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https://github.com/biocypher/biochatter

Backend library for conversational AI in biomedicine
https://github.com/biocypher/biochatter

biocypher chatbot knowledge-graph llm retrieval-augmented-generation vector-database

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Backend library for conversational AI in biomedicine

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README 

        
# BioChatter



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| __License__ | [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) | __Python__ | [![Python](https://img.shields.io/pypi/pyversions/biochatter)](https://www.python.org) |

| __Package__ | [![PyPI version](https://img.shields.io/pypi/v/biochatter)](https://pypi.org/project/biochatter/) [![Downloads](https://static.pepy.tech/badge/biochatter)](https://pepy.tech/project/biochatter) [![DOI](https://zenodo.org/badge/650181006.svg)](https://zenodo.org/doi/10.5281/zenodo.10777945) | __Build status__ | [![CI](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) [![Docs](https://github.com/biocypher/biochatter/actions/workflows/docs.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/docs.yaml) |

| __Tests__ | [![Coverage](https://raw.githubusercontent.com/biocypher/biochatter/coverage/coverage.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) | __Docker__ | [![Latest image](https://img.shields.io/docker/v/biocypher/chatgse)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) [![Image size](https://img.shields.io/docker/image-size/biocypher/chatgse/latest)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) |

| __Development__ | [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://black.readthedocs.io/en/stable/) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) | __Contributions__ | [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CONTRIBUTING.md) |



## Description



🤖 BioChatter is a community-driven Python library that connects biomedical

applications to conversational AI, making it easy to leverage generative AI

models in the biomedical domain.



### 🌟 Key Features

- Generic backend for biomedical AI applications

- Seamless integration with multiple LLM providers

- Native connection to BioCypher knowledge graphs

- Extensive testing and evaluation framework

- Living benchmark of specific biomedical applications



### 🚀 Demo Applications and Utilities



- [BioChatter Light](https://light.biochatter.org) - Simple Python frontend

([repo](https://github.com/biocypher/biochatter-light))



- [BioChatter Next](https://next.biochatter.org) - Advanced Next.js frontend

([repo](https://github.com/biocypher/biochatter-next))



- [BioChatter Server](https://github.com/biocypher/biochatter-server) - RESTful

API server



📖 Learn more in our [paper](https://www.nature.com/articles/s41587-024-02534-3).



## Installation



To use the package, install it from PyPI, for instance using pip (`pip install

biochatter`) or Poetry (`poetry add biochatter`).



### Extras



The package has some optional dependencies that can be installed using the

following extras (e.g. `pip install biochatter[xinference]`):



- `xinference`: support for querying open-source LLMs through Xorbits Inference



- `podcast`: support for podcast text-to-speech (for the free Google TTS; the

paid OpenAI TTS can be used without this extra)



- `streamlit`: support for streamlit UI functions (used in BioChatter Light)



## Usage



Check out the [documentation](https://biochatter.org/) for examples, use cases,

and more information. Many common functionalities covered by BioChatter can be

seen in use in the [BioChatter

Light](https://github.com/biocypher/biochatter-light) code base.  [![Built with

Material for

MkDocs](https://img.shields.io/badge/Material_for_MkDocs-526CFE?style=for-the-badge&logo=MaterialForMkDocs&logoColor=white)](https://squidfunk.github.io/mkdocs-material/)



## 🤝 Getting involved



We are very happy about contributions from the community, large and small!

If you would like to contribute to BioCypher development, please refer to

our [contribution guidelines](CONTRIBUTING.md) and the [developer

docs](DEVELOPER.md). :)



If you want to ask informal questions, talk about dev things, or just chat,

please join our community at https://biocypher.zulipchat.com!



> **Imposter syndrome disclaimer:** We want your help. No, really. There may be a little voice inside your head that is telling you that you're not ready, that you aren't skilled enough to contribute. We assure you that the little voice in your head is wrong. Most importantly, there are many valuable ways to contribute besides writing code.

>

> This disclaimer was adapted from the [Pooch](https://github.com/fatiando/pooch) project.



## More information about LLMs



Check out [this repository](https://github.com/csbl-br/awesome-compbio-chatgpt)

for more info on computational biology usage of large language models.



## Citation



If you use BioChatter in your work, please cite our

[paper](https://www.nature.com/articles/s41587-024-02534-3).