To do very simple queries on the clinical/phenotype data you can use the LabKey application on the Research Environment desktop. However, in order to do more complex analyses across multiple tables, or query very large tables, it is recommended that you use the provided LabKey APIs.
The LabKey client libraries (APIs) provide secure, auditable, programmatic access to LabKey data and services and allow you to:
Analyse and visualise data stored in LabKey in a statistical tool such as R or Python
Perform routine, automated tasks in a programmatic way.
Query and manipulate data in a repeatable and consistent way.
Currently, LabKey supports working with the following programming languages/environments.
We highly recommend using either the Python LabKey API or the R LabKey API to query the Genomics England clinical/phenotype data.
You firstly need to provide your credentials to the API so that you can access the data you are allowed.
This only needs to be one once in order to use the API.
These credentials are stored in a file called
.netrc (dot net rc), located in your home directory. This file does not exist initially, so you will have to create it. To do this:
pwdin the terminal and hitting return.
cdin the terminal and hitting return.
Once in your home directory, we will create the .netrc file. You can use any text editor to do this, but this guide we will use nano.
.netrcin nano by typing
This file needs the following three lines in it, where you change the username and password fields to your Research Environment credentials:
machine labkey-embassy.gel.zone login username password password
Ctrl+Othen hit return. Exit nano with
Because the file contains your password, it should be set to read-write only for yourself.
ls -alhin the terminal.
-rw------- <username> <username> .netrc
-rw-rw-rw-, they are visible to others and need to be changed.
chmod 600 .netrc, which will set read-write to you only.
For R and Python you will need to make specific changes to your scripts. Please have a look at the following pages for example scripts and how to set up your own script:
R LabKey API
Python LabKey API
Note: For the R LabKey API you will also need, as of April 2020, to create or reconfigure the .Renviron file. See R, RStudio, and R libraries#Creatingan.Renvironfile(alsorequiredfortheRLabKeyAPI).
In case the RLabKey API is incorrectly setup, please have a look here:
- LabKey DOCTYPE error
- LabKey curl_fetch_memory error
If this does not resolve the issue, and you still have problems using the R LabKey API, please contact the Service Desk.