Which integrations are available for this server?

Provides tools for biomedical entity normalization, relation mining, and article search using PubTator3, which annotates PubMed articles with entities, relations, and evidence. Provides tools to search academic papers, retrieve paper metadata, traverse citation graphs, and get paper recommendations using the Semantic Scholar API.

How do I use paperSearch?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@paperSearch Find recent papers on immunotherapy for cancer." That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

paperSearch

by FreddieWho

Overview Schema Related Servers Score Discussions

Python

Local

SearchPaper

中文文档

SearchPaper is a literature-first infrastructure layer for agent-assisted research. It searches open scholarly literature, normalizes identifiers, merges duplicate records conservatively, preserves provenance, and exports traceable results for downstream agents or human review.

SearchPaper is not a full research agent, systematic-review engine, evidence evaluator, PDF parser, or Zotero replacement. It provides structured literature records and provenance; interpretation stays with the user or a downstream research workflow.

🔎 At a Glance

Area	What SearchPaper provides
📚 Sources	PubMed, Crossref, OpenAlex, Europe PMC, arXiv, bioRxiv, medRxiv, Semantic Scholar, Unpaywall, OpenCitations, PubTator3
🧬 Biomedical workflows	MeSH lookup, PubMed related articles, DOI/PMID/PMCID conversion, PubTator3 literature signals
🔗 Identifiers	DOI, PMID, PMCID, arXiv, OpenAlex, Semantic Scholar IDs
🧾 Provenance	Source records, merge reasons, conflicts, warnings, trace fields
🧠 Agent access	CLI plus MCP tools for OpenCode, Codex, Claude, and other MCP clients
📦 Exports	JSON, JSONL, BibTeX, RIS, NBIB, ENW, Markdown, Zotero CSV, Obsidian notes, APA, MLA
🔓 API keys	Core workflows are no-key usable; optional keys improve rate limits and coverage

Related MCP server: PubMed MCP Server

✨ What It Does

Multi-source literature search across open scholarly APIs.
Identifier resolution for common scholarly IDs.
Conservative duplicate merge with provenance and conflict preservation.
Local SQLite cache for speed and reproducibility.
Full-text readiness via OA links, Europe PMC XML anchors, and full-text availability fields.
Structured literature signals from PubTator3 with explicit interpretation warnings.
CLI-first workflows plus a small, stable MCP tool surface.
Agent integration helpers for OpenCode, Codex, and Claude.

⚡ Quick Start

git clone <repo-url> ~/Publish/PaperSearch
cd ~/Publish/PaperSearch
uv sync --extra dev
uv run pytest -q

Task	Command
Search literature	`uv run searchpaper search "HCC TACE PD-1" --json`
Resolve a DOI	`uv run searchpaper resolve --doi 10.1038/s41586-021-03819-2 --json`
Check source health	`uv run searchpaper sources status --json`
Run diagnostics	`uv run searchpaper doctor`
Start MCP server	`uv run searchpaper serve --mcp`

For an editable local install:

uv pip install -e .

After installation, the package provides the searchpaper CLI.

⚙️ Configuration

SearchPaper reads ~/.config/searchpaper/config.json. Environment variables override file values.

{
  "semantic_scholar_api_key": "YOUR_KEY",
  "crossref_email": "you@example.com",
  "openalex_email": "you@example.com",
  "ncbi_api_key": "YOUR_NCBI_KEY",
  "cache_path": "~/.cache/searchpaper/cache.db"
}

Variable	Maps to	Description
`SEARCHPAPER_CACHE`	`cache_path`	SQLite cache file
`SEARCHPAPER_CONFIG`	`config_path`	Config file path
`SEMANTIC_SCHOLAR_API_KEY`	`semantic_scholar_api_key`	Optional Semantic Scholar key
`CROSSREF_EMAIL`	`crossref_email`	Crossref polite-pool email
`OPENALEX_EMAIL`	`openalex_email`	OpenAlex polite-pool email
`NCBI_API_KEY`	`ncbi_api_key`	Optional NCBI key

