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Archive for the ‘NCBI’ Category

New Full Text Access Feature in PubMed: Institutional Repository LinkOut!

PubMed users can now see the icon that links to the full text deposited at an institutional repository (IR) using LinkOut. The LinkOut service provides links to full text, library holdings, and other relevant external resources from PubMed and other NCBI databases. Until this year, there were three quick ways to access full text articles from PubMed:

  • the publisher icon links to the journal web site (may require a subscription to the journal)
  • the PMC icon links to free full text in PubMed Central (PMC)
  • the DOI (Digital Object Identifier) links to the article on the journal web site (may require a subscription to the journal)

The new institutional repository icons will link to free full text of the article at an institutional repository that it is not freely available from the journal or PMC. When an IR is participating in this new LinkOut feature, the linking icon will display in the “Full text links” section next to the abstract in PubMed for any publication with a direct link to a full text that does not have another free full text link. The “LinkOut – more resources” section expands to show the same direct links to full text as the icons. All links to participating IRs will appear whether or not there is a free full text icon displayed in the “Full text links” section. There are only a few IRs participating in the free full text LinkOut at this time but these few already expand access to about 25,000 publications. Some academic and research institutions encourage or require authors to submit their publications in the IR, making them publicly accessible within the terms of publication at a journal. This is often called “green open access.” There might be an embargo period or delay after publication, as there can be with NIH-authored manuscripts in PMC. However, free full texts can be available as soon as an article is published.

LinkOut resources come from organizations that have applied to join LinkOut, providing information or data that are relevant to that specific publication. LinkOut participants include libraries, biological data repositories, and repositories like Dryad and Figshare. If you know of an IR that has publicly available free full texts beyond those available in PMC, please let them know about this service. A list of participating institutional repositories is available from the LinkOut Web site. Instructions for institutional repositories to join LinkOut are also available. For questions about participating in LinkOut, contact NLM. Additional details and sample screen displays are available in the NLM Technical Bulletin.

NN/LM Webinar on March 9: Five Questions You Can Answer Using the NCBI Gene Database

Registration is available for the one-hour NN/LM webinar Five Questions You Can Answer Using the NCBI Gene Database, on Thursday, March 9, 10:00-11:00 AM PST. Presenters will be Peter Cooper and Bonnie Maidak from NCBI. The Gene resource at the National Center for Biotechnology Information (NCBI) is a central hub for accessing nearly all molecular and literature resources for a particular gene. You can easily answer the most common questions and perform the most common tasks by starting in Gene. This webinar will cover the structure and contents of the Gene resource and how to use it to answer the following questions:

  • Where is the gene located (chromosome and position) in the genome assembly?
  • What are the Reference genomic, transcript and protein sequences for the gene?
  • What variations are present in the gene and are they associated with disease?
  • In what tissues and under what conditions is the gene expressed?
  • What are the equivalent genes (homologs) in other species?

NIH Request for Information (RFI) on Processes for database of Genotypes and Phenotypes Data Submission, Access, and Management

The National Institutes of Health has just issued a Request for Information (RFI) seeking public comment on the data submission and access processes for the NIH National Center for Biotechnology (NCBI) database of Genotypes and Phenotypes (dbGaP). The RFI also seeks comment on the management of data in dbGaP in order to consider options to improve and streamline these processes and to maximize the use and utility of dbGaP. The complete RFI, as well as instructions on how to comment, are available on the NIH website. Electronic responses will be accepted through April 7, 2017. NIH will consider all public comments before taking next steps. No proprietary, classified, confidential, or sensitive information should be included in responses. Comments received, including any personal information, will be posted without change after the close of the comment period to the NIH Genomic Data Sharing website.

Additional information about the importance of this RFI is included in a new Under the Poliscope blog posting, published by Dr. Carrie D. Wolinetz. For more information or additional questions, please contact the NIH Office of Science Policy.

NCBI Webinar: PubMed for Clinicians in November

On November 9, NLM staff will show health care professionals how to search PubMed for the most relevant and recent literature, explore specific clinical research areas, set up email alerts and more.

Date and time: Wednesday, November 9, 2016, 10:00-11:00am PST

Visit the PubMed for Clinicians registration page to register. 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 homepage.

