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Table of Contents: 2016 NOVEMBER–DECEMBER No. 413

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MEDLINE Data Changes — 2017

Tybaert S. MEDLINE Data Changes — 2017. NLM Tech Bull. 2016 Nov-Dec;(413):e4a.

2016 December 01 [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 2017:

MeSH Vocabulary 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.

You can download 2017 MeSH from links on the MeSH homepage:

  • Under the section "What’s New," click on 2017 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 2017 MeSH Hierarchy section on the download page.

For highlights about 2017 MeSH, see What's New for 2017 MeSH.

The PubMed MeSH database and translation tables will be updated to reflect 2017 MeSH in mid-December 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 in mid-December 2016. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.

Changes to MeSH Headings

This year 77 MeSH headings were either changed or deleted and replaced with more up-to-date terminology. During YEP, NLM updates MeSH headings on MEDLINE citations.

New MeSH Headings and Concepts

629 new MeSH headings, including two new Publication Types, were added to MeSH in 2017.

All of the new 2017 concepts are available in PDF format, 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:

Brain Injuries, Traumatic: Promoted to a MeSH heading. Previously an Entry Term to Brain Injuries. Note that Mild Traumatic Brain Injury was added as an Entry Term to Brain Concussion. Both MeSH headings are children to Brain Injuries.

SCR Protein Terms: A number of protein terms were promoted to MeSH terms in 2017. An example is the 2016 SCR record for lumican. For 2017 lumican was promoted to a MeSH heading. At the same time, three new SCR records were created for the specific species and all three new SCRs were mapped to the new MeSH heading Lumican:

Molecular Sequence Data: The indexing policy has changed. Between 1988-2016 this term was indexed for articles that contained:

  • Accession numbers for sequences deposited in a molecular sequence databank, such as Genbank
  • Articles with base sequences of 50 or more bases
  • Articles with Amino acid sequences of 15 or more amino acids
  • Carbohydrate sequences of 3 or more carbohydrate units

Starting with 2017 MeSH indexing, Molecular Sequence Data will only be indexed for general articles about sequence data.

Postoperative Complications: The indexing policy has changed. This term will be added unstarred to prospective citations that are indexed with any Surgical Procedures, Operative/adverse effects heading as an aid to searchers. The policy change was not applied retrospectively to existing indexed citations.

Disease headings: The indexing policy was clarified to coordinate with either Humans or Animals, as appropriate to the article. If not specified in the article, then indexers will add Humans, based on a review of existing citations that guided this recommendation.

Animal Diseases: A MeSH Scope Note was added: Diseases that occur in VERTEBRATE animals. By indexing policy, this heading:

  • is used for:
    • general articles on veterinary diseases
    • diseases in specific animals when there is no precoordinated term, such as:
      Animal Diseases
  • is not applied when:
    • disease term/veterinary is assigned.
    • the article is about experimental studies of disease in animals

Multimodal Imaging: Note the new specific terms for 2017:

Adult Stem Cells: This term has a new MeSH Scope Note. Some Entry Terms were removed. Selected related headings are:

Peripheral Blood Stem Cells: The MeSH Scope Note: Hematopoietic stem cells found in peripheral blood circulation. Note that Peripheral Stem Cells is an Entry Term to Peripheral Blood Stem Cells.

Immunogenicity, Vaccine and Vaccine Potency: The emphasis of Vaccine Potency is on the dose. Sometimes both headings may be used to cover the general and specific concepts.

Immunotherapy: Indexing policy on when to use /drug therapy or /therapy on the disease term:

  • if a named drug, then use /drug therapy
  • if the immunologic factor is not named, then use /therapy
  • for therapeutic use of vaccines, use /therapy
  • for genetic therapy, use /therapy plus /genetics on the protein expressed to treat the disease

Persons and Professions: Forty-one new headings were added to the M Tree.

Network Meta-Analysis: Indexing policy is to coordinate with Meta-Analysis [Publication Type] if pertinent.

Protein Domains: Many new headings were added to the G2 Tree.

MeSH Publication Types

Two new Publication Types, Calendars and Study Guide, are available for catalogers but will not be used by MEDLINE indexers.

MeSH Qualifier (Subheading) Changes

In order to improve indexing consistency and efficiency and to make MEDLINE searching easier and more straightforward, a new subheading, diagnostic imaging, was added.

Three existing subheadings were deleted and replaced by the new subheading, /diagnostic imaging.

  • Deleted subheadings: /radiography, /radionuclide imaging, and /ultrasonography.

