a vivid mosaic of open scientific literature, assembled in seconds

Multi-sOurce Scientific Article Indexer and Collector

Search, discover, and download scientific papers from multiple open databases — with a single command. Send results directly to Google NotebookLM for AI-powered summaries, podcasts, and more.

Full documentation

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What MOSAIC does

# Search 21 sources at once, deduplicate, download OA PDFs
mosaic search "attention is all you need" --oa-only --download

# Discover related literature from any DOI or arXiv ID — no query needed
mosaic similar 10.48550/arXiv.1706.03762 --sort citations

# Bulk-download your entire Zotero / JabRef library
mosaic get --from refs.bib --oa-only

# Turn results into an AI-powered notebook: podcast, slides, quiz, mind map…
mosaic notebook create "Transformers" --query "transformer architecture" --oa-only --podcast

Authors

Stefano Zaghi · stefano.zaghi@gmail.com

Creator & Maintainer

Andrea Giulianini

Grand Pixel Overlord & Architect of the Sacred Button — world-class web UI designer, responsible for making MOSAIC actually look good

Claude (Anthropic)

Omniscient Code Oracle & Tireless Rubber Duck — AI pair programmer, responsible for writing the boring parts so humans don't have to

Web UI

Launch with mosaic ui (requires [ui] extra — see Web UI docs).

Key features

🌐 21 sources, one command arXiv · Semantic Scholar · OpenAlex · PubMed · PubMed Central · Europe PMC · DOAJ · Crossref · Springer · IEEE · NASA ADS · Zenodo · BASE · CORE · DBLP · HAL · ScienceDirect · bioRxiv/medRxiv · and more	🔭 Find similar papers mosaic similar <doi> — discover related literature from any DOI or arXiv ID via OpenAlex graph + Semantic Scholar ML, no query needed	✨ Smart deduplication Results merged by DOI: best citation count, richest abstract, earliest PDF URL wins
📥 OA PDF downloads Direct links · Unpaywall fallback · browser-session authenticated access · bulk download from .bib/.csv	🎛️ Sort & filter Year · author · journal · open-access · citation count — composable, applied at API level where supported	📤 Export anywhere Markdown · CSV · JSON · BibTeX · Zotero (local & web API)
🤖 NotebookLM integration Podcast · video · slides · quiz · mind map · flashcards · briefing — queued in one command	⚡ Offline-first cache SQLite — repeated queries are instant, no re-fetching	🧩 Custom sources Wire any JSON REST API as a new source with a few lines of TOML — no Python needed
📚 Zotero integration Push results directly into your Zotero library — local API (Zotero running on your machine) or web API (api.zotero.org). Organise into collections, link downloaded PDFs as attachments, and sync across devices — all with a single --zotero flag.

Sources

Source	Shorthand	Coverage	Auth	OA PDF
arXiv	arxiv	Physics, CS, Math, Biology…	None	Always
Semantic Scholar	ss	214 M papers, all disciplines	Optional key	When indexed
ScienceDirect	sd	Elsevier journals & books	API key or browser session	OA articles
Springer Nature	sp	Springer, Nature & affiliated journals (browser)	None ([browser] extra)	Via Unpaywall
Springer Nature API	springer	OA articles from Springer, Nature & affiliated journals	Free API key	Direct PDF link
DOAJ	doaj	8 M+ fully open-access articles	None	Always
Europe PMC	epmc	45 M biomedical papers	None	PMC articles
OpenAlex	oa	250 M+ works, all disciplines	None	When available
BASE	base	300 M+ docs from 10 000+ repos	None	When OA + PDF format
CORE	core	200 M+ OA full-text from repos	Free API key	downloadUrl field
NASA ADS	ads	15 M+ astronomy & astrophysics records	Free API token	OA articles
IEEE Xplore	ieee	5 M+ IEEE journals, transactions & conference proceedings	Free API key	OA articles
Zenodo	zenodo	3 M+ OA research outputs (papers, datasets, software)	None (token optional)	Attached PDF files
Crossref	crossref	150 M+ scholarly works (DOI registry)	None (email optional)	When deposited by publisher
DBLP	dblp	6 M+ CS publications (journals, conferences)	None	Via ee field (arXiv/OA links)
HAL	hal	1.5 M+ OA documents, strong for French academic output	None	Direct PDF when deposited
PubMed	pubmed	35 M+ biomedical citations (NCBI)	None (API key optional)	PMC PDF for OA articles
PubMed Central	pmc	5 M+ free full-text biomedical articles	None (API key optional)	Always — all PMC articles are OA
bioRxiv / medRxiv	rxiv	Life-science and medical preprints	None	Always (all preprints are OA)
PEDro	pedro	Physiotherapy evidence database	None (fair-use ack)	No (abstracts only)
Scopus	scopus	90 M+ abstracts from Elsevier's citation database	API key or browser session	Via Unpaywall
Unpaywall	—	PDF resolver for any DOI	Email only	Legal OA copy

