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

[Tanya Berardini]

Hey everyone,


> 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.


Yes, I agree.


> 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.


In your solution below, where these types of terms fall into the
real-function sub-branch, are they still errors or not?  I think we might be
able to clean some up, as David suggests (transcription regulator activity,
for instance) but some things like 'protein tag' may have to stay.

>David: "Are they really useful?"

Yes, I think that some of them are.  What else would we assign as a function
to ubiquitin or sumo but protein tag?


>
> 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 bfo declarations could be made at the level of the sub-branches rather
> than MF as a whole


Yes, this makes sense.

>>Alan: The second one seems completely wrong. At best one can have the
realization of a function regulating something.
>David:I disagree. This means that the function that is executed by the gene
product modulates some inherent quality of the >execution of  the function
of a calcium channel, such as the rate at which it moves calcium across the
membrane. It's function >could be to plug up the channel, or to open it.

I tried to find an example and found this:

http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:1921831&session_id=1845amigo1218834880

Have a look at this paper from which Sbf2 was annotated to the term
'phosphatase regulator activity':

http://www.ncbi.nlm.nih.gov/pubmed/16399794?dopt=Abstract

I suppose one could easily annotate to something like 'regulation of
phosphatase activity' instead/as well.  If we did the 'regulation of
phosphatase activity' annotation and removed the term 'phosphatase regulator
activity',  I wonder if we could live with annotating such gene products to
the root term 'molecular function' ? Not with the ND evidence code though.

>David: Tanya and I just returned from the Society for Developmental Biology
meeting and we heard talk after talk after talk about >processes that
regulate developmental processes. In my opinion, we can't ignore this view
(Tanya feel free to pipe up). In fact >during one talk someone specifically
said we know that molecule X regulates process Y, but what don't know how.
Of course >what we want to know is what X is doing to regulate Y.

We need to be able to represent regulation in GO, both in the terms we use
for annotation and in the relationships between the terms.  I don't think
that any biologist would argue with that point.  Especially not the
biologists whose talks we attended or who presented posters at the SDB
meeting.  The stumbling point, really, is getting what regulation is across
to the ontologists.  Just because we haven't yet figured out how to define
regulation clearly in their language, doesn't mean that we can't or that
it's not relevant or important or that it doesn't exist.  I realize that I'm
just preaching to the choir here but we need to stay committed to serving
the needs of the biologists.


> Anhyway, I would like to make some kind of statement satisfying Alan soon.


Yes, and it would be good for such a statement to come as a unified
statement from GO.


Tanya


>
> 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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-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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