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Paper Search MCP Server

Python MCP server and CLI for searching, deduplicating, downloading, and reading academic papers across open and public sources such as arXiv, PubMed, bioRxiv, Semantic Scholar, OpenAlex, CORE, Europe PMC, Zenodo, HAL, and more.

by openags · submitted by oktofeesh1·added 2026-06-05·
Review first review before installing

Open the source and read safety notes before installing.

Citation facts

Source-backed facts for citing this resource, derived directly from the registry — also available as plain text for AI assistants.

Source URLs
https://github.com/openags/paper-search-mcp/blob/main/README.md, https://github.com/openags/paper-search-mcp
Brand
Paper Search MCP
Brand domain
github.com
Safety notes
Prefer open-access and publisher-permitted sources. The README describes Sci-Hub as optional, unstable, jurisdiction-dependent, and user-responsibility-only., Download and read tools can retrieve PDFs and extract text; confirm copyright, license, institutional, and project-policy requirements before downloading or sharing papers., Optional source credentials, proxy URLs, and API keys can change access levels and rate limits; store them as secrets rather than in prompts or committed configs., Google Scholar, SSRN, CORE, OpenAIRE, BASE, and other sources may rate-limit, block, or return incomplete results depending on network conditions and provider policies., Paid or restricted connectors should stay disabled unless the user has valid credentials and rights to use those services.
Privacy notes
Queries may reveal research topics, grant interests, product plans, biomedical topics, legal theories, security research, or competitive intelligence., Downloaded PDFs, extracted text, search results, DOI lists, API keys, proxy URLs, emails, and source-specific logs can contain sensitive research or credential data., MCP transcripts and model-provider logs may retain paper queries, abstracts, titles, authors, downloaded text, and notes outside library or institutional systems., Do not paste private API keys, proxy credentials, unpublished manuscripts, review assignments, patient-adjacent research details, or embargoed paper content into prompts.
Author
openags
Submitted by
oktofeesh1
Claim status
unclaimed
Last verified
2026-06-05

Decision playbook

Review trust signals before you adopt

Signals are present but mixed. Use the checklist below to confirm the source and operational safety for your environment.

Compare context
Selected

0

Current score

63

Baseline

Delta

No baseline selected

No major trust-signal divergence detected in the current selection.

Source and provenance checks

Needs review

Confirm ownership and provenance before trusting install instructions.

  • Source link availableRequired

    Open the canonical repository and verify ownership.

    Done
  • Source provenance statusRequired

    Marked as source-backed.

    Done
  • Metadata reviewed

    No reviewed flag detected in metadata.

    Pending

Safety and privacy checks

Complete

Validate risk disclosures before installation or API wiring.

  • Safety notes presentRequired

    Review the listed safety guidance before running commands.

    Done
  • Privacy notes presentRequired

    Review data handling notes before connecting accounts or secrets.

    Done
  • Trust level risk gateRequired

    Trust level does not block evaluation.

    Done

Package and install checks

Needs review

Check package metadata and artifact integrity signals.

  • Install payload available

    Install or copy payload is available for review.

    Done
  • Package verification flag

    No package verification flag provided.

    Pending
  • Checksum metadata

    No checksum provided for downloaded artifact.

    Pending

Compare-driven decision checks

Needs review

Use compare context to validate trade-offs before adoption.

  • Compare tray has multiple entries

    Add at least one more entry to compare trust differences.

    Pending
  • Baseline comparison available

    No baseline peer selected yet.

    Pending
  • Diverging trust signals identified

    No major trust-signal divergence found.

    Pending

Setup at a glance

CLI install

Copy-ready — paste the snippet to get started.

15 minutes

Adoption plan

Balanced adoption plan

Current risk score 24/100. Use staged verification before broader rollout.

Risk 24

Pre-adoption checks

Validate source and review signals before any execution.

  • Confirm source provenanceRequired

    Source URL/provenance metadata is present.

    Done
  • Confirm metadata review state

    No review metadata found; increase manual validation.

    Pending
  • Verify install payload

    Install/config payload exists and can be inspected.

    Done

Security checks

Confirm safety, privacy, and package integrity signals.

  • Review safety notesRequired

    Safety notes are present.

    Done
  • Review privacy notesRequired

    Privacy notes are present.

