title: Enhancing phylogeography by improving geographical information from GenBank.
abstract: Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the species over time within a geographical area, the impact of geography over the evolutionary history, or the expected population of the species within the area. Molecular sequence data from NCBI, specifically GenBank, provide an abundance of available sequence data for phylogeography. However, geographical data is inconsistently represented and sparse across GenBank entries. This can impede analysis and in situations where the geographical information is inferred, and potentially lead to erroneous results. In this paper, we describe the current state of geographical data in GenBank, and illustrate how automated processing techniques such as named entity recognition, can enhance the geographical data available for phylogeographic studies.
authors: Department of Biomedical Informatics, Arizona State University, Tempe, AZ, USA. Electronic address: matthew.scotch@asu.edu.
authors: Matthew
authors: M
authors: Scotch
authors: Center for Clinical and Translational Science, University of Vermont, Burlington, VT, USA; Department of Microbiology & Molecular Genetics, University of Vermont, Burlington, VT, USA; Department of Computer Science, University of Vermont, Burlington, VT, USA. Electronic address: neil.sarkar@uvm.edu.
authors: Indra Neil
authors: IN
authors: Sarkar
authors: Department of Biomedical Informatics, Arizona State University, Tempe, AZ, USA. Electronic address: changjiang.mei@asu.edu.
authors: Changjiang
authors: C
authors: Mei
authors: Department of Biomedical Informatics, Arizona State University, Tempe, AZ, USA. Electronic address: bob.leaman@asu.edu.
authors: Robert
authors: R
authors: Leaman
authors: Yale Center for Medical Informatics, Yale University, New Haven, CT, USA. Electronic address: kei.cheung@yale.edu.
authors: Kei-Hoi
authors: KH
authors: Cheung
authors: Department of Biomedical Informatics, Arizona State University, Tempe, AZ, USA.
authors: Pierina
authors: P
authors: Ortiz
authors: Department of Biomedical Informatics, Arizona State University, Tempe, AZ, USA. Electronic address: ashutosh.singraur@asu.edu.
authors: Ashutosh
authors: A
authors: Singraur
authors: Department of Biomedical Informatics, Arizona State University, Tempe, AZ, USA. Electronic address: graciela.gonzalez@asu.edu.
authors: Graciela
authors: G
authors: Gonzalez
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D014714:Vertebrates / Q000235:genetics; D014780:Viruses / Q000235:genetics