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eds-scikit

eds-scikit is a Python library providing tools to process and analyse OMOP data

https://github.com/aphp/eds-scikit

Science Score: 67.0%

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: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (18.0%) to scientific vocabulary

Keywords

clinical-data-warehouse data-science medical omop python
Last synced: 6 months ago · JSON representation ·

Repository

eds-scikit is a Python library providing tools to process and analyse OMOP data

Basic Info
Statistics
  • Stars: 40
  • Watchers: 1
  • Forks: 5
  • Open Issues: 14
  • Releases: 8
Topics
clinical-data-warehouse data-science medical omop python
Created about 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

#

![Tests](https://img.shields.io/github/actions/workflow/status/aphp/eds-scikit/testing.yml?branch=main&label=tests&style=flat-square) [![Documentation](https://img.shields.io/github/actions/workflow/status/aphp/eds-scikit/publish_doc.yml?branch=main&label=docs&style=flat-square)](https://aphp.github.io/eds-scikit/latest/) [![PyPI](https://img.shields.io/pypi/v/eds-scikit?color=blue&style=flat-square)](https://pypi.org/project/eds-scikit/) [![Supported Python](https://img.shields.io/badge/python-%3E%3D%203.7.1%20%7C%20%3C%203.8-brightgreen?style=flat-square)](https://www.python.org/) [![Black](https://img.shields.io/badge/code%20style-black-black?style=flat-square)]([https://www.python.org/](https://github.com/psf/black)) [![Coverage](https://raw.githubusercontent.com/aphp/eds-scikit/coverage/coverage.svg)](https://raw.githubusercontent.com/aphp/eds-scikit/coverage/coverage.txt) [![DOI](https://zenodo.org/badge/571584236.svg)](https://zenodo.org/badge/latestdoi/571584236&style=flat-square)

eds-scikit is a tool to assist data scientists working on the AP-HP's Clinical Data Warehouse. It is specifically targeted for OMOP-standardized data. It main goals are to:

  • Ease access and analysis of data
  • Allow a better transfer of knowledge between projects
  • Improve research reproducibility

Development

This library is developed and maintained by the core team of AP-HP’s Clinical Data Warehouse (EDS) with the strong support of Inria's SODA team.

How to use

Please check the online documentation for more informations. You will find - Detailed explanation of the project goal and working principles - A complete API documentation - Various Jupyter Notebooks describing how to use various functionnalities of eds-scikit - And more !

Requirements

eds-scikit stands on the shoulders of Spark 2.4 which requires:

  • Python ~3.7.1
  • Java 8 ## Installation

You can install eds-scikit via pip:

bash pip install "eds-scikit[aphp]"

:warning: If you get an an error during installation, please try downgrading pip via pip install -U "pip<23" before installeds-scikit`

:warning: If you don't work in AP-HP's ecosystem (EDS), please install via:

bash pip install eds-scikit

You can now import the library via

python import eds_scikit

Contributing

  • You want to help on the project ?
  • You developped an interesting feature and you think it could benefit other by being integrated in the library ?
  • You found a bug ?
  • You have a question about the library ?
  • ...

Please check our contributing guidelines.

Citation

If you use eds-scikit, please cite us as below.

bibtex @misc{eds-scikit, author = {Petit-Jean, Thomas and Remaki, Adam and Maladière, Vincent and Varoquaux, Gaël and Bey, Romain}, doi = {10.5281/zenodo.7401549}, title = {eds-scikit: data analysis on OMOP databases}, url = {https://github.com/aphp/eds-scikit} }

Acknowledgment

We would like to thank the following funders: - Assistance Publique – Hôpitaux de Paris - AP-HP Foundation - Inria

Owner

  • Name: Greater Paris University Hospitals (AP-HP)
  • Login: aphp
  • Kind: organization
  • Location: Paris

