salmon-domain-ontology

Shared salmon interoperability ontology for cross-organization data integration.

Integration context: See the Salmon Data Integration System overview page (https://br-johnson.github.io/salmon-data-integration-system/) and walkthrough video (https://youtu.be/B0Zqac49zng?si=VmOjbfMDMd2xW9fH).

Project status

This repository is under active development as we build out the Salmon Domain Ontology as a reusable, cross-organization semantic layer for salmon data.

Contributions welcome

We welcome contributions from domain experts, data stewards, and ontology practitioners.

If you want to contribute:

• Open an issue describing the use case, gap, or term request.
• Use issue templates under .github/ISSUE_TEMPLATE/ for new terms, missing parents, definition updates, and obsoletions.
• Reference relevant domain standards, vocabularies, or source schemas where possible.
• Submit a pull request for proposed ontology/module updates.
• Follow CONVENTIONS.md for namespace and modeling rules.

Current structure

• ontology/salmon-domain-ontology.ttl - modular primary build (imports modules 01-07 + conservative alignment)
• salmon-domain-ontology.ttl - flattened, import-free master TTL artifact for one-file consumers (generated)
• ontology/salmon-domain-ontology-research.ttl - optional research build (adds exploratory alignment module)
• ontology/salmon-domain-ontology-rda-case-study.ttl - optional case-study bridge build (adds profile bridge mappings from the RDA juvenile-condition graph, including Hakai + Neville decomposition terms)
• ontology/modules/ - category modules + alignment modules + profile bridge modules
• ontology/views/ - optional, non-normative metamodel views for maintainers and salmon biologists
• CONVENTIONS.md - modeling and namespace conventions (smn: canonical)
• docs/context/widoco.md - WIDOCO publication workflow and output contract
• docs/migrations/README.md - migration map, boundary rules, adoption checklist, cutover runbook, smoke-run templates, and release-readiness notes
• docs/publishing/namespace-decision.md - namespace stabilization decision and freeze rule
• docs/publishing/w3id-request-payload.md - merged smn W3ID registration record + follow-up publication checklist
• docs/guides/modules-and-bridges-for-biologists.md - beginner-friendly guide to modules, local profiles, and bridge mapping

Where non-core terms live

For teams using MetaSalmon Data GPT / R package with local or program-specific terms:

1. File-first (recommended first step): keep local terms in a project-local profile file (their own namespace), map conservatively to shared smn:.
2. Collaborative profile artifact (optional): if multiple teams need shared access to the same local contract, use https://w3id.org/smn/profile/<program>/ as a temporary bridge namespace.
3. Shared-core promotion (rare): promote to smn: only when term reuse is broad and semantics are stable.

If a team wants an independent WIDOCO site for profile terms, run WIDOCO against their own profile ontology source and host that site under their own namespace/hosting. SMN's own publication workflow remains centered on the shared ontology plus curated pilot profiles, so this is the simplest way to serve a separate profile docs site without expanding the core namespace.

Docs / publication workflow

The repo now has a first-pass publication pipeline matching the DFO pattern in a lighter form.

Core commands:

• make install-widoco
• make install-robot
• make compose-case-study-modules
• make compose-flat-ttl
• make verify-ontology-parse
• make verify-year-age-semantic-contract
• make verify-term-definitions
• make verify-flat-ttl
• make verify-doc-term-anchors
• make verify-doc-version-metadata
• make test
• make ci
• make verify-generated-artifacts
• make docs-refresh
• make release-snapshot VERSION=X.Y.Z
• make release VERSION=X.Y.Z

Generated publication targets:

• docs/index.html
• docs/smn.ttl
• docs/smn.owl
• docs/smn.jsonld
• docs/releases/<version>/

Note: Java 17+ is required for WIDOCO and ROBOT. The repo now carries generated latest assets under docs/ plus immutable release snapshots under docs/releases/<version>/. make release VERSION=X.Y.Z is the canonical release path: it updates ontology version metadata, refreshes the WIDOCO publication surface, runs validation, and writes the immutable snapshot. Root, SemVer, and canonical term-path W3ID routing use those published targets; term paths such as https://w3id.org/smn/Escapement dereference to WIDOCO anchors by default and remain content-negotiable for Turtle, RDF/XML, and JSON-LD.

New to ontologies?

Start with docs/guides/modules-and-bridges-for-biologists.md. It explains the module + bridge approach in plain language for dataset teams.

If you want the optional mental-model view of how entity/property/variable/constraint/method/result pieces fit together, then read ontology/views/README.md next.