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

[David Hill]

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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>>>   
>>>       
>
>   

-- 
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