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  eds-scikit: data analysis on OMOP databases
message: If you use eds-scikit, please cite us as below.
type: software
authors:
  - given-names: Thomas
    family-names: Petit-Jean
    orcid: "https://orcid.org/0000-0002-4433-442X"
    affiliation: Assistance Publique – Hôpitaux de Paris
  - given-names: Adam
    family-names: Remaki
    orcid: "https://orcid.org/0000-0002-8902-8207"
    affiliation: Assistance Publique – Hôpitaux de Paris
  - given-names: Vincent
    family-names: Maladière
    orcid: "https://orcid.org/0000-0001-7276-936X"
    affiliation: Inria
  - given-names: Gaël
    family-names: Varoquaux
    orcid: "https://orcid.org/0000-0003-1076-5122"
    affiliation: Inria
  - given-names: Romain
    family-names: Bey
    orcid: "https://orcid.org/0000-0002-6413-5188"
    affiliation: Assistance Publique – Hôpitaux de Paris
repository-code: "https://github.com/aphp/eds-scikit"
url: "http://aphp.github.io/eds-scikit"
abstract: >-
  eds-scikit is a Python library providing tools to
  process and analyse OMOP data.
keywords:
  - OMOP
  - clinical
license: BSD-3-Clause
year: 2021

GitHub Events

Total
  • Issues event: 2
  • Watch event: 4
  • Issue comment event: 3
  • Pull request event: 1
  • Create event: 1
Last Year
  • Issues event: 2
  • Watch event: 4
  • Issue comment event: 3
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 124
  • Total Committers: 8
  • Avg Commits per committer: 15.5
  • Development Distribution Score (DDS): 0.556
Past Year
  • Commits: 9
  • Committers: 2
  • Avg Commits per committer: 4.5
  • Development Distribution Score (DDS): 0.111
Top Committers
Name Email Commits
Thomas PETIT-JEAN t****n@a****r 55
Vincent M m****t@y****r 37
svittoz 1****z 15
Matthieu Doutreligne m****e@h****r 7
Adam a****i@a****r 6
Théo Jolivet t****t@e****r 2
Perceval Wajsburt p****t@g****m 1
JCharline 2****e 1
Committer Domains (Top 20 + Academic)
aphp.fr: 2 ens-paris-saclay.fr: 1 has-sante.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 11
  • Total pull requests: 62
  • Average time to close issues: 21 days
  • Average time to close pull requests: 29 days
  • Total issue authors: 7
  • Total pull request authors: 8
  • Average comments per issue: 0.45
  • Average comments per pull request: 1.31
  • Merged pull requests: 51
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 2.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • strayMat (4)
  • TheooJ (2)
  • Thomzoy (2)
  • Vincent-Maladiere (1)
  • paul-bssr (1)
  • PPPinson (1)
  • JCharline (1)
  • OlivierHassanaly (1)
Pull Request Authors
  • svittoz (28)
  • Thomzoy (20)
  • Vincent-Maladiere (17)
  • percevalw (5)
  • Aremaki (3)
  • TheooJ (1)
  • strayMat (1)
  • JCharline (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 51 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 19
  • Total maintainers: 3
proxy.golang.org: github.com/aphp/eds-scikit
  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 6.5%
Average: 6.7%
Dependent repos count: 6.9%
Last synced: 6 months ago
pypi.org: eds-scikit

eds-scikit is a Python library providing tools to

  • Documentation: https://aphp.github.io/eds-scikit
  • License: Copyright (c) 2021, Assistance Publique - Hôpitaux de Paris, Inria Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.1.8
    published over 1 year ago
  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 51 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 11.9%
Forks count: 15.3%
Average: 18.0%
Dependent repos count: 21.7%
Downloads: 31.4%
Maintainers (3)
ThomasPJ RomainBeyAPHP Vincent-Maladiere
Last synced: 6 months ago

Dependencies

.github/workflows/publish_doc.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/release.yml actions
  • actions/checkout master composite
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/testing.yml actions
  • actions/cache v2 composite
  • actions/checkout v3 composite
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3 composite
  • mstachniuk/ci-skip master composite
pyproject.toml pypi
  • altair >=5.0.0, <6.0.0
  • catalogue *
  • ipython >=7.32.0, <8.0.0
  • koalas >=1.8.1, <2.0.0
  • loguru ==0.7.0
  • numpy >=1.0.0, <1.20
  • packaging ==21.3
  • pandas >=1.3.0, <2.0.0
  • pgpasslib >=1.1.0, <2.0.0
  • pretty-html-table >=0.9.15, <0.10.0
  • psycopg2-binary >=2.9.0, <3.0.0
  • pyarrow ==0.17.0
  • pypandoc ==1.7.5
  • pyspark ==2.4.3
  • schemdraw >=0.15.0, <1.0.0
  • tomli ==2.0.1