MOSAIC

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MOSAICMulti-source Scientific Article Indexer and Collector

a vivid mosaic of open scientific literature, assembled in seconds

Get Started
Agent Workflows
Local RAG Guide
View on GitHub
MOSAIC logoMOSAIC logo
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Multi-source Search

Query arXiv, Semantic Scholar, ScienceDirect, Springer Nature (browser + API), DOAJ, Europe PMC, OpenAlex, BASE, CORE, NASA ADS, IEEE Xplore, Zenodo, Crossref, DBLP, HAL, PubMed, PubMed Central, and bioRxiv/medRxiv simultaneously. Results are deduplicated by DOI so you never see the same paper twice.

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PDF Download

Download open-access PDFs directly. When no PDF link is known, MOSAIC queries Unpaywall to find a legal open-access copy automatically.

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Local Cache

All search results and download history are stored in a local SQLite database. Re-run queries instantly without hitting the network.

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Source-aware

Enable or disable individual sources, set per-source API keys, and control rate limits — all from a single TOML config file.

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Rich Terminal UI

Results are displayed as a formatted table with open-access and PDF indicators. Progress spinners keep you informed during long searches.

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Web Interface

Launch a browser-based UI with `mosaic ui`. Search, filter, download, and export from a responsive dashboard with dark mode, per-source progress, and keyboard shortcuts.

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Local RAG

Index your paper library and ask questions in natural language — synthesis, gap analysis, method comparison, structured extraction. Runs fully locally via Ollama or any OpenAI-compatible server. No data leaves your machine.

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Relevance Ranking

Re-rank any result set by semantic similarity to your query with --sort relevance. BM25 by default (instant, no model). Optionally delegate to your configured LLM for higher-quality scores.

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NotebookLM Integration

Turn any search into a Google NotebookLM notebook — podcast, video overview, slides, quiz, flashcards, mind map, and briefing doc queued in one command with mosaic notebook create.

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Claude Code Skill & AI Agent Mode

Install the bundled Claude Code skill with `mosaic skill install` — gives Claude Code full knowledge of every command, source, and option. The `--json` flag on search and similar emits a structured JSON envelope to stdout for piping, scripting, and CI pipelines.

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Open & Extensible

Each source is a small self-contained class. Adding a new database takes fewer than 50 lines of Python.

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Custom Sources

Wire any number of JSON REST APIs as new search sources directly in config.toml — one block per source, no Python required. Supports GET and POST, nested field paths, API keys, and author objects.

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Zotero Integration

Push results directly into your Zotero library with --zotero. Works with Zotero desktop (local API) and Zotero web (api.zotero.org). Organise into named collections and link downloaded PDFs as attachments.

Quick start ​

bash
pipx install mosaic-search   # or: uv tool install mosaic-search
mosaic config --unpaywall-email you@example.com
mosaic search "attention is all you need" --oa-only --download

AI features ​

Local RAG — mosaic index / ask / chat ​

Index your cached papers once and interrogate your library in natural language. Four structured analysis modes produce cited, grounded answers:

ModeWhat it produces
synthesisComprehensive state-of-the-art summary
gapsOpen problems, contradictions, methodological limitations
compareSide-by-side comparison of methods, datasets, metrics, results
extractPer-paper structured extraction: Task · Method · Dataset · Metric · Result
bash
pipx inject mosaic-search sqlite-vec          # install vector extension once

mosaic index                                  # embed all cached papers
mosaic ask "What are the main approaches to graph neural networks?" --show-sources
mosaic ask "What open problems remain in protein structure prediction?" --mode gaps
mosaic chat                                   # interactive multi-turn session

Runs entirely on your machine via Ollama or any OpenAI-compatible server. → RAG guide

Relevance ranking — --sort relevance ​

Re-rank any result set by semantic similarity to the query. BM25 by default (no model, no network, instant). Configure your LLM for higher-quality scores.

bash
mosaic search "diffusion models" --sort relevance          # live, ranked
mosaic search "diffusion models" --cached --sort relevance # offline, from local cache

→ Relevance ranking guide

NotebookLM — mosaic notebook ​

Turn any search into a Google NotebookLM notebook in one command. Podcast, video overview, slides, quiz, flashcards, mind map, briefing doc — all queued automatically.

bash
mosaic notebook create "Transformers" --query "attention mechanism" --oa-only --podcast --briefing

→ NotebookLM guide

Claude Code Skill & AI agent mode — mosaic skill install ​

MOSAIC ships a bundled Claude Code skill. Install it once and the /mosaic slash command gives Claude Code expert knowledge of every command, source shorthand, filter, export format, and scripting pattern — so you can describe your bibliography goal in plain English and let Claude Code build and run the right commands for you.

bash
# Install into the current project's .claude/skills/ directory
mosaic skill install

# Or globally, for all your projects
mosaic skill install --global

All search and similar commands support --json for structured stdout — a clean {status, query, count, papers[], errors[]} envelope designed for piping, agent scripts, and CI:

bash
# Pipe directly to jq
mosaic search "attention mechanism" --max 30 --oa-only --json \
  | jq -r '.papers[] | "\(.year)  \(.doi)  \(.title)"'

# Combine file export and stdout JSON in one run
mosaic search "FDTD methods" --json --output refs.bib

→ Agent Workflows guide

Architecture ​

Authors ​

Stefano Zaghi · stefano.zaghi@gmail.com

Chief Yak Shaver & Accidental Package Maintainer — Fortran programmer who needed one paper, opened 21 browser tabs, and six months later found himself maintaining a Python library

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

Contributions are welcome.

License ​

MOSAIC is available under your choice of license: GPL-3.0-or-later, BSD-2-Clause, BSD-3-Clause, or MIT. See LICENSE.gpl3.md, LICENSE.bsd-2.md, LICENSE.bsd-3.md, LICENSE.mit.md.

© Stefano Zaghi