DRAFT: New Principle 19 - for OBO Operations Review

[nataled]

No description provided.

[cmungall]

I don't think this has anything directly to do with OBO format. GO, Uberon, CL, all phenotype ontologies all use the same simple data model e.g. making use of comments because this is what browsers show more prominently, because it's simpler and more consistent. Nothing to do with format. OBO Format can represent annotation assertions at exactly the same level of expressivity as OWL

[nataled]

These alternatives are listed for OBO format because they are used 'in the field' so to speak. That is, unlike ontologies in OWL format--which all seem to use the same deprecation methods--OBO formatted ontologies have been using different means. I've confirmed that either way is fine, so we say all this to acknowledge these alternatives.

[cmungall]

See comments, some minor. Overall I recommend not mixing up orthogonal file syntax issues with OMO profiles

[matentzn]

I like this principle very much; some general feedback:

1. the principle is about "term stability", yet the focus is entirely about definitions (IAO:0000115). I think the principle text should clearly refer to all ways a meaning can significantly change, including in cases where there is no human readable definition, but a rich axiomatic structure (like say in PRO or CHEBI).
2. I like the concept of "referents" very much; but what I am missing here is that the source of the mapping between and ID and its referent is solely in the head of the ontology developer. So I would like the text to reflect the idea of "as intended by the ontology developer". I think this is important because the referents are never explicit, and we need to have a source of truth for who gets to define these somewhere in the text. This also helps with deciding "if the referent changed or not" - as you say, only the ontology author can decide this.