Changes to SRA Data Access on the Google Cloud Platform (GCP)

Sequence Read Archive (SRA) data available via the Google Cloud Platform (GCP) are migrating from multi-region to single region us-east-1. This migration is projected to be complete by May 2024. To minimize the impact of this change, we recommend updating your workflow to access SRA data in us-east-1 region as soon as conveniently possible.

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

Preview Upcoming Improvements to PubMed Central (PMC)

Updated article display and journal list

Since announcing the launch of a more modern PubMed Central (PMC) website in March 2022, NLM’s NCBI continues to make improvements based on your feedback. We invite you to preview the latest improvements planned for the PMC website. These improvements will become the default in October 2024 and include an updated article display, enhanced PMC journal list, and other features to help you access information quickly and easily. Click on the “Try it out now” link in the banner on the top of any ncbi.nlm.nih.gov/pmc page to preview and experience these improvements for yourself. Continue reading “Preview Upcoming Improvements to PubMed Central (PMC)” →

Announcing NCBI’s First Ever BioEd Summit!

An in-person training opportunity for science educators

Calling all high school, community college, and undergraduate science educators! NCBI is excited to host our first BioEd Summit on the National Institutes of Health (NIH) campus in Bethesda, MD, from August 5-9, 2024. Join us for a week-long, in-person event where you will collaborate with other educators and NCBI experts to create data-driven curricula. You’ll leave the event with an exciting, novel lesson you can use in your classroom to prepare your students for real-world scientific research.

Event details

Interactive training workshops on NCBI resources
Panel discussion on employing data-driven, active learning exercises in science classes
Codeathon-style curricula-thon with team projects to create a curricular package (learning objectives, course materials, and assessments)

Continue reading “Announcing NCBI’s First Ever BioEd Summit!” →

Now Available: RefSeq Release 223

Check out RefSeq release 223, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of March 4, 2024, this full release incorporates genomic, transcript, and protein data containing:

425,594,654 records
316,329,937 proteins
60,886,133 RNAs
sequences from 147,591 organisms

Continue reading “Now Available: RefSeq Release 223” →

Foreign Contamination Screen Tool: Now Available in Galaxy!

Check out our latest enhancements

Do you submit genome assembly data to GenBank? If so, try out NCBI’s Foreign Contamination Screen (FCS) tool, a quality assurance process that you can run yourself. We will screen all prokaryotic and eukaryotic genome submissions to GenBank with this tool, but we encourage you to screen your data before submitting to save time. FCS offers sensitive contaminant detection to increase the quality of your genome submissions to GenBank. As part of our ongoing effort to improve your experience, we recently made several enhancements. Continue reading “Foreign Contamination Screen Tool: Now Available in Galaxy!” →

Celebrating the Building Transparent ML/AI Solutions for Biological Research Codeathon

Machine Learning and Artificial Intelligence (ML/AI) are reshaping data science and scientific discovery. Recognizing the important role of collaboration and knowledge sharing in this space, NCBI hosted the “Building transparent ML/AI solutions to advance biological research codeathon” from February 26 to March 1, 2024. This virtual event brought together biologists, developers, and data scientists passionate about using responsible AI in biological research. Continue reading “Celebrating the Building Transparent ML/AI Solutions for Biological Research Codeathon” →

Submit Your Somatic Variation Data to ClinVar

NCBI’s ClinVar is now accepting submissions for somatic variants classified for cancer. As recently announced, we updated the ClinVar website as part of our effort to better support the display of submitted somatic variation data.

Access to somatic variation data is essential for understanding tumor biology and will help researchers advance cancer treatment. It also helps clinical cancer testing laboratories provide better patient reports. Make ClinVar as useful for somatic variants as it is for germline by contributing your data! To submit your data, use our new somatic spreadsheet template (SubmissionTemplateSomatic.xlsx) and follow these step-by-step instructions. Once your submission is prepared, you can go to the ClinVar Submission Portal to upload and send your file. See an example below. Continue reading “Submit Your Somatic Variation Data to ClinVar” →

Join NCBI at TAGC 2024

March 6-10 in Washington, D.C.

We look forward to seeing you in person at The Allied Genetics Conference (TAGC), March 6-10, 2024, in the Washington D.C. metro area. NCBI staff will participate in a variety of activities and events, including hosting a hands-on workshop: Exploring and downloading NCBI data with NCBI Datasets. We’re also excited to share our recent efforts on the NIH Comparative Genomics Resource (CGR) in a talk during Sunday’s Technology, Tools, and Resources session.

Check out NCBI’s schedule of activities and events:

Continue reading “Join NCBI at TAGC 2024” →

Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools

As part of our ongoing effort to enhance your experience, we are updating the NCBI Datasets application programming interfaces (APIs). Beginning in June 2024, the v2alpha APIs will be promoted to the stable v2 version. At this time, the v1 API, the command-line interface (CLI) version 13 and older versions, and the Python library v1 will be deprecated and thus no longer supported for bug fixes or updates. Effective December 31, 2024, these will no longer be available for use.

Our updated APIs and CLI tools include new features and functionality based on your feedback. We’re committed to making this transition as smooth as possible and encourage you to review our FAQs for more details. If you use NCBI Datasets web pages and command-line tools v14+, no action is required. Continue reading “Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools” →

NCBI Celebrates International Love Data Week

Providing free and open access to scientific literature and data

Do you love biological data? Join NCBI in celebrating International Love Data Week, February 12-16, 2024! Love Data Week is an international celebration of data, which takes place every year during the week of Valentine’s Day. This year’s theme is “My Kind of Data,” focusing on data equity and inclusion, disciplinary communities, and creating a kinder world through data.

NCBI is one of the largest sources of free and open biological data on the web with over 300 TB retrieved every day. There’s something for everyone to love! Continue reading “NCBI Celebrates International Love Data Week” →