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

[Amelia Ireland]

Back in Gotham City, David Hill wrote:
> Hi Chris,

[snip]
>> 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.
> Jane, Midori and I talked about these types of terms in Cambridge, and Tanya 
> and I have talked about them as well. There are not many of them. Are they 
> really useful?

They are useful in as much as they allow annotators to give something a 
name. I wouldn't say they gain us much in terms of concrete knowledge of 
what the gene product is actually up to!

>> 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)

I would prefer the former, but I realize it would be a huge paradigm shift 
for people, so a gradual introduction would certainly be required. I think 
as we create more links between the ontologies and methods of annotation 
become more sophisticated (e.g. more use of composite terms with parts 
taken from different ontologies, such as 'regulation of systemic 
arterial blood pressure by circulatory epinephrine-norepinephrine'), the 
ontology from which something originated will become less important than
finding a term, or combination of terms, that captures a biological 
phenomenon. That's my dream, anyway... ;)

[snip]
> I guess what I'm saying is I don't really have a problem with 
> a function being a BP at the molecular level of granularity. I think we have 
> always thought of it that way.

Just to play devil's advocate: I think there are two ways in which 
functions have been viewed; the first is the bio process at the molecular 
level, and the second is the 'purpose' or 'job' of the entity, which is 
often a conglomeration of the various processes the entity is involved in, 
its location, its structure, and so on; a more colloquial interpretation 
of 'function'. Who knows what might have happened if the MF ontology had 
been differently named! ;)

Cheers,
Amelia.