Neurobagel

[alyssadai]

Title

Enabling subject queries based on longitudinal phenotypic data across datasets

Leaders

Sebastian Urchs (@surchs on GitHub/Mattermost)
Alyssa Dai (@alyssaydai on Twitter/GitHub, alyssadai on Mattermost)

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Montreal

Project Description

Neurobagel is a tool ecosystem that allows researchers to easily annotate their dataset (both phenotypic and imaging attributes) with standardized terms and provides tools to search for subjects across datasets that have been semantically harmonized.

For BrainHack, we have a primary project as well as mini projects available for folks at any level of experience:

Primary project: Modeling longitudinal/session-level phenotypic attributes of subjects

For phenotypic data available in a dataset, Neurobagel currently supports annotation and query of a core set of cross-sectional (subject-level) attributes including age, sex, diagnosis, and cognitive assessment data availability.

We want to expand this data model to be able to represent these phenotypic attributes at the session level, with the goal of supporting more sophisticated queries of longitudinal data (e.g., "I want to find subjects who had Montreal Cognitive Assessment data collected for at least 2 sessions").

Resources:
To learn more about the attributes described by our current data model: https://neurobagel.org/dictionaries/
To see our data model in action: https://github.com/neurobagel/bagel-cli/blob/main/bagel/models.py

Mini project 1: Tell us about your needs for sample search and phenotypic data annotation

Neurobagel includes web tools for annotating a dataset (https://annotate.neurobagel.org) subject-level sample search across datasets (https://query.neurobagel.org/). We want to hear about how you are interested in using these tools, specific use cases you may have as someone working with/needing to find samples for studies, replication, etc., and more generally collect challenges data users face that Neurobagel may be able to help with.

Resources:
For an overview of the current Neurobagel tools and their purposes: https://neurobagel.org/overview/

Mini project 2: Try out our tools to help us annotate OpenNeuro datasets!

We have internally annotated >340 datasets from OpenNeuro using our tools, and made them searchable at the subject-level via our web query tool at https://query.neurobagel.org/?node=OpenNeuro. We would like your help in annotating a few of the remaining OpenNeuroDatasets using our fully browser-based annotation tool.

Resources:
Our annotation tool: https://annotate.neurobagel.org
To learn more about the annotation process: https://neurobagel.org/annotation_tool/

Link to project repository/sources

Organization: https://github.com/neurobagel

Relevant repos for the project:
https://github.com/neurobagel/bagel-cli

Goals for Brainhack Global

See Project Description!

Good first issues

Please look for the good first issue label (or simply type is:open label:"good first issue" in the issue filter) in the issue list for any of our repos!

e.g.,
https://github.com/neurobagel/bagel-cli/labels/good%20first%20issue

Communication channels

(To be added)

Skills

Primary project: Modeling longitudinal/session-level phenotypic attributes of subjects

Any or all of:

• Python
• Bash
• Git/GitHub
• Any knowledge of longitudinal imaging or demographic/clinical data
• BIDS (optional)

Mini project 1: Tell us about your needs for sample search and phenotypic data annotation

• Experience working with any neuroimaging dataset, study replication, or phenotypic data wrangling
• No coding experience required!

Mini project 2: Try out our tools to help us annotate OpenNeuro datasets!

• Experience working with tabular (CSV/TSV) demographic/clinical data
• Nice to have: familiarity with OpenNeuro or BIDS
• No coding experience required / beginner coders welcome!

Onboarding documentation

No response

What will participants learn?

Primary project: Modeling longitudinal/session-level phenotypic attributes of subjects

• Python functions
• Data modeling using Pydantic and classes in Python
• Command-line interfaces in Python
• pyBIDS
• Working with Git repos

Mini project 1: Tell us about your needs for sample search and phenotypic data annotation

• Learn about Neurobagel and the world of semantic data harmonization!

Mini project 2: Try out our tools to help us annotate OpenNeuro datasets!

• Dataset semantic annotation using Neurobagel
• BIDS
• Working with Git repos

Data to use

No response

Number of collaborators

3

Credit to collaborators

We welcome direct contributions through pull requests, and will eventually employ some organization-level variant of all-contributors to credit any contributors on our website: https://neurobagel.org/

Image

Leave this text if you don't have an image yet.

Type

coding_methods, data_management, method_development

Development status

0_concept_no_content

Topic

reproducible_scientific_methods, other

Tools

BIDS, Datalad

Programming language

Python, unix_command_line, other

Modalities

behavioral, DWI, EEG, fMRI, MRI, other

Git skills

0_no_git_skills, 1_commit_push, 2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.

[alyssadai]

Hi @brainhackorg/project-monitors my project is ready!

[Remi-Gau]

project should already be online 😉