted the issue at
> the GO site, and with any luck they'll handle it quite soon (if it  
> is in
> fact their problem).
>
>> Note that you also have the --computetc switch which will compute the
>> transitive closure for you automatically.
>
> :D Excellent!  Thanks for the pointer, and again for your efforts,
>
> L.
...

If you do find anything that is BioSQL- or Bioperl-related then file  
a bug report so we can track it.  I agree with Hilmar that it's  
likely the parser is partly to blame.

http://bugzilla.open-bio.org/

We really appreciate the work you're putting into this!

chris


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