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

[Chris Mungall]

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.