Creating a custom ontology for peptides

Question

[Mathew]

We are working on a project to create a custom ontology for peptides using Protege, did some research on the existing ones (Sequence Ontology, BioAssay Ontology, OLS Ontology Search). Are there any other sources related to the peptides?

The objective is to build a peptide dataset for the prediction of potential binders. In that case, what are the classes, properties and relationships that needs to be considered? Your suggestions would be highly appreciated. Many thanks in advance.