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

[Midori Harris]

yes, there's another email thread and a long SF item, all converging on 
the same thing

m

On Thu, 12 Mar 2009, Tanya Berardini wrote:

> 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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