ArticleJournal of the American Medical Informatics Association : JAMIA2016
A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records.
Article in Journal of the American Medical Informatics Association : JAMIA, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it, 23 citations in OpenAlex.
- 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
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- Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition.Biological reviews of the Cambridge Philosophical Society · 2022Review
- Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates.Molecular ecology · 2022Article
- The U.S. National Library of Medicine's impact on precision and genomic medicine.Information services & use · 2022Article
- Article
- 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
- Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2019Article
- GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records.Bioinformatics (Oxford, England) · 2018Article
- The Effects of Sampling Location and Predictor Point Estimate Certainty on Posterior Support in Bayesian Phylogeographic Generalized Linear Models.Scientific reports · 2018Article
- Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research.Database : the journal of biological databases and curation · 2017Article
- Extracting geographic locations from the literature for virus phylogeography using supervised and distant supervision methods.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2017Article
- Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
objectiveThe 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 more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases. MATERIALS AND
methodsWe developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, based on data assimilated from these sources, are then disambiguated and mapped to their respective geo-coordinates. We evaluated our approach on a manually annotated dataset comprising of 5728 GenBank records for the influenza A virus.
resultsWe found the precision, recall, and f-measure of our system for linking GenBank records to the latitude/longitudes of their LOIH to be 0.832, 0.967, and 0.894, respectively. DISCUSSION: Our system had a high level of accuracy for linking GenBank records to the geo-coordinates of the LOIH. However, it can be further improved by expanding our database of geospatial data, incorporating spell correction, and enhancing the rules used for extraction.
conclusionOur system performs reasonably well for linking GenBank records for the influenza A virus to the geo-coordinates of their LOIH based on record metadata and information extracted from related full-text articles.
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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.