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

[Midori Harris]

On Thu, 14 Aug 2008, 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

Yup.

Pity we happened to glom onto the word "function" 10 years ago (hindsight 
is such a wonderful thing), since it has a specific meaning within the 
formal ontology community, but we have never actually thought of MF terms 
representing function-in-the-ontological-sense. We've always intended for 
MF terms to represent activities, basically the ontologists' 
molecular-scale processes (with some exceptions that we tolerated mainly 
for lack of other ontologies to use to capture some information).

>
> 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.

I agree.

> 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).

Fine by me.

> 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.

By a curious coincidence, these exceptions/errors are pretty much the same 
terms that have given the GO editors the most headaches.

> 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)

No objections, though it does sound like a longish-term prospect.

m

>
> 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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