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

[Chris Mungall]

On Aug 15, 2008, at 11:29 AM, Amelia Ireland wrote:

> 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... ;)

I think 'regulation of systemic arterial blood pressure by circulatory  
epinephrine-norepinephrine' should always stay in the ontology, as  
it's differentium is non-trivial and non-arbitrary (I would expect).  
There is something biologically interesting in what distinguishes this  
kind of RoSABP. The pathway diagram would look different.

However, if someone wants to annotate to 'regulation of systemic  
arterial blood pressure by circulatory epinephrine-norepinephrine  
DURING some-arbitrary-process' then the during differentium should be  
done via an annotation-time composition. We may later discover the  
during part to be non-arbitrary, in which case it's trivial to upgrade  
this is a named term in GO.

http://wiki.geneontology.org/index.php/Annotation_Cross_Products


>
> [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.
>