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

[Midori Harris]

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

What do you think?

m