Coming Soon! Rapid Access to Influenza Data

Improved Influenza GenBank submission process

Do you submit flu sequences to GenBank? Thanks to community feedback, NCBI is excited to announce that we are improving the Influenza GenBank submission process. We continue to play a key role in providing the biomedical community free and easy access to genome sequences from viruses. To further advance public health research, in the coming weeks we will begin to expedite the release of influenza data. This means you will see the rapid assignment of accession numbers and data becoming publicly accessible within hours. In addition, we will automatically process all Influenza genomes to produce standardized, consistent annotation which saves you time and benefits the researchers who find your data valuable. Continue reading “Coming Soon! Rapid Access to Influenza Data” →

Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus

NCBI Virus now offers genomes for viruses such as Influenza A by using an automated process to group segments from the same samples. We group these segments into genomes based on metadata for the sample including species, isolate name, host organism, collection date, and location. Newly released GenBank records are added daily.

Access these genome assemblies through NCBI Virus using the new “NCBI Virus Assembly” tab above the Results Table as shown below. Continue reading “Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus” →

NCBI Taxonomy Updates to Birds (Aves)

Recent molecular comparisons have better defined relationships among high-level taxonomic groups in birds. To reflect new data and classification changes, NCBI is improving our Taxonomy resource. As previously announced, we updated the higher-level classification of birds (Aves) with the introduction of a new major taxonomic group (clade).

What’s new?

The new clade, Neoaves, comprises about 95% of all birds. The Neoaves contain six major superordinal clades:

Aequornithes (core water birds)
Telluraves (core land birds)
Columbimorphae (pigeons, sandgrouse and mesites)
Otidimorphae (cuckoos, roadrunners, turacos and bustards)
Strisores (nightjars, nighthawks, potoos, swifts and hummingbirds)
Mirandornithes (flamingos and grebes)

Continue reading “NCBI Taxonomy Updates to Birds (Aves)” →

Open Access! Million Veteran Program Genome-Wide PheWAS Results Now Available in dbGaP!

The Million Veteran Program (MVP) is a research program from the U.S. Department of Veterans Affairs (VA) that has collected and analyzed health information from over one million veteran volunteers. The data include genes, lifestyles, military experiences, and exposures that may impact health and wellness.

The results of the MVP phenome-wide association study (PheWAS) analysis are now available in NLM-NCBI’s database of Genotypes and Phenotypes (dbGaP). The PheWAS summary data is based on information from approximately 600,000 veterans from four broad ancestry groups, with hundreds of phenotypic traits recorded in medical records. This is one of the largest publicly available PheWAS datasets to date and does not require an application to access the data. Continue reading “Open Access! Million Veteran Program Genome-Wide PheWAS Results Now Available in dbGaP!” →

Get Faster, More Focused Search Results with NCBI’s New BLAST Core Nucleotide Database (core_nt)

Effective August 2024, core_nt will become the default

Interested in faster nucleotide BLAST searches with more focused search results? As previously announced, NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it more compact and more efficient. Thanks to your feedback, NCBI’s BLAST is excited to introduce the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size.

Benefits of BLAST core_nt over nt

Enables faster searches
Returns similar top results for most searches
Reduces redundancy for some highly represented organisms
Allows easier download and requires less storage space for database download for standalone BLAST

Continue reading “Get Faster, More Focused Search Results with NCBI’s New BLAST Core Nucleotide Database (core_nt)” →

NIH Genetic Testing Registry (GTR®) Annual Review Process Ensures High-Quality Data

Do you rely on high-quality and up-to-date genetic test information from the NIH Genetic Testing Registry (GTR)? Laboratories are expected to regularly review their tests, lab contacts, and license data for accuracy. GTR is making the annual review process for submitters easier and more intuitive to ensure we provide you the most current information.

Attention submitters!

To perform an annual review, you can log into the GTR Submission Portal and click the “Perform Annual Review” button. Learn how to get started and view our updated annual review process policies. Continue reading “NIH Genetic Testing Registry (GTR®) Annual Review Process Ensures High-Quality Data” →

RefSeq Release 225 Now Available!

Check out RefSeq release 225, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of July 8, 2024, this full release incorporates genomic, transcript, and protein data containing:

448,507,905 records
334,845,613 proteins
63,542,774 RNAs
Sequences from 152,668 organisms

The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 225 Now Available!” →

Universal Reference Numbers for Ig Domains Now Available in NCBI’s iCn3D Structure Viewer

The Immunoglobulin (Ig) fold is the most common protein structure unit in the human proteome and is involved in many cellular signaling pathways. NCBI along with researchers at the National Cancer Institute and California State University, Northridge have developed a universal reference numbering scheme for Ig folds, now available in the iCn3D structure viewer, to help you compare and analyze proteins with this common fold. iCn3D can also automatically detect Ig domains in structures by comparing them to a library of diverse Ig template structures. Continue reading “Universal Reference Numbers for Ig Domains Now Available in NCBI’s iCn3D Structure Viewer” →

Quickly Find Chemical Information with PubChem

Did you know NCBI’s PubChem is the world’s largest collection of freely accessible chemical information? You can search chemicals by name, molecular formula, structure, and other identifiers, as well as find chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations and more. We are constantly adding new data and working on improving interfaces to chemical information.

What is in PubChem?

118M Compounds
319M Substances
295M Bioactivity Assay Results
41M Literature Citations
51M Patents

Continue reading “Quickly Find Chemical Information with PubChem” →

A Modern ClinicalTrials.gov Website

Classic website no longer available effective June 25, 2024

We appreciate all the feedback received since the launch of the modernized ClinicalTrials.gov website in June 2023, and we’ve incorporated many of your suggestions. As announced last month, the classic website has remained available to help you transition to the modernized website. Effective today, the classic ClinicalTrials.gov website and its application programming interface (API) are retired and no longer available.

The modernized ClinicalTrials.gov website includes the following improvements:

Improved navigation and searchability – easier to use, more functional, streamlined design
Optimization for mobile devices
Plain language guidance and support materials
An updated, modernized API that aligns with other publicly accessible APIs and standardized data

Continue reading “A Modern ClinicalTrials.gov Website” →