[Ontology-editors] CC, PRO and CORUM

Chris Mungall cjm at berkeleybop.org
Wed Nov 26 08:09:39 PST 2008 

Does "inactive" mean permanently inactived? If not then the potential  
is still there.

But if this still seems unnatural, one solution would be to implicitly  
treat all GO CCs as the active form. For the more specific PRO  
inactive form, PRO would represent a complex that is_a  
"inactivated_complex" and transformation_of the GO active CC.

A similar solution could be used with derives_from, where PRO wants to  
represent specific forms that have gained or lost parts.

On Nov 26, 2008, at 7:32 AM, Darren Natale wrote:

> Yes, that is exactly my understanding.  So, if GO had "unicornase  
> complex" and PRO were to have something like "inactive unicornase  
> complex" and "active unicornase complex," it seems to me that only  
> the active version has the potential function.  I think we'd want to  
> connect both to GO somehow, but which relation to use isn't yet  
> clear to me.
>
> Midori Harris wrote:
>> Hi Darren,
>> In addition to what Judy says, I think it's reasonable to interpret  
>> the function-centric portions of many GO CC definitions as  
>> indicating that a complex has the potential to execute a function  
>> (though it's true that the defs aren't explicitly worded that way).
>> Midori
>> On Wed, 26 Nov 2008, Judith Blake wrote:
>>> Darren,
>>>
>>> I think the complexes in GO are not meant to be function-specific,  
>>> they are meant to be location-specific.  So is_a would be  
>>> correct.  If the definitions are not location specific, such as XX  
>>> complex is_a cellular component, then the GO definition should be  
>>> modified.
>>>
>>> judy
>>>
>>> -----Original Message-----
>>> From: Darren Natale [mailto:dan5 at georgetown.edu]
>>> Sent: Wednesday, November 26, 2008 10:20 AM
>>> To: Judith Blake
>>> Cc: Midori Harris; Chris Mungall; Ontology Editors
>>> Subject: Re: [Ontology-editors] CC, PRO and CORUM
>>>
>>>
>>>
>>> Judith Blake wrote:
>>>> I concur with Midori here.  The purpose of the generation of this  
>>>> set was to expand the representation in GO for those complexes  
>>>> missing that are important in the mammalian system.  For this  
>>>> CORUM provided a great portal for my summer intern to identify  
>>>> and work with generating the intersection of the GO and CORUM sets.
>>>>
>>>> However, as Midori notes, the definitions provided need to be  
>>>> generalized for the GO context.  And, as noted, there are more  
>>>> complexes to be represented as well.  I think the use of the  
>>>> CORUM set as a starting point is proving productive however, and  
>>>> I'm glad to see the extension of complex representation in GO.
>>>>
>>>> The work of the moment, then, is to establish how we will  
>>>> represent the relationship between the context-dependent (species/ 
>>>> celltype/space/time) representation in PRO and the generic  
>>>> representation in GO.
>>>
>>> My initial thought was that is_a would be appropriate.  I think  
>>> Chris
>>> expressed the same idea.  However, I'm no longer certain that this  
>>> is
>>> the case.  For example, the inactive form of a complex--which  
>>> would also
>>> be represented in PRO--would not fit the function-based  
>>> definitions that
>>> are sometimes used in GO.  Technically speaking I suppose part_of  
>>> could
>>> be used (Chris, correct me if I am wrong but I think the  
>>> definition of
>>> part_of allows for saying some whole part_of itself).  I don't  
>>> really
>>> like that, however.  Needs more thought.
>>>
>>>> This does not address the other issue as to whether 'complexes',  
>>>> because of their context dependence should be classified  
>>>> differently than the cellular structures such as the mitochondria  
>>>> or golgi.
>>>>
>>>> Judy
>>>>
>>>> -----Original Message-----
>>>> From: Midori Harris [mailto:midori at ebi.ac.uk]
>>>> Sent: Wednesday, November 26, 2008 9:29 AM
>>>> To: Chris Mungall
>>>> Cc: Ontology Editors; Darren Natale; Judith Blake
>>>> Subject: Re: [Ontology-editors] CC, PRO and CORUM
>>>>
>>>> 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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>>>
>

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