Oracle Open Data

Using Oracle Open Data to publish and access open data on OSF

This tutorial was created by Steffen Bollmannn.
Github: @stebo85

Getting Setup with Neurodesk

For more information on getting set up with a Neurodesk environment, see here

Oracle Open Data is an open platform for scientific data

Publish a dataset

To publish your data there you need to get in touch with Oracle and create a project. The upload then is done via the OCI command line tool. We for example uploaded one our datasets there: https://opendata.oraclecloud.com/ords/r/opendata/opendata/details?data_set_id=28&clear=RR,5

Access a dataset

To download a dataset from Oracle Open data you can use curl or wget:


wget https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/TOMCAT/o/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_IV1_defaced.nii.gz
curl -OL https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/TOMCAT/o/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_IV1_defaced.nii.gz

Or you can mount the object storage bucket inside NeuroDesk using rlcone (requires rclone v1.60.1 + this does not work on the hosted Neurodesk instances on play.neurodesk.org due to limited privileges):

mkdir -p ~/TOMCAT
rclone mount opendata3p:TOMCAT ~/TOMCAT &

This assumes the following ~/.config/rclone/rclone.conf configuration (which is setup already for you inside Neurodesk):

[opendata3p]
type = oracleobjectstorage
provider = no_auth
namespace = idrvm4tkz2a8
region = us-ashburn-1

Last modified September 25, 2023: update to new version 2023-09-20 (088e1f8)