Sorry for the delay, have spent part of the afternoon looking at ontologies via OBO and I think the answer is there are none that serve the purpose I was after at the time. Perhaps it is more helpful if I say what I was trying to do on the occassion I was thinking of?

What I was trying to do was find examples of subtilisin like proteases being used in the synthesis of peptides. In particular I was trying to figure out what range of amino acid substrates had been successfully turned into peptides using proteases. I was using GoPubMed to try and find whether it wasas a better way of figuring out what had been made using these proteases than doing the pubmed search subtilisin + peptide + synthesis and then reading all the papers.

Now using GO or EC numbers or perhaps structural similarity ontologies I can find subtilisin like proteases, and probably somewhat more effectively than by searching on subtilisin. There isn't, as far as I know, any regularly used indexing vocabulary applied to literature in PubMed that focusses on either the inputs to chemical reactions or the products. These are not pathways so KEGG or pathway ontologies are no good.

I think I am just asking a question that is kind of orthogonal to the purpose and aims of the existing ontologies. This is not perhaps anyone else's problem but mine. But it is this kind of thing that makes me suspicious of the idea that existing ontologies are either suitable or helpful for my work.

Appreciate your interest and help though! And I do like the product!