Prerequisites: This tutorial assumes that you have already completed the steps required to gain access to the MIMIC dataset on PhysioNet.
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Note that this install was written and tested using Mac OS X and Ubuntu 15.04. If you feel there are key details missing, please raise an issue with your suggested improvements - we would love to incorporate them!
There are two options for installing MIMIC-III locally in a PostgreSQL database:
- Manually, by following the tutorial below
- Automatically, using the make files available in the mimic-code repository
These steps are roughly equivalent, though you may learn more about the database configuration by installing the data manually.
0. Prepare
Note that before proceeding with this tutorial you will need to:
- Download the MIMIC-III Clinical Database (see here for details on gaining access).
- Place the MIMIC-III Clinical Database as either .csv or .csv.gz files somewhere on your local computer.
- Download the PostgreSQL scripts from here - only the files which end in
.sql
are required.
It’s easiest to move all the MIMIC data files and the scripts to load the data into a single folder (usually called the working directory). Most of the commands below will assume that files are located in the current folder.
1. Install Postgres
Pirate Lilou Cormac Mac Os Catalina
Postgres (also known as PostgreSQL) is a database management system. To create an instance of MIMIC-III on your local machine, you’ll first need to make sure that Postgres is installed. Island of disaster mac os. For installation, please refer to: http://www.postgresql.org/download/
On Mac OSX with the Homebrew package manager, simply type
brew install postgres
. On Ubuntu Linux, try sudo apt-get install postgresql
.2. Place the CSV data files in a local directory
Assuming that you have completed the steps required to gain access to the MIMIC dataset, you should be able to access the CSV data files on PhysioNet at: https://physionet.org/content/mimiciii/.
Download these files to a local folder and decompress them if desired (it is possible to load the data directly into a database from compressed data files). The program
gzip
can be used to decompress the data (e.g. gzip -d *.gz
).3. Create a user to access the data
It’s bad practice to use a superuser account for day to day querying as you may accidentally drop raw data or something similar which would take effort to rectify.
To avoid this issue, we will create a user account on the database with the same username as the operating system user. To find out the local operating system username, type the following in the terminal:
That should return a username. For the rest of this tutorial, we will use
mimicuser
, but it’s recommended to replace this with your local username. If you do, you can use operating system authentication and avoid having to password protect the user for the database. We can use a terminal command to create the user:This user is a superuser - we will remove this privilege later.
4. Connect to the database with psql
Now that Postgres is running, you should be able to connect to the system using the
psql
command line tool. With new installations, the default database name is ‘postgres’, so try connecting with:5. Create an empty database containing a MIMIC-III schema
From this point onwards we will be referring to scripts in the ‘buildmimic’ directory of the MIMIC code repository.You should have already downloaded the SQL scripts to your working directory.
After connecting with psql, create a new database called “mimic”:
6. (Optional, recommended) Create a schema to hold the data
Note that postgres uses the
public
schema by default. We recommend creating an independent schema to host the data. To do this, create the mimiciii schema:In the future, you will need to inform postgres that it should use the
mimiciii
schema.You will need to run the above every time you launch psql.
7. Create a set of empty tables on a mimiciii schema, ready to populate with the data
Refer to the ‘postgres_create_tables’ script in the MIMIC code repository to create the mimiciii schema and then build a set of empty tables. Each table is created by running a
CREATE TABLE
command in psql.First, exit from psql with
q
which should bring you back to the shell command prompt. Now run the “postgres_create_tables.sql” script as follows:If the script runs successfully, you should see the following output:
If you get the error
postgres_create_tables.sql: No such file or directory
that means that the file postgres_create_tables.sql
is not in your current directory. Either download the file to the local directory, or specify the directory in the above command.If you see warnings about being unable to drop tables, don’t worry, this is expected (see #224).
8. Import the CSV data files into the empty tables
Using the Postgres
COPY
or COPY
commands, you should now be able to import the CSV data into the empty set of tables. You can run the “postgres_load_data.sql” script from the command prompt using:If the script runs successfully, you should see the following output:
Importing the data can be slow, particularly for larger tables like CHARTEVENTS which may take several hours.
Note also that above, we have included a line which states
COPY 0
. This is expected: CHARTEVENTS acts as a “mapping” table to multiple sub-tables, and no data is actually stored within it, so postgres reports that 0 rows were inserted. This is expected behaviour for CHARTEVENTS.9. Add indexes to improve performance
Indexes provide additional structure for the database that can help to improve the speed of queries. The MIMIC code repository includes a script with a set of suggested indexes. As before, you can run this script from the command line:
10. Run checks
We have included a script which verifies all rows have been loaded in. Run those checks now:
If all tables have the expected number of rows, you should see the phrase ‘PASSED’ for every table.
11. MIMIC-III is ready for analysis
You should now have a working copy of MIMIC-III ready to query with the psql command line tool. First start the PSQL client from the command line:
Before going further, you should grant all privileges needed to the mimic user, then revoke the superuser privilege:
Now try, for example, counting the number of patients in the database:
Note that, because we specified the search_path in the connection string above (
--search_path=mimiciii
), we can omit it in the query:12. Install a graphical user interface (optional)
It is sometimes convenient to use a graphical user interface (GUI) for working with the database. There are a few options here:
- pgadmin - http://www.pgadmin.org/download/
- dbeaver - https://dbeaver.jkiss.org/
- valentina - https://www.valentina-db.com/en/
Catalina
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Affinity Photo
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macOS Catalina
The power of Mac.
Taken further.
Featuring all-new, dedicated apps for music, TV and podcasts. Smart new features in the apps you use every day. And Sidecar, which lets you use iPad as a second Mac display.
See if your Mac can run macOS Catalina.
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Learn moreNew tools to build new worlds.
If you can imagine it, you can create it. ARKit 3 gives you new tools to build incredible experiences on the world’s largest AR platform.
Develop for macOS Catalina.
The Apple SDK offers enormous possibilities for developers to create apps that will work across Mac, iPhone and iPad.