ArticleBioinformatics (Oxford, England)2020
GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- A FAIR gold-standard benchmark for geographic entity recognition in cancer genomics literature for biomedical NLP.Bioinformatics advances · 2026Article
- Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics.Briefings in bioinformatics · 2025Review
- 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
- Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016-Early 2022.International journal of environmental research and public health · 2023Article
- Classifying literature mentions of biological pathogens as experimentally studied using natural language processing.Journal of biomedical semantics · 2023Article
- GenBank as a source to monitor and analyze Host-Microbiome data.Bioinformatics (Oxford, England) · 2022Article
- Bioinformatics for the Origin and Evolution of Viruses.Advances in experimental medicine and biology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
summaryWe 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. AVAILABILITY AND IMPLEMENTATION: 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 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.