[Chebi-ontology] Overlap between PR and CHEBI

[Chris M. <cjm...@lb...>]

There is a bit of redundancy between CHEBI and PR. For example

CHEBI:

            is_a CHEBI:16670 ! peptide
             is_a CHEBI:25905 ! peptide hormone
              is_a CHEBI:65311 ! corticotropin-releasing hormone
               is_a CHEBI:65312 ! corticotropin-releasing hormone 
(human)

PR:

    is_a CHEBI:23367 ! molecular entity
     is_a PR:000018263 ! amino acid chain
      is_a PR:000000001 ! protein
       is_a PR:000005867 ! corticoliberin
        is_a PR:P06850 ! corticoliberin (human)

These are equivalent  (but note the classification difference, in that 
CHEBI doesn't classify this as a protein).

Why put proteins in CHEBI? I mean do you intend to put TTN in there in 
order to break everyone's autocomplete-by-synonym capabilities?

There are some benefits - e.g. from a GO perspective we like having the 
classification under peptide hormone, which we don't get from PR. But 
there may be better ways to achieve the same thing.

We are making use of both PR and CHEBI for axiomatization in GO. Ideally 
there would be no overlap and an obvious choice of which class in which 
ontology to use. Failing that, or as an interim step, it would be 
extremely useful to have OWL axioms that connect the two ontologies, 
e.g. in a bridging ontology. Does such an artefact exist already?

And a related minor issue that would make things a lot easier for our 
automation processes: can CHEBI and PR agree on leading uppercase 
conventions for proteins. CHEBI says "Elastin", PR says "elastin". I 
prefer the lowercase, it's more in line with OBO conventions.