@DrZZ 'I also think it is very important for researchers to recognize that what’s in the bottle doesn’t always line up with what is supposed to be in the bottle'

Couldn't agree more, that is why we are planning to log every bottle of stuff into our system individually. Each bottle gets its own URI. Part of our aim is actually to be able to make a precise (and machine readable) assertion when something in that bottle is not what someone else asserts it to be.

I take your point that using a system for something its not built for can cause problems. I think the concern that people had with PubChem is that there are misattributions and ambiguities but as you say as long as you can point at something that makes the assertion. The key point is being able to do that pointing (and that the assertion can be pinned down to an authority of some description - the triple has to be a 'quad'). For my purposes the substance ID's are perfectly adequate I think, especially as we use many things, like yeast extract, that aren't identifiable chemicals.

If we go down the SID route we will need buy in from both suppliers and PubChem.