# SkillGraph

> A knowledge graph of 78 bioinformatics pipeline skills with 483 transitions, extracted from PubMed Central papers using a fine-tuned PubMedBERT NER model and EDAM ontology data type validation. Powers Claude Skills and AI agents for genomics, RNA-seq, single-cell, drug discovery, and metagenomics workflows.

SkillGraph is built and maintained by [Pipette.bio](https://pipette.bio) — agentic bioinformatics for wet-lab biologists.

## MCP server (for AI agents)

The full graph is queryable via Model Context Protocol:

- Endpoint: https://skillgraph.pipette.bio/mcp
- Transport: HTTP (streamable)
- Auth: none (public)
- Tools: `get_skill`, `list_skills`, `search_skills`, `get_transitions`, `find_path`, `get_graph_stats`

Setup for Claude Code and other MCP clients: https://github.com/variomeanalytics/bioinformatics-agent-skills

## Resources

- [Interactive graph explorer](https://skillgraph.pipette.bio): web UI for browsing the graph
- [Full skill catalog (machine-readable)](https://skillgraph.pipette.bio/llms-full.txt): every skill with overview, tools, and triggers
- [GitHub repository](https://github.com/variomeanalytics/bioinformatics-agent-skills): MCP setup, examples, license
- [Pipette.bio main site](https://pipette.bio): about Pipette.bio and Variome Analytics

## Optional

- [Open Graph preview image](https://skillgraph.pipette.bio/screenshot.png)
- [Pipette.bio logo](https://skillgraph.pipette.bio/pipette-logo.png)