October Midday at the Oasis Recording Now Available!

On October 19, NN/LM PSR presented NLM Drug Information Services for the Midday at the Oasis monthly webinar. Patrick McLaughlin, from MEDLARS Management, covered a wealth of NLM websites. He covered MedlinePlus, PubMed Health, DailyMed, Dietary Supplement Label Database, Pillbox, RxImage, TOXNET’s HSDB and LactMed, and PubChem. For terminologies, he showed RxNorm, RxNav, RxClass, and UMLS. Last but not least, the Drug Information Portal was highlighted! You can view the webinar by visiting our Midday at the Oasis Archives page or by clicking on the YouTube video player below.

screen capture of Youtube controls with full screen icon encircled
Note: To switch to full screen, click on the full screen icon in the bottom corner of the video player. To exit the full screen, press Esc on your keyboard or click on the Full screen icon again. If you have problems viewing full screen videos, make sure you have the most up-to-date version of Adobe Flash Player.

New Webinar Series: Insider’s Guide to Accessing NLM Data

On Wednesday, October 19, 11:00am – 12:00pm PDT, NLM will host the first session of a new Insider’s Guide to Accessing NLM Data series of webinars, beginning with Welcome to E-utilities for PubMed. The webinar series will promote more powerful and flexible ways of accessing NLM data, starting with an introduction to the Application Programming Interfaces (APIs) for PubMed and other NCBI databases. The series is geared toward librarians and other information specialists who have experience using PubMed via the traditional Web interface, but now want to dig deeper. This class will start with the very basics of APIs, and then move on to showing how to get started using the E-utilities API to search and retrieve records from PubMed. The class will also showcase some specific tools and utilities that information specialists can use to work with E-utilities, helping to prepare for subsequent Insider’s Guide classes. The session will conclude by looking at some practical examples of E-utilities in the real world, and hopefully inspire you to get out and put these lessons to use!

University of Michigan Offers Live Streaming of NCBI Discovery Workshops October 4-6

Remote site registration is available for a series of three three-hour NCBI Discovery Workshops hosted by the Taubman Health Sciences Library at the University of Michigan on October 4-6, with instructors Peter Cooper, Ph.D., and Wayne Matten, Ph.D. The sessions will be streamed using BlueJeans. The workshops are:

  • Tuesday, 10/4, – Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST
  • Wednesday, 10/5, – A Practical Guide to NCBI BLAST
  • Thursday, 10/6, – EDirect: Command Line Access to NCBI’s Biomolecular Databases

NCBI Web Site Permanent Redirect to HTTPS Begins November 9

green padlock

To improve security and privacy, and to comply with a Federal government mandate, NCBI is moving all of its Web sites and services, including Web APIs, to HTTPS only by September 30, 2016, which was subsequently extended to November 9. At that point, HTTP traffic for GET and HEAD requests will be redirected. All other requests will be rejected. This change will provide users with greatly increased privacy and security on the NCBI site. To prepare for this change, NCBI ran a series of tests, which are now completed.

NCBI to Retire Leiden Open Variation Database (LOVD) on September 30

NCBI is retiring the Leiden Open Variation Database (LOVD) on September 30, 2016. LOVD has been used to capture information about novel human variants. Past submitters of human genetic variations to LOVD are encouraged to transfer their information to the ClinVar database. To add new human variation data, please review the instructions on submitting to ClinVar. The submission wizard may ease the process. While the LOVD site will be retired on September 30, an FTP archive will continue to store LOVD data for download after this date.

Find, Browse and Follow Biomedical Literature with NCBI’s New PubMed Journals Resource

Following the latest biomedical literature can be a challenge, but NCBI’s new PubMed Journals resource will help you keep up-to-date.

Use PubMed Journals to:

  • Easily find and follow journals of interest.
  • Browse new articles in your favorite journal(s).
  • Keep up-to-date with a Journal News Feed containing new arrivals, news links, trending articles, and important article updates (retractions and more!).

To follow a journal, you’ll need to be logged in to your NCBI account. PubMed Journals is an experiment of PubMed Labs, NCBI’s  product incubator for delivering new features and capabilities to NCBI end users.