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Quickstart

Get started with linkml-reference-validator in 5 minutes.

Installation

pip install linkml-reference-validator

Or with uv:

uv pip install linkml-reference-validator

Validate a Single Quote

The most common use case - verify that a quote appears in its cited reference:

linkml-reference-validator validate text \
  "MUC1 oncoprotein blocks nuclear targeting of c-Abl" \
  PMID:16888623

Output:

Validating text against PMID:16888623...
  Text: MUC1 oncoprotein blocks nuclear targeting of c-Abl

Result:
  Valid: True
  Message: Supporting text validated successfully in PMID:16888623

The reference is automatically fetched from PubMed and cached locally in references_cache/.

Validate Data Files

For batch validation, create a LinkML schema and data file:

schema.yaml:

id: https://example.org/my-schema
name: my-schema

prefixes:
  linkml: https://w3id.org/linkml/

classes:
  Statement:
    attributes:
      id:
        identifier: true
      supporting_text:
        slot_uri: linkml:excerpt
      reference:
        slot_uri: linkml:authoritative_reference

data.yaml:

- id: stmt1
  supporting_text: MUC1 oncoprotein blocks nuclear targeting of c-Abl
  reference: PMID:16888623

Validate:

linkml-reference-validator validate data \
  data.yaml \
  --schema schema.yaml \
  --target-class Statement

Validate Against a DOI

You can also validate text against DOIs using the Crossref API:

linkml-reference-validator validate text \
  "Nanometre-scale thermometry" \
  DOI:10.1038/nature12373

This works the same way as PMID validation - the reference is fetched and cached locally.

Validate Against Local Files

You can also validate against local markdown, text, or HTML files:

linkml-reference-validator validate text \
  "JAK1 binds to the receptor complex" \
  file:./research/jak-notes.md

Validate Against URLs

Web pages can also be used as references:

linkml-reference-validator validate text \
  "Climate change affects biodiversity" \
  url:https://example.org/climate-report.html

Key Features

  • Automatic Caching: References cached locally after first fetch
  • Editorial Notes: Use [...] for clarifications: "MUC1 [mucin 1] oncoprotein"
  • Ellipsis: Use ... for omitted text: "MUC1 ... nuclear targeting"
  • Title Validation: Verify reference titles with dcterms:title
  • Deterministic Matching: Substring-based (not AI/fuzzy matching)
  • PubMed & PMC: Fetches from NCBI automatically
  • DOI Support: Fetches metadata from Crossref API
  • Local Files: Validate against markdown, text, or HTML files
  • URL Support: Validate against web pages

Next Steps