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. 2025 Jan 6;53(D1):D1711-D1715.
doi: 10.1093/nar/gkae967.

NCBI Taxonomy: enhanced access via NCBI Datasets

Eric Cox  1 , Mirian T N Tsuchiya  1 , Stacy Ciufo  1 , John Torcivia  1 , Robert Falk  1 , W Ray Anderson  1 , J Bradley Holmes  1 , Vichet Hem  1 , Laurie Breen  1 , Emily Davis  1 , Anne Ketter  1 , Peifen Zhang  1 , Vladimir Soussov  1 , Conrad L Schoch  1 , Nuala A O'Leary  1
Affiliations

NCBI Taxonomy: enhanced access via NCBI Datasets

Eric Cox et al. Nucleic Acids Res. .

Erratum in

Abstract

The NCBI Taxonomy resource (https://www.ncbi.nlm.nih.gov/taxonomy) has long been a trusted, curated hub for organism names, classifications, and links to related data for all taxonomic nodes. NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/) is an improved way to leverage the rich data available at NCBI so users can effectively browse, search, and download information. While taxonomy data has been a cornerstone of NCBI Datasets since its inception, we recently extended the taxonomy information available via NCBI Datasets by updating the existing NCBI Datasets taxonomy page, implementing a new taxonomy name details page, expanding programmatic access to taxonomic information via command-line tools and APIs and improving the way we handle taxonomic queries to connect users to gene and genome data. This paper highlights these improvements and provides examples to help users effectively harness these new features.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Screenshots of NCBI Datasets taxonomy pages and features. (A) Search box from the NCBI Datasets homepage showing the autosuggest feature for the taxon Candida tropicalis. (B) Main taxonomy page, where users can find taxonomy information, images, links to genomic resources and other databases. (C) Detail of the top of the main taxonomy page. The red arrow points to the ‘type material’ label, which indicates that a genome assembly derived from type material is available for that species. (D) Detail of the bottom of the main taxonomy page showing links to other databases. The red arrow points to the type material section. (E) Names page for Candida tropicalis, showing synonyms, type material information, current scientific name, basionym, and name authority. (F) Group name, which corresponds to the NCBI BLAST name in the legacy interface (G) Detail showing the expanded lineage for Candida tropicalis (H) Taxonomy Browser showing hierarchical taxonomy information for C. tropicalis, with both parent and children nodes, and the count of assembled genomes available for each taxon.
Figure 2.
Figure 2.
Schematic image showing the command hierarchy and syntax of the datasets command-line tool. Highlighted in red are the newly implement taxonomy commands. In blue, we show the existing endpoints that benefit from better handling of ambiguous names.
See this image and copyright information in PMC

References

    1. Schoch C.L., Ciufo S., Domrachev M., Hotton C.L., Kannan S., Khovanskaya R., Leipe D., McVeigh R., O’Neill K., Robbertse B.et al. .. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020; 2020:baaa062. - PMC - PubMed
    1. Arita M., Karsch-Mizrachi I., Cochrane G.. The international nucleotide sequence database collaboration. Nucleic Acids Res. 2021; 49:D121–D124. - PMC - PubMed
    1. Bornstein K., Gryan G., Chang E.S., Marchler-Bauer A., Schneider V.A.. The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health. BMC Genomics. 2023; 24:575. - PMC - PubMed
    1. Hobern D., Barik S.K., Christidis L., T.Garnett S., Kirk P., Orrell T.M., Pape T., Pyle R.L., Thiele K.R., Zachos F.E.et al. .. Towards a global list of accepted species VI: the Catalogue of Life checklist. Organ. Divers. Evol. 2021; 21:677–690.
    1. O’Leary N.A., Cox E., Holmes J.B., Anderson W.R., Falk R., Hem V., Tsuchiya M.T.N., Schuler G.D., Zhang X., Torcivia J.et al. .. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets. Sci. Data. 2024; 11:732. - PMC - PubMed

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