title: Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application.
abstract: We describe the WhiteText project, and its progress towards automatically extracting statements of neuroanatomical connectivity from text. We review progress to date on the three main steps of the project: recognition of brain region mentions, standardization of brain region mentions to neuroanatomical nomenclature, and connectivity statement extraction. We further describe a new version of our manually curated corpus that adds 2,111 connectivity statements from 1,828 additional abstracts. Cross-validation classification within the new corpus replicates results on our original corpus, recalling 67% of connectivity statements at 51% precision. The resulting merged corpus provides 5,208 connectivity statements that can be used to seed species-specific connectivity matrices and to better train automated techniques. Finally, we present a new web application that allows fast interactive browsing of the over 70,000 sentences indexed by the system, as a tool for accessing the data and assisting in further curation. Software and data are freely available at http://www.chibi.ubc.ca/WhiteText/.
authors.affiliation: Rotman Research Institute, University of Toronto Toronto, ON, Canada.
authors.forename: Leon
authors.initials: L
authors.lastname: French
authors.affiliation: Department of Psychiatry, University of British Columbia Vancouver, BC, Canada.
authors.forename: Po
authors.initials: P
authors.lastname: Liu
authors.affiliation: Department of Psychiatry, University of British Columbia Vancouver, BC, Canada.
authors.forename: Olivia
authors.initials: O
authors.lastname: Marais
authors.affiliation: Department of Psychiatry, University of British Columbia Vancouver, BC, Canada.
authors.forename: Tianna
authors.initials: T
authors.lastname: Koreman
authors.affiliation: Department of Psychiatry, University of British Columbia Vancouver, BC, Canada.
authors.forename: Lucia
authors.initials: L
authors.lastname: Tseng
authors.affiliation: Department of Psychiatry, University of British Columbia Vancouver, BC, Canada.
authors.forename: Artemis
authors.initials: A
authors.lastname: Lai
authors.affiliation: Department of Psychiatry, University of British Columbia Vancouver, BC, Canada ; Centre for High-Throughput Biology, University of British Columbia Vancouver, BC, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Pavlidis
keywords: connectome; information retrieval; natural language processing; text mining