MEDLINE Data Changes — 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 2014.

For information about how this maintenance affects the NLM schedule for adding indexed MEDLINE citations to PubMed, see the article, MEDLINE/PubMed Year-End Processing Activities. Two additional resources, Annual MEDLINE/PubMed Year-End Processing (YEP): Impact on Searching During Fall 2013 and Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information, include examples of typical changes that take place in MEDLINE citations during YEP.

MeSH Vocabulary Updated for 2014

The MeSH Browser currently points to the 2014 MeSH vocabulary with a link to the 2013 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 2014 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 2014 MeSH, see the forthcoming article, What's New for 2014 MeSH.

The PubMed MeSH database and translation tables will be updated to reflect 2014 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 2013. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.

[Editor's note: added June 9, 2014: MEDLINE citation maintenance XML files are no longer available for download.]
The MeSH Section homepage provides links to descriptions of MeSH maintenance. The About Updates link under the "MEDLINE Citation Maintenance" section explains how NLM prepares the changes in a machine-readable form for others to use. To access the XML files for the tasks processed for this maintenance, click on the "Download XML Files" link under this same section; the 2014 changes should be available sometime in January 2014. This information is helpful for those individuals or organizations using MeSH headings in their own application (such as indexing curricula guides) and want to update those applications with the new version of MeSH.

New MeSH Headings

304 new MeSH Headings were added to MeSH in 2014.

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 48 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 2014 concepts on the MeSH New Descriptors Web page.

Category A - Anatomy

Allografts

Autografts

Back Muscles

Bone-Patellar Tendon-Bone Grafts

Composite Tissue Allografts

Dander

Heterografts

Intermediate Back Muscles

Isografts

Paraspinal Muscles

Superficial Back Muscles

Category B - Organisms

Cephalochordata

Influenza A Virus, H7N9 Subtype

Lancelets

Category C – Diseases

Ankle Fractures

Carcinogenesis

Chemically-Induced Disorders

Chemotherapy-Induced Febrile Neutropenia

Dandruff

Drug-Related Side Effects and Adverse Reactions

Febrile Neutropenia

Fetal Alcohol Spectrum Disorders

Myalgia

Pediatric Obesity

Prostatic Neoplasms, Castration-Resistant

Scorpion Stings

Teratogenesis

Tick Bites

Triple Negative Breast Neoplasms

Category D - Chemicals and Drugs

Ammonium Compounds

Biodegradable Plastics

Biological Products

Filamins

Gasotransmitters

Hand Sanitizers

Medical Marijuana

Minichromosome Maintenance Proteins

Minichromosome Maintenance Complex Component 2

Minichromosome Maintenance Complex Component 3

Minichromosome Maintenance Complex Component 4

Minichromosome Maintenance Complex Component 5

Minichromosome Maintenance Complex Component 6

Minichromosome Maintenance Complex Component 7

Minichromosome Maintenance Complex Component 8

Minichromosome Maintenance Complex Component 9

Multifunctional Enzymes

Non-Nutritive Sweeteners

Nutritive Sweeteners

Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment

Alveolar Bone Grafting

Cell- and Tissue-Based Therapy

Hand Transplantation

Multimodal Imaging

Papanicolaou Test

Polypharmacology

Therapy, Soft Tissue

Vascularized Composite Allotransplantation

Category F - Psychiatry and Psychology

Hope

Type B Personality

Type D Personality

Category G - Phenomena and Processes

Cool-Down Exercise (ET: Warm-Down Exercise)

Immunity, Heterologous

Microbiota

Organogenesis, Plant

Physical Conditioning, Human

Portion Size

Secondary Metabolism

Serving Size

Warm-Up Exercise

Category H - Disciplines and Occupations

Veterinary Sports Medicine

Category I - Anthropology, Education, Sociology and Social Phenomena

Drug Trafficking

Human Trafficking (ET: Sex Trafficking)

Identity Theft

Medical Identity Theft

Organ Trafficking

Prenatal Education

Slavery

Sports for Persons with Disabilities

Category K - Humanities

Influenza Pandemic, 1918-1919

Category L - Information Science

Biological Ontologies

Gene Ontology (ET: Gene Ontology Project)

Mobile Applications

Web Browser

Category M - Named Groups

Disaster Victims

Family Nurse Practitioners

Healthy Volunteers

Nurses, Community Health

Nurses, International

Nurses, Public Health

Pediatric Nurse Practitioners

Prisoners of War

Slaves

Category N - Health Care

Critical Care Nursing

Home Health Nursing

Hospice and Palliative Care Nursing

Parish Nursing

Preexisting Condition Coverage

Nocebo Effect

Patient Harm

Rural Nursing

Safety-net Providers

Senior Centers

Category V – Publication Characteristics

Dataset

Observational Study

Pragmatic Clinical Trial

Category Z – Geographicals

Asia, Northern

Mesopotamia

Changes of particular interest include:

