EcoMech is a curated knowledge base of ecological process mechanisms, with structured evidence from the scientific literature. It is modeled after DisMech but focused on ecological processes rather than diseases.
Each entry documents an ecosystem process (drawn from the ENVO ecosystem process branch) with:
- Mechanisms — the ecological, biological, and physicochemical steps involved
- Indicators — observable ecological outcomes and measurements
- Drivers — abiotic, biotic, and anthropogenic factors that initiate or modulate the process
- Interventions — management, conservation, and restoration actions
All data are backed by primary literature references with exact quoted snippets, validated against PubMed abstracts.
| Entity Type | Ontology |
|---|---|
| Ecosystem processes | ENVO (ecosystem process branch) |
| Ecological / biological processes | GO (Gene Ontology) |
| Organisms / taxa | NCBITaxon |
| Phenotypic qualities / measurements | PATO |
| Environmental exposures / stressors | ECTO |
| Habitats / biomes / environmental conditions | ENVO |
| Chemicals (nutrients, pollutants) | CHEBI |
# Install dependencies
just install
# Run all quality checks
just qc
# Validate a single process entry
just validate kb/processes/Nitrogen_Cycling.yaml
# Validate ontology term references
just validate-terms
# Fetch and cache a PubMed reference
just fetch-reference PMID:12345678kb/processes/ # YAML knowledge base entries (one per ecological process)
kb/modules/ # Reusable mechanism modules
kb/groupings/ # Process groupings
src/ecomech/ # Python source: validation, rendering, CLI
src/ecomech/schema/ # LinkML schema definition
conf/ # OAK configuration for term validation
references_cache/ # Cached PubMed abstracts (auto-generated)
templates/ # HTML rendering templates
pages/processes/ # Generated HTML pages (derived, not committed)
tests/ # Test suite
See CONTRIBUTING.md for curation guidelines.
Use the /curate skill in Claude Code to perform a full literature-driven curation workflow for a new ecological process.
BSD-3-Clause