Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: https://www.ncbi.nlm.nih.gov/taxonomy
Full name: NCBI Taxonomy Database
Description: The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.
Year founded: 1991
Last update: 2020
Version: v1.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: National Center for Biotechnology Information
Address: Bethesda,MD 20894,USA
City: Bethesda
Province/State: MD
Country/Region: United States
Contact name (PI/Team): Scott Federhen
Contact email (PI/Helpdesk): federhen@ncbi.nlm.nih.gov

Publications

32761142
NCBI Taxonomy: a comprehensive update on curation, resources and tools. [PMID: 32761142]
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.

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.

Database (Oxford). 2020:2020() | 35 Citations (from Europe PMC, 2021-10-16)
25398905
Type material in the NCBI Taxonomy Database. [PMID: 25398905]
Federhen S.

Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species. For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria. The NCBI Taxonomy Database (http://www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes. This has important implications for many NCBI resources, some of which are outlined below. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Nucleic Acids Res. 2015:43(Database issue) | 69 Citations (from Europe PMC, 2021-10-16)
22139910
The NCBI Taxonomy database. [PMID: 22139910]
Federhen S.

The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.

Nucleic Acids Res. 2012:40(Database issue) | 435 Citations (from Europe PMC, 2021-10-16)

Ranking

All databases:
173/5052 (96.595%)
Phylogeny and homology:
9/216 (96.296%)
Standard ontology and nomenclature:
17/203 (92.118%)
173
Total Rank
539
Citations
59.889
z-index

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Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2020-11-26]
Lina Ma [2018-06-08]
lin liu [2016-04-11]
lin liu [2016-03-27]
Li Yang [2015-06-26]