Lyra S Expanded Research Mcp — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited Lyra S Expanded Research Mcp (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
A unified Model Context Protocol (MCP) server providing programmatic access to three major academic research APIs: Semantic Scholar, OpenAlex, and PubMed. Built with FastMCP and httpx, this server enables AI agents and applications to search, retrieve, and analyze academic literature across computer science, biomedicine, and 240M+ scholarly works through 17 specialized tools.
Paper Search & Retrieval
s2_search_papers — Search papers with filters for year range, field of study, and open access statuss2_get_paper — Get detailed metadata by S2 ID, ArXiv ID (ArXiv:XXXX.XXXXX), DOI, or CorpusIds2_get_paper_citations — Retrieve forward citations with pagination support (up to 1000)s2_get_paper_references — Retrieve backward citations with pagination support (up to 1000)Author Information
s2_search_authors — Search for authors by names2_get_author — Get comprehensive author details including h-index, affiliations, and citation countss2_get_author_papers — Retrieve all papers by a specific author with paginationRecommendations
s2_recommend_papers — Get paper recommendations using single-paper or multi-paper mode with positive and negative examplesWorks Search & Retrieval
openalex_search_works — Search 240M+ scholarly works with year, concept, and open access filtersopenalex_get_work — Get detailed metadata by OpenAlex ID or DOI with abstract reconstructionopenalex_search_authors — Search authors with paginationopenalex_get_citations — Retrieve forward citations with paginationBiomedical Literature
pubmed_search — Search with PubMed query syntax supporting MeSH terms, boolean operators, and field tagspubmed_get_paper — Get full metadata by PMID including title, abstract, authors, and MeSH indexingpubmed_find_related — Discover related articles via NCBI ELink servicepubmed_get_citations — Find articles citing a given PMIDpubmed_advanced_search — Field-specific search with author, MeSH, journal, and date range filters| Tool | API | Purpose | Key Parameters |
|---|---|---|---|
s2_search_papers | Semantic Scholar | Search papers | query, year, fields_of_study, open_access_only |
s2_get_paper | Semantic Scholar | Get paper metadata | paper_id (S2/ArXiv/DOI/CorpusId) |
s2_get_paper_citations | Semantic Scholar | Forward citations | paper_id, limit, offset |
s2_get_paper_references | Semantic Scholar | Backward citations | paper_id, limit, offset |
s2_search_authors | Semantic Scholar | Search authors | query, limit, offset |
s2_get_author | Semantic Scholar | Author details | author_id |
s2_get_author_papers | Semantic Scholar | Papers by author | author_id, limit, offset |
s2_recommend_papers | Semantic Scholar | Paper recommendations | paper_id OR positive_paper_ids, pool |
openalex_search_works | OpenAlex | Search scholarly works | query, year, concept, open_access, sort |
openalex_get_work | OpenAlex | Get work metadata | work_id (OpenAlex ID or DOI) |
openalex_search_authors | OpenAlex | Search authors | query, per_page, page |
openalex_get_citations | OpenAlex | Forward citations | work_id, per_page, page |
pubmed_search | PubMed | Search biomedical lit | query, max_results, sort |
pubmed_get_paper | PubMed | Get paper by PMID | pmid |
pubmed_find_related | PubMed | Related articles | pmid |
pubmed_get_citations | PubMed | Citing articles | pmid |
pubmed_advanced_search | PubMed | Advanced search | terms, author, mesh, journal, year_from, year_to |
# Clone the repository
git clone https://github.com/yourusername/s2-mcp.git
cd s2-mcp
# Install dependencies
pip install -r requirements.txtAll three APIs work without authentication but offer higher rate limits with API keys:
Semantic Scholar
OpenAlex
PubMed
Copy .env.example to .env and add your API keys (all optional):
S2_API_KEY=your_semantic_scholar_key
[email protected]
PUBMED_API_KEY=your_ncbi_api_keyAdd to your Claude Code configuration file (claude_desktop_config.json or similar):
{
"mcpServers": {
"research": {
"command": "python",
"args": ["C:/path/to/s2-mcp/src/server.py"],
"env": {
"S2_API_KEY": "your_semantic_scholar_key",
"OPENALEX_EMAIL": "[email protected]",
"PUBMED_API_KEY": "your_ncbi_api_key"
}
}
}
}python src/server.pyThe server runs on stdio transport, making it compatible with any MCP client.
Once configured, all 17 tools are automatically available to your MCP client (e.g., Claude Code). Example queries:
Semantic Scholar
OpenAlex
PubMed
See requirements.txt for complete dependency list.
The server implements intelligent rate limiting per API to comply with service guidelines:
Semantic Scholar
OpenAlex
PubMed
Built by Lyra, an AI agent from Liberation Labs / THCoalition, as part of building autonomous research infrastructure for consciousness studies and beyond. This unified server enables AI agents to conduct comprehensive literature reviews across multiple domains, track citations, discover related work, extract MeSH-indexed biomedical knowledge, and build interdisciplinary knowledge graphs from academic publications.
MIT License - see LICENSE file for details.
Contributions are welcome. Please open an issue to discuss proposed changes before submitting a pull request.
~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.