BioMCP‑Examples

A companion repository of worked examples that demonstrate how the BioMCP toolkit can be used (and tested) by a variety of large‑language‑model "personas".

Each example poses a real biomedical question, records several independent answers produced by different LLM systems, and includes third‑party judgment runs so you can compare quality side‑by‑side.

Why keep these examples?

• Build a public, reproducible corpus for benchmarking BioMCP and future MCP‑compatible agents.
• Provide ready‑made testbeds for debugging new tools, prompts, or evaluation pipelines.
• Offer concrete reference material for presentations and tutorials.

Repository layout

biomcp-examples/
│  README.md          ← you are here
│  LICENSE            ← MIT, same as BioMCP
└─ researcher_hnscc/  ← one experiment (HNSCC treatment strategies)
   ├─ example_*.md    ← answers produced by different models
   ├─ evals/          ← judgment runs by Claude 3.7, Gemini 2.5 Pro, OpenAI o3
   └─ README.md       ← experiment‑specific notes

Adding a new experiment

Pull requests welcome! Please follow the MIT license and respect citations.

Create a folder at the repo root (e.g. my_new_question/) with: - README.md – describe the question, prompt, model settings, etc. - One or more example_?.md files with the raw model outputs. - Optionally an evals/ sub‑folder with judge outputs.

Experiments

ID	Primary Question / Task	BioMCP capabilities exercised	Folder
researcher_hnscc	“What are the emerging treatment strategies for head and neck cancer?”	PubMed & ClinicalTrials.gov search, evidence aggregation, Sequential‑Thinking outer loop, tool chaining; judged by Claude 3.7, Gemini 2.5 Pro & OpenAI o3	researcher_hnscc

More rows to come – feel free to add yours!

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License

This repository is released under the MIT License (see LICENSE).

Maintainers

@imaurer • GenomOncology Engineering