[Ontology-editors] Precoordination of "response to" terms & drugs

[Jennifer Deegan (nee Clark)]

I thought we decided that 'response to drug' went into column 16. The 
minutes would be the place to find out.

Jen

David Hill wrote:
> coannotation? we discussed this, but I don't remember what we decided.
> 
> 
> 
> Gwinn Giglio, Michelle wrote:
>> That works, but then what about people coming to look for annotations to
>> "response to insulin".  Are we going to assume our users will properly 
>> use
>> and parse column 16 info?  I'm not opposed to making that assumption, but
>> depending on whether we assume that or not it changes how we decide to
>> structure things.
>>
>>
>> On 3/13/09 11:01 AM, "David Hill" <dph at informatics.jax.org> wrote:
>>
>>  
>>> I thought we would annotate to response to drug and then put insulin in
>>> column 16.
>>>
>>> David
>>>
>>> Gwinn Giglio, Michelle wrote:
>>>    
>>>> Hi Chris,
>>>>
>>>> I  thought we decided that "response to drug" would not have any 
>>>> children.
>>>> People would annotate to "response to insulin" (for example) which 
>>>> would
>>>> have parentage under whatever proper chemical terms it usually does, 
>>>> then if
>>>> they new that in this particular case it was acting as a drug they 
>>>> could
>>>> co-annotate to "response to drug". I really don't think we should make
>>>> children of response to drug.
>>>>
>>>> If using column 16 I would expect the we would annotate "response to
>>>> insulin" and then we would need to somehow indicate that insulin in a
>>>> particular case was a drug - not sure how to do that.
>>>>
>>>> Michelle
>>>>
>>>>
>>>>
>>>>
>>>> On 3/12/09 4:55 PM, "Chris Mungall" <cjm at berkeleybop.org> wrote:
>>>>
>>>>        
>>>>> What's our policy here?
>>>>>
>>>>> We already have a fair number of "response to X" terms.
>>>>>
>>>>> On the surface there is a potential for explosion here. You could
>>>>> imagine a high-throughput assay testing against a massive
>>>>> combinatorial chemistry library and measuring gene expression levels,
>>>>> each experiment yielding an annotation where there is upregulation or
>>>>> downregulation of genes. And if we go beyond chemical entities,
>>>>> there's a huge variety of behaviors an organism could potentially
>>>>> respond to.
>>>>>
>>>>> We can restrict the number of declared GO terms by applying our rule:
>>>>> is response to X substantially different from response to Y? Are
>>>>> different receptors or pathways used? If not then one term will do.
>>>>> The additional information can go in col 16. But it seems that this
>>>>> may be hard for us to determine in many cases.
>>>>>
>>>>> Even so, I feel we should continue to pre-coordinate here. I don't
>>>>> fear the explosion here - this part of the graph can be managed almost
>>>>> entirely automatically, like we are beginning to do with regulation.
>>>>>
>>>>> This is related to the response to drug issue: some people don't like
>>>>> the "response to drug" term, and we came up with a way of doing this
>>>>> using annotation xps. But this maybe isn't necessary.
>>>>>
>>>>> CHEBI have moved from an overloaded is_a hierarchy to using has_role
>>>>> relations between some entities and drugs. We can define "response to
>>>>> drug" as "response to a chemical entity that is sometimes used as a
>>>>> drug", and not worry about whether the gene product is acting in
>>>>> response to the chemical in its drug-role or non-drug role. is_a
>>>>> parentage under "response to drug" would be determined entirely
>>>>> automatically based on CHEBI.
>>>>>
>>>>> Personally I don't think "response to drug" is a great scientific
>>>>> term, but it seems it's useful for grouping and analysis purposes, it
>>>>> doesn't really do anyone any harm. We could tag it in a slim.
>>>>>
>>>>> So I am thinking that precoordination is the way to go here.
>>>>>
>>>>> This arose from lakshmi's test GAF file with col 16 - they want to
>>>>> annotate to "response to ryanodine". Should we just suggest that they
>>>>> request this term? Looking at the paper it wasn't clear to me
>>>>>
>>>>> Another question: should every "X receptor activity" term be linked to
>>>>> "response to X (stimulus)" via part_of? I don't see why not, given
>>>>> current definitions.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>             
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>>
>>   
>