title: Using nanoinformatics methods for automatically identifying relevant nanotoxicology entities from the literature.
abstract: Nanoinformatics is an emerging research field that uses informatics techniques to collect, process, store, and retrieve data, information, and knowledge on nanoparticles, nanomaterials, and nanodevices and their potential applications in health care. In this paper, we have focused on the solutions that nanoinformatics can provide to facilitate nanotoxicology research. For this, we have taken a computational approach to automatically recognize and extract nanotoxicology-related entities from the scientific literature. The desired entities belong to four different categories: nanoparticles, routes of exposure, toxic effects, and targets. The entity recognizer was trained using a corpus that we specifically created for this purpose and was validated by two nanomedicine/nanotoxicology experts. We evaluated the performance of our entity recognizer using 10-fold cross-validation. The precisions range from 87.6% (targets) to 93.0% (routes of exposure), while recall values range from 82.6% (routes of exposure) to 87.4% (toxic effects). These results prove the feasibility of using computational approaches to reliably perform different named entity recognition (NER)-dependent tasks, such as for instance augmented reading or semantic searches. This research is a "proof of concept" that can be expanded to stimulate further developments that could assist researchers in managing data, information, and knowledge at the nanolevel, thus accelerating research in nanomedicine.
authors.affiliation: Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Boadilla del Monte, 28660 Madrid, Spain. mgarcia@infomed.dia.fi.upm.es
authors.forename: Miguel
authors.initials: M
authors.lastname: García-Remesal
authors.forename: Alejandro
authors.initials: A
authors.lastname: García-Ruiz
authors.forename: David
authors.initials: D
authors.lastname: Pérez-Rey
authors.forename: Diana
authors.initials: D
authors.lastname: de la Iglesia
authors.forename: Víctor
authors.initials: V
authors.lastname: Maojo
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D016206:Databases, Bibliographic; D006801:Humans; D050997:Nanomedicine / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software