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

[Midori Harris]

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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