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

[Harold Drabkin]

No; to me as a biochemist, I fear that this is getting far too convoluted. 

h


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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>
>