Merge pull request #1034 from MIT-LCP/new_consol

MIMIC repo code consolidation

Author: tompollard

.gitignore

@@ -1,9 +1,3 @@
-# Data files
-*.csv
-
-# Picture files
-*.png
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -65,12 +59,5 @@ target/
 # OSX .DS_Store
 .DS_Store
 
-# Jupyter Notebook checkpoints
-.ipynb_checkpoints/
-
-# data files
-travisdata/
-
-# R project files
-.Rproj
-.Rproj.user
+# PyCharm / JetBrains
+.idea

.travis.yml

@@ -21,4 +21,4 @@ install:
 - pip install pytest --quiet
 
 script:
-   - 'pytest tests'
+   - 'pytest mimic-iii/tests'

ISSUE_TEMPLATE.md

@@ -1,7 +1,7 @@
 ### Prerequisites
 
 * [ ] Put an X between the brackets on this line if you have done all of the following:
-    * Checked the online documentation: https://mimic.physionet.org/about/mimic/
+    * Checked the online documentation: https://mimic.mit.edu/
     * Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
 
 ### Description
@@ -11,3 +11,6 @@ Description of the issue, including:
 * what you have tried
 * references to similar issues
 * queries demonstrating your question (if applicable)
+
+### Labels
+* Please add one or more of these labels when creating an issue: ![](https://img.shields.io/github/labels/MIT-LCP/mimic-code/mimic-iv), ![](https://img.shields.io/github/labels/MIT-LCP/mimic-code/mimic-iii), ![](https://img.shields.io/github/labels/MIT-LCP/mimic-code/mimic-cxr). If your issue applies to more than one of these please feel free to select multiple labels as appropriate.

LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) 2015 MIT Laboratory for Computational Physiology
+Copyright (c) 2019 MIT Laboratory for Computational Physiology
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

README.md

@@ -1,36 +1,16 @@
-# 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=main)](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)
 
-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. Source code for the website is in the [mimic-website GitHub repository](https://github.com/MIT-LCP/mimic-website/).
+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.mit.edu). To find out more about MIMIC, please see: https://mimic.mit.edu. Source code for the website is in the [mimic-website GitHub repository](https://github.com/MIT-LCP/mimic-website/).
 
 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 consists of a number of Structured Query Language (SQL) scripts which build the MIMIC-III database in a number of systems and extract useful concepts from the raw data.
-Jupyter notebooks are also provided which detail analyses performed on MIMIC-III.
-
-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, and a README in the subfolder lists concepts generated.
-* [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
-* [notebooks/aline-aws](/notebooks/aline-aws) - As above, [launchable immediately on AWS](#launch-mimic-iii-in-aws)
-* [tests](/tests) - You should always have tests!
-* [tutorials](/tutorials) - Similar to the notebooks folder, but focuses on explaining concepts to new users
-
-\* A Makefile build system has been created to facilitate the building of the MIMIC database, and optionally contributed views from the community. Please refer to the [Makefile guide](https://github.com/MIT-LCP/mimic-code/blob/master/Makefile.md) for more details.
-
 ## Cloud access
 
-The MIMIC-III database is now available on two major cloud platforms: Google Cloud Platform (GCP) and Amazon Web Services (AWS). To access the data on the cloud, simply add the relevant cloud identifier to your PhysioNet profile. Further instructions are available on [the MIMIC-III website](https://mimic.physionet.org/gettingstarted/cloud/).
-
-Derived concepts can be immediately accessed by querying them directly on BigQuery under the `mimiciii_derived` dataset in the `physionet-data` project (see [cloud instructions for accessing MIMIC-III on the cloud](https://mimic.physionet.org/gettingstarted/cloud/)).
+The MIMIC database is now available on two major cloud platforms: Google Cloud Platform (GCP) and Amazon Web Services (AWS). To access the data on the cloud, simply add the relevant cloud identifier to your PhysioNet profile. Further instructions are available on [the MIMIC website](https://mimic.mit.edu/iv/access/cloud/).
 
 ### Launch MIMIC-III in AWS
 
-Use the below Launch Stack button to deploy access to the MIMIC-III dataset into your AWS account.  This will give you real-time access to the MIMIC-III data in your AWS account without having to download a copy of the MIMIC-III dataset.  It will also deploy a Jupyter Notebook with access to the content of this GitHub repository in your AWS account.    Prior to launching this, please login to the [MIMIC PhysioNet website](https://mimic.physionet.org/), [input your AWS account number](https://physionet.org/settings/cloud/), and [request access to the MIMIC-III Clinical Database on AWS](https://physionet.org/projects/mimiciii/1.4/request_access/2).  
+MIMIC-III is available on AWS (and MIMIC-IV will be available in the future). Use the below Launch Stack button to deploy access to the MIMIC-III dataset into your AWS account.  This will give you real-time access to the MIMIC-III data in your AWS account without having to download a copy of the MIMIC-III dataset.  It will also deploy a Jupyter Notebook with access to the content of this GitHub repository in your AWS account.    Prior to launching this, please login to the [MIMIC PhysioNet website](https://mimic.mit.edu/), [input your AWS account number](https://physionet.org/settings/cloud/), and [request access to the MIMIC-III Clinical Database on AWS](https://physionet.org/projects/mimiciii/1.4/request_access/2).  
 
