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.
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downloaded text, and notes outside library or institutional systems., Do not paste private API keys, proxy credentials, unpublished manuscripts, review assignments, patient-adjacent research details, or embargoed paper content into prompts.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.
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.
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.
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.
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.
Show that Paper Search MCP Server is listed on HeyClaude. Paste this Markdown into your README — it renders the badge and links back to this page.
[](https://heyclau.de/entry/mcp/paper-search-mcp-server)
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).
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.
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.
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.
✓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.
✓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 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.
✓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