Neuroinformatic techniques for provenance & data sharing
Transcript of Neuroinformatic techniques for provenance & data sharing
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Camille Maumet
GlaxoSmithKline - Neurophysics Workshop on Skeptical Neuroimaging
January 14th, 2014
Neuroinformatic techniques for provenance & data sharing
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Outline
1. Data sharing: current practice in neuroimaging 2. How to become less skeptical? 3. Neuroinformatics techniques for provenance and
data sharing
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Outline
1. Data sharing: current practice in neuroimaging 2. How to become less skeptical? 3. Neuroinformatics techniques for provenance and
data sharing
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Pre-processing
Statistical analysis
Overview of a neuroimaging study
Publication
• MR scanner: 1.5T, 3T… • Type of coils: 32-channels, 16-channels… • Imaging sequence: TR, TE, FOV… • fMRI paradigm
• Pre-processing pipeline • Method employed for each processing • Parameters for each method, software…
• Model • (Non-)parametric • Parameters
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Acquisition
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Acquisition
Pre-processing
Statistical analysis
Neuroimaging and data sharing
Publication
Data shared with my collaborators
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Acquisition
Pre-processing
Statistical analysis
Sharing data with my collaborators
Publication
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Acquisition
Pre-processing
Statistical analysis
Neuroimaging and data sharing
Publication
Data shared with my collaborators
Data shared with the whole community
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A neuroimaging publication • Methods section: metadata in free-form text.
• Results section: Acquisition
Pre-processing Statistical analysis
Publication
2D plot(s) of the detections Description of the detections Table of local maxima
Table
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Outline
1. Data sharing: current practice in neuroimaging 2. How to become less skeptical? 3. Neuroinformatics techniques for provenance and
data sharing
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Reproducibility Acquisition Pre-processing Statistical
analysis Publication
Acquisition Pre-processing Statistical analysis Publication
? ? New conclusions
?
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Full provenance
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Acquisition Pre-processing Statistical analysis Publication
Pre-processing Statistical analysis
Statistical analysis
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Meta-analysis: analyzing the analyses
Paper 1 Paper 2 Paper n
New results!
Study 1 Study 2 Study n
…
• Coordinate-Based Meta-Analysis (CBMA) • Image-Based Meta-Analysis (IBMA).
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Statistical analysis Publication
…
Statistical analysis Publication
…
…
New results!
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How to become less skeptical?
• Reproducibility – Confirm results by re-running an analysis
• Provenance – Needed for reproducibility – Avoid selection bias.
• Meta-analysis – Strengthen results by combining studies.
• What do we need? – Sharing data, meta-data and provenance.
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Data sharing: obstacles
• Psychological – “My” data
• Ethical constraints • Technical: difficulties to share data with enough
metadata to be really useful – Available data versus usable data.
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“Less than a few percents of acquired neuroimaging data is available in public repositories” [Poline 2012]
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Outline
1. Data sharing: current practice in neuroimaging 2. How to become less skeptical? 3. Neuroinformatics techniques for provenance and
data sharing
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Acquisition
Pre-processing
Statistical analysis
Data sharing tools
Publication
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A standard format for meta-data
• Sharing data across the data sharing tools… • First attempt of an agnostic format: XML-Based
Clinical Experiment Data Exchange Schema (XCEDE): www.xcede.org – Describes subject, study, activation – Limited provenance encoding – Initiative of the BIRN
• NeuroImaging Data Model NI-DM: www.nidm.nidash.org – Based on web-semantic tools. – Initiative of the BIRN and INCF
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Three major players
• Bottom-up approach. • Lean on existing
analysis software (SPM, FSL, AFNI) to disseminate the standard.
18 Automatically created with Neurotrends based on over 16 000 journal articles
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Work in progress
Vocabulary Data model
• Define a format to represent the results of a neuroimaging study with a focus on meta-analysis.
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Neuroimaging terms
• Define a vocabulary to support the format.
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Data model
• Based on PROV-DM a W3C recommendation to encode provenance.www.w3.org/TR/prov-dm/
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Data model
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Data model: activities
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Data model: agent
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Data model: entities
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Data model: entities
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Conclusion
• Data sharing is one key to reduce skepticism. • There is already a number of technical solutions for
data sharing in neuroimaging. • A meta-data standard would beneficiate to all of
these efforts – NI-DM: http://nidm.nidash.org
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Q & A
This work is supported by the