Remove BFO:processual entity

EnvironmentOntology / environmental-exposure-ontology

Modular environmental exposures ontology

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Remove BFO:processual entity #65

Open wdduncan opened 4 years ago

wdduncan commented 4 years ago

The term 'processual entity' should not be in the ontology. BFO now endorses the term 'process'.

cmungall commented 4 years ago

is this an ecto problem?

matentzn commented 4 years ago

processual entity is not a BFO class: it is an UBERON class.

We cant not use it :P If anything, you can make an UBERON ticket to ask to align processual entity with BFO:process.. Again, not an ECTO issue but feel free to re-open if you disagree.

wdduncan commented 4 years ago

Yes. I disagree :) When you do your import from UBERON, you placed the entities under process. You do not have to be beholden to processual entity.

matentzn commented 4 years ago

Oh ok.. I am afraid I dont quite understand yet; which entities have we placed under process? Can you give an example? I believe, but @diatomsRcool correct me if I am wrong, we have not actually added a single axiom to ECTO:

https://github.com/EnvironmentOntology/environmental-exposure-ontology/blob/master/src/ontology/ecto-edit.owl

everything is either generated by dosdp (no manual assertions) or coming from external ontologies..

wdduncan commented 4 years ago

Under process (BFO_0000015) I see:

biological process
environmental system process
exposure event or process
molecular function
planned process
regulation of behavior

In regard to 'processual entity', this was originally a BFO 1.1 class. @cmungall Are you able to use the BFO 'process' class instead of 'processual entity'? I am not familiar with how UBERON is built.

matentzn commented 4 years ago

Ah you say that UBERON added processual entity as a replacement for BFO:processual entity, and your suggestion is to obsolete UBERON:processual entity in favour of BFO:process?

wdduncan commented 4 years ago

Processual entity used to be included in BFO 1. In BFO 2, the authors created a process class that replaced processual entity.

UBERON, for reasons I am not aware of, retained processual entity. Processual entity has an UBERON IRI, but the definition is the same as the BFO 1 class. It would make more sense (IMHO) to move the entities under processual entity to be under process.

matentzn commented 4 years ago

Ok, maybe move that ticket there then?

https://github.com/obophenotype/uberon/issues

wdduncan commented 4 years ago

We should discuss with @cmungall

diatomsRcool commented 3 years ago

Where are we with this? Is this an ECTO issue?