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zot: full-text PDF retrieval via Zotero built-in connectors #257

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opened 2026-03-25 19:31:21 +00:00 by kert · 0 comments
kert commented 2026-03-25 19:31:21 +00:00
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Objective

Use Zotero OOB capabilities (not SciHub) to retrieve full-text PDFs for the 10K+ evidence base articles.

Approach

Zotero has built-in PDF retrieval via:

  1. Find Available PDF — uses Unpaywall, PubMed Central, and configured proxy
  2. OpenURL resolver — institutional access via link resolver
  3. Zotero Connector — browser-based retrieval with institutional authentication

Tasks

  • Configure Zotero proxy settings in container for institutional access (if available)
  • Batch "Find Available PDF" via Zotero JS API (run from within container)
  • Track retrieval success rate by source (Unpaywall, PMC, proxy)
  • For items with PMCIDs: direct PMC PDF download
  • Attach PDFs to Zotero items, sync storage to data/zotero/data/storage/
  • Index full text for search via Zotero built-in full-text indexing
  • Report: coverage by pub type (expect ~60% for reviews, ~40% for RCTs)

Why Zotero OOB, not SciHub

  • Legal, auditable, institutional-compatible
  • Unpaywall covers ~50% of recent literature
  • PMC covers all NIH-funded research
  • PDF metadata (DOI linking) is automatic
  • Full-text search is built in

Supersedes #248

This approach replaces the planned SciHub/Unpaywall custom module.

## Objective Use Zotero OOB capabilities (not SciHub) to retrieve full-text PDFs for the 10K+ evidence base articles. ## Approach Zotero has built-in PDF retrieval via: 1. **Find Available PDF** — uses Unpaywall, PubMed Central, and configured proxy 2. **OpenURL resolver** — institutional access via link resolver 3. **Zotero Connector** — browser-based retrieval with institutional authentication ## Tasks - [ ] Configure Zotero proxy settings in container for institutional access (if available) - [ ] Batch "Find Available PDF" via Zotero JS API (run from within container) - [ ] Track retrieval success rate by source (Unpaywall, PMC, proxy) - [ ] For items with PMCIDs: direct PMC PDF download - [ ] Attach PDFs to Zotero items, sync storage to `data/zotero/data/storage/` - [ ] Index full text for search via Zotero built-in full-text indexing - [ ] Report: coverage by pub type (expect ~60% for reviews, ~40% for RCTs) ## Why Zotero OOB, not SciHub - Legal, auditable, institutional-compatible - Unpaywall covers ~50% of recent literature - PMC covers all NIH-funded research - PDF metadata (DOI linking) is automatic - Full-text search is built in ## Supersedes #248 This approach replaces the planned SciHub/Unpaywall custom module.
kert added this to the P29: Skin Substitutes — predatory pricing, distribution, and utilization analysis milestone 2026-03-25 19:31:53 +00:00
kert closed this issue 2026-03-26 06:14:39 +00:00
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Reference: homelab/stack#257
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