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

[Tanya Berardini]

I was just going to add it but someone has beaten me to the punch.

On Thu, Mar 12, 2009 at 3:16 PM, Chris Mungall <cjm at berkeleybop.org> wrote:

>
> I think putting this on the agenda is a good idea
>
>
> On Mar 12, 2009, at 2:49 PM, David Hill wrote:
>
>  I think we need to re-explore the definition of the 'response to' terms. I
>> would like to see them (and all other processes for that matter) defined
>> with a beginning and an end, specifically with respect to whether we want to
>> make them pertain to a cellular level, or an organismal level in
>> multicellular organisms.  I think we need to discuss this at the meeting. I
>> know that there are good arguments for annotating gene products that, for
>> example change after exposure to a stimulus. I have seen excellent examples
>> of why these types of annotations can be useful. However, Alex has valid
>> points in his argument for not including these. I can present some ideas
>> about how to handle this at the consortium meeting. One way would be to
>> create 'regulation of gene expression in response to X' terms. These would
>> then get the IDs of the responding genes as targets in column 16. This would
>> differentiate these from gene products in the signaling pathways that
>> transduce the response on a cellular level. The issue would then be, how to
>> relate these gene expression  terms to the 'response to' terms themselves.
>> If they become a part_of, then the response to terms would remain as global
>> as they currently are defined.
>>
>>
>>
>> Chris Mungall 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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>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>
>>
>> --
>> 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
>>
>>
>>
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-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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