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chemkg / chemrof

Schema for chemistry ontology classes
https://chemkg.github.io/chemrof
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valence #3

Closed cmungall closed 3 years ago

cmungall commented 3 years ago

cc @realmarcin

realmarcin commented 3 years ago

Thinking of ways to represent valency vs oxidation number vs formal charge, as distinguished here: https://pubs.acs.org/doi/abs/10.1021/ed083p791

One use case it to be able to represent different oxidation states of what is the same molecule (up to eg protonation) -- but in a different environment (eg pH). This could be useful for example in predicting environments or their features, where we known eg that certain molecular states imply hi/lo pH. It would even be useful to have a parent molecule, and then different children representing different states.

This is also relevant to function annotations, chemical reactions, pathways, and metabolic models e.g. NAD+ central metabolism. In many cases data on the different molecular states in biological samples was sparse because measurements were more difficult (NAD+ example).