🧭 Core CLI Workflows

Workflow	Command
Plan source routing	`searchpaper plan "query" --profile auto --json`
Search literature	`searchpaper search "query" --json`
Get work by PMID	`searchpaper get --pmid 12345 --json`
Resolve identifier	`searchpaper resolve --doi 10.xxx --json`
Expand from a seed work	`searchpaper expand --doi 10.xxx --by citations,references --json`
Build context pack	`searchpaper context --doi 10.xxx --json`
Fetch full-text anchors	`searchpaper get --pmcid PMC8371605 --sources europepmc --anchors --json`
Probe sources	`searchpaper sources preflight --sources pubmed,arxiv --json`
Explain source behavior	`searchpaper sources explain pubmed`
Diagnose source health	`searchpaper sources diagnose --json`
Save project trace	`searchpaper search "query" --json --save`
Export saved trace	`searchpaper project export <trace_id> --format bibtex`
Lookup MeSH	`searchpaper pubmed mesh "term" --json`
Find related PubMed articles	`searchpaper pubmed related 12345 --json`
Convert PubMed IDs	`searchpaper pubmed convert-ids 10.xxx --json`
Batch process inputs	`searchpaper batch queries.jsonl --format jsonl --output results.jsonl`
Verify references	`searchpaper references verify refs.txt --output-format markdown`
Export results	`searchpaper export results.json --format bibtex`
Inspect capabilities	`searchpaper capabilities --json`

🧩 MCP and Agent Integration

Start the default stdio MCP server:

searchpaper serve --mcp

Start a remote HTTP/SSE MCP server with searchpaper[remote] installed:

searchpaper serve --mcp --transport http --host 127.0.0.1 --port 8000 --path /mcp

Tool	Purpose
`search_literature`	Multi-source literature search
`plan_literature_search`	Source-routing plan without a live search
`get_work`	Fetch one work by identifier
`resolve_identifiers`	Resolve and merge multiple identifiers
`get_source_status`	Source health and optional catalog
`lookup_mesh`	PubMed MeSH descriptor lookup
`find_related_articles`	PubMed related article IDs
`convert_identifiers`	DOI/PMID/PMCID conversion
`search_literature_signals`	Biomedical entity/relation signals
`expand_from_work`	Citations, references, and related papers
`export_records`	Export structured records

Agent	Install command	Output
OpenCode	`searchpaper install --target opencode`	MCP config plus `literature-search` skill
Codex	`searchpaper install --target codex`	MCP snippet plus SearchPaper instructions
Claude	`searchpaper install --target claude`	MCP snippet plus SearchPaper instructions
All	`searchpaper install --target all`	Scaffolds all supported integrations

Review generated files and enable the searchpaper MCP server in your agent settings.

📖 Full-Text Readiness

SearchPaper reports full-text availability without requiring PDF parsing. Records may include full_text_availability, open_access_pdf, and canonical URLs such as doi, pubmed, pmc, oa_url, and oa_pdf_url.

searchpaper resolve --doi 10.1038/s41586-021-03819-2 --json
searchpaper get --pmcid PMC8371605 --sources europepmc --anchors --json
searchpaper context --doi 10.1038/s41586-021-03819-2 --json
searchpaper get --doi 10.1038/s41586-021-03819-2 --download-pdf paper.pdf --json
searchpaper get --pmcid PMC8371605 --download-xml paper.xml --json

PDF parsing remains optional and out of scope.

🛡️ Failure Modes and Signal Rules

Topic	Behavior
Source degradation	Public APIs can fail; optional sources warn and continue
Required sources	`--require pubmed` or `--source-mode pubmed:required` returns exit code 1 on failure
Preferred sources	`source:preferred` emits louder warnings but does not fail the full search
Biomedical signals	PubTator3/co-mention signals are not proof of causality
Evidence evaluation	Out of scope; SearchPaper returns records, provenance, and signals

🗂️ Cache, Privacy, and Project Mode

Default cache: ~/.cache/searchpaper/cache.db
Bypass cache: searchpaper search "query" --no-cache --json
Project mode:

searchpaper init
searchpaper search "HCC TACE PD-1" --json --save
searchpaper project traces
searchpaper project export <trace_id> --format bibtex

The cache may contain raw API responses and query identifiers. Store it accordingly.

🧪 Development

uv sync --extra dev
uv run pytest -q
uv run ruff check .
uv run ruff format .

CI should rely on fixture-backed tests. Live public APIs are useful for manual checks but should not be required for routine validation.

📜 License

MIT

This server cannot be installed

license - permissive license

quality - not tested

maintenance

How are these scores calculated?

Maintenance

–Maintainers

–Response time

0dRelease cycle

2Releases (12mo)

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