    Done
  • Verify package integrity metadata

    No package verification/checksum metadata.

    Pending

Rollout

Adopt in controlled steps based on the selected plan.

  • Run in isolated sandbox firstRequired

    Use a constrained sandbox and observe behavior across multiple tasks.

    Pending
  • Roll out graduallyRequired

    Roll out to a small cohort before wider usage.

    Pending
  • Set monitoring and fallback

    Define rollback path and monitor errors after adoption.

    Pending

Evidence readiness

Evidence readiness matrix · balanced

Missing required evidence: Metadata review. Risk score 31.

Risk 31

Source provenance

Present

Source repository/provenance is listed.

Required in this preset

Metadata review

Missing

Review metadata is missing.

Required in this preset

Safety notes

Present

Safety notes are present.

Required in this preset

Privacy notes

Present

Privacy notes are present.

Optional in this preset

Package integrity

Missing

Package integrity metadata is missing.

Optional in this preset

Install payload

Present

Install payload is available.

Required in this preset

Required gaps: Metadata review

Decision timeline

Decision timeline · balanced

Blocking gaps: Check metadata review status. Risk 28.

Risk 28

triage

Confirm source provenanceRequired

Source/provenance metadata is available.

Done

triage

Check metadata review statusRequired

Review metadata is missing.

Pending

verify

Review safety notesRequired

Safety notes are available.

Done

verify

Review privacy notes

Privacy notes are available.

Done

verify

Validate package integrity metadata

Package integrity metadata is missing.

Pending

rollout

Verify install payload and commandsRequired

Install payload is available.

Done

Blockers: Check metadata review status

Prerequisite readiness

Prerequisite readiness

5 prerequisites to line up before setup. Have accounts and credentials ready first. Includes a review or approval gate.

0/5 ready
Account & credentials1Install & runtime1Network & hosting2Review & approval115 minutes

Safety & privacy surface

Safety & privacy surface

5 safety and 4 privacy notes across 4 risk areas. Review closely: credentials & tokens, permissions & scopes, network access.

4 areas
  • SafetyGeneralPrefer open-access and publisher-permitted sources. The README describes Sci-Hub as optional, unstable, jurisdiction-dependent, and user-responsibility-only.
  • SafetyNetwork accessDownload and read tools can retrieve PDFs and extract text; confirm copyright, license, institutional, and project-policy requirements before downloading or sharing papers.
  • SafetyCredentials & tokensOptional source credentials, proxy URLs, and API keys can change access levels and rate limits; store them as secrets rather than in prompts or committed configs.
  • SafetyNetwork accessGoogle Scholar, SSRN, CORE, OpenAIRE, BASE, and other sources may rate-limit, block, or return incomplete results depending on network conditions and provider policies.
  • SafetyCredentials & tokensPaid or restricted connectors should stay disabled unless the user has valid credentials and rights to use those services.
  • PrivacyPermissions & scopesQueries may reveal research topics, grant interests, product plans, biomedical topics, legal theories, security research, or competitive intelligence.
  • PrivacyCredentials & tokensDownloaded PDFs, extracted text, search results, DOI lists, API keys, proxy URLs, emails, and source-specific logs can contain sensitive research or credential data.
  • PrivacyNetwork accessMCP transcripts and model-provider logs may retain paper queries, abstracts, titles, authors, downloaded text, and notes outside library or institutional systems.
  • PrivacyCredentials & tokensDo not paste private API keys, proxy credentials, unpublished manuscripts, review assignments, patient-adjacent research details, or embargoed paper content into prompts.

Safety notes

  • Prefer open-access and publisher-permitted sources. The README describes Sci-Hub as optional, unstable, jurisdiction-dependent, and user-responsibility-only.
  • Download and read tools can retrieve PDFs and extract text; confirm copyright, license, institutional, and project-policy requirements before downloading or sharing papers.
  • Optional source credentials, proxy URLs, and API keys can change access levels and rate limits; store them as secrets rather than in prompts or committed configs.
  • Google Scholar, SSRN, CORE, OpenAIRE, BASE, and other sources may rate-limit, block, or return incomplete results depending on network conditions and provider policies.
  • Paid or restricted connectors should stay disabled unless the user has valid credentials and rights to use those services.

