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

[David Hill]

Just realized my proposed term won't work unless we know at least one 
gene product that is regulating the gene expression. I will think about 
this more.

David

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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-- 
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