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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Proposal for managing naming conventions #2956

Closed matentzn closed 3 years ago

matentzn commented 3 years ago

Depending on applications, some users prefer different naming schemes (ideally let's not discuss those in this ticket - its just clear there are some conflicting preferences). @nicolevasilevsky and I suggest the following:

  1. rdfs:label is the default label
  2. skos:prefLabel can be used to curate preferred labels.
  3. Every skos:prefLabel annotation must have at least one source annotation to a subset, for example: 
    http://purl.obolibrary.org/obo/mondo#clingen
  4. When exporting a clingen view of mondo, we replace all rdfs:label annotation with a skos:prefLabel annotation where they exist.

Does this make sense?

cmungall commented 3 years ago

This seems unusual. Intuitively prefLabel should not be multivalued. E.g. if we were to make shex for obo/mondo/skos there would be max one prefLabel per language.

However, AFAIK there is nothing in skos saying we must use it in this way.

Note also that prefLabel is not considered a label/syn field by a lot of tooling. So would we have a procedure to materialize prefLabels as synonyms?

An alternative proposal is that we just tag select exactSynonyms with an annotation hasSynonymType CLINGEN_PREFERRED, FOO_PREFERRED etc. This is consistent with uberon, etc.

matentzn commented 3 years ago

Perfect, lets do that then! I have no objections to this, so @nicolevasilevsky and I will get started on this. Thank you for the feedback!

matentzn commented 3 years ago

Its decided, we do as @cmungall suggests.