smrgeoinfo
commented
3 years ago Problem-- for mapping the CHEBI, its not clear which CHEBI concept of element matches the GSO concept of element. For instance CHEBI has gold atom, molecular gold, and elemental gold, non of which appear to precisely match the GSO concept of 'gold as aggregation of gold atoms' This does surface some interesting ontological problems w.r.t. precisely what is meant to say that e.g. copper is a constituent of cuprite. I'm sure this is a problem that has seen lots of discussion that I'm not up to speed on, so for the time being, we're going to stick with what we've got in GSO, with the URI for the 'atom' CHEBI version of an element in the gsel:chebiid property until we have a clearer picture of the landscape.
copied from https://github.com/ESIPFed/sweet/pull/224#issuecomment-811512124 Follow ups: @smrgeoinfo : That would be a good thing. The chebi URIs are in the GSO elements module. But we don't want to import CHEBI-- it brings a lot of baggage. @nicholascar Well I think the solution is as per QUDT: we profile CHEBI. Let’s make a vocabulary profile of CHEBI with just the chemicals needed and just the properties of those chemicals that we care about. @smrgeoinfo I'm studying CHEBI to see what might reasonably be extracted for a profile. I'd follow the pattern we used for the GSO QUDT profile.