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As previously announced, NCBI is improving the way that functional data are submitted to ClinVar and how they are represented in the XML format and on the website. We have started enhancing support for functional data and would like your feedback!
We have updated the GitHub repository with:
Continue reading “Update! Improving the Representation of Functional Data in ClinVar”
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”
The next release (v1.4) of Matched Annotation from NCBI and EMBL-EBI (MANE) is here! MANE is a collaborative dataset produced jointly by NCBI and EMBL-EBI that provides a representative transcript (MANE Select) for human protein-coding genes, to be used as universal standards for variant reporting and browser display. A second transcript, MANE Plus Clinical, is provided for genes where MANE Select alone is not sufficient to report all known variants. The new MANE release adds another important component to this high-value dataset – non-coding genes, some of which are known to be associated with human disease. Continue reading “MANE v1.4 with MANE Select for Non-Coding Genes”
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:
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.
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”
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”
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”
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”
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)”
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”