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Table of Contents: 2017 NOVEMBER–DECEMBER No. 419

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MEDLINE Data Changes—2018

Tybaert S. MEDLINE Data Changes—2018. NLM Tech Bull. 2017 Nov-Dec;(419):e5a.

2017 November 16 [posted]

This article collects the notable data changes made to MEDLINE during annual National Library of Medicine (NLM) maintenance known as Year-End Processing (YEP) for 2018:

MeSH Vocabulary Updated for 2018

The MeSH Browser currently points to the 2018 MeSH vocabulary with a link to the 2017 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.

You can download 2018 MeSH from links on the MeSH homepage:

  • Under the section "What’s New," click on 2018 MeSH files or
  • Under the section "Obtaining MeSH," click on Download electronic copies of MeSH

The MeSH Tree Structures are available online under the "Changes to 2018 MeSH Hierarchy" section on the download page.

For highlights about 2018 MeSH, see the forthcoming article What's New for 2018 MeSH.

The PubMed MeSH database and translation tables will be updated to reflect 2018 MeSH by the end of November when YEP activities are complete and the newly maintained MEDLINE data are available in PubMed.

Updated MeSH in MEDLINE Citations

MEDLINE records with updated MeSH are anticipated to be in PubMed by the end of November 2017. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.

Changes to MeSH Headings

This year 113 MeSH headings were either changed or deleted and replaced with more up-to-date terminology. During YEP, NLM updates these MeSH headings on MEDLINE citations.

New MeSH Headings and Concepts

471 new MeSH Headings, plus three new Publication Types, were added to MeSH in 2018.

A complete list of the new 2018 MeSH headings is available in PDF format, see New Headings with Scope Notes, Annotations and Tree Locations.

Typically, NLM does not retrospectively re-index MEDLINE citations with new MeSH heading concepts. Therefore, searching PubMed for a new MeSH term tagged with [mh] or [majr] effectively limits retrieval to citations indexed after the term was introduced. PubMed Automatic Term Mapping (ATM) expands an untagged subject search to include both MeSH Terms and All Fields index terms and may retrieve relevant citations indexed before the introduction of a new MeSH term. Searchers may consult the MeSH Browser or the MeSH database to see the previous indexing terms most likely used for a particular concept before the new MeSH Heading was introduced.

Changes of particular interest to searchers:

MeSH Publication Types

Three new Publication Types are available for 2018. Two of the new Publications Types are types of clinical trials.

1. Adaptive Clinical Trial: Clinical study in which a prospectively planned opportunity is included to modify trial designs and hypotheses based on analysis of data from subjects in the study.

2. Equivalence Trial: Trial that aims to show a new treatment is no better and no worse than the standard treatment. This Publication Type is a child to Randomized Controlled Trial in the MeSH tree hierarchy.

New related MeSH headings:

  • Adaptive Clinical Trials as Topic and Equivalence Trials as Topic are available for 2018. These are headings are used for the general design, methodology, and economics of the trials.
  • Proof of Concept: This heading is a child to Research in the MeSH tree hierarchy. It is used for an empirical investigation which pertains to the development of prototypes or models that demonstrate the feasibility of novel concepts, ideas, principles, schema or their practical application.

3. Expression of Concern: This new Publication Type is for a notification about the integrity of a published article that is typically written by an editor and should be labeled prominently in the item title. It is the responsibility of the editor to initiate appropriate investigative procedures, discover the outcome of the investigation, and notify readers of that outcome in a subsequent published item. The outcome may require the publication of a retraction notice.

MeSH Qualifier (Subheading) Changes

In order to improve indexing consistency and efficiency and to make MEDLINE searching easier and more straightforward, the subheading /contraindications was deleted. This change also helps to eliminate confusion between the use of the subheadings /adverse effects and /contraindications.

  • Deleted Subheading: /contraindications

Three new MeSH headings were created to replace /contraindications. These new headings separate the concepts of contraindications for drugs from the contraindications for procedures. Note that Contraindications, Drug and Contraindications, Procedure are children to Contraindications in the MeSH tree hierarchy.

Indexing Policy:

  • Use Contraindications for general or unspecified contraindications. Note that Contraindications can be coordinated with specific physical agent heading(s). Coordinate the physical agent heading(s) with the subheading /adverse effects.
  • Coordinate Contraindications, Drug with specific drug heading(s). Coordinate the specific drug heading(s) with the subheadings /therapeutic use or /adverse effects.
  • Coordinate Contraindications, Procedure with procedure heading(s). Coordinate the procedure heading(s) with the subheadings /adverse effects.

MEDLINE Citation Maintenance:

  • The subheading /contraindications was deleted and an additional action replaced /contraindications with the new MeSH heading Contraindications on MEDLINE citations.

To eliminate the confusion between /adverse effects and the new MeSH Contraindications headings, two Entry Terms were deleted from the subheading /adverse effects:

  • injurious effects
  • undesirable effects

MeSH Tree Changes

See New Headings by major Tree Category for 2018 (PDF format).

Or see Descriptor Tree with Headings (PDF format) for a complete list of the MeSH heading tree hierarchy.

Other changes of particular interest include:

Several special projects undertaken by MeSH Section for the 2018 MeSH vocabulary.

Isotope and Radioisotope Terminology

This project expanded and updated the isotope terminology with the goal of making more of the isotope terminology found in the literature available in the MeSH vocabulary.

The most common isotope was added as an Entry Term to the MeSH heading for the specific element.

  • Example: Helium-4 is a new Entry Term for Helium.

New Supplementary Concept Records (SCRs) were created for specific isotopes that occur frequently in the literature.