Additional reasons for these changes are:

  • /diagnostic imaging is a broader subheading that covers many other existing diagnostic imaging techniques other than just radiography, radionuclide imaging, and ultrasonography
  • /diagnostic imaging can be used in coordination with specific multimodal imaging techniques MeSH headings (such as Positron Emission Tomography Computed Tomography) that are becoming increasingly important. This will add specificity to indexing and searching.

Indexing policy for the new subheading /diagnostic imaging is:

  • Use for the Disease and/or Organ MeSH headings.
  • Coordinate with the specific diagnostic technique.
  • Do not coordinate with the MeSH heading Diagnostic Imaging; this heading is reserved for general articles only.


1. Multimodal imaging in detection of pancreatic cancer.

2016 Indexing 2017 Indexing
PANCREATIC NEOPLASMS / *diagnosis PANCREATIC NEOPLASMS / *diagnostic imaging

2. Automatic 3D motion estimation of left ventricle from C-arm rotational angiocardiography using a prior motion model and learning based boundary detector.

2016 Indexing 2017 Indexing
HEART VENTRICLES / *radiography HEART VENTRICLES / *diagnostic imaging

3. PET imaging of prostate cancer.

2016 Indexing 2017 Indexing
PROSTATIC NEOPLASMS / *radionuclide imaging PROSTATIC NEOPLASMS / *diagnostic imaging

4. Color Doppler sonography for evaluation of portal venous system in hepatocellular carcinoma.

2016 Indexing 2017 Indexing
CARCINOMA, HEPATOCELLULAR / *ultrasonography CARCINOMA, HEPATOCELLULAR / *diagnostic imaging
LIVER NEOPLASMS / *ultrasonography LIVER NEOPLASMS / *diagnostic imaging
PORTAL VEIN / *ultrasonography PORTAL VEIN / *diagnostic imaging

5. Quality of reporting noninferiority/similarity in research studies of diagnostic imaging.

Indexing: No Change

MeSH Tree Changes

See MeSH Tree Changes for 2017 for a complete list of the MeSH heading tree hierarchy changes in PDF format.

Changes of particular interest include:

Non-Medical Public and Private Facilities [J03]: This new tree was introduced for 2017 MeSH and gathers about 40 MeSH headings in one spot. Most of these headings remain in their original tree locations as well. Note that there are no children for Private Facilities or Public Facilities. Indexing policy is to coordinate with these headings only when the specific type of facility is discussed. Indexers will not try to determine if a facility is private or public.


1. Board diving regulations in public swimming pools and risk of injury.
DIVING / *injuries
2. Prevention of respiratory tract infections: Situation in 12 private day care centers in the city of Buenos Aires.
RESPIRATORY TRACT INFECTIONS / *prevention & control

Phenomena and Processes [G]: This tree was reorganized.

For 2016 MeSH:

  • Process terms were treed under the corresponding Phenomena terms.
  • Specifics were treed either directly under the Phenomena term or under the Process term.

For 2017 MeSH:

  • Process terms became Entry Terms to the corresponding Phenomena terms.
  • Terms that were treed under the Process terms are now treed directly under the Phenomena terms.
  • Note: Metabolism has been retained as the preferred term for Metabolic Phenomena.

Subheading Tree Modifications for 2017

The /diagnosis tree was modified (see Figure 1).

  • Removed the deleted subheadings: /radiography, /radionuclide imaging, and /ultrasonography.
  • Added the new subheading /diagnostic imaging.
  • Removed /pathology from under diagnosis.
screenshot of diagnosis subheading tree from 2016 to 2017 Figure 1: The subheading tree modifications for /diagnosis.
  • /pathology is now only treed under /anatomy & histology as a sibling to /cytology (see Figure 2).
  • Note: Previously, /pathology was often indexed with a Disease MeSH headings (rather than /diagnosis) when microscopy techniques were used as diagnostic tools. For 2017 forward, /pathology is reserved for indexing the histological description of the organ/tissue in disease.
screenshot of anatomy and histology subheading tree from 2016 to 2017 Figure 2: The subheading tree modification for /pathology in the anatomy & histology tree.

Do not confuse:

  • Chocolate and Cacao. Chocolate was promoted to a MeSH Heading. Previously it was an Entry Term to Cacao.

Other Changes:

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2017 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 2017 MeSH include the following:

  • Gizzard was replaced by Gizzard, Avian while a new term Gizzard, Non-avian was introduced. Because the ambiguous old term Gizzard was split into two concepts, the citations were adjusted accordingly.
  • Obsessive Hoarding was replaced by Hoarding. The concept of Obsessive Hoarding was transferred as an Entry Term to the existing MeSH heading Hoarding Disorder. The citations about obsessive hoarding were adjusted to add Hoarding Disorder rather than Hoarding.

