biochatter

Backend library for conversational AI in biomedicine

https://github.com/biocypher/biochatter

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 1 DOI reference(s) in README
✓
Academic publication links
Links to: nature.com, zenodo.org
✓
Committers with academic emails
1 of 22 committers (4.5%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary

Keywords

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

Keywords from Contributors

surrogate standardization hack

Last synced: 6 months ago · JSON representation ·

Repository

Backend library for conversational AI in biomedicine

Basic Info

Host: GitHub
Owner: biocypher
License: mit
Language: Jupyter Notebook
Default Branch: main
Homepage: http://biochatter.org/
Size: 197 MB

Statistics

Stars: 178
Watchers: 7
Forks: 50
Open Issues: 113
Releases: 85

Topics

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

Created over 2 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

BioChatter

| | | | | | --- | --- | --- | --- | | License | | Python | | | Package | | Build status | | | Tests | | Docker | | | Development | | Contributions | |

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 - Simple Python frontend (repo)
BioChatter Next - Advanced Next.js frontend (repo)
BioChatter Server - RESTful API server

📖 Learn more in our paper.

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 for examples, use cases, and more information. Many common functionalities covered by BioChatter can be seen in use in the BioChatter Light code base.

🤝 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 and the developer docs. :)

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 project.

Git LFS Configuration

This repository uses Git LFS for some large files. If you're a developer and don't need to work with these files, you have two options:

Disable Git LFS smudge globally (set once for all repositories): bash git lfs install --skip-smudge git clone https://github.com/biocypher/biochatter.git
Skip LFS files for a one-time clone: bash GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/biocypher/biochatter.git

Both options will prevent Git LFS from downloading the large files while still allowing you to work with the repository normally.

More information about LLMs

Check out this repository for more info on computational biology usage of large language models.

Citation

If you use BioChatter in your work, please cite our paper.

Owner

Name: biocypher
Login: biocypher
Kind: organization

Website: https://biocypher.org
Repositories: 1
Profile: https://github.com/biocypher

Citation (CITATION.cff)

cff-version: 1.2.0
message: >-
  If you use this software, please cite it using the
  preferred-citation below.
type: software
preferred-citation:
  type: article
  title: A platform for the biomedical application of large language models
  authors:
    - given-names: Sebastian
      family-names: Lobentanzer
      orcid: 'https://orcid.org/0000-0003-3399-6695'
    - given-names: Shaohong
      family-names: Feng
    - given-names: Noah
      family-names: Bruderer
    - given-names: Andreas
      family-names: Maier
    - name: The BioChatter Consortium
      type: consortium
    - given-names: Cankun
      family-names: Wang
    - given-names: Jan
      family-names: Baumbach
    - given-names: Jorge
      family-names: Abreu-Vicente
    - given-names: Nils
      family-names: Krehl
    - given-names: Qin
      family-names: Ma
    - given-names: Thomas
      family-names: Lemberger
    - given-names: Julio
      family-names: Saez-Rodriguez
      orcid: 'https://orcid.org/0000-0002-8552-8976'
  doi: 10.1038/s41587-024-02534-3
  journal: Nature Biotechnology
  year: 2025
repository: 'https://github.com/biocypher/biochatter'
repository-code: 'https://github.com/biocypher/biochatter'
repository-artifact: 'https://pypi.org/project/biochatter/'
url: 'https://biochatter.org/'
license: MIT

GitHub Events

Total

Create event: 62
Issues event: 56
Release event: 15
Watch event: 98
Delete event: 32
Member event: 3
Issue comment event: 106
Push event: 395
Pull request review comment event: 26
Pull request review event: 48
Pull request event: 96
Fork event: 26

Last Year

Create event: 62
Issues event: 56
Release event: 15
Watch event: 98
Delete event: 32
Member event: 3
Issue comment event: 106
Push event: 395
Pull request review comment event: 26
Pull request review event: 48
Pull request event: 96
Fork event: 26

Committers

Last synced: 9 months ago

All Time

Total Commits: 1,048
Total Committers: 22
Avg Commits per committer: 47.636
Development Distribution Score (DDS): 0.258

Past Year

Commits: 340
Committers: 15
Avg Commits per committer: 22.667
Development Distribution Score (DDS): 0.271

Top Committers

Name	Email	Commits
slobentanzer	s**r@g**m	778
fengsh	s**8@g**m	63
Tatan47	n**r@g**m	30
Nils Krehl	n**l@p**e	29
drAbreu	j**u@e**g	23
Luna Zetsche	l**e@s**e	18
Tatan47	5****7	15
Yuyao Song	4****8	13
AndiMajore	a**e@g**m	13
fengsh27	1****7	11
emmaver	e**n@h**m	9
melis	m**i@s**e	9
marlis@engelke.me	m**s@e**e	8
Yasmin Tehranchian	y**n@h**e	8
Patrick Dittrich	s**r@g**m	6
Ubuntu	u**u@u**l	6
Francesco Carli	f**4@g**m	3
github-actions[bot]	4****]	2
Ikko Eltociear Ashimine	e**r@g**m	1
Newton Winter	7****t	1
sturmcmaper	s**r@g**m	1
let20	t**e@b**m	1

Committer Domains (Top 20 + Academic)

stud.hs-heilbronn.de: 2 bms.com: 1 hs-heilbronn.de: 1 engelke.me: 1 embo.org: 1 posteo.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 110
Total pull requests: 132
Average time to close issues: 2 months
Average time to close pull requests: 12 days
Total issue authors: 17
Total pull request authors: 24
Average comments per issue: 0.85
Average comments per pull request: 1.33
Merged pull requests: 98
Bot issues: 0
Bot pull requests: 6

