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

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” →

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

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

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

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” →

Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome”

NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowly converged on the term reference to refer to both sets.

A genome is labeled reference if it is deemed to be the best available genome for the species based on assembly, annotation metrics (when available), and, in a small number of cases, curatorial review. The set of eukaryotic reference assemblies is updated continuously as new assemblies are submitted to GenBank. The set of prokaryotic references are recalculated three times a year.

Important Note: Classification of “reference genome” is separate from inclusion in RefSeq – while genomes in RefSeq are preferentially used to pick the reference genome, a reference genome can also be chosen for species not included in RefSeq. Continue reading “Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome”” →

Access Public Reports of Foreign Contamination Screen (FCS) Tool Results

Do you use genomes from NCBI and are concerned they may contain contaminant sequences? Now you can view reports generated for all prokaryotic and eukaryotic genomes with NCBI’s quality assurance tool, Foreign Contamination Screen (FCS), to better understand possible issues that may affect your studies.

What reports are available?

Summary reports to select better assemblies at thresholds of your choosing.
Detailed reports to remove or mask contaminant sequences so they don’t adversely affect analyses. This is particularly useful for building k-mer databases.
Individual assembly reports available through the FTP link located on NCBI Datasets genome pages.
Reports are available for all eukaryotic and prokaryotic GenBank and RefSeq assemblies, currently covering over 2.7 million assemblies.
A README to understand how to interpret and use contamination reports.

Continue reading “Access Public Reports of Foreign Contamination Screen (FCS) Tool Results” →

Updated Bacterial and Archaeal Reference Genome Collection now Available!

Download the updated bacterial and archaeal reference genome collection! We built this collection of 20,403 genomes by selecting the “best” genome assembly for each species among the 350,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference). Changes have been made to the selection criteria including upgrades for type and complete assemblies resulting in a much larger set of changes as compared to previous updates.

What’s New?

2,298 species have an updated reference
1,123 species are represented in this collection for the first time
1,125 species have a better reference assembly than in the April 2024 set
50 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment

Continue reading “Updated Bacterial and Archaeal Reference Genome Collection now Available!” →