Privacy notes

  • Queries may reveal research topics, grant interests, product plans, biomedical topics, legal theories, security research, or competitive intelligence.
  • Downloaded PDFs, extracted text, search results, DOI lists, API keys, proxy URLs, emails, and source-specific logs can contain sensitive research or credential data.
  • MCP transcripts and model-provider logs may retain paper queries, abstracts, titles, authors, downloaded text, and notes outside library or institutional systems.
  • Do not paste private API keys, proxy credentials, unpublished manuscripts, review assignments, patient-adjacent research details, or embargoed paper content into prompts.

Prerequisites

  • Python 3.10 or newer, with uv recommended for the documented no-install and persistent-install paths.
  • Network access to public academic sources and repositories.
  • Optional API keys or emails configured only for sources the user is authorized to access.
  • A policy decision on whether download, read, optional Sci-Hub fallback, paid-platform skeleton connectors, and proxy-based Google Scholar discovery are allowed.
  • Output directories and downloaded PDF retention reviewed for research workflows.

Schema details

Install type
cli
Troubleshooting
No
Source repository stats
Scope
Source repo
Collection metadata
Estimated setup
15 minutes
Difficulty
intermediate
Full copyable content
{
  "mcpServers": {
    "paper-search-mcp": {
      "command": "uvx",
      "args": ["paper-search-mcp"],
      "env": {
        "PAPER_SEARCH_MCP_UNPAYWALL_EMAIL": "YOUR_EMAIL",
        "PAPER_SEARCH_MCP_SEMANTIC_SCHOLAR_API_KEY": "OPTIONAL_API_KEY",
        "PAPER_SEARCH_MCP_CORE_API_KEY": "OPTIONAL_API_KEY"
      }
    }
  }
}

About this resource

Content

Paper Search MCP Server is a Python MCP server and CLI for academic literature workflows. It can search papers, deduplicate results across sources, download open-access PDFs where available, and extract text so an MCP client can work with paper metadata and content.

The project is broader than a single-source server: the README describes connectors for arXiv, PubMed, bioRxiv, medRxiv, Semantic Scholar, Crossref, OpenAlex, PubMed Central, CORE, Europe PMC, dblp, OpenAIRE, CiteSeerX, DOAJ, BASE, Zenodo, HAL, SSRN, Unpaywall, and optional restricted or paid-platform connectors. It also includes a Claude Code skill path for users who prefer a skill plus CLI workflow instead of an MCP server.

Source Review

These sources were reviewed on 2026-06-05. Prefer the live repository, README, license, Python package metadata, environment example, Dockerfile, Smithery config, Claude Code skill, server and CLI modules, config model, paper model, representative connectors, and PyPI metadata for current installation, source support, and caveats.

Features

  • Search papers across multiple academic sources.
  • Deduplicate and standardize search results.
  • Download open-access PDFs through source-native and fallback paths.
  • Extract readable paper text for MCP workflows.
  • Use optional API keys for Unpaywall, CORE, Semantic Scholar, DOAJ, Zenodo, and other supported services.
  • Use a Claude Code skill plus CLI workflow as an alternative to MCP configuration.
  • Run through uvx, uv tool install, pip, Smithery, Docker, or source checkout.
  • Keep optional restricted or unstable connectors separate from the open-access-first path.

Installation

Run the MCP server with uvx:

uvx paper-search-mcp

For Claude Desktop-style JSON configuration:

{
  "mcpServers": {
    "paper-search-mcp": {
      "command": "uvx",
      "args": ["paper-search-mcp"],
      "env": {
        "PAPER_SEARCH_MCP_UNPAYWALL_EMAIL": "YOUR_EMAIL",
        "PAPER_SEARCH_MCP_SEMANTIC_SCHOLAR_API_KEY": "OPTIONAL_API_KEY",
        "PAPER_SEARCH_MCP_CORE_API_KEY": "OPTIONAL_API_KEY"
      }
    }
  }
}

Leave optional keys unset unless you need the corresponding provider and have permission to use it.

Use Cases

  • Search recent papers across several academic indexes.
  • Find open-access PDFs for a DOI or title.
  • Read paper text into a literature-review workflow.
  • Compare arXiv, PubMed, Semantic Scholar, Crossref, and OpenAlex metadata.
  • Use Claude Code skills to trigger paper search without MCP server setup.
  • Build a free-first research assistant for public academic sources.
  • Keep restricted connectors disabled unless policy and credentials allow them.