 To start this deployment, click the Launch Stack button.  On the first screen, the template link has already been specified, so just click next.  On the second screen, provide a Stack name (letters and numbers) and click next, on the third screen, just click next.  On the forth screen, at the bottom, there is a box that says **I acknowledge that AWS CloudFormation might create IAM resources.**.  Check that box, and then click **Create**.  Once the Stack has complete deploying, look at the **Outputs** tab of the AWS CloudFormation console for links to your Juypter Notebooks instance.
 
@@ -45,9 +25,7 @@ To start this deployment, click the Launch Stack button.  On the first screen, t
 
 ## 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.
+If you use code or concepts available in this repository, we would be grateful if you would add a citation as described on the website: [MIMIC-III citation](http://mimic.mit.edu//iii/about/acknowledgments/#mimic-iii-citation) , [MIMIC-IV citation](http://mimic.mit.edu/iv/overview/acknowledgments/#mimic-iv-citation)
 
 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
 
@@ -59,12 +37,12 @@ Our team has worked hard to create and share the MIMIC dataset. We encourage you
 * Commit your changes to the forked repository.
 * Submit a pull request to the [MIMIC code repository](https://github.com/MIT-LCP/mimic-code), using the method described at: https://help.github.com/articles/using-pull-requests/
 
-We encourage users to share concepts they have extracted by writing code which generates a materialized view. These materialized views can then be used by researchers around the world to speed up data extraction. For example, ventilation durations can be acquired by creating the ventdurations view in [concepts/durations/ventilation_durations.sql](https://github.com/MIT-LCP/mimic-code/blob/master/concepts/durations/ventilation_durations.sql).
+We encourage users to share concepts they have extracted by writing code which generates a materialized view. These materialized views can then be used by researchers around the world to speed up data extraction. For example, ventilation durations can be acquired by creating the ventdurations view in [concepts/durations/ventilation_durations.sql](https://github.com/MIT-LCP/mimic-code/tree/new_consol/mimic-iii/concepts/durations/ventilation_durations.sql).
 
 ### License
 
-By committing your code to the [MIMIC Code Repository](https://github.com/mit-lcp/mimic-code) you agree to release the code under the [MIT License attached to the repository](https://github.com/mit-lcp/mimic-code/blob/master/LICENSE).
+By committing your code to the [MIMIC Code Repository](https://github.com/mit-lcp/mimic-code) you agree to release the code under the [MIT License attached to the repository](https://github.com/mit-lcp/mimic-code/blob/main/LICENSE).
 
 ### Coding style
 
-Please refer to the [style guide](https://github.com/MIT-LCP/mimic-code/blob/master/styleguide.md) for guidelines on formatting your code for the repository.
+Please refer to the [style guide](https://github.com/MIT-LCP/mimic-code/blob/main/styleguide.md) for guidelines on formatting your code for the repository.

mimic-cxr/README.md

@@ -0,0 +1,5 @@
+# MIMIC-CXR
+
+MIMIC-CXR is a publicly available database of chest x-rays with free-text radiology reports. You can read more about the dataset on [the PhysioNet project page](https://mimic.mit.edu//iv/modules/cxr/about/).
+
+This repository is intended to support use of the data by providing code, documentation, and a central location for discussion (in the form of GitHub issues). Feedback and contributions are always welcome!

mimic-cxr/awesome-mimic-cxr.md

@@ -0,0 +1,28 @@
+# Awesome MIMIC-CXR [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/sindresorhus/awesome)
+
+A curated list of MIMIC-CXR resources.
+
+## Contributing
+
+Please feel free to send in [pull requests](https://github.com/mit-lcp/mimic-cxr/pulls) to add links.
+
+## Table of Contents
+
+<!--
+ - [Books](#books)
+ - [Courses](#courses)
+ - [Tutorials and Talks](#tutorials-and-talks)
+ - [Resources for students](#resources-for-students)
+ - [Blogs](#blogs)
+ - [Links](#links)
+-->
+
+ - [Papers](#papers)
+ - [Software](#software)
+ - [Datasets](#datasets)
+
+ ## Papers
+
+ ## Software
+
+ ## Datasets