Zotseek

Skill dahliasan/researchskills/skills/zotseek

Semantic search over a Zotero library via ZotSeek MCP (search, find_similar, index_status). Use when the user asks for ZotSeek, semantic Zotero search, related papers from embeddings, manuscript citation curation from the library, or PDF-page snippets with zotero:// deep links. Prefer this over keyword-only Zotero search when relevance ranking or passage evidence matters. Not a substitute for project RAG or for listing a named collection (use zotero for collection membership and PDF paths).From its SKILL.md

Install

npx -y skills add dahliasan/researchskills --skill zotseek

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

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SKILL.md

4.9 KB, as published. Nobody here has run it

ZotSeek (semantic Zotero MCP)

ZotSeek is a Zotero plugin that embeds library PDFs locally and exposes MCP tools at http://localhost:23119/zotseek/mcp (same port family as the Zotero Connector).

Download / install the plugin (not this skill): introfini/ZotSeek → Releases (.xpi) → Zotero Tools → Plugins → Install Plugin From File. Then enable AI Agent Access in ZotSeek settings and allow Zotero local HTTP access (Settings → Advanced). MCP setup notes: docs/MCP.md.

This skill documents agent workflow. It does not install ZotSeek, and it is unrelated to 54yyyu/zotero-mcp (a separate Python MCP server; that is routed by skill zotero when present).

When to use

Goal	Tooling
Natural-language / semantic paper find	ZotSeek `search`
More like this paper	ZotSeek `find_similar`
Items in a named collection + PDF paths	`zotero` (MCP if present, else local scripts)
BibTeX / cite / write collections	`zotero`
OpenAlex discovery (new papers)	`discover-papers`

Preconditions

Zotero is running with ZotSeek installed and indexed.
MCP registered in the harness (see reference.md).
ZotSeek reachable on localhost:23119 (or tunneled there). If Zotero runs on another machine:

ssh -fN -L 23119:127.0.0.1:23119 your-zotero-host
# Check: lsof -i :23119

If skill zotero-private is installed, load it first for this machine’s tunnel alias and MCP bridge path.

Smoke test: curl -sS http://localhost:23119/zotseek/mcp should not connection-refuse.

Agent workflow

Ensure port 23119 is listening (tunnel if remote; follow zotero-private when present).
index_status — confirm ready, coverage, lastIndexed. If not ready, stop and tell the user to index in ZotSeek.
search — write a concrete scholarly query (species + place + process), not a single vague keyword.
Present results with title, authors, year, snippet + page, and clickable links:
- Prefer links.selectHttp / links.openPdfHttp in clients that do not linkify zotero://.
For expansion from a known hit, call find_similar with that itemKey.
Curate, do not dump: mark keep / maybe / skip against the user's section goal.
Collection membership is not in ZotSeek results — cross-check with zotero when needed.

Query tips

One claim or section theme per query; run several targeted queries rather than one mega-query.
Default mode: hybrid. Use semantic for paraphrase recall; keyword for exact author/title.
granularity: passages when drafting and you need page-level quotes; papers for shortlists.

Tools (names)

Tool	Required args	Notes
`index_status`	—	Call first
`search`	`query`	Optional: `max_results`, `mode`, `min_similarity`, `granularity`, `library_key`
`find_similar`	`item_key`	Optional: `library_key`, `max_results`

library_key: omit for all indexed libraries; user for personal; group:<id> for a group.

MCP fallback (no harness tool)

If the zotseek MCP server is not loaded but port 23119 is up, call JSON-RPC over HTTP (initialize → tools/call). Full recipe: reference.md.

Setup (once per harness)

Prefer stdio bridge in Cursor when HTTP MCP shows SSE errors. Point at this pack's bridge script:

"zotseek": {
  "command": "/usr/bin/python3",
  "args": ["/ABSOLUTE/PATH/TO/researchskills/skills/zotseek/scripts/zotseek_stdio_mcp.py"]
}

Use an absolute path (expand ~). The bridge calls REST GET /zotseek/* on 127.0.0.1:23119.

HTTP transport still works in clients that do not require SSE GET:

claude mcp add --transport http --scope user zotseek http://localhost:23119/zotseek/mcp

Details: reference.md.

Related skills

zotero-private — optional host overlay (tunnel / remote library); load when present
zotero — library router (prefer MCP if present, else local API scripts)
zotero-mcp — install/config for 54yyyu/zotero-mcp
manuscript-writing — how cites land in prose
discover-papers — find new papers outside the library