In the example at https://github.com/MI2CAST/MI2CAST/blob/master/examples/PKA_regulation.md, UniProtKB: is used as the prefix for UniProt entries. I think it would make sense to also include in the MI2CAST specification that users defer to a community-accepted registry for prefixes, namely https://identifiers.org, which suggests using uniprot as the prefix instead.

I'm aware that Identifiers.org is not a complete registry, and at times it also has conflicting views about preferred prefixes with the OBO community, from which I can see several important figures are your co-authors.

A prime example of this conflict is over taxonomy identifiers - the OBO world loves using NCBITaxon:, Identifiers.org says to use taxonomy:, and the NCBI says to use NCBI:txid. This problem won't be solved within the scope of MI2CAST, but at least it makes sense to defer to a body that's organizing around improving the situation. Not to self promote, but I wrote a bit more about this exact problem in this blog post if you want to know more