crossref-local
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@crossref-localsearch for papers on CRISPR gene editing"
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.
CrossRef Local (crossref-local)
Demo
# Search 167M papers locally — no API rate limits, ~22 ms full-text query
crossref-local search "epilepsy seizure prediction"
# Resolve a DOI to full record (title, abstract, citations, journal IF)
crossref-local search-by-doi 10.1038/nature11247
# Drive from MCP / Claude Code
crossref-local mcp serveThe image is a live capture against the local DB; the <details>
block below has a 6m55s MCP-driven demo video.
Related MCP server: paper-fetch-mcp
Architecture
┌──────────────────────────┐ ┌──────────────────────────┐
│ CrossRef public dump │ │ JCR / OpenAlex IF tables │
│ (~100 GB compressed) │ │ │
└──────────────┬───────────┘ └──────────────┬───────────┘
│ dois2sqlite │
▼ ▼
┌─────────────────┐ ┌──────────────┐
│ crossref.db │ ◀── joins ──▶ │ impact-factor│
│ (SQLite + FTS5) │ │ table │
└────────┬────────┘ └──────────────┘
│
▼
┌──────────────────────────────────┐
│ crossref-local — Python / CLI / MCP │
│ search · search-by-doi · cache │
│ stats · check-citations · relay │
└──────────────────────────────────┘The DB lives entirely on disk; crossref-local is a thin facade over
SQLite + FTS5 + a small impact-factor table. No network calls during
queries; rebuild scripts under make fts-build-screen /
citations-build-screen are the only producers of state.
Live demonstration of MCP server integration with Claude Code for epilepsy seizure prediction literature review:
Full-text search on title, abstracts, and keywords across 167M papers (22ms response)
📄 Full demo documentation | 📊 Generated diagrams
Built for the LLM era - features that matter for AI research assistants:
Feature | Benefit |
📝 Abstracts | Full text for semantic understanding |
📊 Impact Factor | Filter by journal quality |
🔗 Citations | Prioritize influential papers |
⚡ Speed | 167M records in ms, no rate limits |
Perfect for: RAG systems, research assistants, literature review automation.
pip install crossref-localFrom source:
git clone https://github.com/ywatanabe1989/crossref-local
cd crossref-local && make installDatabase setup (1.5 TB, ~2 weeks to build):
# 1. Download CrossRef data (~100GB compressed)
aria2c "https://academictorrents.com/details/..."
# 2. Build SQLite database (~days)
pip install dois2sqlite
dois2sqlite build /path/to/crossref-data ./data/crossref.db
# 3. Build FTS5 index (~60 hours) & citations table (~days)
make fts-build-screen
make citations-build-screenfrom crossref_local import search, get, count
# Full-text search (22ms for 541 matches across 167M records)
results = search("hippocampal sharp wave ripples")
for work in results:
print(f"{work.title} ({work.year})")
# Get by DOI
work = get("10.1126/science.aax0758")
print(work.citation())
# Count matches
n = count("machine learning") # 477,922 matchesAsync API:
from crossref_local import aio
async def main():
counts = await aio.count_many(["CRISPR", "neural network", "climate"])
results = await aio.search("machine learning")crossref-local search "CRISPR genome editing" -n 5
crossref-local search-by-doi 10.1038/nature12373
crossref-local status # Configuration and database statsWith abstracts (-a flag):
$ crossref-local search "RS-1 enhances CRISPR" -n 1 -a
Found 4 matches in 128.4ms
1. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency (2016)
DOI: 10.1038/ncomms10548
Journal: Nature Communications
Abstract: Zinc-finger nuclease, transcription activator-like effector nuclease
and CRISPR/Cas9 are becoming major tools for genome editing...Start the FastAPI server:
crossref-local relay --host 0.0.0.0 --port 31291Endpoints:
# Search works (FTS5)
curl "http://localhost:31291/works?q=CRISPR&limit=10"
# Get by DOI
curl "http://localhost:31291/works/10.1038/nature12373"
# Batch DOI lookup
curl -X POST "http://localhost:31291/works/batch" \
-H "Content-Type: application/json" \
-d '{"dois": ["10.1038/nature12373", "10.1126/science.aax0758"]}'
# Citation endpoints
curl "http://localhost:31291/citations/10.1038/nature12373/citing"
curl "http://localhost:31291/citations/10.1038/nature12373/cited"
curl "http://localhost:31291/citations/10.1038/nature12373/count"
# Collection endpoints
curl "http://localhost:31291/collections"
curl -X POST "http://localhost:31291/collections" \
-H "Content-Type: application/json" \
-d '{"name": "my_papers", "query": "CRISPR", "limit": 100}'
curl "http://localhost:31291/collections/my_papers/download?format=bibtex"
# Database info
curl "http://localhost:31291/info"HTTP mode (connect to running server):
# On local machine (if server is remote)
ssh -L 31291:127.0.0.1:31291 your-server
# Python client
from crossref_local import configure_http
configure_http("http://localhost:31291")
# Or via CLI
crossref-local --http search "CRISPR"Run as MCP (Model Context Protocol) server:
crossref-local mcp startLocal MCP client configuration:
{
"mcpServers": {
"crossref-local": {
"command": "crossref-local",
"args": ["mcp", "start"],
"env": {
"CROSSREF_LOCAL_DB": "/path/to/crossref.db"
}
}
}
}Remote MCP via HTTP (recommended):
# On server: start persistent MCP server
crossref-local mcp start -t http --host 0.0.0.0 --port 8082{
"mcpServers": {
"crossref-remote": {
"url": "http://your-server:8082/mcp"
}
}
}Diagnose setup:
crossref-local mcp doctor # Check dependencies and database
crossref-local mcp list-tools # Show available MCP tools
crossref-local mcp installation # Show client config examplesSee docs/remote-deployment.md for systemd and Docker setup.
