[Go] recent change, "maternal behavior" relationship to "parental behavior"?

[Jane Lomax]

Chris - the verification checker is currently not working properly in OE2, 
so when that's fixed in the upcoming release these sorts of mistakes 
should be caught before the file is committed.

Jane

On Tue, 23 Jun 2009, Chris Mungall wrote:

>
> I have added a check for this to the production script[*] that checks the 
> editors file prior to publishing it to the public URL. Subsequent mistakes 
> like this will generate errors for go-admin and block publishing.
>
> This is a 'last line of defense' sort of thing though. Perhaps we need to 
> improve the checks at the OE level.
>
> Cheers
> Chris
>
> [*] http://wiki.geneontology.org/index.php/Ontology_publishing_pipeline_2009
>
> On Jun 23, 2009, at 8:45 AM, Midori Harris wrote:
>
>> Yup. Will fix that too. Thanks!
>> 
>> midori
>> 
>> On Tue, 23 Jun 2009, John Matese wrote:
>> 
>>> 
>>> Addendum:  this term is also in the wrong namespace?
>>> 
>>> [Term]
>>> id: GO:0060747
>>> name: oral incubation
>>> namespace: cellular_component
>>> def: "A parental behavior in which fertilized eggs are taken into the 
>>> mouth and held until hatching." [GOC:dph]
>>> is_a: GO:0060746 ! parental behavior
>>> 
>>> 
>>> 
>>> On Jun 23, 2009, at 11:33 AM, John Matese wrote:
>>> 
>>>> Hi,
>>>> One of our tools (Generic GO Term Mapper), is currently nonfunctional, 
>>>> and our current best guess is that it may be problem with the ontology?
>>>> Error message contains :
>>>> "There is an error in the obo file, where the relationship between 
>>>> GO:0042711 and one or more of its parents is not correctly defined. 
>>>> Please check the obo file. The program is unable to continue."
>>>> When I check the OBO file we have downloaded, I see that
>>>> [Term]
>>>> id: GO:0042711
>>>> name: maternal behavior
>>>> namespace: biological_process
>>>> def: "Female behaviors associated with the care and rearing of 
>>>> offspring." [GOC:curators]
>>>> exact_synonym: "maternal behaviour" []
>>>> is_a: GO:0060746 ! parental behavior
>>>> [Term]
>>>> id: GO:0060746
>>>> name: parental behavior
>>>> namespace: cellular_component
>>>> def: "A reproductive behavior in which a parent cares for and rears 
>>>> offspring." [GOC:dph]
>>>> is_a: GO:0033057 ! reproductive behavior in a multicellular organism
>>>> I don't see parental behavior in AmiGO and parental behavior appears to 
>>>> be in the wrong aspect?
>>>> Just letting you know,
>>>> John
>>>> John Matese
>>>> Director, PUMAdb
>>>> jcmatese at genomics.princeton.edu
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>>> 
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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
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