From 780c3363c787f4f546084f9d2150cf73b58a3515 Mon Sep 17 00:00:00 2001 From: Alistair Johnson Date: Fri, 7 Sep 2018 07:55:14 -0400 Subject: [PATCH] add an overview of the repo --- README.md | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 820308d50..d13a6befd 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,28 @@ -# MIMIC Code Repository [![Build Status](https://travis-ci.org/MIT-LCP/mimic-code.svg?branch=master)](https://travis-ci.org/MIT-LCP/mimic-code) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.821872.svg)](https://doi.org/10.5281/zenodo.821872)[![Join the chat at https://gitter.im/MIT-LCP/mimic-code](https://badges.gitter.im/MIT-LCP/mimic-code.svg)](https://gitter.im/MIT-LCP/mimic-code?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) +# MIMIC Code Repository [![Build Status](https://travis-ci.org/MIT-LCP/mimic-code.svg?branch=master)](https://travis-ci.org/MIT-LCP/mimic-code) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.821872.svg)](https://doi.org/10.5281/zenodo.821872) [![Join the chat at https://gitter.im/MIT-LCP/mimic-code](https://badges.gitter.im/MIT-LCP/mimic-code.svg)](https://gitter.im/MIT-LCP/mimic-code?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) This is a repository of code shared by the research community. The repository is intended to be a central hub for sharing, refining, and reusing code used for analysis of the [MIMIC critical care database](https://mimic.physionet.org). To find out more about MIMIC, please see: https://mimic.physionet.org You can read more about the code repository in the following open access paper: [The MIMIC Code Repository: enabling reproducibility in critical care research](https://doi.org/10.1093/jamia/ocx084). +## Brief introduction + +The repository is organized as follows: + +* [benchmark](/benchmark) - Various speed tests for indices +* [buildmimic](/buildmimic) - Scripts to build MIMIC-III in a relational database management system (RDMS), in particular [postgres](/buildmimic/postgres) is our RDMS of choice +* [concepts](/concepts) - Useful views/summaries of the data in MIMIC-III, e.g. demographics, organ failure scores, severity of illness scores, durations of treatment, easier to analyze views, etc. The paper above describes these in detail. +* [notebooks](/notebooks) - A collection of R markdown and Jupyter notebooks which give examples of how to extract and analyze data +* [notebooks/aline](/notebooks/aline) - An entire study reproduced in the MIMIC-III database - from cohort generation to hypothesis testing +* [tests](/tests) - You should always have tests! +* [tutorials](/tutorials) - Similar to the notebooks folder, but focuses on explaining concepts to new users + +## Acknowledgement + If you use code or concepts available in this repository, we would be grateful if you would cite the above paper as follows: > Johnson, Alistair EW, David J. Stone, Leo A. Celi, and Tom J. Pollard. "The MIMIC Code Repository: enabling reproducibility in critical care research." Journal of the American Medical Informatics Association (2017): ocx084. -You can also directly cite the repository using the above DOI from Zenodo. +If including a hyperlink to the code, we recommend you use the DOI from Zenodo rather than a GitHub URL: https://doi.org/10.5281/zenodo.821872 ## How to contribute