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Add biological accession crosswalk guard#397

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haki203:biological-accession-crosswalk-guard-17
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Add biological accession crosswalk guard#397
haki203 wants to merge 1 commit into
SCIBASE-AI:mainfrom
haki203:biological-accession-crosswalk-guard-17

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@haki203 haki203 commented May 23, 2026

/claim #17

Summary

Adds a distinct biological-accession-crosswalk-guard/ slice for issue #17.

The guard validates canonical biological accession nodes before entity pages or graph recommendations are shown. It checks:

  • namespace-specific formats for NCBI Gene, UniProtKB, PubChem, and MeSH identifiers
  • deprecated aliases that should be replaced by canonical accessions
  • taxon mismatches on biological nodes
  • missing DOI-backed crosswalk evidence
  • low crosswalk confidence
  • duplicate canonical targets
  • unsafe recommendation paths that depend on unresolved crosswalk nodes

It emits deterministic JSON, Markdown, SVG, and MP4 reviewer artifacts from synthetic data only.

Non-overlap

This is not another broad knowledge graph extractor/navigator, link-audit, ontology drift/alias/synonym, relationship conflict, author-affiliation disambiguation, artifact lineage, evidence freshness, instrument-method compatibility, reproducibility route planner, recommendation visibility/diversity guard, negative-result replication signal, measurement harmonization, claim qualifier, ethics provenance, funder award lineage, clinical trial registry guard, software/runtime compatibility guard, or geospatial sample provenance guard.

It focuses specifically on canonical biological accession crosswalk quality for gene/protein/compound/ontology nodes before graph publication or recommendation display.

Validation

  • npm --prefix biological-accession-crosswalk-guard test -> 4 tests passed
  • npm --prefix biological-accession-crosswalk-guard run check -> syntax check passed
  • npm --prefix biological-accession-crosswalk-guard run demo -> generated JSON/Markdown/SVG artifacts
  • npm --prefix biological-accession-crosswalk-guard run video -> generated reports/demo.mp4
  • ..\..\node_modules\ffmpeg-static\ffmpeg.exe -v error -i biological-accession-crosswalk-guard\reports\demo.mp4 -f null NUL -> MP4 decoded without errors
  • git diff --check and git diff --cached --check -> passed
  • Sensitive-pattern scan over biological-accession-crosswalk-guard returned no matches

Safety

Synthetic data only. No private research objects, external ontology services, registry calls, recommendation services, credentials, network calls, payment data, or payout details are included.

AI-assisted with OpenAI Codex; I reviewed and locally verified the diff before submitting.

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