GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records

Tasnia Tahsin; Davy Weissenbacher; Karen O'Connor; Arjun Magge; Matthew Scotch; Graciela Gonzalez-Hernandez

doi:10.1093/bioinformatics/btx799

GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records

Tasnia Tahsin, Davy Weissenbacher, Karen O'Connor, Arjun Magge, Matthew Scotch, Graciela Gonzalez-Hernandez

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH. Availability and implementation Binaries and resources required for running GeoBoost are packed into a single zipped file and freely available for download at https://tinyurl.com/geoboost. A video tutorial is included to help users quickly and easily install and run the software. The software is implemented in Java 1.8, and supported on MS Windows and Linux platforms. Contact gragon@upenn.edu Supplementary informationSupplementary dataare available at Bioinformatics online.

Original language	English (US)
Pages (from-to)	1606-1608
Number of pages	3
Journal	Bioinformatics
Volume	34
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/btx799
State	Published - May 1 2018

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btx799

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abstract = "GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH. Availability and implementation Binaries and resources required for running GeoBoost are packed into a single zipped file and freely available for download at https://tinyurl.com/geoboost. A video tutorial is included to help users quickly and easily install and run the software. The software is implemented in Java 1.8, and supported on MS Windows and Linux platforms. Contact gragon@upenn.edu Supplementary informationSupplementary dataare available at Bioinformatics online.",

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AU - Scotch, Matthew

AU - Gonzalez-Hernandez, Graciela

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GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records

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