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

[David Hill]

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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-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430