Zotero Research Library

Zotero Research Library

Operating Rules

• Prefer read-only local access first. Use Zotero Local API if enabled, or open zotero.sqlite with mode=ro&immutable=1.
• Never write directly to zotero.sqlite while Zotero is running. Treat direct SQLite writes as a last-resort experiment requiring explicit user approval, a backup, and Zotero closed.
• For edits, prefer official Zotero Web API writes with an API key. Local API is currently GET-only.
• For native PDF highlights/annotations, prefer Zotero UI or a Zotero-side bridge/plugin/MCP. Do not promise reliable native annotation creation via local API or SQLite alone.
• Preserve provenance: include Zotero item key, itemID, attachment key, page labels, colors, comments, DOI/URL, and local attachment path in digests.

Tool Selection

Use this skill as the default for lightweight paper-reading work:

• inspect papers already in Zotero
• export notes/highlights/annotations into a digest
• answer questions about the user's reading state
• create a child note only after an explicit write request

Reach for a community tool instead when the request exceeds this skill's scope:

• 54yyyu/zotero-mcp: best broad MCP choice for semantic search, full-text indexing, native annotation access, DOI import, collections, and hybrid local-read/web-write workflows.
• cli-anything-zotero: strongest local-write option when a Zotero JS Bridge plugin is acceptable and the user wants local write operations without a Zotero Web API key.
• llm-for-zotero: best in-reader experience when the user wants LLM help inside Zotero while reading PDFs.
• WenyuChiou/zotero-skills or c0mm4nd/zotero-skills: better than this skill for full Web API CRUD over items, notes, collections, tags, and attachments.
• drguptavivek/zotero-use: useful for writing workflows that involve Zotero references and Word .docx citation fields.
• ketthub/zotero-skill: useful as a minimal read-only search implementation; this skill already covers a similar local-read niche but with annotation digest support.

Quick Start

Use the bundled read-only helper for local inspection:

python3 "$CODEX_HOME/skills/zotero-research-library/scripts/zotero_read.py" --db "$HOME/Zotero/zotero.sqlite" search "SABER"
python3 "$CODEX_HOME/skills/zotero-research-library/scripts/zotero_read.py" --db "$HOME/Zotero/zotero.sqlite" digest --item-key ITEMKEY --output reading-digest.md

On a remote Mac, run through SSH:

ssh sourya-mac 'python3 /path/to/zotero_read.py --db "$HOME/Zotero/zotero.sqlite" digest --item-key ITEMKEY'

Use the Web API note helper only when the user explicitly wants a Zotero note written:

ZOTERO_API_KEY=... ZOTERO_USER_ID=... \
python3 "$CODEX_HOME/skills/zotero-research-library/scripts/zotero_web_note.py" \
  --parent ITEMKEY --title "Codex reading synthesis" --markdown notes.md

Dry-run is the default. Add --execute only after confirming the target item and note body.

Common Workflows

Inspect a paper the user is reading

1. Search by title/DOI/arXiv ID with zotero_read.py search.
2. Identify the clean parent item, not stale webpage or troubleshooting items.
3. Run zotero_read.py digest --item-key ....
4. Read the digest plus, if needed, extract the attached PDF text with the pdf skill.
5. Summarize the user's highlights and answer their margin questions.

Create a reading digest

Include:

• metadata: title, creators, year, DOI, URL, item key
• child notes
• attachments and local paths
• annotation count by color
• annotations ordered by attachment sort/page order
• comments separately from selected text
• an interpretation section only after raw evidence is captured

Add or update notes

• Use Zotero Web API writes with a key that has write access.
• Prefer creating a new child note over editing an existing note unless the user asks to modify a specific note.
• Use --dry-run first and show the target parent key/title.
• Remind the user that Zotero desktop may need sync before Web API changes appear locally.

Annotation/highlight edits

• Reading existing annotations is safe via local DB/Local API/Web API.
• Creating native PDF annotations is not reliably supported by Zotero Local API alone. Web API exposes annotations as child items, but local GET-only API cannot create them, and direct DB insertion may not appear in the reader due to runtime/cache internals.
• If native annotation creation is important, consider installing a Zotero MCP/plugin/JS bridge. See references/web-findings.md.
• A safe alternative is to create a child note with quoted passages and page labels, then ask the user to apply highlights manually in Zotero.

Resources

• scripts/zotero_read.py: read-only local SQLite search/detail/digest exporter.
• scripts/zotero_web_note.py: explicit Web API child-note creation helper with dry-run default.
• references/web-findings.md: current API/MCP findings and constraints.