B. Nolan Nichols
Graduated: January 1, 2014
Reproducibility in Human Cognitive Neuroimaging: A Community-Driven Data Sharing Framework for Provenance Information Integration and Interoperability
ccess to primary data and the provenance of derived data are increasingly recognized as an essential aspect of reproducibility in biomedical research. While productive data sharing has become the norm in some biomedical communities, human brain imaging has lagged in open data and descriptions of provenance. The overarching goal of my dissertation was to identify barriers to neuroimaging data sharing and to develop a fundamentally new, granular data exchange standard that incorporates provenance as a primitive to document cognitive neuroimaging workflow.
For my dissertation research, I led the development of the Neuroimaging Data Model (NIDM), an extension to the W3C PROV standard for the domain of human brain imaging. NIDM provides a language to communicate provenance by representing primary data, computational workflow, and derived data as bundles of linked Agents, Activities, and Entities. Similar to the way a sentence conveys a standalone thought, a bundle contains provenance statements that parsimoniously express the way a given piece of data was produced. To demonstrate a system that implements NIDM, I developed a modern, semantic Web application platform that provides neuroimaging workflow as a service and captures provenance statements as NIDM bundles. The course of this work necessitated interaction with an international community, which adopted and extended central elements of this work into prevailing brain imaging software. My dissertation contributes neuroinformatics standards to advance the current state of computational infrastructure available to the cognitive neuroimaging community.
Last Known Position:
Bioinformatics Software Engineer, Genentech
James F. Brinkley (Chair), Nicholas R. Anderson, Thomas Grabowski, Susan E. Coldwell (GSR)