MedGen Users, We Want Your Feedback!

MedGen Users, We Want Your Feedback!

Do you use NCBI’s MedGen? If so, then you probably know it’s NCBI’s one-stop-shop for genetic phenotype information. If you are a healthcare provider, genetic professional, researcher, or anyone who uses MedGen, we want to hear from you to help us make this resource better meet your needs!  

We want to know: 

  • How you currently use MedGen 
  • How we can make MedGen data more useful to you 
How to provide feedback

There are two ways you can provide feedback:

  1. Take this short online survey 
  2. Contact us at medgen@ncbi.nlm.nih.gov to schedule an interview with a MedGen team member 
About MedGen
  • Aggregates information from authoritative sources and provides links to useful, actionable information 
  • Links professional practice guidelines to relevant phenotypes, related articles in PubMed and on NCBI’s Bookshelf 
  • Standardizes genetic phenotype nomenclature across NCBI resources  
  • Includes information on infectious diseases (since 2020) 
  • Search by clinical features to find disease records  
  • Provides the phenotypic data and vocabularies used by ClinVar and Genetic Testing Registry (GTR) 

Please note: MedGen data is available for you to use in your own projects. Contact us if you would like us to help you adopt the MedGen dataset.

Stay up to date

Follow us on social @NCBI_clinical and join NCBI’s mailing list to keep up to date with MedGen and other NCBI news.    

Questions?

Please reach out to us if you have questions or would like to provide feedback. 

 

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

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)

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!

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

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!

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

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

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

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

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”