Researchers: Now it’s easier to find the data you want in BioProject


We’ve improved BioProject to give you a better way to find all data from a specific project. We think you’ll love the new interface that lets you quickly choose the right BioProject with links to the data you want in other NCBI databases.

The updated BioProject browser makes it easier than ever to filter the data by a variety of attributes so you can quickly pick BioProjects that interest you.

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Figure 1. The BioProject home page showing links to the BioProject browser. To use the new browser, click the ‘Browse by Project Attributes link below the search bar on any BioProject page or the ‘By Project attributes’ link on the BioProject home page.

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Human annotation release 109 for GRCh38.p12 is available in RefSeq


You can now download human annotation release 109 on FTP or explore it in the Genome Data Viewer, in the Gene database, and with BLAST.

Highlights in release 109:

  • A total of 20,203 protein-coding genes and 17,871 non-coding genes were annotated.
  • The number of annotated curated transcripts increased by 17% and genes with two or more curated alternative variants increased by 8%.
  • The annotation includes 6,862 features and 2,075 GeneIDs for non-genic functional elements, such as regulatory regions and known structural elements. For example, see the opsin locus control region (OPSIN-LCR).

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NCBI retires Map Viewer web interface


On October 24, 2017, we announced the replacement of NCBI’s Map Viewer with the Genome Data Viewer (GDV) . As described in that announcement, the Map Viewer web interface will be removed in one week on May 2, 2018. Map Viewer links will be redirected to the GDV home page. Map Viewer static data will remain on the NCBI FTP site. Please review details related to the FTP content in our February announcement.

Please contact us with any comments and concerns, or if you need more help with the transition from Map Viewer to GDV.

May 2 webinar: Using NCBI’s MedGen in Clinical Practice


Join us next Wednesday, May 2, 2018, 12:00 PM – 12:30 PM EDT for a webinar on MedGen, NCBI’s portal to clinical genetics. We’ll show you how to find information in MedGen on genetic phenotypes, clinical features of disorders, and more. You’ll also learn how to retrieve actionable information such as practice guidelines for a condition and get a list of available genetic tests in GTR, and how to easily access resources like GeneReviews, OMIM and ClinicalTrials.gov, the Genetic and Rare Diseases Information Center, and Medline Plus.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

NCBI releases enhanced Pathogen Detection (Beta) Isolates Browser


NCBI has introduced a new and improved Pathogen DetectionBeta Isolates Browser. The browser is a key component of NCBI’s Pathogen Detection Project, a collaboration with FDA, CDC, USDA, and others to use whole genome sequencing data to monitor and investigate outbreaks of foodborne disease. Federal, state and other labs sequence pathogens (such as Salmonella and Listeria) isolated from patients, food, and environmental samples and submit the data in real time to NCBI. We then use our analysis pipeline to assemble the sequences and cluster them with all other isolates in the database to identify closely related sequences, thereby making it easier to identify cases that could be involved in an outbreak.

What’s new?

The browser is a completely updated interface that offers many improvements, like:

  • An enhanced search and browse interface
  • A new tree viewer that allows easy navigation of large SNP clusters

The NCBI Pathogen DetectionBeta home page allows direct access to sequence data, submission resources, and documentation.

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Testing Periods for New API Keys


You’ll want to pay attention to this if you regularly use the E-utilities API. As we announced last fall, we are in the process of introducing API keys for the E-utilities. This post will update the schedule of this process and outline our release plan, which will include a series of testing periods.

So what’s happening?

We’re learning a lot from you!

Thanks for all of your feedback! Ongoing conversations with our users are helping us plan this release in a way that will benefit everyone as much as possible. Please continue to reach out to us with ideas and suggestions!

The effective date for release of API keys has been pushed back.

We will not be activating API keys on May 1, 2018 as originally announced. That date is being moved to be no earlier than September 1, 2018.

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April 25 NCBI Minute: Revised Release Plan for the New NCBI API Keys


As previously announced, NCBI is introducing API keys for the E-utilities. This NCBI Minute will review these keys and their benefits for API users, and will update the schedule for when we will activate these keys. We will also describe plans for a test site and a series of testing periods during which these keys will be fully active. These periods are an ideal opportunity for developers to test their products in this new environment.

Please register and join us for this webinar to be presented on Wednesday, April 25, 2018 at noon, Eastern time.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

BLAST is transitioning to accession.version-based databases


As you may have read in previous posts, NCBI is phasing out sequence GIs and transitioning to accession.version identifiers.  To help you prepare for this transition, we created sample BLAST databases that will help you make code changes to your programs and workflows for the switch to accession identifiers.

The sample databases, env_nr_v5 and tsa_nr_v5, are on FTP.

If you have any questions or concerns, please contact our Help Desk.

April 11 webinar: Getting the most out of web BLAST tabular format


Next Wednesday, April 11, 2018, at 12:00PM EDT, we will present a webinar that will help you enhance and expand your tabular saved BLAST results with basic Unix tools and the NCBI EDirect suite of programs. You will see how to add useful information to tabular format results like taxonomy, sequence titles, and links to sequence records and publications.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

The NCBI web BLAST service has many useful download formats, including the traditional pairwise output, tabular formats and highly structured formats. These formats allow you to easily save your BLAST results for later processing, editing and annotating.