[Ontology-editors] CC, PRO and CORUM

[Chris Mungall]

Thanks for the clarification.

Yes, I think we will want to grab the xrefs out the spreadsheet when  
we're done

On Nov 26, 2008, at 6:28 AM, Midori Harris wrote:

> Hi Chris,
>
> As noted briefly yesterday, I'm gradually working my way through the  
> many suggested new complex terms in SF 2049652, and Jane has taken  
> on a subset in SF 2125996. It's very slow going, because I'm finding  
> that I have to check each term manually, and that often requires  
> reading (or at least skimming) much of the full text of a paper.
>
> Based on what I'm finding, I would not incorporate anything into GO  
> based on importing or mapping anything from CORUM or MIPS. The Sin3  
> complex example is fine, but there are problems with enough of the  
> CORUM entries I've looked at to make me very leery of trying to  
> speed up adding the complex terms. For example, CORUM cites PMID: 
> 11713266 for more different complexes than the paper shows; CORUM: 
> 3284 is a separate entry based on a paper that actually shows that a  
> particular protein is a member of a previously identified complex;  
> for CORUM:832 the paper cited actually says that two of the listed  
> subunits are found in *different* complexes.
>
> Even for the accurately described complexes, the localization (and  
> maybe also function and process) may be species-specific in some  
> cases, and those wouldn't meet our all-some criteria. Like the  
> composition (and existence!) of the complexes themselves,  
> localizations might have to be individually vetted.
>
> For those CORUM complexes that do pass the curator vetting  
> procedure, I'll be able to pull GO IDs and CORUM IDs out of a  
> spreadsheet if we want to add dbxrefs.
>
> midori
>
> [snip PRO stuff]
>
>> * 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
>>
>>
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>