[Ontology-editors] CC, PRO and CORUM

[Judith Blake]

Hi Chris

Source forge item 2049652 Protein Complex terms for the GO.
Assignee hjdrabkin

To this item is appended a zip file xl spreadsheet.

Also see  S-2125996, a subset that Midori is working on

Judy

-----Original Message-----
From: Chris Mungall [mailto:cjm at berkeleybop.org]
Sent: Tuesday, November 25, 2008 2:06 PM
To: Ontology Editors
Cc: Judith Blake; Darren Natale
Subject: CC, PRO and CORUM

Reading Judy's slides from PRO.

* Relationship between PRO and CC
The slides suggest: contributes_to
I think it would be <CC complex term> has_part <PRO protein term>
Optionally with cardinality restrictions

Also, if PRO also represents, and these are intended to be more
specific than the ones in GO, is_a should be used.

We may want to keep the inter-ontology links in a separate bridging
file.

* Mapping CORUM to GO.

I see we have 18 CC terms with synonyms with CORUM as provenance. It
may be an idea to have a separate xref too (e.g. if the CORUM name is
identical). So there's another ~1200 to be added? I couldn't find the
tracker item for this.

There are quite a few that could be trivially mapped. E.g:

[Term]
id: GO:0016580
name: Sin3 complex
namespace: cellular_component
def: "A multiprotein complex that functions broadly in eukaryotic
organisms as a transcriptional repressor of protein-coding genes,
through the gene-specific deacetylation of histones. Amongst its
subunits, the Sin3 complex contains Sin3-like proteins, and a number
of core proteins that are shared with the NuRD complex (including
histone deacetylases and histone binding proteins). The Sin3 complex
does not directly bind DNA itself, but is targeted to specific genes
through protein-protein interactions with DNA-binding proteins." [PMID:
10589671, PMID:11743021, PMID:12865422]
is_a: GO:0000118 ! histone deacetylase complex

To:

http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=54

Note that MIPS localizes this to the nucleus. Can we just import MIPS
localizations, or are they not as rigorous as us in forcing an all-
some relation?

Once we have these we can also use mips2go and the mips funcat entry
for each complex to get CC->MF/MP links