Neurobagel

[surchs]

Title

Enable subject level cohort search across BIDS datasets

Short description and the goals for the OHBM BrainHack

Neurobagel’s goal is to make it easy for researchers to annotate their own BIDS data with standardized terms and to provide solutions to make these harmonized metadata searchable.

As a proof of concept, we have done this for a large part of the OpenNeuro MRI data and put them here: https://github.com/OpenNeuroDatasets-JSONLD. The metadata can be searched here: https://query.neurobagel.org/

We are going to work on two projects for folks at any level of experience. Our goals are:

• Understand better how users want to interact with our tools. Sit down with us, try the query tool or our "Getting started" documentation, and tell us what is easy and what can be improved. We specifically want to hear from people who are interested in a cross-dataset cohort search about how they would like to use Neurobagel in the future.
• Increase alignment with the BIDS community. Neurobagel annotations are currently stored inside BIDS participant.json files with additional json keys. We would like to discuss how we can create these files in a way that makes them maximally useful to people in the wider BIDS ecosystem, and hopefully eventually fully BIDS compatible.
• Collaborate on automating the processing of OpenNeuro annotations. We would like to have an automatic process that can be triggered (e.g. via some Github Action or hook) to pull a BIDS datalad dataset and run the Neurobagel metadata extractor to create a linked data view of the BIDS dataset that we can search over. All of the steps are already in place but done manually at the moment. We hope to find ways to automate this via Github or a different CI.

Link to the Project

https://github.com/neurobagel

Image for the OHBM brainhack website

No response

Project lead

Who	Where	Github	Discord
Alyssa Dai	In person	@alyssadai	alyssadai#5780
Arman Jahanpour	On Discord	@rmanaem	rmanaem
Sebastian Urchs	In person	@surchs	_surchs

Main Hub

Montreal

Other Hub covered by the leaders

• Montreal
• Asia / Pacific
• Europe / Middle East / Africa
• Americas

Skills

User feedback

• everybody is welcome
• having an interest in cross dataset cohort search or dealing with messy data

Discussing semantic annotation in BIDS

• BIDS (beginner)
• Experience working with messy (clinical) data
• Research interest that wants to ask questions across several dataset
• Interest in data harmonization and metadata

Automating processing of OpenNeuro metadata

• Datalad
• git, Github Actions, CI workflows in general
• Python
• Docker (nice to have)

Recommended tutorials for new contributors

• Set up a brainhack friendly computing environment
• A introduction to Bash
• Python: Writing a script
• Python: Data analysis with Python
• Python: Visualisation
• Machine learning basics
• BIDS
• Machine learning for neuroimaging
• VCS: Using Git and Github
• VCS: Data management with Datalad
• Virtualization
• High Performance Computing: Oracle cloud resource

Good first issues

No response

Twitter summary

No response

Short name for the Discord chat channel (~15 chars)

neurobagel

Please read and follow the OHBM Code of Conduct

• I agree to follow the OHBM Code of Conduct during the hackathon

[ufangYang]

hi @surchs can you provide the content and/or figure for this project to be added into Brainhack Proceeding 2023 by 15th May? Also please don't forgot to fill out your team member's details using this form: https://forms.gle/Ku3AVHcXvpUqVVkV7 . Cheers