add pertubation ontologies

[davidsebfischer]

Genetic perturbations:

• [ ] gene IDs
• [ ] perturbation type: {KO, inhibition, over-expression}
• [ ] free text for vector specifics

small molecules

• [ ] Chembl IDs
• [ ] free text for concentration
• [ ] free text for delivery

as suggested by @ilibarra

[ilibarra]

ChEMBL is the largest public database so it cover most cases (1st table here). Having said that, two future things

• PubChem/DrugBank not fully covered by ChEMBL, so also relevant to consider those. I would expect user highlighting this as an issue before solving this. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916886/figure/fig02/
• SigmaAldrich and ThermoFisher reagents are independent, and sometimes unlisted in public databases (e.g. X chemical solution and mostly sold by one vendor due to purity/market trends). Those cases are much rarer, so not so relevant in your current timeline I suppose.

[stefanpeidli]

Some comments / thoughts:

• ChEMBL is nice and has an easy to use python package for it's web API: https://github.com/chembl/chembl_webresource_client. But I don't see any obo or owl format download link for their ontology.
• ChEBI might be the way to go: They do have owl and obo files to download. @davidsebfischer is this easy to add to sfaira? https://chembl.gitbook.io/chembl-interface-documentation/downloads

[stefanpeidli]

In turn, ChEBI maps to ChEMBL ids. See here for example: https://www.ebi.ac.uk/chebi/displayAutoXrefs.do?chebiId=CHEBI:114785