Literature DB >> 29240889

GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records.

Tasnia Tahsin1, Davy Weissenbacher1, Karen O'Connor2, Arjun Magge1, Matthew Scotch1,3, Graciela Gonzalez-Hernandez2.   

Abstract

Summary: 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 information: Supplementary data are available at Bioinformatics online.

Entities:  

Mesh：

Year:  2018        PMID： 29240889      PMCID： PMC5925778          DOI： 10.1093/bioinformatics/btx799

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

1.  A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records.

Authors:  Tasnia Tahsin; Davy Weissenbacher; Robert Rivera; Rachel Beard; Mari Firago; Garrick Wallstrom; Matthew Scotch; Graciela Gonzalez
Journal:  J Am Med Inform Assoc       Date:  2016-01-17       Impact factor: 4.497

2.  Leveraging biomedical ontologies and annotation services to organize microbiome data from Mammalian hosts.

Authors:  Indra Neil Sarkar
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

3.  Enhancing phylogeography by improving geographical information from GenBank.

Authors:  Matthew Scotch; Indra Neil Sarkar; Changjiang Mei; Robert Leaman; Kei-Hoi Cheung; Pierina Ortiz; Ashutosh Singraur; Graciela Gonzalez
Journal:  J Biomed Inform       Date:  2011-06-24       Impact factor: 6.317

4.  Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion.

Authors:  Daniel Magee; Rachel Beard; Marc A Suchard; Philippe Lemey; Matthew Scotch
Journal:  Arch Virol       Date:  2014-10-30       Impact factor: 2.574

5.  Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies.

Authors:  Elizabeth S Chen; Indra Neil Sarkar
Journal:  AMIA Jt Summits Transl Sci Proc       Date:  2011-03-07

6.  Knowledge-driven geospatial location resolution for phylogeographic models of virus migration.

Authors:  Davy Weissenbacher; Tasnia Tahsin; Rachel Beard; Mari Figaro; Robert Rivera; Matthew Scotch; Graciela Gonzalez
Journal:  Bioinformatics       Date:  2015-06-15       Impact factor: 6.937

7.  GenBank.

Authors:  Dennis A Benson; Mark Cavanaugh; Karen Clark; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Eric W Sayers
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

8.  Influenza A H5N1 immigration is filtered out at some international borders.

Authors:  Robert G Wallace; Walter M Fitch
Journal:  PLoS One       Date:  2008-02-27       Impact factor: 3.240

Review 9.  Global spread of dengue virus types: mapping the 70 year history.

Authors:  Jane P Messina; Oliver J Brady; Thomas W Scott; Chenting Zou; David M Pigott; Kirsten A Duda; Samir Bhatt; Leah Katzelnick; Rosalind E Howes; Katherine E Battle; Cameron P Simmons; Simon I Hay
Journal:  Trends Microbiol       Date:  2014-01-24       Impact factor: 17.079
  9 in total
  7 in total

1.  Linking dimensions of data on global marine animal diversity.

Authors:  Thomas J Webb; Bart Vanhoorne
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-11-02       Impact factor: 6.237

2.  Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature.

Authors:  Arjun Magge; Davy Weissenbacher; Abeed Sarker; Matthew Scotch; Graciela Gonzalez-Hernandez
Journal:  Pac Symp Biocomput       Date:  2019

3.  High-throughput methods for efficiently building massive phylogenies from natural history collections.

Authors:  Ryan A Folk; Heather R Kates; Raphael LaFrance; Douglas E Soltis; Pamela S Soltis; Robert P Guralnick
Journal:  Appl Plant Sci       Date:  2021-02-27       Impact factor: 1.936

4.  GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography.

Authors:  Arjun Magge; Davy Weissenbacher; Karen O'Connor; Tasnia Tahsin; Graciela Gonzalez-Hernandez; Matthew Scotch
Journal:  Bioinformatics       Date:  2020-12-22       Impact factor: 6.937

5.  A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks.

Authors:  Rachel Beard; Elizabeth Wentz; Matthew Scotch
Journal:  Int J Health Geogr       Date:  2018-10-30       Impact factor: 3.918

6.  Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography.

Authors:  Matthew Scotch; Tasnia Tahsin; Davy Weissenbacher; Karen O'Connor; Arjun Magge; Matteo Vaiente; Marc A Suchard; Graciela Gonzalez-Hernandez
Journal:  Virus Evol       Date:  2019-02-28

7.  Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty.

Authors:  Matteo A Vaiente; Matthew Scotch
Journal:  Infect Genet Evol       Date:  2020-08-13       Impact factor: 3.342
  7 in total

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