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

[Chris Mungall]

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
>
>