title: Automatic extraction of nanoparticle properties using natural language processing: NanoSifter an application to acquire PAMAM dendrimer properties.
abstract: In this study, we demonstrate the use of natural language processing methods to extract, from nanomedicine literature, numeric values of biomedical property terms of poly(amidoamine) dendrimers. We have developed a method for extracting these values for properties taken from the NanoParticle Ontology, using the General Architecture for Text Engineering and a Nearly-New Information Extraction System. We also created a method for associating the identified numeric values with their corresponding dendrimer properties, called NanoSifter. We demonstrate that our system can correctly extract numeric values of dendrimer properties reported in the cancer treatment literature with high recall, precision, and f-measure. The micro-averaged recall was 0.99, precision was 0.84, and f-measure was 0.91. Similarly, the macro-averaged recall was 0.99, precision was 0.87, and f-measure was 0.92. To our knowledge, these results are the first application of text mining to extract and associate dendrimer property terms and their corresponding numeric values.
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: David E
authors.initials: DE
authors.lastname: Jones
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, United States of America ; Center for High Performance Computing, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Sean
authors.initials: S
authors.lastname: Igo
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Hurdle
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, United States of America ; Center for High Performance Computing, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Julio C
authors.initials: JC
authors.lastname: Facelli
mesh_terms: D057225:Data Mining / Q000379:methods; D050091:Dendrimers / Q000737:chemistry; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D053758:Nanoparticles / Q000737:chemistry*; D009323:Natural Language Processing; D015203:Reproducibility of Results
chemical_list: D050091:Dendrimers; C104700:PAMAM Starburst