Tag: NCBI Taxonomy

An Updated Bacterial and Archaeal Reference Genome Collection is Available!

An Updated Bacterial and Archaeal Reference Genome Collection is Available!

Download the updated bacterial and archaeal reference genome collection! We built this collection of 22,420 genomes by selecting the “best” genome assembly for each species among the 450,000+ prokaryotic genomes in RefSeq. 

What’s new? 
  • One species is represented in this collection for the first time 
  • 323 species are represented by a better assembly
  • Six species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment 

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

An Updated Bacterial and Archaeal Reference Genome Collection is Available!

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. 

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 

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

NCBI Taxonomy Updates to Virus Classification

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. 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” →

RefSeq Release 229 is Now Available!

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. 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 

Continue reading “RefSeq Release 229 is Now Available!” →

New Ranks in NCBI Taxonomy: Domain & Realm

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.”

As previously announced, NCBI continues to make improvements to our Taxonomy resource. 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

Continue reading “New Ranks in NCBI Taxonomy: Domain & Realm” →

NCBI Resources Highlighted in 2025 Nucleic Acids Research Database Issue

NCBI Resources Highlighted in 2025 Nucleic Acids Research Database Issue

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. 

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.

Continue reading “NCBI Resources Highlighted in 2025 Nucleic Acids Research Database Issue” →

NCBI Taxonomy: Upcoming Changes to Viruses

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!

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

NCBI Taxonomy Updates to Prokaryotes

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” →