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Archive for the ‘PubMed’ Category

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.

New Online Class in PubMed® for Librarians Series: Using Evidence-Based Search Features!

Registration is available for the new 90-minute instructional webinar PubMed® for Librarians: Using Evidence-Based Search Features, on Wednesday, November 16, from 10:00-11:30 AM PST. It is a synchronous online session that includes hands-on exercises. The session will explore Medical Subject Headings (MeSH) used for indexing study design and how they work in PubMed, introduce three PubMed products that facilitate evidence based searching, and demonstrate how to customize My NCBI Filters to quickly locate specific publication types. It is an expansion of the popular PubMed for Librarians series from the National Network of Libraries of Medicine Training Office (NTO).

PubMed for Librarians is made up of six 90-minute sessions, which are presented via WebEx and recorded for archival access. Each session is meant to be a stand-alone module designed for each user to determine how many and in what sequence they attend. Each session is certified for 1.5 MLA (Medical Library Association) CE (Continuing Education) hours. CE credit is not available for viewing recordings.

MEDLINE Marks Its 45th Year!

October 2016 marks the 45th anniversary of MEDLINE! The NLM Technical Bulletin has published an article with a timeline chart showing notable MEDLINE and current events occurring in 1971, 2006, and the present day. Also included is an infographic presentation of some of the information in the chart. Much has changed since 1971, when MEDLINE included 236 indexed journals and operated on an IBM 360/50 mainframe computer. Today it includes 5,618 indexed journals and PubMed runs on approximately 62 standard Linux servers! In 1971 The French Connection won the Best Picture Academy Award and Joy to the World by Three Dog Night was the #1 song according to Billboard Magazine. In 2016, the final videocassette recorder was manufactured by the Japanese company Funai and in January Adele’s Hello was the #1 song.

Report Citation Errors in PubMed Directly to Publishers

The PubMed Data Management System (PMDM), which allows publishers or their authorized representatives to update or correct nearly all elements of their citations, is now available. PubMed users should report basic citation errors in PubMed data directly to the publisher, including errors in author names, affiliations, or citation bibliographic information (such as date of publication, volume, issue, and page or e-location), typographical errors in titles or abstracts, and errors in grants or databanks. PMDM is a secure Web application for PubMed data providers to access and edit their PubMed citation data. Nearly all citation elements can be updated at any time after initial receipt of their records by PubMed. The vast majority of PubMed citations are supplied electronically by publishers or their representatives, and the PMDM was created to improve the ease and timeliness for publishers to update and correct their own citations. Changes made in the PMDM are reflected in PubMed within 24-48 hours.

With the implementation of PMDM, NLM is no longer routinely updating or correcting publisher-supplied citations. Users who report citation errors in PubMed to NLM will be directed to contact the publisher directly. NLM will continue to receive and investigate error reports about value-added data on the citations, for example, MeSH Headings and Subheadings, Supplementary Concepts, and Publication Types. Use the Contact Us form for these reports.

NLM Announces Important Dates for MEDLINE/PubMed 2017 Year-End Processing Activities

The National Library of Medicine is currently involved in MEDLINE year-end processing (YEP) activities. These include changing the Medical Subject Headings (MeSH) main headings and subheadings as well as Supplementary Concept Records that standardize names and associated numbers for chemicals, protocols, and diseases that are not main headings. The MeSH edits include maintaining existing MEDLINE citations to conform with the 2017 version of MeSH, and other global changes.

Important Dates

  • November 15, 2016: NLM expects to temporarily suspend the addition of fully-indexed MEDLINE citations to PubMed. NLM will continue to add Publisher-supplied and in process citations.
  • Mid-December 2016: PubMed MEDLINE citations, translation tables, and the MeSH database will have been updated to reflect 2017 MeSH.

For details about the impact on searching from November 16 to mid-December, visit Annual MEDLINE/PubMed Year-End Processing (YEP): Impact on Searching During Fall 2016. For background information on the general kinds of changes made annually, visit Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information.

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.