The NCBI Taxonomy database

By S. Federhen. 2011

1,405 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Minoru Kanehisa
2. Jinbo Xu
3. Rob Knight
4. Sheng Wang
5. K. Cohen
6. Yoko Sato
7. Mosè Manni
8. Danso Ako-Adjei

In Molecular Biology

1. Rob Knight
2. Curtis Huttenhower
3. Jinbo Xu
4. Sheng Wang
5. Steven L. Salzberg
6. J. Gregory Caporaso
7. Minoru Kanehisa
8. Florian P. Breitwieser

Citations in the corpus

• ProGen: Language Modeling for Protein Generation (2020, methodology): “We curate the protein sequences and associated tags available in Uniparc [24], UniprotKB [7], SWISS-PROT [6], TrEMBL [10], Pfam [8], and NCBI taxonomic information [16].”
• ColabFold: making protein folding accessible to all (2022, methodology): “To pair MSAs for complex prediction, we retrieve for each found UniRef100 member sequence the taxonomic identifier from the NCBI (National Center for Biotechnology Information) Taxonomy database 30 .”
• SIFTS: Structure Integration with Function, Taxonomy and Sequences resource (2012, neutral): “When a new structure is deposited in the PDB, the wwPDB annotation staff add appropriate cross-references to other resources such as PubMed (9), UniProtKB, the NCBI taxonomy database (10), NORINE (11) and EMDB (12,13), to capture the biological, chemical and structural context of the entry.”
• BPGA- an ultra-fast pan-genome analysis pipeline (2016, background): “S5, while the gene-families present exclusively in M-1 and M-12 serotypes are enlisted in Supplementary file 2 41–44 .”
• A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life (2018, background): “Phylum (99) Class (263) Order (705) Family (1,594) Genus (5,389) Total (8,050) Active changes Passive changes Unchanged”