Salmon data package + guided review + SPSR intake path

Use this page when your goal is to move from mapped data to a submission-ready salmon data package and a route-scoped SPSR upload.

Canonical package specification (Markdown): https://github.com/dfo-pacific-science/smn-data-pkg/blob/main/SPECIFICATION.md

Operational Intake Path Package-first Route-scoped
Note

This page is for packaging, optional guided review, and intake.

For the maintained package creation/review workflow, use the metasalmon docs:

If you need to propose new vocabulary terms or ontology changes, use the canonical ontology docs: conventions and term requests.

Quick summary

  • Start with a salmon data package (SDP) as the source of truth.
  • The canonical package layout is metadata/ + data/, with an optional root datapackage.json.
  • metasalmon is the canonical package creation, review, and validation workflow before submission.
  • SPSR wizard uploads and bulk uploads should converge on the same package-first path.
  • Current minimum route-scoped support story includes CU/composite, SMU, and Population routes.
  • Guided review tools such as SMN-GPT can help with ambiguity triage after the package exists, but validation remains the quality gate.

Practical workflow

  1. Find canonical terms in GC DFO Salmon Ontology (WIDOCO) and use the metasalmon reusing-standards vignette for the maintained lookup flow.
  2. Create the package with metasalmon (preferred) or assemble it manually to the specification if your project already owns that path.
  3. Review the generated package in the metasalmon package-native loop.
  4. Validate locally with metasalmon::validate_salmon_datapackage(pkg_path, require_iris = TRUE).
  5. Choose the SPSR route scope that matches your data grain:
    • CU/composite
    • SMU
    • Population
  6. Generate or align route-scoped upload CSV(s) from the same package using the current SPSR templates.
  7. Upload through SPSR and review validation feedback.

For bulk uploads, use the same package-first flow. Do not maintain a separate spreadsheet-only bulk route that drifts away from the package metadata.

Package + review references

SPSR touchpoints

Validation gates

Before upload, confirm:

  • all required metadata fields are present
  • all semantic links use canonical full IRIs
  • categorical values are mapped to controlled concepts
  • provenance notes are present for major transformations
  • the selected SPSR route scope matches the grain of the package data
  • bulk upload files and wizard upload files still trace back to the same package version

Cookbook + examples

References