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Archive for the ‘Search Tools’ Category

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.

NLM’s ChemIDplus Now Includes New Internet Locator Link for EPA Chemical Safety for Sustainability CompTox

A new internet locator link, CompTox, has been added to the National Library of Medicine’s ChemIDplus resource. The link connects ChemIDplus users to over 155,000 chemicals in the U.S. Environmental Protection Agency’s Chemical Safety for Sustainability CompTox. The interactive CompTox dashboard is part of a suite of databases and web applications developed by the EPA interactive Chemical Safety for Sustainability (iCSS) Research Program. These databases, dashboards, and apps support EPA’s computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. Information for over 720,000 chemicals is accessible in CompTox. Other locators recently added to ChemIDplus include DrugBank and European Medicines Agency (EMA).

ChemIDplus is a dictionary of over 400,000 chemicals (names, synonyms, and structures). ChemIDplus includes links to NLM and other databases and resources, including links to federal, state and international agencies. ChemIDplus Lite is designed for simple searching on name or registry. ChemIDplus Advanced helps users draw their own structures and perform similarity and substructure searches.

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.

September 7 NCBI Webinar: E-Utilities in an Age without GI Numbers

On Wednesday, September 7, the National Center for Biotechnology Information (NCBI) will host a 30-minute webinar briefly describing future plans for the E-utilities API in a time where GI (GenInfo Identifier) numbers are no longer used as the primary identifiers for sequence records. You will learn how to convert GI numbers to accession.version identifiers and how to quickly determine the most recent version of an accession. You’ll also learn about a new E-utility parameter, to be released this fall, that allows these tools to work only with accession.version identifiers.

Date and time: Wednesday, September 7, 9:00 AM PDT

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.

Beta Version of the MeSH Browser Available for Testing!

A new beta version of the Medical Subjects Heading (MeSH) Browser is available for user testing for approximately two months. It accesses the same data as the current production MeSH Browser, so that users can compare the search and retrieval functionality between the two systems. The new version is being developed to take advantage of new technology and improve functionality. NLM welcomes feedback on the beta version of the MeSH Browser during the test period. Comments and questions may be sent to NLM Customer Service with “MeSH Browser beta version” in the Subject field.

Health Information Outreach Funding Opportunities from NLM and NIH

Do you know where to find grant and funding opportunities from the National Library of Medicine (NLM) and National Institutes of Health (NIH) related to health information outreach? The Outreach and Special Populations Branch (OSPB) of the National Library of Medicine provides a webpage with links for locating Information Outreach Funding Opportunities from NLM, NIH, and the National Network of Libraries of Medicine (NN/LM). Some examples of funding search resources include:

  • NLM Grants and Funding – Browse grants and funding opportunities under a number of categories, such as “Research Grants,” “Awards Supporting Career Development and Training,” “Support for Outreach Initiatives to Improve Access and Eliminate Health Disparities,” and “Trans NIH Programs and Initiatives Supported by NLM.”
  • NN/LM Funding Opportunities – Browse by region for funding opportunities from the National Network of Libraries of Medicine.
  • NIH Funding Sources – Search or browse funding opportunities (published daily) from NIH, learn how to apply for grants, and explore previous NIH-funded research through NIH RePORT.

NLM Resources on Precision Medicine

The new Director of the National Library of Medicine, Patricia Flatley Brennan, RN, PhD, puts a strong focus on precision medicine in the vision she describes for NLM: “I believe the National Library of Medicine has an important role to play in the Precision Medicine Initiative…and I believe that role’s going to be showing up in a number of the existing services already seen in the Library…” The National Institutes of Health defines precision medicine as “an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.” To learn more about precision medicine and how NIH is already playing an important role in the Precision Medicine Initiative, visit the following NLM resources:

August Midday at the Oasis Recording Now Available!

On August 17, NN/LM PSR presented Mapping Your Community’s Health for the Midday at the Oasis monthly webinar. Colette Hochstein, D.M.D., MLS and Jennifer Rewolinski, B.S. Community Health, National Library of Medicine, Division of Specialized Information Service, were the presenters. Colette talked about the Community Health Maps blog for information on low cost mapping tools for community-based organizations. Jennifer covered a case study on mapping curb ramp accessibility for an assisted living facility as an example of community maps. 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.

PMC Updates: New Search Result Filters and Updated Reference List Display

As of August 2016, PMC is now home to four million articles! A few updates have been implemented to make this full-text content easier to navigate:

Search Result Filters
On all search results pages, you will now see filters (similar to PubMed’s filters) on the left-hand side that allow you to filter your results by article attributes, publication date, research funder, and search fields. These filters replace the Limits page and allow you to more readily:

You can now also quickly add articles that are under a 12-month or less embargo in PMC to your search results by selecting the “Include embargoed articles” filter option under Text Availability. More information about these filters is available in the PMC User Guide and a sample screen shot is available from the NLM Technical Bulletin.

Reference List Display
Using related article data available in PMC, articles that cite papers that have been either retracted or named in a Findings of Research Misconduct issued by the HHS Office of Research Integrity and not yet retracted will now include a red hyperlink to the relevant notice directly from the article’s reference list. This update will help users more easily identify post-publication updates to existing research.

PMC Retraction Flag Screenshot

Institute of Education Sciences (IES) Biographical Sketch Format Now Available for SciENcv Profiles

SciENcv users can now create biosketches in the Institute of Education Sciences (IES) biographical sketch format which can be used to apply for IES funding. In addition, users can also export their citations from the IES Education Resources Information Center (ERIC) database to My Bibliography. This newly added biosketch format is available to download in PDF, MS Word or XML, and users are able to share their SciENcv IES biosketches through a public URL.

The IES biographical sketch consists of five sections:

Creating SciENcv Profiles Using the IES Biographical Sketch Format
There are three ways to create a SciENcv profile in the IES biographical sketch format: entering information manually, copying information from an existing SciENcv biosketch, or using an external data source to populate a biosketch. Further details are available in the NLM Technical Bulletin.