Safety and Privacy

Paper search and download workflows can run into copyright, license, rate-limit, and institutional-access constraints. Prefer open-access sources, keep optional restricted connectors disabled by default, and treat Sci-Hub as a user-enabled fallback with jurisdiction and policy risk rather than a recommended path.

Protect source credentials and research topics. Queries, DOI lists, downloaded PDFs, extracted text, abstracts, API keys, proxy URLs, and emails can reveal private research interests or restricted content. Keep sensitive literature review work out of shared prompts and logs unless approved.

Duplicate Check

No openags/paper-search-mcp entry, Paper Search MCP entry, or matching source URL was found in content/mcp. The existing arXiv MCP entry covers a narrower single-source arXiv server.

Source citations

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How it compares

Paper Search MCP Server side by side with 3 alternatives on trust, install, platform support, and disclosed safety notes — all from reviewed registry metadata.

1 trust signal differ across this comparison (Submitter).

Field

Python MCP server and CLI for searching, deduplicating, downloading, and reading academic papers across open and public sources such as arXiv, PubMed, bioRxiv, Semantic Scholar, OpenAlex, CORE, Europe PMC, Zenodo, HAL, and more.

Open dossier

MCP server for searching, downloading, reading, and analyzing arXiv papers through Claude and other MCP clients.

Open dossier

MCP server for connecting Claude, ChatGPT, Cursor, and other MCP clients to a local or web Zotero research library for paper search, metadata, full text, annotations, notes, collections, semantic search, and citation workflows.

Open dossier

Local-first codebase intelligence MCP server that indexes repositories with tree-sitter, stores searchable chunks in DuckDB, and gives Claude semantic search, regex search, daemon status, and deep code research tools.

