[Ontology-editors] use of regulates

[Chris Mungall]

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
>
>