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Open Source Science

https://github.com/aidh-ms/medminer

https://github.com/aidh-ms/medminer

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: aidh-ms
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 2.68 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 7
  • Releases: 0
Created over 1 year ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

MedMiner

MedMiner leverages large language models (LLMs) and SmolAgents from Hugging Face to extract and analyze data from medical documents efficiently.

Getting Started

[!NOTE] Use the included dev container to automatically install all the necessary dev tools and dependencies.

  1. Clone the repository: sh git clone https://github.com/aidh-ms/MedMiner.git cd python-project-template

  2. Open the project in Visual Studio Code: sh code .

  3. (Optionally) Enable Snowstorm server

to enable the snowstorm server for snomedct go to the .env file in the .devcontainer folder and add the following line.

bash COMPOSE_PROFILES=dev

  1. Reopen in Container:
    • Press F1 to open the command palette.
    • Type Remote-Containers: Reopen in Container and select it.
    • VS Code will build the Docker container defined in the .devcontainer folder and open the project inside the container.

Owner

  • Name: AIDH MS
  • Login: aidh-ms
  • Kind: organization
  • Email: christian.porschen@ukmuenster.de
  • Location: Germany

Anaesthesiology and Intensive Care Digital Health Münster

GitHub Events

Total
  • Create event: 133
  • Issues event: 53
  • Watch event: 1
  • Delete event: 115
  • Member event: 1
  • Issue comment event: 72
  • Push event: 317
  • Pull request review comment event: 11
  • Pull request review event: 116
  • Pull request event: 246
  • Fork event: 1
Last Year
  • Create event: 133
  • Issues event: 53
  • Watch event: 1
  • Delete event: 115
  • Member event: 1
  • Issue comment event: 72
  • Push event: 317
  • Pull request review comment event: 11
  • Pull request review event: 116
  • Pull request event: 246
  • Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 27
  • Total pull requests: 139
  • Average time to close issues: 8 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.15
  • Average comments per pull request: 0.3
  • Merged pull requests: 97
  • Bot issues: 0
  • Bot pull requests: 129
Past Year
  • Issues: 27
  • Pull requests: 139
  • Average time to close issues: 8 days
  • Average time to close pull requests: 1 day
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.15
  • Average comments per pull request: 0.3
  • Merged pull requests: 97
  • Bot issues: 0
  • Bot pull requests: 129
View more stats
Top Authors
Issue Authors
  • Paul-B98 (18)
  • aegis301 (9)
Pull Request Authors
  • dependabot[bot] (129)
  • Paul-B98 (8)
  • aegis301 (2)
Top Labels
Issue Labels
enhancement (7)
Pull Request Labels
dependencies (129) python (129)

Dependencies

.github/workflows/continuous_delivery.yaml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
.github/workflows/continuous_integration.yml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • coverallsapp/github-action v2.3.6 composite
.devcontainer/Dockerfile docker
  • mcr.microsoft.com/devcontainers/python 3.13 build
.devcontainer/docker-compose.yml docker
poetry.lock pypi
  • 147 dependencies
pyproject.toml pypi
  • coverage ^7.6.12 develop
  • mypy ^1.15.0 develop
  • pytest ^8.3.5 develop
  • pytest-asyncio ^0.25.3 develop
  • pytest-cov ^6.0.0 develop
  • pytest-random-order ^1.1.1 develop
  • pytest-recording ^0.13.1 develop
  • ruff ^0.9.9 develop
  • jupyter ^1.1.1 docs
  • mkdocs ^1.6.1 docs
  • mkdocs-gen-files ^0.5.0 docs
  • mkdocs-jupyter ^0.25.1 docs
  • mkdocs-literate-nav ^0.6.1 docs
  • mkdocs-macros-plugin ^1.3.7 docs
  • mkdocs-material ^9.6.7 docs
  • mkdocs-section-index ^0.3.9 docs
  • mkdocstrings-python ^1.16.2 docs
  • pymdown-extensions ^10.14.3 docs
  • python ^3.13