Open dossier
Next steps
Trust
Review statusNot reviewedNot reviewedNot reviewedNot reviewed
Package trustPackage not verifiedPackage not verifiedPackage not verifiedPackage not verified
Source provenanceSource-backedSource-backedSource-backedSource-backed
SubmitterDiffersoktofeesh1oktofeesh1oktofeesh1
Install riskReview firstReview firstReview firstReview first
Notes Safety ✓ Privacy ✓ Safety ✓ Privacy ✓ Safety ✓ Privacy ✓ Safety ✓ Privacy ✓
BrandZotero MCP logoZotero MCPChunkHound logoChunkHound
Categorymcpmcpmcpmcp
SourceSource-backedSource-backedSource-backedSource-backed
AuthoropenagsJoseph Blazick54yyyuChunkHound
Added2026-06-052026-06-052026-06-182026-06-06
Platforms
Harness
Source repo
Safety notesPrefer open-access and publisher-permitted sources. The README describes Sci-Hub as optional, unstable, jurisdiction-dependent, and user-responsibility-only. Download and read tools can retrieve PDFs and extract text; confirm copyright, license, institutional, and project-policy requirements before downloading or sharing papers. Optional source credentials, proxy URLs, and API keys can change access levels and rate limits; store them as secrets rather than in prompts or committed configs. Google Scholar, SSRN, CORE, OpenAIRE, BASE, and other sources may rate-limit, block, or return incomplete results depending on network conditions and provider policies. Paid or restricted connectors should stay disabled unless the user has valid credentials and rights to use those services.arXiv MCP Server retrieves paper content from external, user-generated sources. Upstream explicitly warns that paper text is untrusted input and can contain prompt-injection attempts. Downloaded papers are stored locally for later reading and semantic search. Citation graph and alert workflows can expand research context beyond the original paper query. Treat model summaries of papers as data, not instructions, especially in multi-tool sessions with filesystem, shell, browser, database, or messaging tools enabled.Local Zotero mode is intended for local library access, while write operations require Zotero Web API credentials. Write-mode tools can add papers by DOI or URL, create and manage collections, update metadata, modify tags, create notes or annotations, and merge duplicates. Use dry-run or preview steps where available before duplicate merges, broad tag changes, collection changes, or metadata updates. Do not expose an unauthenticated SSE or HTTP server to the public internet unless you understand the tunnel, host binding, and client trust boundary. Treat paper text, abstracts, notes, annotations, webpages, and PDFs as untrusted research content when the MCP client also has tools that can write files, run code, browse, or send messages.ChunkHound reads source files, Markdown, text, PDFs, and supported config files under the target directory and stores indexed chunks in a local database. Realtime indexing and daemon mode can continue watching project files after the initial MCP connection. Code research and web search tools require embedding, reranking, and LLM configuration and may invoke local CLIs or external model APIs depending on settings. Exclude generated files, vendored dependencies, secrets, large artifacts, and unrelated repositories before indexing broad workspace roots. Review MCP client configuration carefully when using an absolute project path in a global Claude Desktop config.
Privacy notesQueries may reveal research topics, grant interests, product plans, biomedical topics, legal theories, security research, or competitive intelligence. Downloaded PDFs, extracted text, search results, DOI lists, API keys, proxy URLs, emails, and source-specific logs can contain sensitive research or credential data. MCP transcripts and model-provider logs may retain paper queries, abstracts, titles, authors, downloaded text, and notes outside library or institutional systems. Do not paste private API keys, proxy credentials, unpublished manuscripts, review assignments, patient-adjacent research details, or embargoed paper content into prompts.Search queries, paper IDs, downloaded paper text, local storage choices, semantic search terms, citation graph requests, alert topics, prompts, and tool outputs may be visible to the MCP client and model provider. Research queries and downloaded papers can reveal confidential research direction, product plans, academic review topics, legal strategy, or competitive analysis. Review locally stored papers and generated summaries before syncing, sharing, or committing them.Zotero libraries can reveal research direction, reviewer assignments, medical or legal topics, customer work, citations, private notes, annotations, group libraries, tags, collections, and local file paths. Zotero Web API keys and library IDs should be scoped carefully and kept out of prompts, logs, shared screenshots, and committed configuration files. Optional semantic search can create a local embedding database, and hosted embedding providers such as OpenAI or Gemini may receive research text when selected. Tunneled ChatGPT or web-client setups may expose library search and document context outside the local machine; review the tunnel URL, session handling, and tool permissions before use.Indexed chunks, file paths, symbols, comments, Markdown, PDFs, configuration values, database files, daemon state, and search results can reveal proprietary source code and internal architecture. Embedding, reranking, LLM, and web search providers may receive code-derived queries or snippets if configured. Local ChunkHound database files, logs, daemon state, and MCP transcripts may retain code-derived context after the session ends. Avoid sharing ChunkHound databases, config files with API keys, verbose logs, research outputs, and screenshots from private repositories.
Prerequisites
  • Python 3.10 or newer, with uv recommended for the documented no-install and persistent-install paths.
  • Network access to public academic sources and repositories.
  • Optional API keys or emails configured only for sources the user is authorized to access.
  • A policy decision on whether download, read, optional Sci-Hub fallback, paid-platform skeleton connectors, and proxy-based Google Scholar discovery are allowed.
  • Python 3.11 or newer available to the MCP client runtime.
  • uvx available for package execution.
  • Local storage available for downloaded papers.
  • Optional PDF extra if you need older papers that do not have HTML content.
  • Python 3.10 or newer available to the MCP client runtime.
  • Zotero 7 or newer with the local API enabled for local library access.
  • `uv`, `pip`, or `pipx` available for installing `zotero-mcp-server`.
  • A Zotero API key, library ID, and library type when using Zotero Web API or write-mode workflows.
  • Python 3.10 or newer and the `uv` package manager.
  • A local repository or workspace you are authorized to index.
  • ChunkHound JSON config reviewed for database path, excludes, embeddings, and LLM provider settings.
  • Optional embedding provider credentials for semantic search, or regex-only usage when no embedding key is configured.
Install
uvx paper-search-mcp
uvx arxiv-mcp-server
uv tool install zotero-mcp-server
uv tool install chunkhound
Config
Manual-only setup:
uv tool install paper-search-mcp
uv tool run paper-search-mcp
{
  "mcpServers": {
    "arxiv": {
      "command": "uvx",
      "args": ["arxiv-mcp-server"]
    }
  }
}
{
  "mcpServers": {
    "zotero": {
      "command": "zotero-mcp",
      "env": {
        "ZOTERO_LOCAL": "true"
      }
    }
  }
}
{
  "mcpServers": {
    "chunkhound": {
      "command": "chunkhound",
      "args": ["mcp", "/path/to/approved/project"]
    }
  }
}
Citations
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