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” →

GenBank Release 261.0 is Available!

GenBank release 261.0 (6/18/2024) is now available on the NCBI FTP site. This release has 32.04 trillion bases and 4.51 billion records.

The current release has:

251,094,334 traditional records containing 3,387,240,663,231 base pairs of sequence data
3,380,877,515 WGS records containing 27,900,199,328.,333 base pairs of sequence data
746,753,803 bulk-oriented TSA records containing 695,405,769,319 base pairs of sequence data
135,446,337 bulk-oriented TLS records containing 54,512,778,803 base pairs of sequence data

Continue reading “GenBank Release 261.0 is Available!” →

Upcoming Changes to NCBI Taxonomy Classifications

NCBI is continually making improvements to our Taxonomy resource in response to new data and changes in biological nomenclature and classification. In the coming months, we will update the higher-level classification of birds (Aves), budding yeasts (Saccharomycotina), prokaryotes (Bacteria and Archaea) and Viruses. This update will also change the formal ranks of several high-level taxonomic names including Eukaryota. Except for the new species names for Viruses, none of these changes will affect organism names at the species level or below.

Here is a brief overview of changes to each group in the order we plan to make them. Stay tuned for upcoming posts, which will describe the changes for each category in more detail. Continue reading “Upcoming Changes to NCBI Taxonomy Classifications” →

Explore Population Genetics in dbSNP with NCBI’s Allele Frequency Aggregator (ALFA)

Access to comprehensive and accurate allele frequency data is essential to understanding the impact of genetic variations on human health and disease. Allele Frequency Aggregator (ALFA) provides the Database of Single Nucleotide Polymorphisms (dbSNP) with allele frequency data for 200K subjects from the Database of Genotypes and Phenotypes (dbGaP). ALFA adheres to the Findable, Accessible, Interoperable, and Reusable (FAIR) Data Principles providing open access to valuable allele frequency data. Continue reading “Explore Population Genetics in dbSNP with NCBI’s Allele Frequency Aggregator (ALFA)” →

NCBI & NIAID Join Forces to Co-Host Virtual AMR Codeathon

Resistance is Futile: A codeathon to combat antimicrobial resistance

Do you perform antimicrobial resistance (AMR) research, or would you like to join a team to work on microbial and AMR data analysis? NCBI is joining forces with the National Institute of Allergy and Infectious Diseases (NIAID) to co-host a virtual codeathon, Resistance is Futile: A codeathon to combat antimicrobial resistance, which will take place September 23-27, 2024. Continue reading “NCBI & NIAID Join Forces to Co-Host Virtual AMR Codeathon” →

New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI

Sequence data from the ongoing avian influenza A (H5N1) virus outbreak in cattle are now available through NLM’s NCBI resources NCBI Virus and NCBI Datasets.

These data were submitted by the U.S. Department of Agriculture (USDA), U.S. Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO), Iowa State University, and St. Jude Children’s Research Hospital. Continue reading “New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI” →

Ortholog Groups Added for ~2 Million Insect Genes

Find evolutionarily related genes across insects and other arthropods on our new Ortholog webpages

NCBI recently released a set of orthologs for approximately 2 million insect genes. You can now find and access the orthologous genes, transcripts, and proteins by searching a species and gene name in NCBI All Databases, NCBI Gene, or NCBI Datasets. As previously described, these orthologs are based on comparisons to the Drosophila melanogaster annotated genome. Using Drosophila gene nomenclature for orthologs should lead to more informative gene symbols for insects and other arthropods. Continue reading “Ortholog Groups Added for ~2 Million Insect Genes” →

International Nucleotide Database Collaboration (INSDC) Introduces Enhanced Website

Aims to broaden INSDC membership and attract diverse new members

The National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) and other Founding Members of the International Nucleotide Database Collaboration (INSDC) have enhanced its website, www.insdc.org, to provide comprehensive information on how interested parties from around the world can evaluate their readiness to participate in the INSDC. This effort supports INSDC’s aim to broaden membership and attract qualified nucleotide sequence databases. Web content now includes a formalized Founders Arrangement and a Membership Arrangement, along with other updated information about the INSDC mission, vision, governance, and technical documentation. In doing so, INSDC encourages interested parties to visit the INSDC website to learn more. Continue reading “International Nucleotide Database Collaboration (INSDC) Introduces Enhanced Website” →