[Ontology-editors] use of regulates

[Jane Lomax]

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