Deep neural networks and distant supervision for geographic location mention extraction
Motivation Virus phylogeographers rely on DNA sequences of viruses and the locations of
the infected hosts found in public sequence databases like GenBank for modeling virus …
the infected hosts found in public sequence databases like GenBank for modeling virus …
[HTML][HTML] Assessing information congruence of documented cardiovascular disease between electronic dental and medical records
Dentists are more often treating patients with Cardiovascular Diseases (CVD) in their clinics;
therefore, dentists may need to alter treatment plans in the presence of CVD. However, it's …
therefore, dentists may need to alter treatment plans in the presence of CVD. However, it's …
Knowledge-driven geospatial location resolution for phylogeographic models of virus migration
Diseases caused by zoonotic viruses (viruses transmittable between humans and animals)
are a major threat to public health throughout the world. By studying virus migration and …
are a major threat to public health throughout the world. By studying virus migration and …
A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records
T Tahsin, D Weissenbacher, R Rivera… - Journal of the …, 2016 - academic.oup.com
Objective The metadata reflecting the location of the infected host (LOIH) of virus sequences
in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting …
in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting …
Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography
Discrete phylogeography using software such as BEAST considers the sampling location of
each taxon as fixed; often to a single location without uncertainty. When studying viruses …
each taxon as fixed; often to a single location without uncertainty. When studying viruses …
Phylodynamics of H5N1 highly pathogenic avian influenza in Europe, 2005–2010: potential for molecular surveillance of new outbreaks
Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza
viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia …
viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia …
GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography
We present GeoBoost2, a natural language-processing pipeline for extracting the location of
infected hosts for enriching metadata in nucleotide sequences repositories like National …
infected hosts for enriching metadata in nucleotide sequences repositories like National …
[HTML][HTML] Extracting geographic locations from the literature for virus phylogeography using supervised and distant supervision methods
The field of phylogeography allows researchers to model the spread and evolution of viral
genetic sequences. Phylogeography plays a major role in infectious disease surveillance …
genetic sequences. Phylogeography plays a major role in infectious disease surveillance …
[HTML][HTML] Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty
MA Vaiente, M Scotch - Infection, Genetics and Evolution, 2020 - Elsevier
Phylogeography is a popular way to analyze virus sequences annotated with discrete,
epidemiologically-relevant, trait data. For applied public health surveillance, a key quantity …
epidemiologically-relevant, trait data. For applied public health surveillance, a key quantity …
Geocoding genomic databases using GBIF
RDM Page - bioRxiv, 2018 - biorxiv.org
Many nucleotide sequences in the publicly available genomics databases lack spatial
information, such as the latitude and longitude coordinates for the locality where the sample …
information, such as the latitude and longitude coordinates for the locality where the sample …