Construction of a Comprehensive Database from the Existing Viral Sequences Available from the International Nucleotide Sequence Database Collaboration

2018 ◽  
pp. 231-243
Author(s):  
Rodrigo García-López
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Database ◽  
International Nucleotide Sequence Database ◽  
Comprehensive Database ◽  
Viral Sequences ◽  
Nucleotide Sequence Database

scholarly journals NCBI Taxonomy: a comprehensive update on curation, resources and tools

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Conrad L Schoch ◽  
Stacy Ciufo ◽  
Mikhail Domrachev ◽  
Carol L Hotton ◽  
Sivakumar Kannan ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Protein Sequence ◽  
Ncbi Taxonomy ◽  
Sequence Database ◽  
External Resources ◽  
International Nucleotide Sequence Database ◽  
Sql Database ◽  
Data Elements ◽  
Taxonomic Groups ◽  
Nucleotide Sequence Database

Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy

scholarly journals The International Nucleotide Sequence Database Collaboration

2010 ◽  
Vol 39 (Database) ◽  
pp. D15-D18 ◽  
Author(s):  
G. Cochrane ◽  
I. Karsch-Mizrachi ◽  
Y. Nakamura ◽  
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Database ◽  
International Nucleotide Sequence Database ◽  
Nucleotide Sequence Database

scholarly journals The international nucleotide sequence database collaboration

2020 ◽  
Vol 49 (D1) ◽  
pp. D121-D124
Author(s):  
Masanori Arita ◽  
Ilene Karsch-Mizrachi ◽  
Guy Cochrane
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Data ◽  
Data Bank ◽  
National Institutes Of Health ◽  
Sequence Database ◽  
National Library ◽  
Nucleotide Sequence Data ◽  
International Nucleotide Sequence Database ◽  
European Nucleotide Archive ◽  
Nucleotide Sequence Database

Abstract The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been the core infrastructure for collecting and providing nucleotide sequence data and metadata for >30 years. Three partner organizations, the DNA Data Bank of Japan (DDBJ) at the National Institute of Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have been collaboratively maintaining the INSDC for the benefit of not only science but all types of community worldwide.

scholarly journals The International Nucleotide Sequence Database Collaboration

2015 ◽  
Vol 44 (D1) ◽  
pp. D48-D50 ◽  
Author(s):  
Guy Cochrane ◽  
Ilene Karsch-Mizrachi ◽  
Toshihisa Takagi ◽  
International Nucleotide Sequence Database Collaboration
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Database ◽  
International Nucleotide Sequence Database ◽  
Nucleotide Sequence Database

scholarly journals The International Nucleotide Sequence Database Collaboration

2011 ◽  
Vol 40 (D1) ◽  
pp. D33-D37 ◽  
Author(s):  
I. Karsch-Mizrachi ◽  
Y. Nakamura ◽  
G. Cochrane ◽  
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Database ◽  
International Nucleotide Sequence Database ◽  
Nucleotide Sequence Database

scholarly journals The International Nucleotide Sequence Database Collaboration

2012 ◽  
Vol 41 (D1) ◽  
pp. D21-D24 ◽  
Author(s):  
Y. Nakamura ◽  
G. Cochrane ◽  
I. Karsch-Mizrachi ◽  
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Database ◽  
International Nucleotide Sequence Database ◽  
Nucleotide Sequence Database

scholarly journals The international nucleotide sequence database collaboration

2017 ◽  
Vol 46 (D1) ◽  
pp. D48-D51 ◽  
Author(s):  
Ilene Karsch-Mizrachi ◽  
Toshihisa Takagi ◽  
Guy Cochrane ◽  
Keyword(s):  
Biological Sciences ◽  
Nucleotide Sequence ◽  
Sequence Data ◽  
Data Bank ◽  
National Institutes Of Health ◽  
Sequence Database ◽  
Nucleotide Sequence Data ◽  
International Nucleotide Sequence Database ◽  
European Nucleotide Archive ◽  
Nucleotide Sequence Database

Abstract For more than 30 years, the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been committed to capturing, preserving and providing access to comprehensive public domain nucleotide sequence and associated metadata which enables discovery in biomedicine, biodiversity and biological sciences. Since 1987, the DNA Data Bank of Japan (DDBJ) at the National Institute for Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have worked collaboratively to enable access to nucleotide sequence data in standardized formats for the worldwide scientific community. In this article, we reiterate the principles of the INSDC collaboration and briefly summarize the trends of the archival content.

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