The appropriate element and appropriate isotope or radioisotope term were added in the Heading Mapped to field for the new SCRs.

  • Example: Helium and Radioisotopes are the Heading Mapping To terms for Helium-6.

The MeSH tree hierarchy was updated when inconsistencies were found.

Transactinide Series Elements was created as a new MeSH heading.

Smoking Terminology

The MeSH vocabulary for smoking and smoking-related terms was updated and expanded.

Several smoking-related terms were promoted from Entry Terms to new MeSH headings.

New MeSH headings were created as children to Smoking.

Other new smoking-related MeSH headings to note are Smokers, Smoking Devices, and Smoking Prevention.

Existing smoking-related headings were re-treed in the MeSH hierarchy to account for the new terminology.

Sugars Terminology

The terminology and treeing in the MeSH hierarchy of sugars were updated to better reflect their structure and properties.

Sugars was created as a new MeSH heading. Prior to 2016, Sugars was an Entry Term to Carbohydrates.

Dietary Sugars was created as a new MeSH heading. Prior to 2017, Dietary Sugars was an Entry Term to Dietary Sucrose.

Virus Terminology and New SCR Class for Organisms

The MeSH vocabulary for viruses was updated to conform to the International Committee on Taxonomy of Viruses (ICTV) nomenclature.

Entry Terms were added to existing virus terms to cover alternate or older names.

New virus MeSH headings were added under Coronavirus.

Note the introduction of SCRs (Class 4) for organisms. 387 new SCRs were created to expand coverage of viruses in the MeSH vocabulary. All SCR organisms are mapped to a MeSH heading. For example:

That is, all citations for articles indexed with Lagos bat lyssavirus will also be indexed with the MeSH heading, Lyssavirus.

Do Not Confuse:

Other Changes:

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2018 MeSH vocabulary and enhance search retrieval. These follow-on adjustments are largely to add additional MeSH headings or Supplementary Concept Record Names to citations in order to help searchers refine retrieval. In some cases, the changes clarify areas where a single concept existed before, but is now represented by two or more specific concepts.

One MeSH Concept Split into Two

Examples for 2018 MeSH include the following:

  • Egypt, Ancient and Greece, Ancient were created as new MeSH headings. They are treed in the MeSH hierarchy under Ancient Lands. The existing MeSH headings Egypt and Greece were removed from the Ancient Lands tree. Because of these treeing changes, the MEDLINE citations indexed with Egypt or Greece were adjusted accordingly.

These types of changes, along with others documented on the Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information Web page, suggest the importance of routinely using the PubMed Details feature when searching to see how terms are mapped with the new year's vocabulary and then checking the MeSH Browser or the MeSH database for clarification. Additional information is also available in the article, Skill Kit: The Effects of Year End Processing (YEP) on Saved Searches or RSS Feeds.

Entry Combination Revisions

This year during YEP, NLM will again retrospectively replace certain MeSH heading/subheading combinations, known as Entry Combinations, with the new precoordinated MeSH heading. If you get no retrieval for a MeSH heading/subheading combination check the heading in the 2018 MeSH Browser to see if the Entry Combination information indicates a different term.

There are seven new Entry Combinations for 2018.

Previous MeSH Heading/Subheading
(Entry Combination)
Replaced-by Heading for 2018
Blood Transfusion/adverse effects Transfusion Reaction
Factor IXa/deficiency Hemophilia B
Factor VIIa/deficiency Factor VII Deficiency
Metals, Heavy/poisoning Heavy Metal Poisoning
Receptors, Enterotoxin/agonists Guanylyl Cyclase C Agonists
Smoking/prevention & control Smoking Prevention
Synovial Membrane/surgery Synovectomy

Other News:

New Databank Sources

During 2017 NLM began including the databank names for the following three World Health Organization (WHO) Primary Registries when they are provided by the publisher in their XML submissions.

  • JapicCTI: Japan Pharmaceutical Information Center (Japan Registry Member)
  • JMACCT: Center for Clinical Trials, Japan Medical Association (Japan Registry Member)
  • UMIN CTR: University Hospital Medical Information Network Clinical Trial Registry (Japan Registry Member)

The MEDLINE Databank Sources Web page is up to date and includes this new listing.

Data Distribution Notes

Beginning with the 2018 baseline, PubMed export files on the FTP server will be named as follows to better reflect the file contents.

  • Baseline files will begin with pubmed18n0001.xml.gz
  • Daily update files will continue with this naming convention: pubmed18nxxxx.xml.gz
  • Associated .md5 files will follow this convention beginning with pubmed18n0001.xml.gz.md5
  • Stats files will follow this convention beginning with pubmed18n0001_stats.html

Changes to 2018 production year PubMed: pubmed_180101.dtd:

  • Added Organism to the allowed values for SupplMeshName @Type.
  • Deleted DateCreated. The allowed value <PubMedPubDate PubStatus="entrez"> indicates the date that a citation was created.

Additional information and announcements can be found at Download MEDLINE/PubMed Data.

Policy Changes and PubMed Notes

As noted in the Data Distribution Notes above, the "DateCreated" element was deprecated and deleted from the 2018 PubMed XML DTD. In PubMed, this is reflected in two ways:

  • The "DA" field was removed from the MEDLINE format view.
  • [DA] was removed as a search tag.

The date a PubMed citation was created will continue to be displayed in the MEDLINE format view in the "CRDT" field.

It is searchable by using the [CRDT] or [Date – Create] search tags.

By Sara Tybaert
MEDLARS Management Section

NLM Technical Bulletin National Library of Medicine National Institutes of Health