[Ontology-editors] use of regulates

[Midori Harris]

> So if A -regulates-> B, the all instances of A regulate some instances of B?

That sounds right.

> What do you mean by "the only difference between process X and process Y is 
> the regulatory context"?

This is where I was struggling for how to phrase it, and where I think 
David and Tanya have done it better. Basically, it means the process is 
the same whenever it occurs ... in the transcription example, there are a 
bunch of regulation terms like 'positive regulation of central gap gene 
transcription', 'regulation of transcription from RNA polymerase II 
promoter involved in forebrain neuron fate commitment', etc. But 
transcription always occurs the same way, and the regulation terms are 
distiguished based on when, where, mediated by what, or in response to 
what, transcription level increase or decrease. So there's no separate 
term for 'central gap gene transcription, or transcription from RNA 
polymerase II promoter involved in forebrain neuron fate commitment'.

Is that clearer, or murkier??
m

>
> cheers,
>
> Jane
>
> Midori Harris wrote:
>> David & Tanya will probably do a better job of this, but they're both away 
>> this week, so ...
>> 
>>> For example, in a situation where you have a term 'regulation of process 
>>> X' but there's no process X in GO, but process X is_a process Y, is it 
>>> okay to say that 'regulation of process X' regulates process Y? Or do we 
>>> have to create a process X?
>> 
>> Usually, yes, except where the only difference between process X and 
>> process Y is the regulatory context. The example D&T used is transcription 
>> -- there's a brief description in the Princeton meeting minutes:
>> 
>> http://wiki.geneontology.org/index.php/GO_18th_Consortium_Meeting_Minutes_Day_1#2.29_Regulation. 
>> 
>> m
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