Installation

# recommended — isolated install, globally available
pipx install mosaic-search        # or: uv tool install mosaic-search

# pip — must be inside a virtualenv (modern systems enforce PEP 668)
python -m venv ~/.venvs/mosaic && source ~/.venvs/mosaic/bin/activate
pip install mosaic-search

# from source
git clone https://github.com/szaghi/mosaic
cd mosaic
python -m venv .venv && source .venv/bin/activate
pip install -e .

Requires Python 3.11+

Quick Start

# 1. Set your email (enables Unpaywall PDF fallback)
mosaic config --unpaywall-email you@example.com

# 2. Optional: add an Elsevier API key to unlock ScienceDirect
mosaic config --elsevier-key YOUR_KEY

# 3. Search and download
mosaic search "transformer architecture" --oa-only --download

Usage

Search

# Search all enabled sources (10 results per source by default)
mosaic search "protein folding"

# More results, open-access only
mosaic search "deep learning" -n 25 --oa-only

# Single source
mosaic search "RNA velocity" --source epmc

Source shorthands: arxiv · ss · sd · doaj · epmc · oa · base · core · sp · springer · ads · ieee · zenodo · crossref · dblp · hal · pubmed · pmc · rxiv · pedro · scopus

Custom sources defined in config.toml are also queried and addressable by their name.

Filters

# By year — single, range, or list
mosaic search "BERT" --year 2019
mosaic search "diffusion models" -y 2020-2023
mosaic search "GPT" -y 2020,2022,2024

# By author (repeatable, OR logic, case-insensitive substring)
mosaic search "attention" -a Vaswani -a Shazeer

# By journal (case-insensitive substring)
mosaic search "CRISPR" --journal "Nature"

# Combine freely
mosaic search "graph neural" -y 2021-2023 -a Kipf -j "ICLR" --oa-only --download

Find similar papers

# Discover related literature from any DOI or arXiv ID
mosaic similar 10.48550/arXiv.1706.03762

# Sort by citation count, open-access only
mosaic similar arxiv:1706.03762 -n 20 --sort citations --oa-only

# Save to BibTeX
mosaic similar 10.1038/s41586-021-03819-2 --output related.bib

Uses OpenAlex related_works (always) and Semantic Scholar recommendations (when ss-key is configured). Results are deduplicated and merged — the higher citation count and richer metadata always win.

Download by DOI

mosaic get 10.48550/arXiv.1706.03762

Checks the local cache first, then tries Unpaywall if no PDF URL is known.

Bulk download from BibTeX / CSV

# Export your Zotero/JabRef/Mendeley library and download everything
mosaic get --from refs.bib

# CSV with a 'doi' column works too
mosaic get --from references.csv --oa-only

Extracts all DOIs from the file, deduplicates, and downloads with the same fallback chain (direct PDF → Unpaywall → browser session).

