title: Automatic target validation based on neuroscientific literature mining for tractography.
abstract: Target identification for tractography studies requires solid anatomical knowledge validated by an extensive literature review across species for each seed structure to be studied. Manual literature review to identify targets for a given seed region is tedious and potentially subjective. Therefore, complementary approaches would be useful. We propose to use text-mining models to automatically suggest potential targets from the neuroscientific literature, full-text articles and abstracts, so that they can be used for anatomical connection studies and more specifically for tractography. We applied text-mining models to three structures: two well-studied structures, since validated deep brain stimulation targets, the internal globus pallidus and the subthalamic nucleus and, the nucleus accumbens, an exploratory target for treating psychiatric disorders. We performed a systematic review of the literature to document the projections of the three selected structures and compared it with the targets proposed by text-mining models, both in rat and primate (including human). We ran probabilistic tractography on the nucleus accumbens and compared the output with the results of the text-mining models and literature review. Overall, text-mining the literature could find three times as many targets as two man-weeks of curation could. The overall efficiency of the text-mining against literature review in our study was 98% recall (at 36% precision), meaning that over all the targets for the three selected seeds, only one target has been missed by text-mining. We demonstrate that connectivity for a structure of interest can be extracted from a very large amount of publications and abstracts. We believe this tool will be useful in helping the neuroscience community to facilitate connectivity studies of particular brain regions. The text mining tools used for the study are part of the HBP Neuroinformatics Platform, publicly available at http://connectivity-brainer.rhcloud.com/.
authors.affiliation: Blue Brain Project, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland ; IBM Systems France ; Laboratoire de Recherche en Neurosciences Cliniques France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Vasques
authors.affiliation: Blue Brain Project, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland.
authors.forename: Renaud
authors.initials: R
authors.lastname: Richardet
authors.affiliation: Blue Brain Project, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland.
authors.forename: Sean L
authors.initials: SL
authors.lastname: Hill
authors.affiliation: Laboratoire de Recherche Neuroimagerie, Université de Lausanne Lausanne, Switzerland ; Département des Neurosciences Cliniques, Centre Hospitalier Universitaire Vaudois, Université de Lausanne Lausanne, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Slater
authors.affiliation: School of Computer and Communication Sciences, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland.
authors.forename: Jean-Cedric
authors.initials: JC
authors.lastname: Chappelier
authors.affiliation: Département des Neurosciences Cliniques, Centre Hospitalier Universitaire Vaudois, Université de Lausanne Lausanne, Switzerland.
authors.forename: Etienne
authors.initials: E
authors.lastname: Pralong
authors.affiliation: Département des Neurosciences Cliniques, Centre Hospitalier Universitaire Vaudois, Université de Lausanne Lausanne, Switzerland.
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Bloch
authors.affiliation: Laboratoire de Recherche Neuroimagerie, Université de Lausanne Lausanne, Switzerland ; Département des Neurosciences Cliniques, Centre Hospitalier Universitaire Vaudois, Université de Lausanne Lausanne, Switzerland.
authors.forename: Bogdan
authors.initials: B
authors.lastname: Draganski
authors.affiliation: Laboratoire de Recherche Neuroimagerie, Université de Lausanne Lausanne, Switzerland ; Département des Neurosciences Cliniques, Centre Hospitalier Universitaire Vaudois, Université de Lausanne Lausanne, Switzerland ; Département de Neurochirurgie, Hôpital Gui de Chauliac, Centre Hospitalier Régional Universitaire de Montpellier, Université Montpellier 1 Montpellier, France.
authors.forename: Laura
authors.initials: L
authors.lastname: Cif
keywords: globus pallidus internus; information extraction; natural language processing; nucleus accumbens; subthalamic nucleus; text mining; tractography