title: Knowledge-driven geospatial location resolution for phylogeographic models of virus migration.
abstract: Diseases caused by zoonotic viruses (viruses transmittable between humans and animals) are a major threat to public health throughout the world. By studying virus migration and mutation patterns, the field of phylogeography provides a valuable tool for improving their surveillance. A key component in phylogeographic analysis of zoonotic viruses involves identifying the specific locations of relevant viral sequences. This is usually accomplished by querying public databases such as GenBank and examining the geospatial metadata in the record. When sufficient detail is not available, a logical next step is for the researcher to conduct a manual survey of the corresponding published articles.
  
  
  BACKGROUND
  In this article, we present a system for detection and disambiguation of locations (toponym resolution) in full-text articles to automate the retrieval of sufficient metadata. Our system has been tested on a manually annotated corpus of journal articles related to phylogeography using integrated heuristics for location disambiguation including a distance heuristic, a population heuristic and a novel heuristic utilizing knowledge obtained from GenBank metadata (i.e. a 'metadata heuristic').
  
  
  RESULTS
  For detecting and disambiguating locations, our system performed best using the metadata heuristic (0.54 Precision, 0.89 Recall and 0.68 F-score). Precision reaches 0.88 when examining only the disambiguation of location names. Our error analysis showed that a noticeable increase in the accuracy of toponym resolution is possible by improving the geospatial location detection. By improving these fundamental automated tasks, our system can be a useful resource to phylogeographers that rely on geospatial metadata of GenBank sequences. .
authors.affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.
authors.forename: Davy
authors.initials: D
authors.lastname: Weissenbacher
authors.affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.
authors.forename: Tasnia
authors.initials: T
authors.lastname: Tahsin
authors.affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Beard
authors.affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.
authors.forename: Mari
authors.initials: M
authors.lastname: Figaro
authors.affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Rivera
authors.affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Scotch
authors.affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.
authors.forename: Graciela
authors.initials: G
authors.lastname: Gonzalez
mesh_terms: D030561:Databases, Nucleic Acid; D058974:Phylogeography / Q000379:methods*; D017421:Sequence Analysis; D014780:Viruses / Q000235:genetics*