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Archive for the ‘Search Tools’ Category

NLM Policy Change for Identification of Partial Retractions in MEDLINE/PubMed

The National Library of Medicine began keeping separate statistics on partial retractions in December 2006 and reporting them on the MEDLINE Key Indicators page when a journal identified an article as partially retracted. In 2006, NLM expected that partial retractions would be a new designation that publishers would be using. These were cases when some aspect of the article, such as a table, chart, image, etc., was determined to be incorrect, but the overall methodology or conclusion(s) of the paper were not affected. Since 2006, only 42 articles have been designated as “partially retracted.” In addition, the Committee on Publication Ethics (COPE) Retraction Guidelines state that partial retractions make it difficult for users to know which parts of an article are or are not reliable or the correct status of the article.

Beginning in October 2016, NLM will discontinue the identification of partial retractions in MEDLINE/PubMed. Previously, the Retracted Publication designation was added as a Publication Type to the citation for the article, which also triggered the Retracted Article banner on the Abstract display in PubMed, and Retraction of Publication was used as the Publication Type for the notice citation. NLM also linked the citations using a “Partial retraction in” label on the article citation and a “Partial retraction of” label on the notice citation. Instead, this type of notice will be treated as a published erratum. NLM will no longer use the retraction-related Publication Types on these citations, and the Retracted Article banner will no longer appear on the Abstract display; the notice citation will have Published Erratum as the Publication Type. The citations will continue to be linked, but will use an “Erratum in” label on the article citation and an “Erratum for” label on the notice citation, as is the case for other errata/correction notices. NLM has edited the existing 42 pairs of citations to reflect the new policy and the “Errata” Fact Sheet has been edited to reflect the new policy.

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!

Health Hotlines Database To Be Retired January 2017

Health Hotlines was developed by NLM as a community service to help the public locate health-related information from organizations with toll free numbers. NLM has decided it will no longer update the Health Hotlines database because most of the information is now readily available through web search engines and many of the organizations no longer have toll-free numbers. Health Hotlines will remain online until the end of January, 2017, at which time it will be retired.

Complementary Therapies and Traditional Healing Resources from NLM

Medical treatments not considered part of mainstream medicine are often called complementary, integrative, or alternative medicine. Examples include herbal supplements, acupuncture, meditation, and other forms of treatment. NLM’s Arctic Health portal defines traditional healing as treatment that focuses on the health and wellness of the individual in the context of culture and community, and it incorporates Native beliefs, practices, and traditional ecological knowledge. Traditional healing may be practiced by Native American communities across the U.S., including Alaska and the Arctic region. Resources for both complementary medicine and traditional healing are available through the National Library of Medicine for many different populations, including:

  • For the General Public – MedlinePlus provides an overview of various complementary and alternative therapy health topics, as well as reliable information on the health benefits and possible side effects for a long list of herbs and supplements.
  • For Older Adults – NIH Senior Health discusses a variety of topics on complementary health approaches, including information on natural products, mind and body practices, the safety of these complementary health approaches, and how to be an informed consumer with complementary health treatments.
  • For Native American Communities – The American Indian Health portal includes a list of traditional healing resources, with resources for community members, researchers, health professionals, educators, and the general public. The Traditional Healing section of the Arctic Health portal lists organizations and programs, stories, research and learning tools, and teaching tools for traditional healing practices of Native American communities in the Arctic region.

Retention of Ceased Abstracting and Indexing Publications Containing MEDLINE Citations

Does your collection include abstracting and indexing titles produced in cooperation with NLM, such as Hospital Literature Index and/or its successor Hospital and Health Administration Index, Index to Dental Literature, or International Nursing Index, all of which had ceased publication by the year 2000? In general, the NLM-derived citations in these publications are available in MEDLINE/PubMed. However, all of these publications also contained separate sections for monographic materials, which may not be available in the NLM collection. Therefore, NLM advises librarians that if access to the monographic materials in these tools are important at your institution, then retain these old print indexes in your collection. More details about each publication are available in this FAQ.

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.