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MEDLINE Data Changes — 2015
Tybaert S. MEDLINE Data Changes — 2015. NLM Tech Bull. 2014 Nov-Dec;(401):e5.
December 01, 2014 [posted]
December 16, 2014
[Editor's note added]
[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