add 'periphytic biofilm' subClass of 'biofilm', with subClasses of it's own

[turbomam]

Periphyton is defined by NEON as 'Mixture of algae, cyanobacteria, microbes, and detritus that coats submerged surfaces in most bodies of water.'

see a precedent for 'periphytic biofilm' here: https://www.frontiersin.org/articles/10.3389/fmicb.2021.684903/full

subclasses:

• Epilithon: Periphyton colonizing rock substrata.
• Epipelon: Periphyton colonizing silt substrata.
• Epiphyton: Periphyton colonizing surface of aquatic plants.
• Epipsammon: Periphyton colonizing sand substrata.
• Epixylon: Periphyton colonizing woody substrata.

cc @aclum @cmungall

[turbomam]

These values can be found in the aquMicrobeType field in the amb_fieldParent table

[aclum]

Definitions of proposed class subclasses come from NEON document number NEON.DOC.003044, revision E, title AOS Protocol and Procedure: AMC – Aquatic Microbial Sampling URL: https://data.neonscience.org/documents/10179/1883159/NEON.DOC.003044vE/05ca8fcc-33ba-a5b2-0e93-8f4001f38c37

[turbomam]

@cmungall @pbuttigieg I don't see any modules or patterns that seem like the right home for these biofilm subclasses, so I'm going to start a PR with direct edits to envo-edit.owl

[turbomam]

Oops, I'm not sure I understand the difference between biofilm and biofilm material

[cmungall]

I propose merging these, keeping a branch under material

On Thu, Nov 9, 2023 at 12:12 PM Mark A. Miller @.***> wrote:

Oops, I'm not sure I understand the difference between biofilm https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00002034 and biofilm material https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_01000156

— Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/issues/1466#issuecomment-1804595980, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOM46HEDACMECFI6GKTYDU2KHAVCNFSM6AAAAAA6YJ7P6KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBUGU4TKOJYGA . You are receiving this because you were mentioned.Message ID: @.***>

[turbomam]

see also

• https://github.com/EnvironmentOntology/envo/issues/1176

compare definitions and superclass before closing that issue