cmungall
commented
2 years ago @EnvironmentOntology/envo-editors: we need to give consistent advice on template-based addition of terms to ENVO
We are confusing two template workflows. For documentation of workflows, see:
https://docs.google.com/document/d/1KXv-Tm3HvypjucFZeLLPjCdgkof5f0Re5_5GbFfQLWU/edit
We are mixing
- workflow 1: seeding
- workflow 2: TSV driven ontology curation
It's fine to mix these for different branches, but not the same term
I think for now it is easiest if you remove that line from the tsv @marieALaporte but I would rather have simpler modularization where the EA/EAL branch of the ontology has the TSVs as SOT
I was trying to propose more concentration terms relevant to soil and liquid water using the pattern approach and the template entity_attribute_location. I used the dedicated ID range for that specific pattern to create IDs for the new terms. I added my terms directly to the corresponding module, and then ran the command that was in the Makefile for making the the modules (dosdp generate and robot annotate).
When looking at the diffs of the entity_attribute_location.owl file that I got in return, I see that one term ('concentration of oxygen in water') was obsoleted at some point, but because I ran the make module command again, the term is created again. See here: https://github.com/marieALaporte/envo/commit/d093bf0eaa9d3914762839c7403a28186c7d06cf
I understand that what I am trying to do it different from what is described in the Wiki. I preferred to use the pattern approach as we have a bunch of concentration and composition terms that we would like to propose to ENVO (we have several issues open for those), and it is a great approach to add both the terms and the equivalent axioms in one shot.
Could you please advise what should be done here? Many thanks !