Table of Contents: 2017 NOVEMBER–DECEMBER No. 419
Tybaert S. MEDLINE Data Changes—2018. NLM Tech Bull. 2017 Nov-Dec;(419):e5a.
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:
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:
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.
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.
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.
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.
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:
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.
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.
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:
MEDLINE Citation Maintenance:
To eliminate the confusion between /adverse effects and the new MeSH Contraindications headings, two Entry Terms were deleted from the subheading /adverse effects:
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.
Several special projects undertaken by MeSH Section for the 2018 MeSH vocabulary.
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.
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.
The MeSH tree hierarchy was updated when inconsistencies were found.
Transactinide Series Elements was created as a new MeSH heading.
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.
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.
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.
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.
Examples for 2018 MeSH include the following:
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.
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 |
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.
The MEDLINE Databank Sources Web page is up to date and includes this new listing.
Beginning with the 2018 baseline, PubMed export files on the FTP server will be named as follows to better reflect the file contents.
Changes to 2018 production year PubMed: pubmed_180101.dtd:
Additional information and announcements can be found at Download MEDLINE/PubMed Data.
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 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
MEDLINE Data Changes—2018