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

[David Hill]

I agree. This is a must in Montreal.

Midori Harris wrote:
> Much as I would love to just do it, I think we have to bring it up at 
> the meeting first. People ain't gonna be happy if we spring a big 
> change like this on them without a discussion, no matter how sensible 
> the change really is. Sigh.
>
> m
>
> On Tue, 2 Sep 2008, Jane Lomax wrote:
>
>> 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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>>
>>
>>
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