[Ontology-editors] What does the MF ontology represent?

[Jane Lomax]

I'm all for this proposal. I think the exercise of splitting the 
molecular processes in MF from the molecular 'functions' will in itself 
be a useful one in improving the broad structure of the node.

David, I think there are more 'dirty' functions (heh) than you 
think...Amelia and I once had a discussion where we came to the 
conclusion that the only true molecular processes in MF are catalysis, 
transporter & regulator and their children (and I agree that 'regulator 
activity' is probably redundant with the regulation BP terms). I think 
that's probably still true, will be interested to see!

Should we take this to the Montreal meeting? Or is this something that 
we can agree on now?

Jane



Chris Mungall wrote:
>
> BFO makes the (I think) very useful distinction between a function and 
> a process/occurrent. Functions are realized as processes. The 
> canonical example being a sperm cell - it has a function even if that 
> function is never realized. bfo:Functions are subtypes of realizables. 
> Another word for them might be potentials.
>
> At first it seemed natural to treat the MF ontology as bfo:Functions.  
> However, it transpired that GO folks don't really think of MFs as 
> bfo:Functions. This lead to a lot of confusing talk between GO and 
> other OBO folks. At the last RO meeting, David, Tanya, Suzi and I 
> decided that the cleanest solution is to simply state that MF is_a 
> bfo:Process. Note that this is implicit in our decision to use part_of 
> / has_part to link MF/BP
>
> Note that so far we are not talking about annotation, just the meaning 
> of the terms themselves. When we make an annotation we are perhaps 
> saying something about function or potential in the bfo sense - not 
> every gene product realizes the function evolution honed it for. That 
> goes for both MF and BP.
>
> If GO is to be part of the OBO Foundry it has to declare what the 
> appropriate bfo superclasses of its roots are such that relations can 
> be made across the foundry coherently. I would like it to be formally 
> stated that MF is_a bfo:Process. This would quell Alan's concerns 
> (below and see also gofriends).
>
> Of course there are some terms in MF for which it makes little sense 
> to state that it is a process - protein tag, structural constituent 
> etc. I propose we acknowledge that there are some errors and we will 
> work to resolve these.
>
> I think the eventual solution will look pretty much exactly what 
> Amelia outlined in St Croix. It may not be as radical as moving most 
> of MF into BP (though I am not against). It could involve splitting MF 
> into a process sub-branch and a real-function sub-branch (logically 
> this is equivalent, but it feels less radical as terms stay in the 
> same namespace for the most part, though this is somehow less satisfying)
>
> The function sub-branch would look like this:
>
> antioxidant
> energy transducer
> enzyme
> motor
> nutrient reservoir
> signal
>  chemoattractant
>  chemorepellant
>  hormone
>  ligand
>  morphogen
>  protein tag
> structural molecule
> receptor
> regulator
>  chaperone regulator
>  enzyme regulator
>  transcription regulator
>  translation regulator
> transporter
> toxin
> triplet codon-amino acid adaptor
>
> the bfo declarations could be made at the level of the sub-branches 
> rather than MF as a whole
>
> The ppt is here if anyone wants a refresher:
>
> http://wiki.geneontology.org/index.php/Function-Process_Links
>
> Anhyway, I would like to make some kind of statement satisfying Alan 
> soon.
>
> Begin forwarded message:
>
>> From: Alan Ruttenberg <alanruttenberg at gmail.com>
>> Date: August 14, 2008 10:57:37 AM PDT
>> To: Barry Smith <phismith at buffalo.edu>
>> Cc: Chris Mungall <cjm at fruitfly.org>
>> Subject: changing function
>>
>> How closely is function tied to physical properties.
>> Can we say that function can change if (some) physical properties 
>> change?
>> This is brought up by the recent announcement by GO that they are 
>> going to have regulates relations between process and functions, e.g. 
>> some process regulates some function.
>>
>> Specifically, we will make the implicit regulatory relationships 
>> between 'regulation of molecular function' BP terms and the 
>> corresponding MF terms explicit. For example:
>>
>>     • regulation of kinase activity (BP) regulates kinase activity (MF)
>> Similarly, we will make the implicit regulatory relationships between 
>> terms within the MF ontology explicit. For example:
>>
>>     • calcium channel regulator activity (MF) regulates calcium 
>> channel activity (MF)
>>
>>
>> The second one seems completely wrong. At best one can have the 
>> realization of a function regulating something.
>>
>> Mess.
>>
>> -Alan
>>
>>
>
>
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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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