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Public Source Notes

This directory contains sanitized source-note pages for citation routing and claim traceability.

The public export intentionally omits:

  • raw PDF files
  • extracted full-text files
  • local absolute paths
  • machine ingest manifests

Ingest Modes

Provisional bulk-ingest mode

Used for batch ingestion of papers Automatically creates/updates: sources, extracted text, tags, index, and logs Does NOT update core knowledge pages (topic / entity / project / digest) Claim-Level Confidence should reflect only biologically supported claims from the text, not processing steps or system actions

Focused manual crystallization mode

Used for deep curation of priority papers Requires manual reading (including figures, methods, and experimental context) Updates core knowledge pages (topic / entity / project / digest) Emphasizes: context, evidence strength, limitations, and contradictions

Use source_index.md as the public source list. Source-note pages may include conservative summaries, evidence profiles, caveats, related pages, and claim-level confidence statements, but they should not be treated as replacements for the original papers.