ArticleBioinformatics (Oxford, England)2018
GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks.International journal of health geographics · 2018Pooled it
- A FAIR gold-standard benchmark for geographic entity recognition in cancer genomics literature for biomedical NLP.Bioinformatics advances · 2026Article
- Detection of patient metadata in published articles for genomic epidemiology using machine learning and large language models.medRxiv : the preprint server for health sciences · 2025Article
- Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis.JMIR research protocols · 2025Article
- Classifying literature mentions of biological pathogens as experimentally studied using natural language processing.Journal of biomedical semantics · 2023Article
- High-throughput methods for efficiently building massive phylogenies from natural history collections.Applications in plant sciences · 2021Article
- GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography.Bioinformatics (Oxford, England) · 2020Article
- Linking dimensions of data on global marine animal diversity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2019Article
- Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography.Virus evolution · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.