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

By C. Schoch, S. Ciufo, M. Domrachev, C. Hotton, S. Kannan, Rogneda Khovanskaya, Detlef D. Leipe, Richard McVeigh, Kathleen O'Neill, B. Robbertse and 6 more. Database J. Biol. Databases Curation, 2020

2,193 citations recorded by the source corpus.

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.

Subfields: Ecological Modeling, Ecology, Evolution, Behavior and Systematics, Plant Science

View Paper: https://www.semanticscholar.org/paper/f7787f0da0258d3015daf00a57929f9d3ad8779a

How researchers see this paper

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

In Ecological Modeling

In Ecology, Evolution, Behavior and Systematics

In Plant Science

Citations in the corpus

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads (2023, methodology): “The tree is derived from NCBI TaxonomyDB [20,21], and was visualised in iToL [22].”
Petabase-scale sequence alignment catalyses viral discovery (2020, background): “genomes; report best-estimate predictions balancing over-classification and under-classification (too many and too few ranks, respectively); and assign an NCBI Taxonomy Database [96] identifier (TaxID).”
The Sequence Read Archive: a decade more of explosive growth (2021, background): “Further, while phylogenetic, the Taxonomy tree is not solely based on sequence similarity (10,11).”
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity (2022, background): “The orthology levels are defined according to the NCBI Taxonomy (12).”
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool (2024, methodology): “In addition to the NCBI taxonomy database ( 16 ), iTOL now also supports GTDB (Genome Taxonomy Database) ( 17 ).”
Protein complex prediction with AlphaFold-Multimer (2021, background): “Chains with empty MSAs are not matched and the resulting paired MSA will be padded with gap (no-match) symbols.”
RESCRIPt: Reproducible sequence taxonomy reference database management (2020, methodology): “The use of genomes sequenced from type material provides these two databases with a robust taxonomic and phylogenetic backbone that enables users to link natural history and experimental science [94,104].”
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 (2023, methodology): “…of outlier labels resulting from misspellings or incorrect assignments by NCBI genome submitters (for example, the Staphylococcus epidermidis SGB7865 is composed of 700 reference genomes, 32 of which have different or unspecified species labels in the NCBI database 49 , Supplementary Table 1).”
BioRAG: A RAG-LLM Framework for Biological Question Reasoning (2024, methodology): “GeneGPT chose the wrong NCBI API.”