Available tools:
search- Full-text search across 167M+ paperssearch_by_doi- Get paper by DOIenrich_dois- Add citation counts and references to DOIsstatus- Database statisticscache_*- Paper collection management
from crossref_local.impact_factor import ImpactFactorCalculator
with ImpactFactorCalculator() as calc:
result = calc.calculate_impact_factor("Nature", target_year=2023)
print(f"IF: {result['impact_factor']:.3f}") # 54.067Journal | IF 2023 |
Nature | 54.07 |
Science | 46.17 |
Cell | 54.01 |
PLOS ONE | 3.37 |
from crossref_local import get_citing, get_cited, CitationNetwork
citing = get_citing("10.1038/nature12373") # 1539 papers
cited = get_cited("10.1038/nature12373")
# Build visualization (like Connected Papers)
network = CitationNetwork("10.1038/nature12373", depth=2)
network.save_html("citation_network.html") # requires: pip install crossref-local[viz]Query | Matches | Time |
| 541 | 22ms |
| 477,922 | 113ms |
| 12,170 | 257ms |
Searching 167M records in milliseconds via FTS5.
openalex-local - Sister project with OpenAlex data:
Feature | crossref-local | openalex-local |
Works | 167M | 284M |
Abstracts | ~21% | ~45-60% |
Update frequency | Real-time | Monthly |
DOI authority | ✓ (source) | Uses CrossRef |
Citations | Raw references | Linked works |
Concepts/Topics | ❌ | ✓ |
Author IDs | ❌ | ✓ |
Best for | DOI lookup, raw refs | Semantic search |
When to use CrossRef: Real-time DOI updates, raw reference parsing, authoritative metadata. When to use OpenAlex: Semantic search, citation analysis, topic discovery.
Installation
Recommended:
uv pip install crossref-local[all]— uv's Rust resolver handles the SciTeX dep set in 1-3 min where pip's serial backtracker can take 30+ min on the full extras. Plainpip installstill works; the install block below shows both.
pip install crossref-local # core
pip install crossref-local[mcp] # + MCP server4 Interfaces
from crossref_local import crossref_search, get_work
results = crossref_search("deep learning EEG", limit=10)
work = get_work("10.1038/nature12373")crossref-local search "query"
crossref-local doi 10.1038/nature12373crossref-local mcp startAgent skill pages live under src/crossref_local/_skills/crossref-local/.
Problem and Solution
# | Problem | Solution |
1 | CrossRef public API is rate-limited + requires internet + slow for bulk queries -- 167M works is the bottleneck for literature tools | Local SQLite + FTS5 -- full CrossRef dump (~60 GB) queryable offline; |
Part of SciTeX
crossref-local is part of SciTeX. Install via
the umbrella with pip install scitex[scholar] to use as
scitex.scholar (Python) or scitex scholar ... (CLI) — crossref-local
provides the local CrossRef backing for scholar's DOI resolution.
import scitex
scitex.scholar.enrich_bibtex("references.bib")
scitex.scholar.check_citations("manuscript.tex")Four Freedoms for Research
The freedom to run your research anywhere — your machine, your terms.
The freedom to study how every step works — from raw data to final manuscript.
The freedom to redistribute your workflows, not just your papers.
The freedom to modify any module and share improvements with the community.
AGPL-3.0 — because we believe research infrastructure deserves the same freedoms as the software it runs on.
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