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inspire_meds

INSPIRE ETL to MEDS

https://github.com/rvandewater/inspire_meds

Science Score: 54.0%

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
  • ✓
    DOI references
    Found 2 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 (10.6%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

INSPIRE ETL to MEDS

Basic Info
  • Host: GitHub
  • Owner: rvandewater
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 180 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 6
Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Contributing License Citation

README.md

INSPIRE-MEDS

PyPI - Version codecov tests code-quality python license PRs contributors DOI

This pipeline extracts the INSPIRE dataset (from physionet, https://physionet.org/content/inspire/) into the MEDS format.

Usage:

bash pip install INSPIRE_MEDS export DATASET_DOWNLOAD_USERNAME=$PHYSIONET_USERNAME export DATASET_DOWNLOAD_PASSWORD=$PHYSIONET_PASSWORD MEDS_extract-INSPIRE root_output_dir=$ROOT_OUTPUT_DIR

When you run this, the program will:

  1. Download the needed raw INSPIRE files for the currently supported version into $ROOT_OUTPUT_DIR/raw_input.
  2. Perform initial, pre-MEDS processing on the raw INSPIRE files, saving the results in $ROOT_OUTPUT_DIR/pre_MEDS.
  3. Construct the final MEDS cohort, and save it to $ROOT_OUTPUT_DIR/MEDS_cohort.

You can also specify the target directories more directly, with

bash export DATASET_DOWNLOAD_USERNAME=$PHYSIONET_USERNAME export DATASET_DOWNLOAD_PASSWORD=$PHYSIONET_PASSWORD MEDS_extract-INSPIRE raw_input_dir=$RAW_INPUT_DIR pre_MEDS_dir=$PRE_MEDS_DIR MEDS_cohort_dir=$MEDS_COHORT_DIR

Examples and More Info:

You can run MEDS_extract-INSPIRE --help for more information on the arguments and options. You can also run

bash MEDS_extract-INSPIRE root_output_dir=$ROOT_OUTPUT_DIR

to run the entire pipeline.

Owner

  • Name: Robin van de Water
  • Login: rvandewater
  • Kind: user
  • Location: Berlin
  • Company: Hasso Plattner Institute

PhD student in Medical Event Prediction at Hasso Plattner Institute in collaboration with the Charité hospital (Berlin)

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "SICdb_MEDS ETL"
doi: "10.5281/zenodo.14891940"
authors:
  - family-names: "van de Water"
    given-names: "Robin Philippus"
    orcid: "https://orcid.org/0000-0002-2895-4872"
date-released: "2025-02-19"
url: "https://github.com/rvandewater/INSPIRE_MEDS"
repository-code: "https://github.com/rvandewater/INSPIRE_MEDS"
license: "MIT"

GitHub Events

Total
  • Release event: 4
  • Watch event: 1
  • Delete event: 1
  • Public event: 1
  • Push event: 14
  • Create event: 6
Last Year
  • Release event: 4
  • Watch event: 1
  • Delete event: 1
  • Public event: 1
  • Push event: 14
  • Create event: 6

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 22
  • Total Committers: 1
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 22
  • Committers: 1
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Robin van de Water r****r@g****m 22

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Dependencies

.github/workflows/code-quality-main.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pre-commit/action v3.0.1 composite
.github/workflows/code-quality-pr.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pre-commit/action v3.0.1 composite
  • trilom/file-changes-action v1.2.4 composite
.github/workflows/python-build.yaml actions
  • actions/checkout v4 composite
  • actions/download-artifact v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
  • sigstore/gh-action-sigstore-python v3.0.0 composite
.github/workflows/tests.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • codecov/codecov-action v4.0.1 composite
  • codecov/test-results-action v1 composite
pyproject.toml pypi
  • beautifulsoup4 *
  • hydra-core *
  • meds-transforms *
  • requests *