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Archive for the ‘PubMed’ 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.

NLM Resources for National Native American HIV/AIDS Awareness Day: March 20, 2017

Today is National Native American HIV/AIDS Awareness Day. Health outreach professionals can access HIV/AIDS resources for Native American communities through multiple National Library of Medicine websites, including the following:

  • American Indian Health – Check the “Health Topics – HIV/AIDS” section of American Indian Health for links to HIV/AIDS resources for Native American individuals and communities, for researchers/health professionals/educators, programs and organizations working to treat and prevent HIV/AIDS among Native Americans, and health information about HIV/AIDS for everyone.
  • AIDSource – Look under the Specific Populations:Native Americans section of AIDSource for HIV/AIDS treatment, prevention, education, and research resources related to HIV/AIDS in Native American communities.
  • PubMed – For the latest biomedical research related to HIV/AIDS among Native American populations, visit PubMed.

Upcoming Enhancements for PubMed!

On March 8 NLM implemented four new enhancements to PubMed:

  1. Conflict of Interest Statements (COIS): PubMed includes conflict of interest statements below the abstract when these statements are supplied by the publisher.
  2. Editorial Expressions of Concern: NLM has added editorial expressions of concern as a new pair of linking elements in the Comments/Corrections suite in PubMed. Expressions of concern, previously handled as comments, are labeled explicitly in the abstract display.
  3. Results Display: The “Per page” menu, which allows users to customize the number of items that appear on the results screen, appears at the top of the results list.
  4. Status Tag: The status tag [PubMed – indexed for MEDLINE] has been replaced with the tag [Indexed for MEDLINE]. The Abstract display in PubMed includes a status tag only if the citation is indexed for MEDLINE. Additional status tags still appear in the MEDLINE and XML displays. The citation status search strategies continue to function as they always have.

For additional details and illustrations of these updates, visit the NLM Technical Bulletin.

NN/LM Webinar on March 15: “What’s New in Post-Publication Activities in PubMed”

Join the one-hour NN/LM Webinar, What’s New in Post-Publication Activities in PubMed, on March 15, 1:00-2:00 PM PDT. Hilda Bastian from the National Center for Biotechnology Information (NCBI) will present a discussion of the changing visibility and accessibility of post-publication activity in PubMed. The webinar is part of the PNR Rendezvous monthly webinar series from the NN/LM Pacific Northwest Region.

PubMed Subject Filter Strategies Updated for 2017

PubMed subject filter strategies are reviewed each year to determine if modifications are necessary. Modifications may include revisions due to changes in Medical Subject Heading (MeSH) vocabulary or MEDLINE journals, adding or deleting terms, and changing parts of a strategy to optimize retrieval. The following subset strategies were recently revised:

  • AIDS
  • Bioethics
  • Cancer
  • Complementary Medicine
  • Dietary Supplements
  • Systematic Reviews
  • Toxicology

New Look for NLM Search Engine Results Display!

The National Library of Medicine has just released a new design for its main Web site search engine results page. The new design is responsive and is a result of usability testing, analytics, and user feedback. Searches for health topics will feature a MedlinePlus result on the right side of the screen. Search results from PubMed and the LocatorPlus catalog record will display separately, also on the right. Searches for an NLM product or service will highlight a curated result in the “NLM Recommended Resources” box. The facets have been combined into four basic categories and now can be found above the results display. They include:

  • Health Information: MedlinePlus encyclopedia pages, drug monographs, health topic pages, supplement pages, and MedlinePlus Magazine pages.
  • Programs and Services: NLM main Web site pages including NCBI and SIS.
  • Exhibits and Collections: History of Medicine Division exhibition sites and the Digital Collections records.
  • Web Archives: Older Web pages from the NLM main Web site.
Snapshot of NLM website search engine page

Further details about the redesigned web site are available in the NLM Technical Bulletin.

Recording for “NN/LM Resource Picks: PubMed Update” Webinar Now Available!

The archived recording of the January 25 session for the NN/LM collaborative webinar series, NN/LM Resource Picks, is available. The topic was PubMed Update with Katherine Majewski, from the National Library of Medicine’s MEDLARS Management Section, Bibliographic Services Division. View the webinar 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.

