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

Midori Harris midori at ebi.ac.uk
Thu Sep 4 03:33:33 PDT 2008 

One clarification from Chris' visit yesterday: this part should not be 
controversial:

    Chris: I would like it to be formally stated that MF is_a bfo:Process.

We (Chris, me, Jane , Jen) think we can and should go ahead with it 
without waiting for the discussion about 'dirty functions'. We agreed that 
Chris will produce a mapping file (consisting of one line!) for GO 
MF-to-BFO process, after David and I mention it to the GO managers next 
week.

m

On Tue, 2 Sep 2008, David Hill wrote:

> 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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