https://github.com/genomoncology/biomcp-examples

Example chats from running BioMCP for demonstrations
https://github.com/genomoncology/biomcp-examples

Last synced: 2 months ago
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Example chats from running BioMCP for demonstrations

• Host: GitHub
• URL: https://github.com/genomoncology/biomcp-examples
• Owner: genomoncology
• License: mit
• Created: 2025-04-17T00:46:34.000Z (7 months ago)
• Default Branch: main
• Last Pushed: 2025-06-20T18:53:47.000Z (5 months ago)
• Last Synced: 2025-06-20T19:55:10.474Z (5 months ago)
• Size: 121 KB
• Stars: 6
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-mcp-servers - **biomcp-examples** - Example chats from running BioMCP for demonstrations `mcp` `git clone https://github.com/genomoncology/biomcp-examples` (💬 Communication)
• awesome-mcp-servers - **biomcp-examples** - Example chats from running BioMCP for demonstrations `mcp` `git clone https://github.com/genomoncology/biomcp-examples` (💬 Communication)

README

          
# BioMCP‑Examples

A companion repository of **worked examples** that demonstrate how

the [BioMCP](https://github.com/genomoncology/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](./researcher_hnscc/) |

*More rows to come – feel free to add yours!*

______________________________________________________________________

### License

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

### Maintainers

[@imaurer](https://github.com/imaurer) • GenomOncology Engineering