yjcyxky / rapex

RAPEX - Response to Air Pollution EXposure

Rapex

A knowledge graph system with graph neural network for drug discovery, disease mechanism, biomarker screening and discovering response to toxicant exposure.

Features

• Knowledge graph studio for graph query, visualization and analysis.
• Graph neural network for drug discovery, disease mechanism, biomarker screening and discovering response to toxicant exposure.
• Support customized knowledge graph schema and data source.
• Support customized graph neural network model.
• Support customized omics datasets.
• Integrated large language models (such as vicuna, rwkv, chatgpt etc. more details on chat-publications) for answering questions.

Demo

Ask questions with chatbot

Find similar diseases with your queried disease

Predict drugs and related genes for your queried disease

Find potential paths between two nodes

Installation

Clone the repo

git clone https://github.com/yjcyxky/rapex.git

Compile it

./bin/lein uberjar

Launch a postgresql instance for testing

bash create-db.sh rapex_dev 54320

Launch rapex

export MIGRATE_DB=true
export JAVA_OPTS='-Dconf=./example-conf.edn'

bash bin/start

Launch frontend

cd studio && yarn start:local-dev

# Release it to GitHub
cd studio && yarn build && yarn gh-pages

Usage

FIXME: explanation

$ java -jar rapex-0.1.0-standalone.jar [args]

Options

FIXME: listing of options this app accepts.

Bugs

...

Any Other Sections

That You Think

Might be Useful

TODO List

• [] Add advanced search for knowledge graph.
  • [] Two modes: add to current canvas & add to new canvas.

License

Copyright © 2022 FIXME

This program and the accompanying materials are made available under the terms of the Eclipse Public License 2.0 which is available at http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary Licenses when the conditions for such availability set forth in the Eclipse Public License, v. 2.0 are satisfied: GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html.