Coming Soon: Updated Algorithm for PubMed Best Match Sort Order

An enhanced relevance algorithm for the “Best Match” sort order is coming to PubMed. The new algorithm incorporates machine learning to re-rank the top articles returned for improved relevance. The standard PubMed Best Match sort is based on a weighted term frequency algorithm. This approach calculates the frequency with which terms appear in PubMed records. Those frequencies are then applied in a weighted fashion to return a ranked list of PubMed citations that match your query terms. The new relevance algorithm includes machine learning to re-rank the top articles returned. This algorithm combines over 150 signals that are helpful for finding best matching results. Most of these signals are computed from the number of matches between the search terms and the PubMed record, while others are either specific to a record (e.g., publication type; publication year) or specific to a search (e.g., search length). The new ranking model was built on relevance data obtained from anonymous PubMed search logs that were aggregated over an extended period of time.

Because the “Best Match” results are calculated using a new machine learning environment, there might be a slight change in total search results when sorting by “Best Match.” Users who sort by “Best Match” are typically clicking through citations on the first page of retrieval; therefore, it is important for NLM to continue to incorporate new tools to improve this ranking. The new machine learning system achieves significant improvement in retrieval performance over the weighted term frequency algorithm alone. Additionally, the “Search details” portlet will be replaced with “Best match search information” that will display translations to MeSH, etc., and additional synonyms under the “See more…” link. The Search button will not be available for the new portlet used for “Best Match” results. To use “Best Match” as the default sort order for PubMed results, change your preferences in My NCBI. For additional details and illustrations, visit the NLM Technical Bulletin.

Registration Available for the February/March 2017 NLM Webinar Series: “Insider’s Guide to Accessing NLM Data: EDirect for PubMed”

Beginning February 21, 2017, the National Library of Medicine will present the three-part Webinar series, Insider’s Guide to Accessing NLM Data: EDirect for PubMed. This series of workshops will introduce new users to the basics of using EDirect to access exactly the PubMed data you need, in the format you need. Over the course of three 90-minute sessions, students will learn how to use EDirect commands in a Unix environment to access PubMed, design custom output formats, create basic data pipelines to get data quickly and efficiently, and develop simple strategies for solving real-world PubMed data-gathering challenges. No prior Unix knowledge is required; novice users are welcome!

Registration is currently open for the February/March 2017 series:

  • Part 1: Getting PubMed Data, Tuesday, February 21, 10:00 – 11:30 AM PST
  • Part 2: Extracting Data from XML, Tuesday, February 28, 10:00 – 11:30 AM PST
  • Part 3: Building Practical Solutions, Tuesday, March 7, 10:00 – 11:30 AM PST

Students are expected to attend Part 1, Part 2, and Part 3 in a single series. Due to the nature of this class, registration will be limited to 50 students per offering.

This series of classes involves hands-on demonstrations and exercises. Before registering for these classes, NLM strongly recommends the following:

  • Watch the first Insider’s Guide class “Welcome to E-utilities for PubMed” or be familiar with the basic concepts of APIs and E-utilities.
  • Be familiar with structured XML data (basic syntax, elements, attributes, etc.)
  • Have access to a Unix command-line environment on your computer (see the Installing EDirect page for more information.)
  • Install the EDirect software (see the Installing EDirect page for more information.)

NNLM Training Office Upcoming Classes: PubMed for Librarians Series, 2017 MeSH Highlights, Classroom Assessment on the Fly, and Discovering TOXNET

There are several class offerings coming up from the NNLM Training Office (NTO). Class details and registration links are available in the NLM Technical Bulletin, or you can visit Training Opportunities to see a schedule of classes that are open to all regions.

PubMed® for Librarians Series: Six Classes

Sessions on January 19 and 25; February 1, 8, 16, and 23, 10:00-11:30 AM PST. Learn about concepts such as using MeSH to build a search, PubMed’s Automatic Term Mapping (ATM) feature, building and refining PubMed searches, using PubMed features that facilitate evidence-based searching, and customizing PubMed searches with the NCBI feature.

Teaching Topics: Classroom Assessment on the Fly

Sessions on either January 11 or February 15, 10:00-11:00 AM PST offer a brief review of the types of assessment available and different methods to use for instantaneous feedback, from low tech polling to one-minute papers.

NLM Webinar: 2017 MeSH Highlights, January 27, 9:00-10:00 AM PST

This session provides a 30-minute highlights tour of the 2017 MeSH, followed by a Q&A with MeSH experts.

Discovering TOXNET

Running from March 1 through 31, this class offers the opportunity to discover TOXNET and other NLM environmental health databases with a guided, self-paced, online format involving thirteen independent modules.