Add terms related to streams

[aclum]

To support NEON we propose adding the follow terms as children of stream http://purl.obolibrary.org/obo/ENVO_00000023 The definitions come from the categoricalCodes csv files NEON provides for DP1.20279, benthic microbial metagenome sequences.

• pool: Typically the deepest habitats in a stream, pools are characterized by smaller substrate size and relatively slow moving water
• run: Shallow to deep stream habitat with swift to moderate flow, characterized by low turbulence (i.e., smooth water surface)
• step pool: In high-gradient streams, a series of pools separated by boulder or cobble steps, causing fast flow over the steps and slow flow in the pools"

@cmungall @turbomam

[turbomam]

Great contributions. Let's think about what class these would be sub-classes of. It seems like both could be _partof a stream or a watercourse, but all pools are not streams, so that would not be a good subclass relationship.

• riffle is a subclass of compound astronomical body part
• waterfall is a subclass of hydroform

Here's all the things that are subclasses of EnvO's river

Here's all the things that are parts of any subclass of EnvO's river

[turbomam]

This closed issue gives a sense of the EnvO term addition process

We can also refer to https://github.com/EnvironmentOntology/envo/blob/master/CONTRIBUTING.md

[cmungall]

It sounds like you made some progress on this! Can you give a quick status update @turbomam?

[aclum]

@cmungall mark and I worked on this but I don't have write permissions on the repo so I couldn't commit my local changes. @turbomam was planning on doing the pull request this week unless you can give me permissions on this repo.

[cmungall]

@aclum - anyone can make PRs on this repo (we need to fill out https://github.com/EnvironmentOntology/envo/blob/master/CONTRIBUTING.md) to make this clear

However, the workflow is slightly easier if you have permissions to work on a branch off origin rather than making a fork

[turbomam]

I'm going to do a PR early tomorrow

[pbuttigieg]

Thanks for the PR - the definitions need rewriting for semantic clarity

@aclum how tolerant are you to changes there ?

[turbomam]

PR updated, including some reshaping of the definitions and splitting additional content out into comments.

[turbomam]

I also updated the PR title.

[turbomam]

GH Action still failing on

2023-09-01 02:00:51,345 ERROR org.obolibrary.robot.ReasonOperation - Only equivalent classes that have been asserted are allowed. Inferred equivalencies are forbidden. 2023-09-01 02:00:51,345 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_03600095 == http://purl.obolibrary.org/obo/ENVO_03600094 2023-09-01 02:00:51,345 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_03600096 == http://purl.obolibrary.org/obo/ENVO_03600095 2023-09-01 02:00:51,345 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_03600096 == http://purl.obolibrary.org/obo/ENVO_03600094

All of the new classes are logically equivalent?

Can't they all be subClassOf 'liquid astronomical body part' and subClassOf 'part of' some stream?

[turbomam]

I updated the subclass axioms to

• 'part of' some stream|'part of' some 'forested area'
• 'part of' some stream|'part of' some desert
• 'part of' some stream|'part of' some farm

in the three new class definitions to test my understanding of inferred logical equivalence. It still didn't pass the GH actions.

I'm going to manually remove all mentions/definitions of the three new terms fromenvo-edit.owl in order to remove the EquivalentClasse assertions ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/ENVO_00000023>) that seem to have gotten stuck in there from previous commits.

[turbomam]

It passed. Apologies for all of the drama, poor documentation reading and poor advice giving to @aclum.

[aclum]

@turbomam Okay to close?