Structuring data from echocardiography reports

This repository contains code for structuring data from echocardiography reports. This data can be used in studying the relationship between cardiac function and patient health.

How to access the data

If you are simply interested in accessing the data, it is available on PhysioNetWorks: https://physionet.org/users/

PhysioNet Works is an online repository allowing selective access to data for credentialed users. In order to directly access the data, users must be accredited to use the MIMIC-III clinical database. If you do not have the appropriate access, you can acquire it by following the steps detailed here.

Once you have access to the MIMIC-III database, log in to PhysioNetWorks with your username/password. Go to the "MIMIC-III Related Work" project, and scroll down to "Echocardiography data". The CSV files are available to download. They can be linked back to the MIMIC-III database using SUBJECT_ID, HADM_ID or ICUSTAY_ID.

How to use this repository

Before using this repository, you'll need to:

1. Install Python 2.7
   • The numpy, pandas, and psycopg2 packages are also required
2. Install PostgreSQL 9.4 or higher
3. Install MIMIC-III locally on your system
   • This requires access to the MIMIC-III database, detailed here.
   • An install guide is available here (Ubuntu/Mac OS X) or here (Windows).

Once these are available on your system, you can begin running the Python script which will generate