[Ontology-editors] use of regulates

[Chris Mungall]

This should all be automatable. What do you have so far? Term names?

On Aug 5, 2008, at 2:25 AM, Jane Lomax wrote:

> 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
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>
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>