[Ontology-editors] use of regulates

[Jane Lomax]

I do (it's all terms in the range (GO:0075***), but the terms aren't in 
the main file yet so you'll have to use my working version (attached)...

j

Chris Mungall wrote:
>
> Do you have an ID block?
>
> If not I'll just rerun obol on everything below MOP and we'll see what 
> we get
>
> On Aug 7, 2008, at 5:47 AM, Jane Lomax wrote:
>
>> Well, they've submitted to me an OBO file with the definitions but no 
>> relations, and a figure embedded in a Word doc (seriously!) to show 
>> the relations. I've so far assigned ids to their new terms and 
>> imported them into the latest version of GO and am now adding the 
>> relations.
>>
>> Can you work with just that file Chris? Or does it need to have all 
>> the relations in for the results to make sense? There are currently 
>> lots of orphan terms...
>>
>> Jane
>>
>>
>> Chris Mungall wrote:
>>>
>>> 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
>>>> Cambridgeshire, UK
>>>> CB10 1SD
>>>>
>>>> p: +44 1223 492516
>>>> f: +44 1223 494468
>>>>
>>>>
>>
>>
>> -- 
>> Dr Jane Lomax
>> GO Editorial Office
>> EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridgeshire, UK
>> CB10 1SD
>>
>> p: +44 1223 492516
>> f: +44 1223 494468
>>
>>


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

p: +44 1223 492516
f: +44 1223 494468

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