SciLEx

SciLEx (Science Literature Exploration) is a Python toolkit for systematic literature reviews. Crawl 10 academic APIs, deduplicate papers, analyze citation networks, and push to Zotero with advanced quality filtering.

Cite this work:

Full text:

Célian Ringwald, Benjamin Navet. SciLEx, Science Literature Exploration Toolkit ⟨swh:1:dir:944639eb0260a034a5cbf8766d5ee9b74ca85330⟩.

Bibtex:

@softwareversion{scilex2026,
  TITLE = {{SciLEx, Science Literature Exploration Toolkit}},
  AUTHOR = {Ringwald, Célian and Navey, Benjamin},
  URL = {https://github.com/Wimmics/SciLEx},
  NOTE = {},
  INSTITUTION = {{University C{\^o}te d'Azur ; CNRS ; Inria}},
  YEAR = {2026},
  MONTH = Fev,
  SWHID = {swh:1:dir:944639eb0260a034a5cbf8766d5ee9b74ca85330},
  VERSION = {1.0},
  REPOSITORY = {https://github.com/Wimmics/SciLEx},
  LICENSE = {MIT Licence},
  KEYWORDS = {Python, Scientific literature, literature research, paper retriva},
  HAL_ID = {},
  HAL_VERSION = {},
}

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Framework

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Key Features

• Multi-API collection with parallel processing (10 academic APIs)
• Smart deduplication using DOI, URL, and fuzzy title matching
• 5-phase quality filtering pipeline with time-aware citation thresholds
• Citation network extraction via CrossRef + OpenCitations + Semantic Scholar
• HuggingFace enrichment: ML models, datasets, GitHub stats, AI keywords
• Export to Zotero (bulk upload) or BibTeX (with PDF links)
• Idempotent collections for safe re-runs

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Installation

# With uv (recommended)
uv sync

# With pip
pip install -e .

# Dev dependencies (pytest, ruff, coverage)
pip install -e ".[dev]"

Quick Start

# 1. Configure APIs and search parameters
cp scilex/api.config.yml.example scilex/api.config.yml
cp scilex/scilex.config.yml.example scilex/scilex.config.yml
cp scilex/scilex.advanced.yml.example scilex/scilex.advanced.yml

# 2. Activate your environment (pip/venv users)
source .venv/bin/activate       # macOS/Linux
# .venv\Scripts\activate        # Windows
# uv users: no activation needed, use: uv run scilex-collect

# 3. Collect papers from APIs
scilex-collect

# 3. Deduplicate & filter
scilex-aggregate

# 4. (Optional) Enrich with HuggingFace metadata
scilex-enrich

# 5. Export to Zotero or BibTeX
scilex-push-zotero          # Push to Zotero
scilex-export-bibtex        # Or export to BibTeX

See the Quick Start Guide for a complete walkthrough.

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Supported APIs

API	Key Required	Best For
SemanticScholar	Optional	CS/AI papers, citation networks
OpenAlex	Optional	Broad coverage, ORCID data
IEEE	Yes	Engineering, CS conferences
Arxiv	No	Preprints, physics, CS
Springer	Yes	Journals, books
Elsevier	Yes	Medical, life sciences
PubMed	Optional	35M biomedical papers
HAL	No	French research, theses
DBLP	No	CS bibliography, 95%+ DOI
Istex	No	French institutional access

See the API Comparison for rate limits, coverage details, and limitations.

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Documentation

Full documentation is available at scilex.readthedocs.io:

• Installation - Setup with uv or pip
• Configuration - API keys, keywords, filters
• Basic Workflow - Step-by-step pipeline guide
• Advanced Filtering - 5-phase filtering pipeline
• BibTeX Export - Field reference, PDF sources
• Troubleshooting - Common issues and fixes

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Contributing

• Report issues: GitHub Issues
• See CONTRIBUTING.md for development guidelines

Requirements

• Python >=3.10
• pip or uv package manager