[Ontology-editors] [Refgenome] CC->MF links

[Valerie Wood]

Makes sense (if they are true)

Chris Mungall wrote:

>
> So far we have only been considering necessary and sufficient  
> conditions (cross-products) in:
>     http://wiki.geneontology.org/index.php/XP:cellular_component_xp_go
>
> But we could extend this to include plain cross-ontology links  
> (necessary conditions) too.
>
> On Feb 10, 2009, at 10:35 AM, Pascale Gaudet wrote:
>
>> Val,
>>
>> that's great, thanks!
>>
>> Chris-- Can this go in the wiki CC-> MF somewhere?
>>
>> Pascale
>>
>> Valerie Wood wrote:
>>
>>>
>>>
>>> I did a quick reccy of the pombe annotations using contributes_to
>>> This accounts for 166 of my 239 using this qualifier. As I am the  
>>> largest user, this probably accounts for most of the complex- 
>>> function links using this qualifier (as SGD s are likely to be  
>>> similar). I would need to check the remaining 73 individually, but  
>>> these look like more of a hotch-potch.
>>>
>>> We could start a list where these are allowed (or disallowed), and  
>>> once we are happy with the contents, reject any annotations using  
>>> "contributes_to" at point of submission unless it is added to the  
>>> list.
>>> I'd be happy to reannotate rejections, it would make me do it.  
>>> Otherwise it will never go up my to-do list.
>>>
>>> I notice there are still two 'types' here.
>>> i) Complexes which do not have the activity on their own
>>> i.e
>>> DNA polymaerase
>>> F1/Fo ATPase
>>> proteasome
>>> etc
>>>
>>> ii) Complexes which are described as having a 'function' which  
>>> isn't really an activity at all.
>>> like
>>> RNA polymerase III transcription factor activity
>>> RNA polymerase II transcription mediator activity
>>> RNA polymerase III transcription factor activity
>>>
>>> Val
>>>
>>>
>>> V-type ATPase and F1/Fo ATPase  -->  proton-transporting ATPase  
>>> activity, rotational mechanism
>>>
>>> mediator complex --> RNA polymerase II transcription mediator  activity
>>>
>>> proteasome  --> endopeptidase activity
>>>
>>> DNA-directed RNA polymerase -->  DNA-directed RNA polymerase activity
>>>
>>> DNA polymerase  --> DNA-directed DNA polymerase activity
>>>
>>> TIM23 translocase complex  --> P-P-bond-hydrolysis-driven protein  
>>> transmembrane transporter activity
>>>
>>> anaphase-promoting complex --> I have this to ubiquitin ligase  
>>> activity but in this case there is specific subunit so the others  
>>> should be removed
>>>
>>> translocon --> protein transporter activity
>>>
>>> ubiquinol-cytochrome-c reductase complex --> ubiquinol-cytochrome-c  
>>> reductase activity
>>>
>>> TFIIIC complex --> RNA polymerase III transcription factor activity
>>>
>>> RNase P and RNase MRP -> ribonuclease P activity ribonuclease MRP  
>>> activity
>>>
>>> mRNA decapping complex --> m7G(5')pppN diphosphatase activity
>>>
>>> signal recognition particle --> endoplasmic reticulum signal  
>>> peptide binding
>>>
>>> translation initiation factor eIF3 --> translation initiation  
>>> factor activity
>>>
>>> mitochondrial respiratory chain complex IV --> cytochrome c  
>>> oxidase  activity
>>>
>>> geranylgeranyltransferase complex --> protein  
>>> geranylgeranyltransferase activity
>>>
>>> origin recognition complex --> DNA replication origin binding
>>>
>>> TIM22 inner membrane protein import complex --> protein transporter  
>>> activity
>>>
>>> glycine decarboxylase complex --> glycine dehydrogenase  
>>> (decarboxylating) activity
>>>
>>> DNA replication factor C  --> DNA clamp loader activity
>>>
>>> DNA replication factor A --> single-stranded DNA binding
>>>
>>> glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI- 
>>> GnT) complex --> phosphatidylinositol N- 
>>> acetylglucosaminyltransferase activity
>>>
>>> CCR4-Not complex  --> poly(A)-specific ribonuclease activity
>>>
>>> ATP citrate synthase complex -->  ATP citrate synthase activity
>>>
>>> mitochondrial TOM complex P-P-bond-hydrolysis-driven protein  
>>> transmembrane transporter activity
>>>
>>> farnesyltransferase  protein farnesyltransferase activity
>>>
>>> ribonuclease H2 complex ribonuclease H activity (I'm not sure this  
>>> one is correct
>>>
>>>
>>>
>>> Pascale Gaudet wrote:
>>>
>>>> Hello everyone,
>>>>
>>>> Minutes from today's call are available:
>>>> http://wiki.geneontology.org/index.php/RefGenome10Feb09_Phone_Conference 
>>>>
>>>>
>>>> I added some suggestion as to where we could move annotations to  
>>>> some of the 'fraction' terms.
>>>>
>>>> Pascale
>>>>
>>>>
>>>>
>>>> Pascale Gaudet wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> This is a reminder that our monthly conference call is tomorrow,  
>>>>> Tuesday, February 10, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST.
>>>>>
>>>>> Agenda is here:
>>>>> http://wiki.geneontology.org/index.php/RefGenome10Feb09_Phone_Conference 
>>>>>
>>>>>
>>>>>
>>>>> Pascale
>>>>>
>>>>> ------------------------------------------------------------------------ 
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Refgenome mailing list
>>>>> Refgenome at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/refgenome
>>>>>
>>>>>
>>>> ------------------------------------------------------------------------ 
>>>>
>>>>
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>>>>
>>>
>>>
>>>
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