[Ontology-editors] CC, PRO and CORUM

[Midori Harris]

Actually, Harold created the main item, and it's assigned to me. Jane has 
the subset. (Judy - you must have looked at the 'submitted by' column.)

I'll reply to Chris in more detail tomorrow.

m

On Tue, 25 Nov 2008, Judith Blake wrote:

> 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
>
>
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>