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      GenBank

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          Abstract

          GenBank ® ( https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species. Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Submission Portal. We also discuss upcoming changes to GI identifiers, a new data management interface for BioProject, and advice for providing contextual metadata in submissions.

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          Most cited references10

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          Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

          Nuala A. O'Leary, Mathew Wright, J. Rodney Brister … (2015)
          The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
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            BLAST: a more efficient report with usability improvements

            Grzegorz M Boratyn, Christiam Camacho, Peter S. Cooper … (2013)
            The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.
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              Is Open Access

              Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

              John Wieczorek, David Bloom, Robert Guralnick … (2012)
              Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.
              Article 0 comments Cited 233 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Eric W Sayers:
                ORCID: https://orcid.org/0000-0001-8394-3802
                Mark Cavanaugh
                Karen Clark
                Kim D Pruitt
                Conrad L Schoch:
                ORCID: https://orcid.org/0000-0003-1839-5322
                Stephen T Sherry
                Ilene Karsch-Mizrachi:
                ORCID: https://orcid.org/0000-0002-0289-7101
                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: 07 January 2022
                Publication date (Electronic): 01 December 2021
                Publication date PMC-release: 01 December 2021
                Volume: 50
                Issue: D1
                Pages: D161-D164
                Affiliations
                National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike , Bethesda, MD 20894, USA
                National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike , Bethesda, MD 20894, USA
                National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike , Bethesda, MD 20894, USA
                National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike , Bethesda, MD 20894, USA
                National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike , Bethesda, MD 20894, USA
                National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike , Bethesda, MD 20894, USA
                National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike , Bethesda, MD 20894, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 301 496 2475; Fax: +1 301 480 9241; Email: sayers@ 123456ncbi.nlm.nih.gov
                Author information
                https://orcid.org/0000-0001-8394-3802
                https://orcid.org/0000-0003-1839-5322
                https://orcid.org/0000-0002-0289-7101
                Article
                Publisher ID: gkab1135
                DOI: 10.1093/nar/gkab1135
                PMC ID: 8690257
                PubMed ID: 34850943
                SO-VID: 21fbbb07-804a-4c02-a2f7-4a9b63c2472a
                Copyright © Published by Oxford University Press on behalf of Nucleic Acids Research 2021.
                License:

                This work is written by (a) US Government employee(s) and is in the public domain in the US.

                History
                Date accepted : 08 November 2021
                Date revision received : 20 October 2021
                Date received : 18 September 2021
                Page count
                Pages: 4
                Funding
                Funded by: Intramural Research Program of the National Library of Medicine;
                Funded by: National Institutes of Health, DOI 10.13039/100000002;
                Categories
                Subject: AcademicSubjects/SCI00010
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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