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

[Chris Mungall]

On May 6, 2009, at 5:28 AM, Midori Harris wrote:

> for the record
>
> ---------- Forwarded message ----------
> Date: Thu, 30 Apr 2009 14:25:19 +0100 (BST)
> From: Midori Harris <midori at ebi.ac.uk>
> To: Chris Mungall <cjm at berkeleybop.org>
> Subject: cell walls - Re: biological_process_xp_cellular_component- 
> unvetted.obo
>
> Hi Chris,
>
> Several of the xps remaining in the bp-xc-cc-unvetted file are for  
> 'cell wall [some molecule] biosynthetic process' terms, for which  
> I've commented to the effect that I thought they might mean  
> synthesis of molecules destined to become part of the cell wall,  
> rather than synthesis that takes place in the cell wall. E.g.:
>
> [Term]
> id: GO:0000032 ! cell wall mannoprotein biosynthetic process
> intersection_of: GO:0006057 ! mannoprotein biosynthetic process
> intersection_of: OBO_REL:occurs_in GO:0005618 ! cell wall
> !! confirm this; the term may mean biosynthesis of mannoproteins  
> destined for the cell wall
>
> I've added a few more terms of this ilk recently, and I've become  
> fully convinced that my hunch was right -- 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.

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

>
> What do you think?
>
> m
>
>
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