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Archive for the ‘PubMed’ Category

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.

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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.

Search PubMed with 2017 MeSH!

As of December 12, PubMed/MEDLINE citations, the NLM Catalog, and the MeSH translation tables were updated to reflect 2017 MeSH, with full searching functionality for Supplementary Concept Record (SCR) data and mapping in place on December 14. The citations newly indexed with 2017 MeSH since November 15 were available in PubMed for searching on December 15. Now that end-of-year processing activities are complete, MEDLINE/PubMed may be searched using 2017 MeSH vocabulary. For details about data changes, visit MEDLINE Data Changes — 2017. NLM has resumed daily MEDLINE updates for PubMed.

2017 MEDLINE Data Changes

MeSH vocabulary has been updated for 2017. The MeSH Browser currently points to the 2017 MeSH vocabulary with a link to the 2016 MeSH Vocabulary. Searchers should consult the Browser to find MeSH headings of interest and their relationships to other headings. The Browser contains MeSH heading records that may include Scope Notes, Annotations, Entry Terms, History Notes, Allowable Qualifiers (Subheadings), Previous Indexing, and other information. It also includes Subheading records and Supplementary Concept Records (SCRs) for substances and diseases that are not MeSH headings. MEDLINE records with updated MeSH are anticipated to be in PubMed in mid-December 2016. This year 77 MeSH headings were either changed or deleted and replaced with more up-to-date terminology, and 629 new MeSH headings, including two new Publication Types, were added to MeSH in 2017. In order to improve indexing consistency and efficiency and to make MEDLINE searching easier and more straightforward, a new subheading, “diagnostic imaging,” was added. It replaces three existing subheadings; “radiography,” “radionuclide imaging,” and “ultrasonography.” For an overview of the many other 2017 MEDLINE data changes, visit the NLM Technical Bulletin.

Register Now for 2017 Sessions of the “PubMed for Librarians” Webinar Series!

Registration is now open for the next round of the highly popular PubMed For Librarians webinar series, offered by the NN/LM Training Office. The class is divided into six segments (90 minutes each). Each segment is a synchronous online session that includes hands-on exercises and is worth 1.5 hours of MLA CE credit. Participants can choose any or all of the six segments that are of interest. The segments are as follows:

  • Introduction to PubMed: Learn about the difference between PubMed and MEDLINE, how to run a PubMed search, assess your search retrieval, analyze search details, employ three ways to search for a known citation, and how to customize with My NCBI.
  • MeSH (Medical Subject Headings): Learn about the NLM Medical Subject Headings (MeSH) database. Explore the four different types of MeSH terms and how searchers can benefit from using MeSH to build a search. Investigate the structure of the MeSH database and look at the components of a MeSH record.
  • Automatic Term Mapping (ATM): Learn about Automatic Term Mapping (ATM) – the process that maps keywords from your PubMed search to the controlled vocabulary of the MeSH database. Learn why searching with keywords in PubMed can be an effective approach to searching. Look at the explosion feature, what is and is not included in search details, and explore how PubMed processes phrases.
  • Building and Refining Your Search: Use some of the tools and features built into PubMed that are designed to help you search more effectively. Explore the filters sidebar and Topic-Specific Queries. Use History, tools in the NLM Catalog, and the Advanced Search Builder to build searches and explore topics.
  • Using Evidence-Based Search Features: Explore terminology used for indexing study design in PubMed, explore three PubMed products that facilitate evidence based searching, and learn how to customize My NCBI Filters to quickly locate specific publication types.
  • Customization – My NCBI: Learn about the advantages of creating a My NCBI account, managing and manipulating your My NCBI page content, locating and identifying available filters on PubMed’s filter sidebar, selecting and setting up to fifteen filters, and creating a custom filter.

New Three-Part NLM Webinar Series Begins November 30, “Insider’s Guide to Accessing NLM Data: EDirect for PubMed”

On November 30, December 7, and December 14, 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, participants 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 will be limited to 50 students per offering. Participants are expected to attend all sessions in a single series:

  • Part 1: Getting PubMed Data: Wednesday, November 30, 10:00 – 11:30 AM PST
  • Part 2: Extracting Data from XML: Wednesday, December 7, 10:00 – 11:30 AM PST
  • Part 3: Building Practical Solutions: Wednesday, December 14, 10:00 – 11:30 AM PST

The entire series will be offered again in January/February 2017. All classes involve hands-on demonstrations and exercises. Before registering for these classes, NLM strongly recommends completion of the following activities:

  • 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. For more information, visit the Installing EDirect page.
  • Install the EDirect software. For more information, visit the EDirect installation page.

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.