Screen and extract data from biomedical literature across PubMed, GEO, and preprints using LLM-assisted analysis. Built for researchers and developers automating systematic reviews, meta-analyses, and literature curation workflows.
io.github.rachadele/biolit
Local install
STDIO
No auth required
How models use it and what it is built for.
Screen and extract data from biomedical literature across PubMed, GEO, and preprints using LLM-assisted analysis. Built for researchers and developers automating systematic reviews, meta-analyses, and literature curation workflows.
Local install — runs as a subprocess.
Configuration this server reads at startup.
Anthropic API key (required when using the default Anthropic provider)
OpenAI API key (required when using LLM_PROVIDER=openai)
LLM provider: anthropic (default), openai, or ollama
Model name override (e.g. claude-sonnet-4-6, gpt-4o)
Semantic Scholar API key for higher rate limits on citation lookup (optional)
Email address for Unpaywall API access to improve PDF retrieval (optional)
Where to find authoritative docs and source for Rachadele Biolit.
Paste any of these into Agent Studio after connecting Rachadele Biolit.
Common questions about connecting and running Rachadele Biolit.
What LLM providers does biolit support?
Biolit supports Anthropic (default), OpenAI, and Ollama. Set LLM_PROVIDER and optionally override the model name with LLM_MODEL (e.g., gpt-4o or claude-sonnet-4-6).
Do I need API keys to use biolit?
Yes, you need either ANTHROPIC_API_KEY or OPENAI_API_KEY depending on your LLM_PROVIDER. SEMANTIC_SCHOLAR_API_KEY and UNPAYWALL_EMAIL are optional but recommended for higher rate limits and better PDF retrieval.
What data sources can biolit query?
Biolit integrates PubMed, GEO (Gene Expression Omnibus), preprint servers, and Semantic Scholar for citation lookup. It can retrieve abstracts, metadata, and PDFs where available.
How does the LLM-assisted screening work?
The server uses your configured LLM to analyze and filter literature based on your criteria—screening abstracts, extracting structured data, and ranking results by relevance without manual review of every paper.
Can I use biolit offline or with a local model?
Yes, set LLM_PROVIDER=ollama to use a local LLM. You'll still need internet access to query PubMed, GEO, and preprint APIs, but LLM inference runs locally.
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