[Ontology-editors] CC->MF links

[Chris Mungall]

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
>>>>
>>>> ------------------------------------------------------------------------
>>>>
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>>>>
>>>>
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>>>
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>>>
>>
>>
>>
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