RefSeq release 83 now public

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RefSeq release 83 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available as of July 17, 2017, and contains 132,052,465 records, including 88,385,530 proteins, 19,634,664 RNAs, and sequences from 71,356 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings. More information about RefSeq release 83 is available in the release notes.

Future changes

NCBI will phase out support for non-human organisms in the dbSNP and dbVar databases. These databases will stop accepting submissions for non-human SNPs in September 2017. The interactive websites for these databases and related NCBI services, including RefSeq flatfiles, will stop presenting non-human variant data in November 2017.

New video on the NCBI YouTube channel: How You and Your Journal Club Can Contribute Using PubMed Commons

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The newest video on the NCBI YouTube channel discusses how eligible individuals and journal clubs can join PubMed Commons and contribute comments.

PubMed Commons enables members to post comments about publications, which appear directly below abstracts in PubMed.

Subscribe to the NCBI YouTube channel to watch and receive alerts about new videos ranging from quick tips to full presentations.

New releases from NCBI: Multiple Sequence Alignment Viewer 1.6, Tree Viewer 1.6.0, and Genome Workbench 2.12.0

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This week, we’ve updated Multiple Sequence Alignment (MSA) Viewer, Tree Viewer, and Genome Workbench . You can see a full list of new features, improvements and bug fixes in each resource’s release notes:

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New on YouTube: “NCBI Minute: Tailor Your PubMed Search Experience with My NCBI”

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The recording of the June 28th webinar on My NCBI is now on YouTube.  In this NCBI Minute, we show you how to automatically highlight keywords, create custom filters that can be active every time you run a search, and permanently display up to 200 items per results page.

The NCBI Minute is a series of short webinars that give a brief introduction to a specific topic or NCBI tool. Learn about future presentations on the Webinars and Courses page.

NCBI Facilitates Hackathons at the Bio-IT World Conference and Silicon Valley Artificial Intelligence

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NCBI usually participates in hackathons as direct organizers and planners. However, NCBI staff recently functioned as facilitators in two hackathons organized by outside groups: one at the Bio-IT World conference, and one at the Silicon Valley Artificial Intelligence (SVAI) incubator.

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July 19th NCBI Minute: Automate PubMed Searches & Save Citation Collections with My NCBI

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Would you like to have new PubMed citations for your topic of interest conveniently appear in your email inbox or quickly collect those records for further review? Join NCBI on July 19, 2017, when we’ll show you how to have your PubMed searches automatically run and the results emailed to you daily, weekly or monthly. You will also learn how to create PubMed collections that you can share with others or keep privately for yourself. Don’t have a My NCBI account yet? Get started at MyNCBI.

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dbSNP architecture redesign supports future human variation data expansion; changes to be introduced over the next year

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To continue providing efficient and timely processing, annotation, and dissemination of data, dbSNP’s architecture and process flow have been redesigned. The technical redesign prepares the database for increasing data volumes and providing timely, effective and trustworthy reference SNP results as submission rates continue to increase.

Highlights of the new system include:

  • Use of data objects instead of a relational database
  • Improved algorithms for clustering data into unique Reference SNPs
  • Automation of the entire process to provide timely releases
  • Guaranteed data consistency across dbSNP data accessed using web-based products or downloaded content, such as VCF and FTP files

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GenBank release 220.0 is available via FTP

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GenBank release 220.0 (6/18/2017) has 201,663,568 traditional records containing 234,997,362,623 base pairs of sequence data. In addition, there are 487,891,767 WGS records containing 2,164,683,993,369 base pairs of sequence data, 176812130 TSA records containing 158,112,969,073 base pairs of sequence data, and 1,628,475 TLS records containing 824,191,338 base pairs of sequence data.

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July 12th NCBI Minute “Crowdsourcing Post-publication Comments: How You and Your Journal Club Can Contribute Using PubMed Commons”

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Join us for the next NCBI Minute, “Crowdsourcing Post-publication Comments”, where you’ll learn how eligible individuals and journal clubs can join PubMed Commons and contribute comments.

Date and time: Wednesday, July 12, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. Any related materials will be accessible on the Webinars and Courses page; you can also learn about future webinars on this page.

PubMed Commons enables members to post comments about publications, which appear directly below abstracts in PubMed. Researchers and practitioners regularly assess articles in exchanges with colleagues and in journal clubs. PubMed Commons is one place where you can make key points from those discussions public and discoverable.