krchristie
commented
3 years ago Hi @kallia-p @zoependlington @paolaroncaglia
To make sure that GO does not obsolete any of the terms that EFO is using, we propose to make a subset for EFO terms so that we know to contact you about any proposed changes in advance.
Here are our existing subsets: subsetdef: goslim_agr "AGR slim" subsetdef: goslim_aspergillus "Aspergillus GO slim" subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_chembl "ChEMBL protein targets summary" subsetdef: goslim_drosophila "Drosophila GO slim" subsetdef: goslim_flybase_ribbon "FlyBase Drosophila GO ribbon slim" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_metagenomics "Metagenomics GO slim" subsetdef: goslim_mouse "Mouse GO slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_synapse "synapse GO slim" subsetdef: goslim_yeast "Yeast GO slim"
Looking at these and thinking about what you've said you are doing with GO terms, here's a proposed label for an EFO subset:
subsetdef: goslim_efo "Experimental Factor Ontology import"
If you're in agreement with this idea, I'll go ahead and make a subset in GO so we know what terms you're using. If you add additional terms in the future, let us know to add them by opening a new ticket.
Thanks,
-Karen
pgaudet
raymond91125
zoependlington
dosumis
rays22
paolaroncaglia
Hi @krchristie @zoependlington @paolaroncaglia
I think, given the timing it would be best if we could both approach the 'response to' terms in a systematic way rather than as part of sporadic tickets about specific drugs. If you agree we could start discussing this in a new ticket. If needed I can join one of your future meetings to discuss and plan around the proposed work with regards to the alignment between GO, EFO and OBA 'response to' terms. Please let me know which of the two you prefer and if you think a meeting is warranted which forthcoming Monday we can allocate to this task.
I provide a bit of background and context to the preliminary work that I have done thus far. I am currently reviewing all of the terms that are in GO and have been imported in EFO (N=75 GO terms, see table below which comprises the EFO created 'response to' specific drug terms as well). I am also examining the OBA cross referenced terms with GO and the overlap between the three ontologies. With regards to EFO some of the imported GO terms are high level grouping terms with the main one being 'response to stimulus' of which 'response to chemical' is a Subclass Of. 'Response to drug' is a Subclass Of 'response to chemical' and I have made a note that you plan to merge this with 'response to xenobiotic'. Further down the GO hierarchy i.e. in the 'response to drug' branch there is some structure incorporated in GO that several EFO terms sit under for example the GO 'response to antipsychotic drug' and GO 'response to antineoplastic agent' have a number of children with either GO or EFO IDs for specific antipsychotic drugs and cancer therapy agents (with one of them being the GO 'response to paclitaxel' which you are planning to obsolete). Small changes like these will have less of an effect to our users but changes in higher level grouping terms will cause much disruption and I wonder why do you think EFO would be a better place for them than GO, and what is the hazard of keeping these kind of terms in GO.
I reviewed the tickets in trying to understand how GO views usage of the 'response to' terms in general. In my view an organism's response to an exogenous stimulus whether this is food intake, stress or a pharmacologic intervention constitutes a biological process; variations in our our genes interact with our environment. Many of the GWAS catalog studies associate variants with phenotypes that measure responses. Pharmacogenomics studies will specifically look for variants that modulate efficacy of a drug or adverse/toxic reactions. The GWAS catalog contains associations from gene x environment interactions studies as well. I think it also useful for researchers to know that (a variant affecting expression or function of) gene X which is associated with an adverse reaction to a drug Y (GO 'response to term') is linked to GO biological process Z.
Thanks!
Summary of discussion at GO Editors call on 9/27/21
Originally posted by @kallia-p in https://github.com/geneontology/go-ontology/issues/21998#issuecomment-926572432