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

[Karen Christie]

I think most biologists really don't care about the theoretical 
distinctions between (ontological) functions and functionings. I think for 
biologists this might even fall into the MEGO (My Eyes Glaze Over) 
category that I just encountered in a National Geographic article. The 
writer explained MEGO as a term journalists use for things that many 
people may find boring, though he was talking about dirt, not ontology 
construction ;)

Personally, I don't have any problems with GO making efforts to comply 
with ontological principles, but at the same time, it needs to remain 
practical for biologists without requiring that they learn about MEGO 
ontological formalisms.

For myself, since I'm an annotator more often than an ontology developer,
I've been kind of thinking of them as:
   Function: how
   Process: what
   Component: where

So, I do see the problem with some of the terms like 'transcription 
regulator activity' and 'translation regulator activity', where the 
function term does not address the how. These two terms are basically 
equivalent to the process terms 'regulation of transcription, 
DNA-dependent' and 'regulation of translation', respectively. We've also 
made comments about how Function and Process should be orthogonal and 
having pairs like these that are essentially indistinguishable seems 
non-orthogonal. But, from my recollection of Amelia's proposal, I think 
that may be too far.

-Karen





On Thu, 4 Sep 2008, Harold Drabkin wrote:

> 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
>>>> 
>>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Ontology-editors mailing list
>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>> 
>> 
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>