NTR: wetland biome (biome for peat-forming wetlands)

[clnsmth]

Requesting wetland biome, built on the biome pattern as wetland ecosystem and ('participates in' some 'climactic ecological succession'), SubClassOf wetland ecosystem.

It would give a MIxS env_broad_scale value to the Microflora Danica "Bogs, mires and fens" habitats (Natura2000/EUNIS 7000), ~530 samples in PRJNA1071982 currently using flooded grassland biome; coastal salt marshes use the existing marine salt marsh biome. Reference: Microflora Danica, Nature 2025, doi:10.1038/s41586-025-09794-2.

Depends on wetland ecosystem being placed under terrestrial ecosystem.

[clnsmth]

@edi-ontology-agent please add this new term

[edi-ontology-agent]

🤖 Working on it...

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[edi-ontology-agent]

I have successfully completed your request to add the new term and update the ontology hierarchy!

Summary of Actions

1. Hierarchical Modification:

   • Re-positioned wetland ecosystem (ENVO:01001209) under terrestrial ecosystem (ENVO:01001790) as its parent class (updated subclass assertions in src/envo/envo-edit.owl), aligning it with its textual definition.

2. Term Creation:

   • Created the new term wetland biome (ENVO:03622000) based on the standard biome design pattern:
     • Label: wetland biome
     • Definition: "A wetland ecosystem that is undergoing climactic ecological succession."
     • Equivalent To: wetland ecosystem and ('participates in' some 'climactic ecological succession')
     • SubClassOf: wetland ecosystem (ENVO:01001209)
     • Reference / Citation: Derived and sourced from Microflora Danica (Nature 2025, DOI: 10.1038/s41586-025-09794-2).
     • Comments: Documented the utility of the class for providing MIxS env_broad_scale values to the Microflora Danica project's "Bogs, mires and fens" habitats (Natura2000/EUNIS 7000).

3. Pattern Compliance:

   • Added pattern conformance metadata for wetland biome to src/envo/patterns/matches/logical/biome.tsv so it is correctly validated against the DOSDP template.

4. Editor Setup:

   • Registered idrange:31 for edi-ontology-agent (ENVO:03622000 to ENVO:03622999) in src/envo/envo-idranges.owl to prevent any potential ID collisions.

5. Validation and Pull Request:

   • Ran local ontology reasoning, syntax profile validation, and SPARQL conformance tests (make test). Everything built successfully and passed reasoning checks!
   • Submitted a Pull Request: EDIorg/envo#9 containing all curated modifications.

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🤖 Generated by @edi-ontology-agent

• Model: gemini-3.5-flash
• Agent harness: antigravity-cli
• Triggered by: @clnsmth
• Run: View workflow run