paperqa-mcp-server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| index_statusA | Check the health of the paper index. Returns a summary of how many papers are indexed, how many have errors, and how many are unindexed. Use this to diagnose why paper_qa queries might be failing or timing out. |
| paper_qaA | Search and synthesize across all papers in the library. Use this for questions that require deep reading and synthesis across multiple scientific papers — e.g. "What methods have been used to recycle lithium from spent batteries?" or "Compare the thermal stability of PEEK vs PTFE in the literature." Returns a detailed answer with inline citations. Each citation includes a file path containing an 8-character Zotero storage key (e.g. ABC123DE from storage/ABC123DE/paper.pdf). You can use these keys with zotero-mcp tools to look up the full bibliographic record, read annotations, or find related items. Not for quick metadata lookups or library browsing — use Zotero tools for that. If this tool returns "Index incomplete", the paper index has not been fully built yet. Tell the user to run the index build command from the terminal (see the paperqa-mcp-server README, step 6). Do not retry the query — it will give the same result until the index is built. This tool can take 30–90 seconds to respond when working normally. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 2 tools
The two tools have completely distinct purposes with no overlap: index_status is for health/status monitoring of the indexing system, while paper_qa is for querying and synthesizing content across papers. Their descriptions clearly differentiate diagnostic vs. query functionality.
Both tools follow a consistent snake_case naming pattern with clear verb_noun structure: index_status (verb: check/status, noun: index) and paper_qa (verb: query/answer, noun: paper). The naming is predictable and readable throughout.
With only 2 tools, the server feels severely under-scoped for a paper query and synthesis domain. A typical paper/library server would need at least basic CRUD operations for papers, search filtering, or metadata management, but here the surface is minimal and relies heavily on external Zotero tools.
The toolset is incomplete for the apparent domain of paper querying and synthesis. There are no tools for managing papers (add/remove), browsing the library, filtering searches, or handling indexing beyond status checks. The server delegates core functionality to Zotero tools, creating significant gaps for agent workflows.