Eric Earl
Eric Earl is a Neuroinformaticist acting as a Data Scientist in the NIMH Data Science & Sharing Team.
BIDS tabular phenotype data software for big neuroimaging studies
Eric Earl1, Jessica Dafflon1,2, Roberto Salamanca-Giron3,
Josh Faskowitz4, Arshitha Basavaraj1, Dustin Moraczewski1,
Samuel Guay5, Francisco Pereira2, Adam Thomas1
Poster #2464, Sessions 3 and 4
Presentation
and references
1 NIMH Data Science & Sharing Team, 2 NIMH Machine Learning Team, 3 NINDS Human Cortical Physiology and Neurorehabilitation Section,
4 NIMH Section on Functional Imaging Methods, 5 Université de Montréal Department of Psychology
Remember this
Our software is FAIR-principled and does the hard work of BIDS-standardizing big neuroimaging tabular phenotype data. You can download some data & dictionaries right now.
outline
What is big neuroimaging tabular phenotype data?
How do you convert this big data to BIDS?
How do you use the software?
outline
What is big neuroimaging tabular phenotype data?
How do you convert this big data to BIDS?
How do you use the software?
phe·no·type
noun, BIOLOGY
The set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.
tab·u·lar
adjective
Consisting of or presented in columns or tables.
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Assessments
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Forms
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Instruments
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Labs
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Questionnaires
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Surveys
Tabular Phenotype Data
big Neuroimaging
A growing wealth of large datasets in neuroimaging
big Neuroimaging
Each study standardizes tabular phenotype data differently
350+ file pairs
TSV data
CSV dictionaries
120+ file pairs
CSV data
Excel dictionaries
1 small file pair
CSV data
PDF dictionary
2 large file pairs
CSV data
Excel dictionary
250+ file pairs
CSV data
CSV dictionaries
1 enormous file pair
CSV data
TSV dictionaries
data dictionary
Centralized repository of information about data such as meaning, relationships to other data, origin, usage, and format
How is race defined?
What is an education of 4?
outline
What is big neuroimaging tabular phenotype data?
How do you convert this big data to BIDS?
How do you use the software?
phenotype/
├── <measurement_tool_name>.tsv
└── <measurement_tool_name>.jsonCONVERSION to bids
At OHBM 2022 Samuel Guay presented our BIDS Extension Proposal 36 (BEP036) Phenotypic Data Guidelines as a poster
outline
What is big neuroimaging tabular phenotype data?
How do you convert this big data to BIDS?
How do you use the software?
demonstration
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BIDS-standardizing tabular phenotype data requires non-trivial work
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Our FAIR-principled software has that work done
- You can download data and dictionaries right now or request new ones
takeaways
meet The collaborators
left to right,
top to bottom
eric earl
Jessica Dafflon
Roberto Salamanca-Giron
Josh Faskowitz
Arshitha Basavaraj
dustin moraczewski
Samuel Guay
Francisco Pereira
Adam Thomas
〞
Why did the bug not want to share his data?
Because it was buggy!
– Martha Earl, 7 years old
Kristen, Eric, Warren & Martha
References and links
This presentation's poster is #2464 and my colleagues' posters are #2444, #2506, and #1283
BIDS tabular phenotype data software for big neuroimaging studies
By Eric Earl
BIDS tabular phenotype data software for big neuroimaging studies
A presentation for the Software Demonstrations oral session during the OHBM 2023 conference, July 25, 12:45pm-2:45pm.