• In 2013 Ammonium Compounds and Ammonium were Entry Terms to Quaternary Ammonium Compounds; however, in 2014 Ammonium Compounds became a MeSH Heading and Ammonium is an Entry Term to this new heading.
• Biological Agents was replaced by Biological Products and Biological Agents is now an Entry Term for the MeSH Heading Biological Factors.
• A number of trees in Category D were refined.
• In 2013 the MeSH Heading Education had an Entry Term of Parenting Education. In 2014 this Entry Term was moved to a different MeSH Heading, "Education, Nonprofessional."
• Fetal Alcohol Syndrome was a MeSH Heading in 2013, but in 2014 it became an Entry Term to the new MeSH Heading, Fetal Alcohol Spectrum Disorder.
• Heterograft was an Entry Term to Transplantation, Heterologous [E04.936.764] but is now promoted to a MeSH Heading in Category A under Transplants [A01.941].
• Microbiota was an Entry Term to Metagenome treed under Genome in Category G. In 2014 it became a MeSH Heading and is treed both under Category G and Category N.
• The Entry Term Papanicolaou Test for Vaginal Smears in 2013 MeSH has been promoted to a MeSH Heading in 2014.
• Slaves was an Entry Term in 2013 for the MeSH Heading, Social Problems, in Category I. In 2014 Slavery became a new MeSH Heading and was moved to Category M.
• Tissue Therapy, Historical replaces Tissue Therapy. The replaced term is more specific; follow-on tasks will insure that Tissue Therapy, Historical is used only for articles related to the procedures by Filatov or Niehans. Users should use Cell- and Tissue-Based Therapy to retrieve articles for contemporary cell or tissue therapy.
• Transplant and Transplantation terms were reviewed and changes were made to treeing and subheadings, plus a few new terms were added. For example Transplants was moved from Category E7 to Category A.
• The Entry Term Tumorigenesis for Cell Transformation, Neoplastic has been moved and is now an Entry Term under Carcinogenesis.

Do not confuse:

• Home Health Nursing with Home Nursing.
• Immunity, Heterologous with Cross Protection or Cross Reactions.
• Multifunctional Enzymes with Multienzyme Complexes.
• Polypharmacology with Polypharmacy; Pharmacology; or Polychemotherapy.
• Secondary Metabolism with Secondary Metabolites.
• Teratogenesis with Teratoma.
• Therapy, Soft Tissue with Cell- and Tissue-Based Therapy.
• Warm-Down Exercise (an Entry Term for Cool-Down Exercise) with Warm-Up Exercise, a new 2014 MeSH Heading.

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2014 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.

New Publication Types (PT) for 2014

Three new publication types have been introduced for 2014 MeSH. They are:

• Dataset
  This publication type is defined as "An organized collection of values stored permanently in a formalized manner suitable for communication, interpretation, or processing." This publication type will not be used in combination with any other publication type as it is not to be used for journal articles that contain or produce datasets as part of the publication (including Supplemental Materials). Rather, it will be used on citations to items that are stand-alone descriptions of the metadata of a particular dataset.
• Observational Study
  The scope note defines this publication type as "A clinical study in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study)." This publication type should not be confused with the MeSH Heading "Observation" which is used for a scientific method. There is a related new MeSH Heading "Observational Studies as Topic," which is used for general design, methodology, economies, etc. of observational studies.
• Pragmatic Clinical Trial
  This publication type refers to "Randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts." There is a related new MeSH Heading, "Pragmatic Clinical Trial as Topic," which is used for general design, methodology, economics, etc. of pragmatic clinical trials.

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 2014 MeSH Browser to see if the Entry Combination information indicates a different term.

There are 21 new Entry Combinations for 2014.

Previous MeSH Heading/Subheading (Entry Combination)	Replaced-by Heading for 2014
3-Hydroxybutyric Acid/analogs & derivatives	Hydroxybutyrates
Alcoholism/congenital	Fetal Alcohol Spectrum Disorders
Aminocaproic Acid/analogs & derivatives	Aminocaproates
Dihydrouracil Dehydrogenase (NADP)/deficiency	Dihydropyrimidine Dehydrogenase Deficiency
DNA Gyrase/antagonists & inhibitors	Topoisomerase II Inhibitors
Drug Therapy/adverse effects	Drug-Related Side Effects and Adverse Reactions
Glutamates/antagonists & inhibitors	Excitatory Amino Acid Antagonists
Glutamic Acid/agonists	Excitatory Amino Acid Agonists
Glutamic Acid/antagonists & inhibitors	Excitatory Amino Acid Antagonists
H(+)-K(+)-Exchanging ATPase/antagonists & inhibitors	Proton Pump Inhibitors
Hand/transplantation	Hand Transplantation
Hyoscyamine/analogs & derivatives	Atropine Derivatives
Pharmaceutical Preparations/adverse effects	Drug-Related Side Effects and Adverse Reactions
Pharmaceutical Preparations/toxicity	Drug-Related Side Effects and Adverse Reactions
Phospholipases A2/antagonists & inhibitors	Phospholipase A2 Inhibitors
Prolyl Hydroxylases/antagonists & inhibitors	Prolyl-Hydroxylase Inhibitors
Proton Pumps/antagonists & inhibitors	Proton Pump Inhibitors
Receptors, Neurokinin-1/antagonists & inhibitors	Neurokinin-1 Receptor Antagonists
Sodium-Potassium-Chloride Symporters/antagonists & inhibitors	Sodium Potassium Chloride Symporter Inhibitors
Solute Carrier Family 12, Member 3/antagonists & inhibitors	Sodium Chloride Symporter Inhibitors
Sports for Persons with Disabilities/injuries	Athletic Injuries

Author Affiliation

Effective with the implementation of the new PubMed system in mid-December and going forward, NLM will include 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. To prepare for and support this change, NLM ceased quality control review and editing of the author affiliation field in the MEDLINE citations as of September 30, 2013.

[Editor's note: For additional information on author affiliation see Author, Corporate Author, and Collaborator Affiliation Display Changes.]

Databanks

Starting soon NLM will be including additional Databank names in MEDLINE citations. Currently NLM includes data from the 13 registries in the Secondary Source (SI) field. The additional data being carried include 13 new WHO Primary Clinical Trial Registries; UniProt databanks; and several NCBI databanks.

Structured Abstracts

In November 2013, NLM added 505 new labels to the list of structured abstract labels. This brings the total of vetted and mapped labels to 2,454.