MEDLINE Data Changes—2019

This article collects the notable data changes made to MEDLINE during the National Library of Medicine (NLM) annual maintenance known as Year-End Processing (YEP) for 2019:

• MeSH Vocabulary Updated for 2019
• Updated MeSH in MEDLINE Citations
• Changes to MeSH Headings
• New MeSH Headings and Concepts
• MeSH Publication Types
• MeSH Qualifier (Subheading) Changes
• MeSH Tree Changes
• Two MeSH Concepts Merged into One
• Special MeSH Projects
• Do Not Confuse
• Entry Combination Revisions
• Data Distribution Notes
• New Databank Source

MeSH Vocabulary Updated for 2019

The MeSH Browser currently points to the 2019 MeSH vocabulary with a link to the 2018 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 2019 MeSH from links on the NLM Data Distribution page for MeSH Data.

For highlights about 2019 MeSH, see What's New for 2019 MeSH.

The PubMed MeSH database and translation tables will be updated to reflect 2019 MeSH by the middle of 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 by mid-December 2018. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.

Changes to MeSH Headings

For 2019, 73 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

402 new MeSH Headings, plus 20 new Publication Types, were added to MeSH in 2019.

A complete list of the new 2019 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.

Exception for 2019: The new publication type Systematic Review (see below) will be added to appropriate existing MEDLINE citations. NLM made the decision to do this re-indexing based on the importance of providing a mechanism to retrieve all MEDLINE citations to articles that are systematic reviews.

Changes of particular interest to searchers:

MeSH Publication Types

Twenty new publication types are available for 2019.

Four new publication types will be used for MEDLINE indexing.

• Clinical Trial, Veterinary
• Clinical Trial Protocol
• Observational Study, Veterinary
• Systematic Review
  Note: The entry term Systematic Review was deleted from Review when this new publication type was created.

Indexing Policy: In 2016, NIH narrowed the definition of a Clinical Trial to specify that it be used for humans only going forward. For that reason, NLM added additional MeSH clinical trial terminology to address animal trials. Note that the publication type Clinical Trial Protocol, however, can be used for both human and animal clinical trials that are being planned. Indexers will coordinate this term with either Humans or Animals.

Sixteen new publication types will be used by NLM Cataloging only:

• Catalog, Commercial
• Catalog, Drug
• Catalog, Union
• Dictionary, Chemical
• Dictionary, Classical
• Dictionary, Dental
• Dictionary, Medical
• Dictionary, Pharmaceutic
• Dispensatory
• Formularies, Dental
• Formularies, Hospital
• Formulary, Homeopathic
• Manuscript, Medical
• Pharmacopoeia, Homeopathic
• Preprint
• Web Archive

Seven publication type strings were changed for publication types that are used for MEDLINE Indexing:

• Addresses to Address
• Congresses to Congress
• Government Publications to Government Document
• Lectures to Lecture
• Legal Cases to Legal Case
• Personal Narratives to Personal Narrative
• Portraits to Portrait

Fifty-four publication type strings were changed for publication types that are used for Cataloging only.

Three MeSH headings were changed to publication types for 2019. These publication types are used by Cataloging only. New "as Topic" MeSH headings were not created.

• Catalogs, Booksellers’ to Catalog, Bookseller
• Catalogs, Publishers’ to Catalog, Publisher
• Dictionaries, Polyglot as Topic to Dictionary, Polyglot

Three new "as Topic" MeSH headings will be used for MEDLINE indexing. Their corresponding publication types will used for MEDLINE indexing as well:

• Clinical Trial Protocols as Topic
• Clinical Trials, Veterinary as Topic
• Systematic Reviews as Topic
  Note: Systematic review protocols are indexed as Systematic Reviews as Topic.

Lastly, five new "as Topic" MeSH headings will be used for MEDLINE indexing. Their corresponding publication types will not be used for MEDLINE indexing:

• Collections as Topic
• Diary as Topic
• Forms as Topic
• Preprints as Topic
• Web Archives as Topic

MeSH Qualifier (Subheading) Changes

For 2019 MeSH, NLM has continued its project of reviewing subheadings in order to improve indexing consistency and efficiency and to make MEDLINE searching easier and more straightforward.

1. One subheading was deleted and replaced by a new MeSH heading.

• Deleted subheading: /manpower
  
  The new MeSH heading Workforce was created to replace /manpower. Note that the existing MeSH heading Health Manpower was changed to Health Workforce, which is a child to Workforce.
  
  MEDLINE Citation Maintenance: The subheading /manpower was deleted and an additional action replaced /manpower with the new MeSH heading Workforce on MEDLINE citations. Note that NLM only replaced /manpower on those citations that were not indexed already with Health Workforce.
  
  

2. In addition, two subheadings were deleted and replaced with existing subheadings. [This section was updated on December 18, 2018.]

• Replaced subheading: /secretion was replaced by /metabolism
  
  The new MeSH heading Insulin Secretion was created. Note that Milk Secretion was added as an entry term (ET) to the MeSH heading Lactation.
  
  MEDLINE Citation Maintenance: The subheading /secretion was changed to /metabolism on MEDLINE citations.
  
  [Editor's note added on December 18, 2018: This item was added to reflect additional MEDLINE citation maintenance.]
  Insulin Secretion was added to MEDLINE citations that were indexed with Insulin/secretion previously. Lactation was added to MEDLINE citations that were indexed with Milk/secretion or Milk, Human/secretion previously.
  
  

• Replaced subheading: /utilization was replaced by /statistics & numerical data
  
  Three new MeSH headings were created related to this change: Equipment and Supplies Utilization, Facilities and Services Utilization, and Procedures and Techniques Utilization.
  
  MEDLINE Citation Maintenance: The subheading /utilization was changed to /statistics & numerical data on MEDLINE citations.

MeSH Tree Changes

See New Headings by major Tree Category for 2019 (PDF format).

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

Other changes of particular interest include:

Two MeSH concepts merged into one:

• Rhamnus merged into Frangula. The preferred string for Frangula then changed to Rhamnus.
• Salicaceae merged into Flacourtiaceae. The preferred string for Flacourtiaceae then changed to Salicaceae.

Special MeSH Projects

Several special projects were undertaken by MeSH staff that resulted in the following new 2019 MeSH headings:

Neoplasm Terms:

• Adenocarcinoma of Lung
• Carcinoma, Ovarian Epithelial
• Chondrosarcoma, Clear Cell
• Esophageal Squamous Cell Carcinoma
• Myopericytoma
• Nasopharyngeal Carcinoma
• Pancreatic Intraductal Neoplasms
• Squamous Cell Carcinoma of Head and Neck
• Thyroid Cancer, Papillary

Data Terms:

• Big Data
• Data Aggregation
• Data Science
• Data Systems
• Data Visualization
• Deep Learning

Drug Combination Terms:

• Artemether, Lumefantrine Drug Combination
• Cilastatin, Imipenem Drug Combination
• Lidocaine, Prilocaine Drug Combination
• Piperacillin, Tazobactam Drug Combination
• Tobramycin, Dexamethasone Drug Combination

Dietary Protein Terms:

• Fish Proteins, Dietary
• Fruit Proteins
• Grain Proteins
• Meat Proteins
• Nut Proteins
• Pea Proteins
• Poultry Proteins
• Shellfish Proteins

Behavior Terms:

• Burnout, Psychological
• Cyberbullying
• Disenfranchised Grief
• Disgust
• Egocentrism
• Embarrassment
• Respect
• Road Rage
• Sadness

Person Term:

• Ex-Smokers

Do Not Confuse:

• Clinical Protocols with Clinical Trial Protocols as Topic or with the publication type Clinical Trial Protocol.
• Drug Development with Drug Discovery, which is the process of finding chemicals for potential therapeutic use.
• Granulins with the viral protein Granulin Matrix Proteins, which is an entry term on Occlusion Body Matrix Proteins.
• Wool Fiber with Wool, which is the hair of sheep or other animals.

Other Changes:

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2019 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.

• The SCR ROB was deleted from MeSH in 2019 because it had multiple meanings.

Entry Combination Revisions

This year during YEP, NLM will again retrospectively replace certain MeSH heading/subheading combinations, known as Entry Combinations, with the new pre-coordinated MeSH heading. If you get no retrieval for a MeSH heading/subheading combination check the heading in the 2019 MeSH Browser to see if the Entry Combination information indicates a different term.

There are seven new Entry Combinations for 2019.

Previous MeSH Heading/Subheading (Entry Combination)	Replaced-by Heading for 2019
Allogeneic Cells/transplantation	Transplantation, Homologous
Enzymes/therapeutic use	Enzyme Therapy
Epidermis/cytology	Epidermal Cells
Heavy Ions/therapeutic use	Heavy Ion Radiotherapy
Intestines/metabolism	Intestinal Mucosa/metabolism
Intestines/secretion	Intestinal Mucosa/metabolism
Jaw/surgery	Orthognathic Surgical Procedures
Nose/metabolism	Nasal Mucosa/metabolism
Nose/secretion	Nasal Mucosa/metabolism
Pharmacy/history	History of Pharmacy
Piperazines/analogs & derivatives	Piperazine
Protons/therapeutic use	Proton Therapy
Sodium-Glucose Transporter 2/antagonists & inhibitors	Sodium-Glucose Transporter 2 Inhibitors
Stomach/metabolism	Gastric Mucosa/metabolism
Stomach/secretion	Gastric Mucosa/metabolism

Other News:

Data Distribution Notes

DTD Changes: On September 13, 2018, NLM announced the release of the 2019 PubMed DTD.

There are several changes from the current 2018 PubMed DTD:

• The 2019 DTD includes the addition of <ReferenceList>, <Reference>, and <Citation> elements. The cites data, currently found in <CommentsCorrections RefType="Cites">, will be moved to the new <ReferenceList> elements when the 2019 Baseline is released.
• The <CitationString> element will be removed from the <BookDocument> element.
  • Four new valid values have been added to the RefType attribute of the <CommentsCorrections> element:
  • CorrectedandRepublishedIn
  • CorrectedandRepublishedFrom
  • RetractedandRepublishedIn
  • RetractedandRepublishedFrom
• A new valid value "plain-language-summary" has been added to the Type attribute of the <OtherAbstract> element to identify Plain Language Summaries.

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

• Other changes maintained during Year-End Processing. Roughly 2 million citations will export because they will have gotten the Indexing Method attribute "Curated" or "Automated". These include citation which had been indexed for OLDMEDLINE and a smaller number of other citations.

New Databank Source

During 2018 NLM added to the list of Databank Sources that may be carried in MEDLINE citations. The Peruvian Clinical Trial Registry (REPEC), which is one of the WHO Clinical Trial Primary Registries, was added.