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

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

2020 | Conrad L. Schoch, Stacy Ciufu, Mikhail Domrachev, Carol L. Hotton, Sivakumar Kannan, Rogneda Khovanskaya, Detlef Leipe, Richard Mcveigh, Kathleen O'Neill, Barbara Robbertse, Shobha Sharma, Vladimir Soussov, John P. Sullivan, Lu Sun, Seán Turner and Ilene Karsch-Mizrachi
The NCBI Taxonomy is a comprehensive resource that provides organism names and classifications for all sequences in the nucleotide and protein databases of the International Nucleotide Sequence Database Collaboration (INSDC). Since its last review in 2012, it has undergone significant improvements, including a shift from a single SQL database to a system of linked databases centered around NameBank. This change allows for more detailed relationships between data elements, enhanced tracking of publications, and improved annotation of scientific authorities and types. The resource also includes informal names and descriptions of taxonomic groups, along with updates to tools and other resources. The NCBI Taxonomy plays a crucial role in structuring communication about all forms of life on Earth, as it links organism names with genetic and genomic data. Accurate taxonomy is essential for research in biomedical, agricultural, and ecological fields. The NCBI Taxonomy includes a hierarchical list of organism names across all domains of life, with names that are correct, current, and valid according to the best authorities in the taxonomic disciplines. It also includes informal names and uses phylogenetic classification to reflect current understanding of organismal relationships. The NCBI Taxonomy has been updated to include type strain and type specimen information, which enhances the development of taxonomic information attached to public sequence records. The resource also includes a variety of tools and databases, such as the NCBI BioCollections database, which verifies data on biorepositories linked to sequence data. The NCBI Taxonomy is used by various databases, including GenBank and RefSeq, to ensure that sequence records are synchronized with changes in the taxonomy. The NCBI Taxonomy is governed by four principal codes of nomenclature, which are used to validate names in different taxonomic groups. These codes include the International Code of Nomenclature for algae, fungi, and plants (ICNafp), the International Code of Nomenclature of Prokaryotes (ICNP), the International Code of Zoological Nomenclature (ICZN), and the International Code of Virus Classification and Nomenclature (ICVCN). These codes provide rules for naming and are used to ensure that names are accurate and consistent. The NCBI Taxonomy also includes a variety of resources, such as the NCBI Taxonomy statistics page, which provides information on the number of species and other taxonomic groups. The resource is used by various databases and tools to ensure that taxonomic information is accurate and up-to-date. The NCBI Taxonomy is also used to curate and verify data on organisms, including prokaryotes, green plants, fungi, and viruses. The resource is continually updated to reflect new information and changes in the taxonomic literature.The NCBI Taxonomy is a comprehensive resource that provides organism names and classifications for all sequences in the nucleotide and protein databases of the International Nucleotide Sequence Database Collaboration (INSDC). Since its last review in 2012, it has undergone significant improvements, including a shift from a single SQL database to a system of linked databases centered around NameBank. This change allows for more detailed relationships between data elements, enhanced tracking of publications, and improved annotation of scientific authorities and types. The resource also includes informal names and descriptions of taxonomic groups, along with updates to tools and other resources. The NCBI Taxonomy plays a crucial role in structuring communication about all forms of life on Earth, as it links organism names with genetic and genomic data. Accurate taxonomy is essential for research in biomedical, agricultural, and ecological fields. The NCBI Taxonomy includes a hierarchical list of organism names across all domains of life, with names that are correct, current, and valid according to the best authorities in the taxonomic disciplines. It also includes informal names and uses phylogenetic classification to reflect current understanding of organismal relationships. The NCBI Taxonomy has been updated to include type strain and type specimen information, which enhances the development of taxonomic information attached to public sequence records. The resource also includes a variety of tools and databases, such as the NCBI BioCollections database, which verifies data on biorepositories linked to sequence data. The NCBI Taxonomy is used by various databases, including GenBank and RefSeq, to ensure that sequence records are synchronized with changes in the taxonomy. The NCBI Taxonomy is governed by four principal codes of nomenclature, which are used to validate names in different taxonomic groups. These codes include the International Code of Nomenclature for algae, fungi, and plants (ICNafp), the International Code of Nomenclature of Prokaryotes (ICNP), the International Code of Zoological Nomenclature (ICZN), and the International Code of Virus Classification and Nomenclature (ICVCN). These codes provide rules for naming and are used to ensure that names are accurate and consistent. The NCBI Taxonomy also includes a variety of resources, such as the NCBI Taxonomy statistics page, which provides information on the number of species and other taxonomic groups. The resource is used by various databases and tools to ensure that taxonomic information is accurate and up-to-date. The NCBI Taxonomy is also used to curate and verify data on organisms, including prokaryotes, green plants, fungi, and viruses. The resource is continually updated to reflect new information and changes in the taxonomic literature.
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