[Ontology-editors] cell walls - Re: biological_process_xp_cellular_component-unvetted.obo (fwd)

[Midori Harris]

On Wed, 6 May 2009, Chris Mungall wrote:

>
> On May 6, 2009, at 5:28 AM, Midori Harris wrote:
>
>> 
>> the differentiae for these terms are 
>> all about what the molecules are made for, not where the synthesis happens. 
>> It fits in with the CC macromolecule biosythesis part_of CC biogenesis 
>> arrangement that we recently implemented, so I'm now thinking that perhaps 
>> these terms would be best represented as bp-xp-bp, where the genus is 
>> '[molecule] biosynthetic process and the differentia is part_of [optional 
>> specific wall type] cell wall biogenesis'. Recasting the GO:0000032 
>> example:
>> 
>> [Term]
>> id: GO:0000032 ! cell wall mannoprotein biosynthetic process
>> intersection_of: GO:0006057 ! mannoprotein biosynthetic process
>> intersection_of: OBO_REL:part_of GO:0042546 ! cell wall biogenesis
>
> The question is whether there are ever other mannoproteins being made as part 
> of cell wall biogenesis that are not destined to become part of the cell 
> wall. My guess would be not.

I think not, too, partly because as far as I know mannoproteins that don't 
become part of the cell wall wouldn't be counted as "made as part of cell 
wall biogenesis".

>
> We don't really have a protocol for shifting xps from one xp file to another. 
> I think it's fine to do this and then email the maintainer of that file or 
> the ontology editors list to say you've done it

OK, this would be that email, to Jen and cc'd to the list. I've added some 
xps to biological_process_xp_self-unvetted.obo (right at the end, 
following a !! comment about them), and commented out corresponding 
entries in biological_process_xp_cellular_component-unvetted.obo.

m