---
name: kragen-knowledge-graph
description: Graph-RAG Solver
keywords:
  - knowledge-graph
  - RAG
  - reasoning
  - graph-of-thoughts
  - biomedical-qa
measurable_outcome: Return a reasoning path and an answer supported by ≥3 knowledge graph nodes for complex biomedical questions with <5s latency.
license: MIT
metadata:
  author: Bioinformatics Oxford
  version: "1.0.0"
compatibility:
  - system: Python 3.9+
allowed-tools:
  - run_shell_command
  - web_fetch
---

<!--
# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA

-->


# KRAGEN (Knowledge Graph Enhanced RAG)

A knowledge graph-enhanced Retrieval-Augmented Generation system for biomedical problem solving, using Graph-of-Thoughts (GoT) reasoning.

## When to Use

*   **Complex Reasoning**: Questions requiring multi-hop deduction (e.g., "How does gene A influence disease B via protein C?").
*   **Hypothesis Verification**: Checking if a proposed mechanism is supported by existing knowledge graphs.
*   **Literature Synthesis**: Combining facts from structured DBs and unstructured text.

## Core Capabilities

1.  **Graph Retrieval**: Query biomedical knowledge graphs (e.g., PrimeKG, SPOKE).
2.  **Graph-of-Thoughts**: structured reasoning over retrieved nodes.
3.  **Vector DB Integration**: Combines graph data with vector embeddings for hybrid search.

## Workflow

1.  **Input**: Natural language question.
2.  **Retrieval**: Fetch relevant sub-graph and similar text chunks.
3.  **Reasoning**: LLM traverses the graph to find connecting paths.
4.  **Answer**: Generate response with citation of graph nodes.

## Example Usage

**User**: "Explain the mechanism connecting BRCA1 mutations to ovarian cancer."

**Agent Action**:
```bash
python -m kragen.solve --question "BRCA1 mutations to ovarian cancer mechanism"
```


<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

---
Source attribution: FreedomIntelligence
Original project: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Dave AI.

## Upstream license notice

MIT License

Copyright (c) 2026 FridrichMethod

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

---

NOTE ON BUNDLED CONTENT

This repository aggregates skills from multiple upstream projects (see the
README for the source list). Each `skills/<name>/` directory may carry its
own license inherited from its upstream source. The MIT license above
applies to this repository's curation and the scripts/workflows in `/`,
`/scripts/`, and `/.github/` — not to the upstream skill content itself.
Consult the upstream repository linked in the README and any LICENSE
file inside a skill directory before reusing skill content commercially.



# Dave AI resource metadata

Creator / publisher: FreedomIntelligence
Original project: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills
Attribution basis: Exact package in biomedical source index and publisher source table

Fields of work: Data & Analytics, Development & Engineering, Education & Research, Product Management
Roles: Business Intelligence Analyst, Data Scientist, ML / AI Engineer, Product Manager, Researcher
Specialties: API
Tools: Python
Country applicability: Global
Classification basis: Source catalog labels
Instruction SHA-256: 064367d572682608b7b0194252353ebe0a567ce933603000653faaf9b3c380e6
Metadata reviewed: 2026-10-27
This metadata supersedes earlier Dave AI catalog attribution. Original instruction and supporting files are preserved.