[go] error in gene_ontology_edit.obo

[Jennifer Deegan (nee Clark)]

I have added that to the tracker.

Thanks,

Jen

Chris Mungall wrote:

> 
> OBO-Edit detects disjointness violations - ie when a term is both a  
> function and a process. Technically this isn't such a violation, as  
> both parents are processes. It's a namespace assignment problem. If  
> there isn't already a check for this can someone add it to the tracker?
> 
> We intend to move to a system with a true editors/deployment version  
> split, this will help prevent some of these issues leaking into the  
> publicly consumed version.
> 
> On Nov 15, 2007, at 1:58 PM, David Hill wrote:
> 
>> Hi Gavin,
>>
>> Thanks for the heads-up. We will fix this error this afternoon when  
>> we are editing.
>>
>> David
>>
>> Gavin Sherlock wrote:
>>
>>> Hi all,
>>>
>>> I have discovered what I presume is an error in the current  
>>> gene_ontology_edit.obo, cvs version: $Revision: 5.551, that I just  
>>> downloaded from the GO site.
>>>
>>> The following entry:
>>>
>>> [Term]
>>> id: GO:0008086
>>> name: light-activated voltage-gated calcium channel activity
>>> namespace: biological_process
>>> def: "Catalysis of the transmembrane transfer of a calcium ion by  a 
>>> voltage-gated channel that is activated in response to  light." 
>>> [GOC:mtg_transport]
>>> synonym: "light-activated voltage gated calcium channel activity"  
>>> EXACT []
>>> synonym: "light-activated voltage-dependent calcium channel  
>>> activity" EXACT []
>>> is_a: GO:0005245 ! voltage-gated calcium channel activity
>>> is_a: GO:0010461 ! light-activated channel activity
>>>
>>> is listed as a biological process, yet its parents are molecular  
>>> functions:
>>>
>>> id: GO:0005245
>>> name: voltage-gated calcium channel activity
>>> namespace: molecular_function
>>>
>>> id: GO:0010461
>>> name: light-activated channel activity
>>> namespace: molecular_function
>>>
>>> I think that's the only error, as fixing it in my local copy of  the 
>>> file fixes the error generated by my parser.  Can it be fixed,  and 
>>> should OBO-Edit detect this type of error automatically?
>>>
>>> Cheers,
>>> Gavin
>>>
>>>
>>>
>>>
>>
>>
>>

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium