Abstract
GenBank is a popular National Center for Biotechnology Information (NCBI) database for submission and analysis of DNA sequences for biomedical research. The resource is part of the Entrez environment which enables for cross-linking of concepts and entries in other participating NCBI databases such as Taxonomy, PubMed and Protein. For example, a GenBank record of an influenza A hemagglutinin gene DNA sequence might have a link to the Taxonomy database for the organism, a link to the related article in PubMed (if published) and a link to the Protein entry for the hemagglutinin protein. Despite its importance in biomedical research such as population genetics, phylogeography and public health surveillance, the host and geospatial metadata of genetic sequences in GenBank are not linked to any database. Therefore, to facilitate biomedical research based on georeferenced DNA sequences and/or DNA sequences with normalized host names, we designed and developed a framework that enriches GenBank entries by linking their host metadata to the NCBI Taxonomy database and their geospatial metadata to a comprehensive knowledge base of geographic locations called GeoNames. Here, we introduce a database created through the application of this framework to virus sequences in GenBank, and evaluate our normalization algorithms on a set of manually annotated records pertaining to viruses. Although currently applied to viruses, our framework can be easily extended to other organisms, and we discuss the potential utilization of our resource for biomedical research. Database URL: https://zodo.asu.edu/zoophydb/
Highlights
GenBank is a public database of nucleotide sequences developed and maintained by the National Center for Biotechnology Information (NCBI), which is part of the U.S National Library of Medicine (NLM) of the National Institutes of Health (NIH) [1]
We provide key statistics pertaining to our database, which currently contains 2 244 971 GenBank records corresponding to 162 043 distinct virus organisms
None of the GenBank records contained a formal link between the host field and an entry in the NCBI Taxonomy database
Summary
GenBank is a public database of nucleotide sequences developed and maintained by the National Center for Biotechnology Information (NCBI), which is part of the U.S National Library of Medicine (NLM) of the National Institutes of Health (NIH) [1]. As one of the most comprehensive sources of virus sequence information, GenBank presents an invaluable resource for a wide range of virus-related research. It is frequently used in fields such as phylogenetics, phylogeography, molecular epidemiology, evolutionary biology and environmental health for studying viruses through a variety of different approaches. In addition to genetic sequence data, the rich metadata present in many GenBank records are vital for analysis and comparison. Http://www.catalogueoflife.org (16 September 2017, date last accessed) Home j Catalogue of Life. http://www.catalogueoflife.org (16 September 2017, date last accessed)
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