Chemical compounds as generically dependent continuants?

[Omar Stradella]

I have a question regarding the classification of entities like chemical compounds using BFO in the context of the pharmaceutical industry.

For patent purposes, an invention requires a "conception" stage, the intellectual act of creating a complete inventive concept, including ideas for making the invention and methods of using it. It also requires an "actual reduction to practice" stage, which involves creating a physical embodiment of the invention and using it successfully for its intended purpose (see  Guide to Patent Law - Rosalind Franklin University)

Therefore, in the pharma domain, we think of entities like chemical compounds or therapeutic proteins (like antibodies) as abstract concepts that get ultimately concretized when produced physically as batches. When a batch is made and experimentally verified to correspond to the conceptual entity, we "register" the conceptual entity and give it a corporate ID.

 
First, within the BFO framework, would it be right to consider the conceptual entities as generically dependent continuants that get concretized by the entity representation? So, for example, a chemical compound would be a generically dependent continuant concretized by the molecular structure, and a protein would be a generically dependent continuant concretized by the amino acid sequence. Second, how should a registered compound be represented? "Registered" seems to be a role that a conceptual compound adopts when it gets a corporate ID. Moreover, the registration happens only when at least one batch is made. How would the batch be represented, and what would the relationships be?

I appreciate any help you can provide.

Omar Stradella

[Colin Batchelor]

Hello,

Janna Hastings and others have done useful work on this - here is a paper from 2011 which I think directly addresses your questions, or at least points to an OWL file that should do:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025513

There is also a detailed discussion of how classifying the molecules themselves happens in practice here:

https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-4-8

All the best,

Colin Batchelor.