[Ontology-editors] use of regulates

[Jane Lomax]

These are new terms I'm adding, David, more than 300 so I thought I may 
as well get the relations right as they go in. However, it doesn't seem 
to be as straightforward as I hoped, so I might just not add any 
regulates relations for them for now and just get the terms themselves in...

Jane


David Hill wrote:
> 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
>>>
>>>
>>>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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