Past Year

Issues: 47
Pull requests: 91
Average time to close issues: 23 days
Average time to close pull requests: 6 days
Issue authors: 13
Pull request authors: 16
Average comments per issue: 0.79
Average comments per pull request: 1.25
Merged pull requests: 69
Bot issues: 0
Bot pull requests: 6

View more stats

Top Authors

Issue Authors

slobentanzer (119)
nilskre (6)
fcarli (5)
mengerj (4)
winternewt (3)
anisdismail (2)
fengsh27 (2)
kvitoslava-yarish (2)
vd-dragan21 (1)
emmaver (1)
WagnerJon (1)
sergeifedorenko (1)
Zeno-kimono (1)
mbaric758 (1)
noahbruderer (1)

Pull Request Authors

slobentanzer (65)
fengsh27 (31)
fcarli (20)
nilskre (9)
mengerj (8)
HansJarchow (8)
bastienchassagnol (7)
github-actions[bot] (6)
kvitoslava-yarish (6)
emmaver (4)
Tatan47 (4)
drAbreu (3)
AndiMajore (2)
AmanSCoder (2)
cpommier (2)

Top Labels

Issue Labels

model request (8) bug (7) enhancement (2) question (1)

Pull Request Labels

enhancement (12) documentation (6)

Packages

Total packages: 1
Total downloads:
- pypi 500 last-month
Total docker downloads: 12

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 78
Total maintainers: 1

pypi.org: biochatter

Backend library for conversational AI in biomedicine

Homepage: https://biochatter.org
Documentation: https://biochatter.org
License: MIT
Latest release: 0.13.5
published 7 months ago

Versions: 78
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 500 Last month
Docker Downloads: 12

Rankings

Downloads: 8.9%

Dependent packages count: 10.1%

Average: 13.5%

Dependent repos count: 21.5%

Maintainers (1)

mrfcharles

Last synced: 6 months ago

Dependencies

poetry.lock pypi

bump2version 1.0.1 develop
exceptiongroup 1.1.2 develop
iniconfig 2.0.0 develop
pluggy 1.2.0 develop
pytest 7.4.0 develop
tomli 2.0.1 develop
aiohttp 3.8.5
aiosignal 1.3.1
altair 5.0.1
async-timeout 4.0.3
attrs 23.1.0
blinker 1.6.2
cachetools 5.3.1
certifi 2023.7.22
charset-normalizer 3.2.0
click 8.1.6
colorama 0.4.6
dataclasses-json 0.5.14
decorator 5.1.1
environs 9.5.0
filelock 3.12.2
frozenlist 1.4.0
fsspec 2023.6.0
gitdb 4.0.10
gitpython 3.1.32
greenlet 2.0.2
grpcio 1.53.0
gtts 2.3.2
huggingface-hub 0.16.4
idna 3.4
importlib-metadata 6.8.0
jinja2 3.1.2
joblib 1.3.2
jsonschema 4.19.0
jsonschema-specifications 2023.7.1
langchain 0.0.147
markdown-it-py 3.0.0
markupsafe 2.1.3
marshmallow 3.20.1
mdurl 0.1.2
multidict 6.0.4
mypy-extensions 1.0.0
nltk 3.8.1
numexpr 2.8.5
numpy 1.25.2
openai 0.27.8
openapi-schema-pydantic 1.2.4
packaging 23.1
pandas 2.0.3
pillow 9.5.0
protobuf 4.24.0
py 1.11.0
pyarrow 12.0.1
pydantic 1.10.12
pydeck 0.8.0
pygments 2.16.1
pymilvus 2.2.8
pympler 1.0.1
pymupdf 1.22.5
python-dateutil 2.8.2
python-dotenv 1.0.0
pytz 2023.3
pytz-deprecation-shim 0.1.0.post0
pyyaml 6.0.1
redis 4.6.0
referencing 0.30.2
regex 2023.8.8
requests 2.31.0
retry 0.9.2
rich 13.5.2
rpds-py 0.9.2
safetensors 0.3.2
six 1.16.0
smmap 5.0.0
sqlalchemy 1.4.49
streamlit 1.25.0
tenacity 8.2.2
tiktoken 0.4.0
tokenizers 0.13.3
toml 0.10.2
toolz 0.12.0
tornado 6.3.2
tqdm 4.66.1
transformers 4.31.0
typing-extensions 4.7.1
typing-inspect 0.9.0
tzdata 2023.3
tzlocal 4.3.1
ujson 5.8.0
urllib3 2.0.4
validators 0.21.2
watchdog 3.0.0
yarl 1.9.2
zipp 3.16.2

pyproject.toml pypi

gTTS ^2.3.2
langchain 0.0.147
nltk ^3.8.1
openai ^0.27.8
pymilvus 2.2.8
pymupdf ^1.22.3
python >=3.10,<3.12
redis ^4.5.5
retry ^0.9.2
streamlit ^1.23.1
tiktoken ^0.4.0
transformers ^4.30.2

biochatter

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

BioChatter

Description

🌟 Key Features

🚀 Demo Applications and Utilities

Installation

Extras

Usage

🤝 Getting involved

Git LFS Configuration

More information about LLMs

Citation

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: biochatter

Rankings

Maintainers (1)

Dependencies