Multiple MeSH Concepts Combined into One

Examples for 2017 MeSH include the following:

When one of these deleted subheadings was replaced with /diagnostic imaging, a MeSH heading for the specific diagnostic technique was added to the citations, if the specific technique or one of its children was not already on the citation:

  • Added Radiography when /radiography was replaced by /diagnostic imaging.
  • Added Radionuclide Imaging for previous /radionuclide imaging was replaced by /diagnostic imaging.
  • Added Ultrasonography for previous /ultrasonography was replaced by /diagnostic imaging.

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 2017 MeSH Browser to see if the Entry Combination information indicates a different term.

There are 12 new Entry Combinations for 2017.

Previous MeSH Heading/Subheading
(Entry Combination)
Replaced-by Heading for 2017
Anterior Cruciate Ligament/injuriesAnterior Cruciate Ligament Injuries
Cardiovascular Diseases/rehabilitationCardiac Rehabilitation
Growth Plate/injuriesSalter-Harris Fractures
In Vivo Dosimetry/instrumentationRadiation Dosimeters
Menisci, Tibial/injuriesTibial Meniscus Injuries
Myocardium/diagnostic imagingHeart/diagnostic imaging
Peripheral Blood Stem Cells/transplantationPeripheral Blood Stem Cell Transplantation
Rotator Cuff/injuriesRotator Cuff Injuries
School Teachers/educationTeacher Training
Shoulder/injuriesShoulder Injuries
Stroke/rehabilitationStroke Rehabilitation

Other News:

New MeSH Browser

The new MeSH Browser was launched on November 16, 2016. For more information see New MeSH Browser Available.

PMDM/IMS and Exports

In October 2016, NLM transitioned from one Data Creation and Maintenance System (DCMS) to two separate systems, the PubMed Data Management System (PMDM) and the Indexing Management System (IMS). This change will separate citation creation and bibliographic data maintenance (PMDM) from assigning MeSH indexing vocabulary (IMS). The new systems facilitate improvements to citation and indexing workflows. To read more about the new model for managing journal citation data in PubMed see MEDLINE/PubMed Production Improvements Underway.

Data Distribution Notes

In October 2016, NLM launched newly redesigned Data Distribution Program Web pages. For an explanation for the changes to the Web pages see Changes to the NLM Data Distribution Program. In conjunction with these changes NLM discontinued the license requirement for obtaining MEDLINE/PubMed citations and switched to a "Terms and Conditions" agreement.

The FTP data file exports are now in a new location as explained on the revised Web pages.

NLM is implementing a new consolidated DTD (Document Type Definition) for users of the FTP server and the E-utilities API. More information will be available in a forthcoming article.

Journal Title Update

The algorithm that creates the journal title name in the NLM Catalog was revised to omit the statement of responsibility (data in the 245 $c) from the journal title name. Data in the MARC 245 $a, $b, $n and $p is still included in the journal title name.

For example (see Figure 3):

screenshot of Journal Title Update Figure 3: Updated journal title name in the NLM Catalog.

This change impacted approximately 540,000 citations in approximately 9,000 PubMed titles.

Policy Changes and PubMed Notes

1. Partial Retractions Policy Change
In September 2016, NLM announced a policy change for citing Partial Retractions. For more information see Partial Retractions: NLM Policy Change.

2. New Expression of Concern Policy
For 2017 NLM will implement a new pair of linking elements to tag notices that express concern about an article. These elements are under the CommentsCorrections suite:
The corresponding tags using 3 letters for the MEDLINE display are:
ECF - appears on the citation for the Expression of Concern
ECI - appears on the citation for the original article

3. Conflict of Interest (COI) Statement
NLM is adding a conflict of interest statement as provided by the publisher. Sometime in 2017, journal citations will contain conflict of interest statements for the article as submitted by the publisher.

The corresponding tag for the MEDLINE display is COI.

4. Authors Who Contribute Equally
In 2017 NLM will implement a method for publishers to indicate when authors "contributed equally" to a journal article. We do not have a target date yet for when publishers will be able to begin submitting these data.

The corresponding tag using 2 letters in the MEDLINE display will be CE.
The contributed equally designation will also appear in the Summary (text) display and the Abstract display.

MEDLINE Celebrates Its 45th Anniversary!

Please see MEDLINE Celebrates Its 45th Anniversary for fun highlights of the changes in the world since MEDLINE launched in 1971.

By Sara Tybaert
MEDLARS Management Section

NLM Technical Bulletin National Library of Medicine National Institutes of Health