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oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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How to relate a post anatomical structure to a taxon of origin #627

Open cmungall opened 2 years ago

cmungall commented 2 years ago

From Damion Dooley:

Today in OBI call about specimens we hashed over the ‘derives from’ issue where a Malus domestica instance ceases to exist if we also have an apple existing:

Apple: equivalent to: 'pome fruit' and 'derives from' some 'Malus domestica'

So with “in taxon” can I do this instead (and not violate our beyond-OWL temporal ambition)?:

Apple: equivalent to: 'pome fruit' and ‘in taxon’ some 'Malus domestica'

Does this apply to anatomical animal parts too? I looked up ‘develops from’ but perhaps that aims more at identifying the connected parts something originates from?

Kind of pressing as I want to finally set the pattern in upcoming release of FoodOn.

ddooley commented 2 years ago

Existing issues pertaining to this: RO https://github.com/oborel/obo-relations/issues/367 RO https://github.com/oborel/obo-relations/issues/621 NTR: [sourced,extracted,...] from or variation of derives from UBERON https://github.com/obophenotype/uberon/issues/2427 (closed) COB https://github.com/OBOFoundry/COB/issues/204

cmungall commented 2 years ago

derives-from is too strong:

a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity

(this is inherited from RO 2005, on reflection I really do not like this definition, it brings in many complicated concepts about temporal change, when this should be an intuitive straightforward relationships)

develop-from is not inconsistent with existing usage but I don't think you would want to use this for say processed apples or butchered hearts

in-taxon is quite broad and covers derivation, development, part-of, and self

def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." []

I think your DP should use in-taxon

ddooley commented 1 year ago

This can be closed! We have adopted "in taxon".

wdduncan commented 1 year ago

Ok. I'll close.