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

[David Hill]

from the meeting minutes:

*10.3 Discuss how we are going to handle 'response to drug'*

SF 1242405 and 1494526 and 'response to toxin' SF1658374. Are they 
normal biological processes? Response to X (drug, toxin) Response to 
Chemical (see also Use of Response To Terms in Annotation, for a related 
issue)(David and Tanya)

1. We keep ‘response to drug’, add response to ‘XX’ response by role 
chemical is playing would be in ontology with co annotation to chemical. 
We keep stub of ‘response to drug’, no children. Roles are basically 
stub terms in ontology

Transport of drug
Degradation of drug

2. Response to Chemical [ ID as Chebi ID ultimately]
	Response to Cocaine[XX}
		Response to Cocaine[XX] as a Drug

sometimes things are toxins, sometimes not; same as drug similiar to 
situation in PAMGO with ‘pathogenesis’, not always deleterious Drugs 
would be put in the chemical organization.

Note added Day 2: Harold's proposal:
annotate to response to X with whatever evidence code
annotate to response to drug with IC

some discussion of this proposal, qualifiers, other gp-term rels, etc.

this is effectively a refinement of yesterday's proposal

/*ACTION ITEM*: Implement Michelle's proposal; decide whether to put 
'response to drug' ID in column 16 or is separate IC annotation. 
Annotate to chemical term ‘response to cocaine’, co-annotate with 
chemical term for now, then later when available, put GO ID for 
“response to drug’ in column 16 (or separate IC annotation)./



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