Tag: NCBI Datasets

Improved Gene Data Access with Redesigned NCBI Gene Pages

We are excited to announce redesigned NCBI Gene pages! The redesigned pages (available through NCBI Datasets) offer a modern, clean interface with an intuitive layout that makes browsing and downloading NCBI Gene data easier. The legacy Gene page will continue to be available during this transition period, and we will continue to communicate updates and changes through NCBI websites and this blog.

What’s new?

Improved Search Capabilities: The new Gene landing page offers improved search functionality, allowing users to find gene information more effectively. Users can now search by taxon, locus tag and symbol (with or without specifying a taxon, and above species level) in addition to NCBI GeneID and accession.

Continue reading “Improved Gene Data Access with Redesigned NCBI Gene Pages” →

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!

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

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

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” →

RefSeq Release 228 is Available!

Check out RefSeq release 228, 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 January 3, 2025, this full release incorporates genomic, transcript, and protein data containing:

513,096,240 records, including
391,903,900 proteins
67,997,702 RNAs
Sequences from 162,138 organisms

Continue reading “RefSeq Release 228 is Available!” →

Access Avian Influenza A (H5N1) Virus Sequences from the Current Outbreak at NCBI

The U.S. Centers for Disease Control and Prevention (CDC) has been monitoring the ongoing outbreak of the avian influenza A (H5N1) virus. This is widespread globally in wild birds, and has led to sporadic outbreaks in poultry, cows, several species of wild animals, and has been detected in exposed humans. The CDC recently sequenced the H5N1 virus in two respiratory specimens collected from a U.S. patient who was severely ill and has now died (PQ809549-PQ809564).

As previously announced, the GenBank sequences, annotations, and metadata including from this patient are available through NLM’s NCBI resources. Continue reading “Access Avian Influenza A (H5N1) Virus Sequences from the Current Outbreak at NCBI” →

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:

Continue reading “Top of 2024: A Look at the NCBI Insights Blog “ →

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!” →