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Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford) 2020; 2020:baaa062. [PMID: 32761142 PMCID: PMC7408187 DOI: 10.1093/database/baaa062] [Citation(s) in RCA: 615] [Impact Index Per Article: 153.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/04/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022]
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.
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Affiliation(s)
- Conrad L Schoch
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Stacy Ciufo
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Mikhail Domrachev
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Carol L Hotton
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Sivakumar Kannan
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Rogneda Khovanskaya
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Detlef Leipe
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard Mcveigh
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Kathleen O'Neill
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Barbara Robbertse
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Shobha Sharma
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Vladimir Soussov
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - John P Sullivan
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Lu Sun
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Seán Turner
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Ilene Karsch-Mizrachi
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
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