GenBank Release 263.0 Now Available!

GenBank Release 263.0 Now Available!

GenBank release 263.0 (10/19/2024) is now available on the NCBI FTP site. This release has 36.50 trillion bases and 5.13 billion records.

The current release has: 

  • 251,998,350 traditional records containing 4,250,942,573,681 base pairs of sequence data
  • 3,745,772,758 WGS records containing 31,362,454,467,668 base pairs of sequence data
  • 948,733,596 bulk-oriented TSA records containing 812,661,461,811 base pairs of sequence data
  • 187,349,395 bulk-oriented TLS records containing 77,037,504,468 base pairs of sequence data 
Continue reading “GenBank Release 263.0 Now Available!”
Upcoming Changes to NCBI’s BioSample Database

Upcoming Changes to NCBI’s BioSample Database

Improving Metadata Quality 

Do you rely on high-quality metadata from NCBI’s BioSample database? BioSample is home to metadata associated with the biological source materials used to generate raw reads, sequences, and other data submitted to NCBI. We are improving our submission process to ensure we provide you with more complete and robust information. 

Attention submitters! 

To improve metadata quality, we are introducing new submission validation steps and providing improved help documentation.  Continue reading “Upcoming Changes to NCBI’s BioSample Database”

Explore NLM’s NCBI Bookshelf With New Learning Tools at Your Fingertips

Explore NLM’s NCBI Bookshelf With New Learning Tools at Your Fingertips

New tutorials, queries, and discovery guides now available 

NLM’s NCBI Bookshelf provides free access to more than 13,000 peer-reviewed books and documents in life science and health care using over a dozen formats including monographs, reviews, reference works, government publications, standards and guidelines, technical reports, and textbooks. In acknowledgement of Open Access Week, we are excited to introduce new learning tools to better access and discover subject- and format-based collections within Bookshelf.

Bookshelf strives to advance open and equitable science and scholarship. To achieve this goal, Bookshelf collaborates with over 150 content providers, more than half of which are nontraditional publishers like government agencies and non-governmental organizations, to make their content publicly accessible. This diverse body of content is organized into user-relevant subcollections, such as “health disparities,” to better facilitate access and discovery. Over half of this content is also available for programmatic reuse through Bookshelf’s Open Access Subset.  Continue reading “Explore NLM’s NCBI Bookshelf With New Learning Tools at Your Fingertips”

PubMed Central (PMC) Transitions to Updated Website

PubMed Central (PMC) Transitions to Updated Website

The next step in the modernization of PMC 

As previously announced, NLM’s NCBI transitioned to an updated PubMed Central (PMC) website, representing the next step in ongoing efforts to modernize NLM’s products and services. As part of this update, the primary URL for the PMC website has changed from ncbi.nlm.nih.gov/pmc to pmc.ncbi.nlm.nih.gov. In addition, you’ll notice a new look, feel, and organization of PMC article pages and the PMC Journal List.   

The updated website runs on cloud services to ensure the website’s long-term sustainability and reliability. It also incorporates U.S. Web Design System (USWDS) components and design principles to improve PMC’s readability and accessibility, whether you are visiting on a desktop computer, mobile device, or accessing its content using assistive technology.  Continue reading “PubMed Central (PMC) Transitions to Updated Website”

CDART: Find Proteins with Similar Domain Architecture

CDART: Find Proteins with Similar Domain Architecture

Are you interested in comparing gene families or exploring the evolution of domain architecture? Try our Conserved Domain Architecture Retrieval Tool (CDART) to retrieve sets of proteins that share the same or similar domain superfamily architecture with your query. We recently updated CDART so it’s faster and more streamlined with simplified navigation and result filtering. 

Check out this example:  Continue reading “CDART: Find Proteins with Similar Domain Architecture”

Changes to SRA Data Access on Amazon Web Services (AWS) and Google Cloud Platform (GCP)

Changes to SRA Data Access on Amazon Web Services (AWS) and Google Cloud Platform (GCP)

Important note! The storage tier for Sequence Read Archive (SRA) data available through Amazon Web Services (AWS) commercial buckets is transitioning to Glacier Instant retrieval and Google Cloud Platform (GCP) is transitioning to Coldline. This change is projected to be complete by the end of October 2024. To mitigate the cost impact of this change, we recommend adjusting your data access workflow to utilize the SRA Toolkit for accessing SRA data from AWS or GCP.  

Please note this change does not impact SRA data access from NCBI servers or AWS Open Data Program.     Continue reading “Changes to SRA Data Access on Amazon Web Services (AWS) and Google Cloud Platform (GCP)”

Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects

Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects

With support from the National Institute of Allergy and Infectious Diseases (NIAID)’s Office of Genomics and Advanced Technologies and the NCBI Pathogen Detection Project Team, NCBI hosted a successful virtual event, Resistance is Futile: A codeathon to combat antimicrobial resistance. This codeathon took place September 23-27, 2024, and brought together experts in the field of antimicrobial resistance and those with bioinformatic, data science skills from around the world.

Because infections caused by antimicrobial-resistant bacteria do not always respond to routinely prescribed antibiotics, they can be difficult for healthcare providers to treat. Unfortunately, this is becoming an increasingly frequent worldwide problem. This codeathon examined the association of antimicrobial resistance (AMR) with genetic sequence adaptations, mutations in bacterial receptors and efflux pumps, and emergence of mobile genetic elements in common and difficult-to-treat bacterial pathogens. Continue reading “Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects”

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”

Viewing Ligand-Protein Interactions in iCn3D

Viewing Ligand-Protein Interactions in iCn3D

Are you interested in viewing how a protein interacts with a ligand? iCn3D, our 3D molecular structure viewer, now offers improved displays of these interactions at an atomic level.  

Check out this example: 

You are now able to see the interactions of an embedded ligand (such as the drug Gleevec in the protein ABL2) within iCn3D. In the image below, the left panel shows Gleevec colored by atom type and the interacting ABL2 protein residues colored in magenta. The right panel displays Gleevec as a 2D structure with interacting protein residues shown as magenta rectangles. In both panels, the dashed lines represent individual interactions, color-coded by interaction type as explained in the “Color Legend.” Hovering over a dashed lines will display the interaction type and length.  Continue reading “Viewing Ligand-Protein Interactions in iCn3D”