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

Bioinformatics
Arjun MaggeMatthew Scotch

Abstract

We present GeoBoost2, a natural language-processing pipeline for extracting the location of infected hosts for enriching metadata in nucleotide sequences repositories like National Center of Biotechnology Information's GenBank for downstream analysis including phylogeography and genomic epidemiology. The increasing number of pathogen sequences requires complementary information extraction methods for focused research, including surveillance within countries and between borders. In this article, we describe the enhancements from our earlier release including improvement in end-to-end extraction performance and speed, availability of a fully functional web-interface and state-of-the-art methods for location extraction using deep learning. Application is freely available on the web at https://zodo.asu.edu/geoboost2. Source code, usage examples and annotated data for GeoBoost2 is freely available at https://github.com/ZooPhy/geoboost2. Supplementary data are available at Bioinformatics online.

References

Jul 5, 2011·Journal of Biomedical Informatics·Matthew ScotchGraciela Gonzalez
Aug 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Oliver G PybusEric L Delwart
Feb 26, 2016·Journal of the American Medical Informatics Association : JAMIA·Tasnia TahsinGraciela Gonzalez
Nov 16, 2017·Nucleic Acids Research·Dennis A BensonEric W Sayers
Dec 15, 2017·Bioinformatics·Tasnia TahsinGraciela Gonzalez-Hernandez
Jun 27, 2018·Virus Evolution·Marc A SuchardAndrew Rambaut
Jun 29, 2018·Bioinformatics·Arjun MaggeGraciela Gonzalez-Hernandez
Mar 7, 2019·Virus Evolution·Matthew ScotchGraciela Gonzalez-Hernandez

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Datasets Mentioned

BETA
KU497555

Software Mentioned

BEAST
ZooPhy
GeoBoost
GeoBoost2
GeoNames
Python

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