search

biolink / biolinkml

DEPRECATED: replaced by linkml
https://github.com/linkml/linkml
Creative Commons Zero v1.0 Universal
23 stars 12 forks source link

add antonymy as a meta model attribute #396

Closed sierra-moxon closed 2 years ago

sierra-moxon commented 3 years ago

to allow tagging of 'opposites in biolink-model. chose antonymy instead of opposite we might want to allow opposition on a gradient. Perhaps there is a more precise way to do this. fixes #395

hsolbrig commented 3 years ago

I would be interested in understanding the use case for this proposal. Antonyms are definitely useful for understanding terminological resources -- the definition of words and their meaning, but I'm not sure I understand how this fits in a modeling language. Is the intent that this would be another annotation property like definition, example, name, comments, etc. or is its intent to enhance the actual semantics of the model the way that inverse declares a dependency in the model itself?

cmungall commented 3 years ago

we should probably call this antonym_of or opposite_of

yes, there is a strong case for keeping this a domain predicate and not part of the core metamodel - at least until we can define semantics (but then we don't really have semantics for closeMatch...)

the main driver here is it's much more convenient and clear to do this:

slots:
  negatively regulates:
   opposite_of: positively_regulates

(which requires the meta-slot be in the metamodel)

vs

slots:
  negatively regulates:
   annotations:
     extension_tag: biolink:opposite_of
     extension_value: positively regulates
   opposite_of: positively_regulates