Enabling subject queries based on longitudinal phenotypic data across datasets
Sebastian Urchs (@surchs on GitHub/Mattermost) Alyssa Dai (@alyssaydai on Twitter/GitHub, alyssadai on Mattermost)
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Brainhack Montreal
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:
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
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/
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/
Organization: https://github.com/neurobagel
Relevant repos for the project: https://github.com/neurobagel/bagel-cli
See Project Description!
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
(To be added)
Any or all of:
Mini project 2: Try out our tools to help us annotate OpenNeuro datasets!
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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/
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coding_methods, data_management, method_development
0_concept_no_content
reproducible_scientific_methods, other
BIDS, Datalad
Python, unix_command_line, other
behavioral, DWI, EEG, fMRI, MRI, other
0_no_git_skills, 1_commit_push, 2_branches_PRs
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Hi @brainhackorg/project-monitors my project is ready!