Tag: NCBI Datasets

New Ranks in NCBI Taxonomy: Domain & Realm

New Ranks in NCBI Taxonomy: Domain & Realm

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  
  • “No rank” 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” →

RefSeq Release 228 is Available!

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

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” →

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!” →

Expansion of Ortholog Data for RefSeq Arthropods

Expansion of Ortholog Data for RefSeq Arthropods

250K+ new Hymenoptera orthologs added 

NCBI is excited to announce the expansion of ortholog data for RefSeq arthropods. This update expands the breadth of arthropod orthology information, offering new insights into evolutionary biology, gene function, and shared pathways. Whether you’re studying insect genetics, developmental biology, or comparative genomics, the expanded ortholog data opens up new possibilities for research. Check out our previous blog to learn how to access the orthologs using NCBI Datasets.  Continue reading “Expansion of Ortholog Data for RefSeq Arthropods” →

New API Key System Coming Soon to NCBI Datasets

New API Key System Coming Soon to NCBI Datasets

Increased flexibility, efficiency, and reliability 

Do you use the NCBI Datasets command-line tools or API? As of January 2025, you will have the option to use an API key to increase your rate of access. This update will provide you more flexibility and efficiency, while still maintaining robust access for everyone. Note that these changes will not affect web users. 

What to expect?

Without an API Key: You will be limited to 5 requests per second.  

With an API Key: You will be able to make 10 requests per second.  Continue reading “New API Key System Coming Soon to NCBI Datasets” →

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” →