[Ontology-editors] use of regulates

[David Hill]

Hi Jane,

We agree with Midori on this. Were we going to try to do these terms 
together?

David and Tanya

Midori Harris wrote:
>
>> 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
>>
>>
>>