Export to Zotero

# Push to your Zotero library (Zotero must be running — no config needed)
mosaic search "CRISPR" --oa-only --zotero

# Push to a named collection (created automatically if missing)
mosaic search "transformers" --zotero --zotero-collection "Deep Learning"

# Download PDFs and link them as Zotero attachments (local mode)
mosaic search "diffusion models" --download --zotero --zotero-collection "Generative AI"

For the web API (Zotero not running locally), configure once:

mosaic config --zotero-key YOUR_API_KEY

Configuration

mosaic config --show                          # print current config
mosaic config --unpaywall-email me@uni.edu
mosaic config --elsevier-key abc123
mosaic config --ss-key xyz789
mosaic config --download-dir ~/papers

Config is stored at ~/.config/mosaic/config.toml. Downloaded PDFs go to ~/mosaic-papers/ by default.

Custom sources

Any number of JSON REST APIs can be added as new sources directly in config.toml — one [[custom_sources]] block per source, no Python required:

[[custom_sources]]
name         = "My Institution Repo"
enabled      = true
url          = "https://repo.myuni.edu/api/search"
method       = "GET"
query_param  = "q"
results_path = "results"

[custom_sources.fields]
title    = "title"
doi      = "doi"
year     = "year"
authors  = "authors"    # flat string array
journal  = "source.title"

See the Custom Sources guide for the full reference.

NotebookLM

Send search results directly to a Google NotebookLM notebook:

# 1. Inject into MOSAIC (--include-apps exposes the notebooklm CLI)
pipx inject --include-apps mosaic-search "notebooklm-py[browser]"

# 2. Install Chromium — playwright lives inside the pipx venv, call it directly
~/.local/share/pipx/venvs/mosaic-search/bin/playwright install chromium

# 3. Authenticate once
notebooklm login

# 4. Search, download, and create a notebook in one command
mosaic notebook create "Transformers" --query "transformer architecture" --oa-only --podcast

# Or import PDFs you already have
mosaic notebook create "My Papers" --from-dir ~/mosaic-papers/

MOSAIC uploads local PDFs when available, falls back to URLs otherwise, and respects NotebookLM's 50-source limit. With --podcast, an Audio Overview is queued automatically.

Architecture

flowchart LR
    CLI -->|query + filters| Search
    Search --> arXiv & SS[Semantic Scholar] & SD[ScienceDirect] & SP[Springer browser] & SPN[Springer API] & DOAJ & EPMC[Europe PMC] & OA[OpenAlex] & BASE & CORE & ADS[NASA ADS] & IEEE[IEEE Xplore] & ZEN[Zenodo] & CR[Crossref] & DBLP[DBLP] & HAL[HAL] & PM[PubMed] & PMC[PubMed Central] & RXV[bioRxiv/medRxiv]
    arXiv & SS & SD & SP & SPN & DOAJ & EPMC & OA & BASE & CORE & ADS & IEEE & ZEN & CR & DBLP & HAL & PM & PMC & RXV -->|Paper list| Dedup{Deduplicate\nby DOI}
    Dedup --> Cache[(SQLite\ncache)]
    Dedup --> Table[Rich table]
    Table -->|--download| DL[Downloader]
    DL -->|no pdf_url| UPW[Unpaywall]
    UPW --> DL
    DL -->|no OA copy| AUTH[Browser session]
    AUTH --> DL
    DL --> Disk[(~/mosaic-papers/)]
    DL -->|mosaic notebook create| NLM[NotebookLM]

Loading

Development

pip install -e ".[dev]"

# with NotebookLM integration (includes Playwright for auth)
pip install -e ".[dev,notebooklm]"
playwright install chromium

# run tests + coverage
pytest

# live docs
cd docs && npm install && npm run docs:dev

Coverage report and badge JSON are written to docs/public/ after every test run.

License

MOSAIC is available under your choice of license:

License	SPDX	File
GNU General Public License v3	GPL-3.0-or-later	LICENSE.gpl3.md
BSD 2-Clause	BSD-2-Clause	LICENSE.bsd-2.md
BSD 3-Clause	BSD-3-Clause	LICENSE.bsd-3.md
MIT	MIT	LICENSE.mit.md

© Stefano Zaghi