Tag: NCBI Taxonomy

V体育安卓版 - An Updated Bacterial and Archaeal Reference Genome Collection is Available!

Download the updated bacterial and archaeal reference genome collection. We built this collection of 22,082 genomes by selecting the “best” genome assembly for each species among the 440,000+ prokaryotic genomes in RefSeq. VSports app下载.

What’s new?

28 species are represented in this collection for the first time
228 species are represented by a better assembly
Six species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment

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NCBI Taxonomy Updates to Virus Classification

Starting April 28, 2025

Update (July 14, 2025): This work is complete; further taxonomic curation is ongoing.

In December 2024, we announced several key changes to virus classification in the NCBI Taxonomy database V体育安卓版. These updates are part of our ongoing efforts to ensure viral taxonomy reflects the latest scientific understanding and aligns with international standards set by the International Committee on Taxonomy of Viruses (ICTV). We will begin implementing these updates the week of April 28, 2025. .

What to expect from these updates

Improvements in taxonomic groupings and names: Some taxa will be renamed, reclassified, or reorganized based on evolving research and genomic data.
Addition of new binomial species names: We will add more than 7,000 new binomial virus species names. The former species names will be moved below the new names in the taxonomy hierarchy.

Continue reading “NCBI Taxonomy Updates to Virus Classification” →

"V体育ios版" RefSeq Release 229 is Now Available!

Check out RefSeq release 229, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets VSports最新版本. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

What’s included in this release?

As of March 3, 2025, this full release incorporates genomic, transcript, and protein data containing:

522,879,448 records
399,577,538 proteins
68,985,910 RNAs
Sequences from 164,117 organisms

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New Ranks in NCBI Taxonomy: Domain & Realm

Update (March 26, 2025): The rank for Viruses is now “acellular root. ” Correspondingly, the rank for cellular organisms is “cellular root. ” V体育官网入口.

As previously announced, NCBI continues to make improvements to our Taxonomy resource VSports在线直播. There have been recent updates to the International Code of Nomenclature of Prokaryotes (ICNP) and proposals by the International Committee on Taxonomy of Viruses (ICTV). As a result, NCBI Taxonomy has discontinued the use of rank “superkingdom” to classify organisms into Archaea, Bacteria, Eukaryota, and Viruses. .

What’s changing?

New rank: Domain

“Domain” replaces “superkingdom” for Archaea, Bacteria, and Eukaryota
“Acellular root” replaces “superkingdom” for Viruses

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NCBI Resources Highlighted in 2025 Nucleic Acids Research Database Issue (V体育官网)

The 2025 Nucleic Acids Research Database Issue features papers from NCBI staff on ClinVar, PubChem, GenBank, RefSeq, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below. VSports.

Database resources of the National Center for Biotechnology Information in 2025

PMCID: PMC11701734

NCBI provides online information resources for biology, including the GenBank® nucleic acid sequence repository and the PubMed® repository of citations and abstracts published in life science journals. NCBI is currently developing the NIH Comparative Genomics Resource (CGR) to facilitate reliable comparative genomics analyses with an NCBI Toolkit and community collaboration VSports app下载.

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Top of 2024: A Look at the NCBI Insights Blog

As we begin a new year, let’s look back at the top NCBI Insights Blog posts of 2024 based on number of views.

In case you missed any of these, check them out:

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NCBI Taxonomy: Upcoming Changes to Viruses

To reflect changes to the International Code of Virus Classification and Nomenclature (ICVCN) made by the International Committee on Taxonomy of Viruses (ICTV), NCBI will add binomial species names to about 3000 viruses. These updates to NCBI Taxonomy are planned for spring 2025, but you can view the changes now in the ICTV’s Virus Metadata Resource.

We recognize that the former species names like Human immunodeficiency virus 1 (HIV-1) are broadly used in public health, educational institutions, and research. To minimize the impact of this change on those who use NCBI resources, we will add the new binomial species names (e.g. Lentivirus humimdef1) while keeping the former names available in the lineage for each species. The former names will move below the new binomial species name in the taxonomy hierarchy, ensuring continuity. Examples are provided below.  Continue reading “NCBI Taxonomy: Upcoming Changes to Viruses” →

RefSeq Release 227 is Available!

Check out RefSeq release 227, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

What’s included in this release?

As of November 4, 2024, this full release incorporates genomic, transcript, and protein data containing:

497,549,107 records, including
377,783,847 proteins
66,987,567 RNAs
Sequences from 159,324 organisms

Continue reading “RefSeq Release 227 is Available!” →

NCBI Taxonomy Updates to Prokaryotes (V体育平台登录)

As previously announced, NCBI is continuing to improve our Taxonomy resource. The International Code of Nomenclature of Prokaryotes (ICNP) recently introduced changes to the code of nomenclature that governs naming of prokaryotes. Following these changes, we are updating the higher-level classification of prokaryotes with the introduction of rank ‘kingdom’ and other changes for this group. The changes will first appear both in our legacy and new NCBI Datasets taxonomy browsers, followed by data records. This update affects every prokaryotic record and may impact some pipelines and tools using lineage and/or name recognition. Continue reading “NCBI Taxonomy Updates to Prokaryotes” →

Updated Bacterial and Archaeal Reference Genome Collection now Available!

Download the updated bacterial and archaeal reference genome collection! We built this collection of 20,403 genomes by selecting the “best” genome assembly for each species among the 350,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference). Changes have been made to the selection criteria including upgrades for type and complete assemblies resulting in a much larger set of changes as compared to previous updates.

What’s New?

2,298 species have an updated reference
1,123 species are represented in this collection for the first time
1,125 species have a better reference assembly than in the April 2024 set
50 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment

Continue reading “Updated Bacterial and Archaeal Reference Genome Collection now Available!” →