Skip to content

Opt-in ECO codes for evidence items in validation reports #9

Description

@NingyuSUN

Since 0.6.0 each extraction_method value carries an ECO term in the LinkML schema (meaning:, see docs/STANDARDS.md), but reports do not show them. Add an opt-in way to include the ECO code for every evidence item in a validation report, so downstream systems that speak ECO can use it directly.

Constraints

  • Opt-in only. The default report must stay byte-for-byte identical, because committed benchmark results and audit hashes depend on it. Suggested: bioevidence validate --annotate-eco and a matching keyword argument in Python.
  • Read the codes from the schema (SchemaView(...).get_enum("ExtractionMethod")), do not hard-code them, so the mapping has one source of truth.

Where to look

  • src/bioevidence_validator/engine.py (RecordValidator.validate builds the report), src/bioevidence_validator/cli.py
  • tests/test_standards.py shows how to read the meanings

Done when

  • With the flag, the report contains, for each evidence item id, its extraction method and ECO CURIE
  • Without the flag, reports are unchanged (the existing replay tests still pass)
  • Tests for both, and a short note in docs/STANDARDS.md and docs/ENGINEERING.md

Activity

  1. NingyuSUN commented on Oct 6, 2026

    @NingyuSUN
    OwnerAuthor

    Closing as not planned. The validation reports and the engine changed substantially in 0.8.0 (grounders, the feedback loop), and opt-in ECO annotations are no longer on the roadmap. The ECO mapping itself stays in the LinkML schema (see docs/STANDARDS.md). Thanks to @PandaHUN777 for the work in #13.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions