MEDLINE Data Changes — 2015

[Editor's note: These changes were implemented in PubMed on December 15, 2014.]

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 2015.

MeSH Vocabulary Updated for 2015

The MeSH Browser currently points to the 2015 MeSH vocabulary with a link to the 2014 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 headings and other information. It also includes Subheading records and Supplementary Concept Records (SCRs) for substances and diseases that are not MeSH Headings.

The MeSH Section homepage provides a link under "All About MeSH" to the Introduction of 2015 MeSH and under "Obtaining MeSH" to download electronic versions.

The MeSH Tree Structures are also available online in both PDF and HTML formats with all indented terms showing.

For highlights about 2015 MeSH, see the article, What's New for 2015 MeSH.

The PubMed MeSH database and translation tables will be updated to reflect 2015 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 will be in PubMed in mid-December 2014. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.

New MeSH Headings

310 new MeSH Headings were added to MeSH in 2015.

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 to MeSH Headings

This year 29 MeSH Headings were either changed or deleted and replaced with more up-to-date terminology. During YEP, NLM updates MeSH headings on MEDLINE citations.

Brand New Concepts

Examples of new MeSH headings of special interest to searchers are highlighted below by Category. You can browse all of the new 2015 concepts on the MeSH New Descriptors Web page.

Category A - Anatomy

Commissural Interneurons

Olfactory Cortex

Renshaw Cells

Category B – Organisms

Influenza A Virus, H10N8 Subtype

Middle East Respiratory Syndrome Coronavirus

Category C – Diseases

Adenocarcinoma in Situ

Atypical Hemolytic Uremic Syndrome

Atypical Squamous Cells of the Cervix

Cardiotoxicity

Infant Death

Morphological and Microscopic Findings

Perinatal Death

Pregnancy, Angular

Pregnancy, Cornual

Pregnancy, Interstitial

Pregnancy, Ovarian

Squamous Intraepithelial Lesions of the Cervix

Transfusion Reaction

Vascular Remodeling

Category D – Chemicals and Drugs

Cytochrome P-450 CYP1B1

Cytochrome P-450 CYP2A6

Cytochrome P-450 CYP2B6

Cytochrome P-450 CYP2C8

Cytochrome P-450 CYP2C9

Cytochrome P-450 CYP2C19

Cytochrome P-450 Enzyme Inducers

Cytochrome P-450 CYP1A2 Inducers

Cytochrome P-450 CYP2B6 Inducers

Cytochrome P-450 CYP2C8 Inducers

Cytochrome P-450 CYP2C9 Inducers

Cytochrome P-450 CYP2C19 Inducers

Cytochrome P-450 CYP2D6 Inducers

Cytochrome P-450 CYP2E1 Inducers

Cytochrome P-450 CYP3A Inducers

Cytochrome P-450 Enzyme Inhibitors

Cytochrome P-450 CYP1A2 Inhibitors

Cytochrome P-450 CYP2B6 Inhibitors

Cytochrome P-450 CYP2C8 Inhibitors

Cytochrome P-450 CYP2C19 Inhibitors

Cytochrome P-450 CYP2C9 Inhibitors

Cytochrome P-450 CYP2D6 Inhibitors

Cytochrome P-450 CYP2E1 Inhibitors

Cytochrome P-450 CYP3A Inhibitors

Metabolic Side Effects of Drugs and Substances

Protein Aggregates

Protein Aggregation, Pathological

Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment

Controlled Before-After Studies

Historically Controlled Study

Interrupted Time Series Analysis

Protective Factors

Category F - Psychiatry and Psychology

Spatial Learning

Spatial Navigation

Spatial Processing

Psychology, Developmental

Social Skills

Category G - Phenomena and Processes

Absorption, Physiochemical

Absorption, Physiological

Absorption, Radiation

Activation, Metabolic

Diet, Paleolithic

Diet, Western

Drug Liberation

Forests

Gastrointestinal Absorption

Gastric Absorption

Grassland

Hepatobiliary Elimination

Intestinal Elimination

Intramuscular Absorption

Lacrimal Elimination

Lacteal Elimination

Nasal Absorption

Ocular Absorption

Oral Mucosal Absorption

Peritoneal Absorption

Permafrost

Pulmonary Elimination

Rainforest

Rectal Absorption

Renal Elimination

Renal Reabsorption

Respiratory Tract Absorption

Salivary Elimination

Subcutaneous Absorption

Taiga

Toxicokinetics

Tundra

Vaginal Absorption

Category J – Technology, Industry, Agriculture

Electronic Cigarettes

Category K - Humanities

Religious Missions

Category L - Information Science

Datasets as Topic

Category M - Named Groups

Missionaries

Changes of particular interest include:

• The Publication Type In Vitro was deleted and replaced by the MeSH Heading In Vitro Techniques.
• In 2015 MeSH the MeSH Tree structures were updated for Neuroanatomy Terms. 54 new terms were added with 281 Entry Terms (ET). 451 new Entry Terms were added to existing neuroanatomy terms.
  • As an example: in 2014 Olfactory Cortex was an ET to Olfactory Pathways but in 2015 Olfactory Cortex was created as a separate MeSH term.
• The term Morphological and Microscopic Findings was created for the grouping of specific terms for morphologic findings, particularly the results of PAP smears reported according to the Bethesda System. It is not used for indexing.
• Transfusion Reaction was created as a separate MeSH term in 2015. In 2014 it had been an ET to Blood Group Incompatibility. After Transfusion Reaction was removed as an ET, Blood Group Incompatibility was re-treed.
• Two new infant death terms were added in 2015: Infant Death and Perinatal Death. It is important to note the difference between death and mortality terms. Mortality terms are used for statistical concepts and death terms are used for biological, physiological and psychological concepts. Please read the annotations for the overlap in the definition between these two, and between Fetal Death and Perinatal Death.
• A number of new Absorption terms were added for concepts related to the pharmacokinetic processes of exogenous chemicals.
• For 2015 MeSH the concept of missions was separated from the persons involved in missionary work.  Two new terms were created: Religious Missions and Missionaries. 

Do not confuse:

• Protein Aggregates with Multiprotein Complexes.
• Historically Controlled Study with Historical Article.

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2015 MeSH vocabulary and to enhance search retrieval. These follow-on adjustments are largely the adding of more MeSH Headings or Supplementary Concept Record Names to citations to help searchers refine retrieval. In some cases, the changes clarify areas where a single concept existed before, but it is now represented by two or more specific concepts.

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 2015 MeSH Browser to see if the Entry Combination information indicates a different term.

There are 38 new Entry Combinations for 2015.

 

Previous MeSH Heading/Subheading (Entry Combination)	Replaced-by Heading for 2015
alpha-Glucosidases /antagonists & inhibitors	Glycoside Hydrolase Inhibitors
Aromatic-L-Amino-Acid Decarboxylases /antagonists & inhibitors	Aromatic Amino Acid Decarboxylase Inhibitors
beta-Lactamases /antagonists & inhibitors	beta-Lactamase Inhibitors
Calcineurin /antagonists & inhibitors	Calcineurin Inhibitors
Catechol O-Methyltransferase /antagonists & inhibitors	Catechol O-Methyltransferase Inhibitors
Cephalosporinase /antagonists & inhibitors	beta-Lactamase Inhibitors
Chloride Channels /agonists	Chloride Channel Agonists
Cornea /injuries	Corneal Injuries
Cytochrome P-450 CYP1A2 /antagonists & inhibitors	Cytochrome P-450 CYP1A2 Inhibitors
Cytochrome P-450 CYP2B6 /antagonists & inhibitors	Cytochrome P-450 CYP2B6 Inhibitors
Cytochrome P-450 CYP2C19 /antagonists & inhibitors	Cytochrome P-450 CYP2C19 Inhibitors
Cytochrome P-450 CYP2C8 /antagonists & inhibitors	Cytochrome P-450 CYP2C8 Inhibitors
Cytochrome P-450 CYP2C9 /antagonists & inhibitors	Cytochrome P-450 CYP2C9 Inhibitors
Cytochrome P-450 CYP2D6 /antagonists & inhibitors	Cytochrome P-450 CYP2D6 Inhibitors
Cytochrome P-450 CYP2E1 /antagonists & inhibitors	Cytochrome P-450 CYP2E1 Inhibitors
Cytochrome P-450 CYP3A /antagonists & inhibitors	Cytochrome P-450 CYP3A Inhibitors
Cytochrome P-450 Enzyme System /antagonists & inhibitors	Cytochrome P-450 Enzyme Inhibitors
DNA-Directed DNA Polymerase /antagonists & inhibitors	Nucleic Acid Synthesis Inhibitors
Dopa Decarboxylase /antagonists & inhibitors	Aromatic Amino Acid Decarboxylase Inhibitors
Estradiol /antagonists & inhibitors	Estrogen Antagonists
Estrogens /antagonists & inhibitors	Estrogen Antagonists
Factor Xa /antagonists & inhibitors	Factor Xa Inhibitors
Factor Xa /deficiency	Factor X Deficiency
Hernia, Diaphragmatic /congenital	Hernias, Diaphragmatic, Congenital
Ornithine Decarboxylase /antagonists & inhibitors	Ornithine Decarboxylase Inhibitors
Penicillinase /antagonists & inhibitors	beta-Lactamase Inhibitors
Receptor, Bradykinin B1 /antagonists & inhibitors	Bradykinin B1 Receptor Antagonists
Receptor, Bradykinin B2 /antagonists & inhibitors	Bradykinin B2 Receptor Antagonists
Receptor, Endothelin A /antagonists & inhibitors	Endothelin A Receptor Antagonists
Receptor, Endothelin B /antagonists & inhibitors	Endothelin B Receptor Antagonists
Receptors, Bradykinin /antagonists & inhibitors	Bradykinin Receptor Antagonists
Receptors, CCR5 /antagonists & inhibitors	CCR5 Receptor Antagonists
Receptors, Dopamine D2 /antagonists & inhibitors	Dopamine D2 Receptor Antagonists
Receptors, Endothelin /antagonists & inhibitors	Endothelin Receptor Antagonists
Receptors, Islet Amyloid Polypeptide /agonists	Amylin Receptor Agonists
Receptors, Opioid /antagonists & inhibitors	Narcotic Antagonists
Receptors, Vasopressin /antagonists & inhibitors	Antidiuretic Hormone Receptor Antagonists
Recurrence /prevention & control	Secondary Prevention

Interview [PT]

In a new change in policy, MEDLINE citations that are cited with the Publication Type [PT] Interview will have both the Interviewee and Interviewer cited as authors. The first author will be the Interviewee and the second author will be the Interviewer. In the past we only cited the Interviewee as the author.

Author Affiliation

Effective with the implementation of the new PubMed system in mid-December and going forward, NLM will allow for multiple Author Affiliations for all Authors, Corporate Authors and Investigators, if the data are supplied by the publisher in their XML submissions for MEDLINE indexed journals.

MeSH Unique Identifier

Also effective with the implementation of the new PubMed system in mid-December and going forward NLM will be including the MeSH Unique Identifier for MeSH Headings, Subheadings, Name of Substance, Supplementary MeSH Name and Publication Types. These Unique Identifiers are displayed in the PubMed XML view only.

Structured Abstracts

In November 2014, NLM added 345 new labels to the list of structured abstract labels. This brings the total of vetted and mapped labels to 2,799. The new 2014 file can be found at: http://structuredabstracts.nlm.nih.gov/Downloads/Structured-Abstracts-Labels-111314.txt.

Additional information is available in the article, Structured Abstracts in MEDLINE: Newly Identified and Mapped Labels Available.

New Indexing Policy

Effective for 2015 indexing forward, the more general MeSH heading Mice, Rats, or Cricetinae will no longer be added to a MEDLINE citation when one of their children terms is selected by the indexer. This change now aligns with the basic indexing policy of indexing to the most specific heading (and not also adding the parent term) and using the Tree structures for retrieval. The MeSH heading Animals will still be added, as usual, to support the Animals search limit.

LR (Modification Date) on In Process Citations

Starting around the last week in November 2014, NLM will tag In Process citations with an LR (Modification Date) when those citations have been edited to add Grant information or PMCIDs that have been identified by NCBI automatic machine detection. The purpose of this change for these particular updates to In Process citations is to facilitate the tracking of compliance for NIH Public Access. NLM already assigns an LR for these updates to completed citations (MEDLINE and PubMed-not-MEDLINE subsets) and to the "as supplied by publisher" citations (publisher subset).

PubMed Notes

The Dataset [PT] value will be used for 2015 indexing.

PubMed will display the following new display labels for linking between a Dataset citation and the original research citation.

Dataset described in: - this would appear on the citation for the original paper

Dataset use reported in: - this would appear on the citation for the dataset description

To retrieve the dataset-related citations use the following new search terms:

hasdatasetdescribedin

hasdatasetusereportedin