From dce20ec808e94a37fd9db9d383d936c8d8c20493 Mon Sep 17 00:00:00 2001 From: Chamath Palihawadana Date: Sat, 30 Dec 2023 19:38:59 +0000 Subject: [PATCH] fix: readme mimic-iv concept postgres links --- mimic-iv/concepts/README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/mimic-iv/concepts/README.md b/mimic-iv/concepts/README.md index 7610be23a..051bad2d8 100644 --- a/mimic-iv/concepts/README.md +++ b/mimic-iv/concepts/README.md @@ -1,7 +1,7 @@ # MIMIC-IV Concepts This folder contains scripts to generate useful abstractions of raw MIMIC-IV data ("concepts"). -The scripts are written using the **BigQuery Standard SQL Dialect**. Concepts are categorized into folders if possible, otherwise they remain in the top-level directory. The [postgres](/mimic-iv/concepts/postgres) subfolder contains automatically generated PostgreSQL versions of these scripts; [see below for how these were generated](#postgresql-concepts). Concepts are categorized into folders if possible, otherwise they remain in the top-level directory. +The scripts are written using the **BigQuery Standard SQL Dialect**. Concepts are categorized into folders if possible, otherwise they remain in the top-level directory. The [postgres](/mimic-iv/concepts_postgres) subfolder contains automatically generated PostgreSQL versions of these scripts; [see below for how these were generated](#postgresql-concepts). Concepts are categorized into folders if possible, otherwise they remain in the top-level directory. The concepts are organized into individual SQL scripts, with each script generating a table. The BigQuery `mimiciv_derived` dataset under `physionet-data` contains the concepts pregenerated. Access to this dataset is available to MIMIC-IV approved users: see the [cloud instructions](https://mimic.mit.edu/docs/gettingstarted/cloud/) on how to access MIMIC-IV on BigQuery (which includes the derived concepts). @@ -26,9 +26,9 @@ In general the concepts may be generated in any order, except for the *first_day ## Generating the concepts on PostgreSQL -These instructions are used to regenerate the [postgres](/mimic-iv/concepts/postgres) scripts from the BigQuery dialect scripts in the concepts folder. +These instructions are used to regenerate the [postgres](/mimic-iv/concepts_postgres) scripts from the BigQuery dialect scripts in the concepts folder. -* **If you just want to create PostgreSQL concepts for your installation of MIMIC-IV, go to the [postgres](/mimic-iv/concepts/postgres) subfolder** +* **If you just want to create PostgreSQL concepts for your installation of MIMIC-IV, go to the [postgres](/mimic-iv/concepts_postgres) subfolder** * If you would like to understand the process better, and possibly improve upon it, read on Analogously to [MIMIC-III Concepts](https://github.com/MIT-LCP/mimic-code/tree/master/concepts), the SQL scripts here are written in BigQuery's Standard SQL syntax. The concepts have been carefully written to allow conversion to PostgreSQL, so that only the following changes are necessary to make them compaible with PostgreSQL: @@ -37,13 +37,13 @@ Analogously to [MIMIC-III Concepts](https://github.com/MIT-LCP/mimic-code/tree/m * modify SQL scripts for incompatible syntax * run the modified SQL scripts and direct the output into tables in the PostgreSQL database -To do this, we have created a (*nix/Mac OS X) compatible shell script which performs regular expression replacements for each script. To simplify the process for users, we output these automatically generated scripts to the [postgres](/mimic-iv/concepts/postgres) folder. +To do this, we have created a (*nix/Mac OS X) compatible shell script which performs regular expression replacements for each script. To simplify the process for users, we output these automatically generated scripts to the [postgres](/mimic-iv/concepts_postgres) folder. Re-running this shell script can be done as follows: 1. Open a terminal in the `concepts` folder. 2. Run [convert_bigquery_to_postgres.sh](convert_bigquery_to_postgres.sh). * e.g. `bash convert_bigquery_to_postgres.sh` - * This file outputs the scripts to the [postgres](/mimic-iv/concepts/postgres) subfolder after applying a few changes. + * This file outputs the scripts to the [postgres](/mimic-iv/concepts_postgres) subfolder after applying a few changes. * This also creates the `postgres_make_concepts.sql` script in the postgres subfolder. ### Known Problems