MEDLINE Data Changes — 2016

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 2016:

• MeSH Vocabulary Updated for 2016
• Updated MeSH in MEDLINE Citations
• New MeSH Headings
• Changes to MeSH Headings
• Brand New Concepts
• Changes of particular interest
• MeSH Publication Types
• MeSH Qualifier (Subheading) Deletion
• MeSH Tree Changes
• MeSH Annotation Projects
• Other Changes: One Concept Split into Two
• Entry Combination Revisions
• Structured Abstracts
• OLDMEDLINE MeSH Mapping
• MEDLINE Journal Title Updates
• MEDLINE Country of Publication
• PubMed Notes

MeSH Vocabulary Updated for 2016

The MeSH Browser currently points to the 2016 MeSH vocabulary with a link to the 2015 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 MeSH from the MeSH homepage:

• Under the section "All About MeSH," click on Introduction to 2016 MeSH
• Under the section "Obtaining MeSH," click on Download electronic copies

The MeSH Tree Structures are available online in PDF format with all indented terms showing.

For highlights about 2016 MeSH, see the article, What's New for 2016 MeSH.

The PubMed MeSH database and translation tables will be updated to reflect 2016 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 2015. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.

New MeSH Headings

434 new MeSH Headings were added to MeSH in 2016. Four new Publication Types were added.

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 66 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 that may be of special interest to searchers are highlighted below by Category. All of the new 2016 concepts are available as a PDF, New MeSH Headings for 2016. Note that headings listed below may be treed in more than one category.

Category A – Anatomy

Human Embryonic Stem Cells

Mouse Embryonic Stem Cells

Category B – Organisms

Calceolariaceae

Clostridiales

Firmicutes

Lamiales

Plantaginaceae

Category C – Diseases

War-Related Injuries

Category D – Chemicals and Drugs

Olive Oil

Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment

Clinical Studies as Topic

Data Accuracy

Health Smart Cards

Isolated Heart Preparation

Mitochondrial Replacement Therapy

Near Miss, Healthcare

Prisoner Dilemma

RNAi Therapeutics

Category F - Psychiatry and Psychology

Autism Spectrum Disorder

Driving Under the Influence

Hoarding Disorder

Underage Drinking

Category G - Phenomena and Processes

Cell Plasticity

Cell Self Renewal

Diet, Food, and Nutrition

Natural Resources

Origin of Life

Category H – Disciplines and Occupations

Data Anonymization

Category I – Anthropology, Education, Sociology, and Social Phenomena

Armed Conflicts

Games, Recreational

Personally Identifiable Information

War Exposure

Warfare and Armed Conflicts

Category L - Information Science

Digital Divide

Libraries, Special

Open Access Publishing

Smartphone

Category M - Named Groups

Miners

Neurosurgeons

Oral and Maxillofacial Surgeons

Orthodontists

Social Workers

Vegans

Vegetarians

Category N – Health Care

Medical Overuse

Time Out, Healthcare

Category V – Publication Characteristics

Clinical Study

Changes of particular interest include:

• The MeSH Heading Intervention Studies was deleted and replaced by the Publication Type Clinical Trial which has a new entry term Intervention Study.
• Random Allocation is now allowed for human as well as animal studies.
• A project was begun for 2016 MeSH that will continue for 2017 MeSH to add Scope Notes to existing MeSH Headings that do not have scope notes.

MeSH Publication Types

• NLM has discontinued the use of the Publication Type [PT] Overall for MEDLINE indexing, effective for the 2016 indexing year. Existing citations with this PT will retain that value, but NLM will no longer create Overall [PT] citations. If publishers submit a single citation for a collection of abstracts presented at a meeting, that citation will be assigned Congresses [PT].
• Three new Publication Types are available for catalogers but will not be used by MEDLINE indexers. These Publication Types are: Blogs, Graphic Novels, and Public Service Announcements.
• A new Publication Type, Clinical Study, was added and will be available for indexers in 2016.
  
  Clinical Study
  Scope Note: A work that reports on the results of a research study to evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies. While most clinical studies concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans.
  
  Annotation: …prefer the specifics: CLINICAL TRIAL or OBSERVATIONAL STUDY

2015 MeSH V03 TREE

2016 MeSH V03 TREE

Study Characteristics [V03]      Clinical Trial [V03.200] Clinical Trial, Phase I [V03.200.100] Clinical Trial, Phase II [V03.200.200] Clinical Trial, Phase III [V03.200.300] Clinical Trial, Phase IV [V03.200.400] Controlled Clinical Trial [V03.200.500] Multicenter Study [V03.200.600] Observational Study [V03.200.650] Randomized Controlled Clinical Trial [V03.200.700]          Pragmatic Clinical Trial [V03.200.700.500]

Study Characteristics [V03]      Clinical Study [V03.175]      Clinical Trial [V03.175.250]           Clinical Trial, Phase I [V03.175.250.100]           Clinical Trial, Phase II [V03.175.250.200]           Clinical Trial, Phase III [V03.175.250.300]           Clinical Trial, Phase IV [V03.175.250.400]           Controlled Clinical Trial [V03.175.250.500]                Randomized Controlled Clinical Trial [V03.175.250.500.500]+      Observational Study [V03.175.500]      Multicenter Study [V03.175.600]

Note: Indexers will assign Clinical Study [PT] only if the authors use "clinical study" and if there are no indications that the study is either a "clinical trial" or "observational study."

MeSH Qualifier (Subheading) Deletion

In order to improve indexing consistency and efficiency and to make MEDLINE searching easier and more straightforward, the subheading diagnostic use was deleted from MeSH.

To cover the concept of Diagnostic Use related to diseases, search:

• diseases with the subheading /diagnosis (or specific subheading treed under it)
• the specific diagnostic technique
• the specific chemical(s) or physical agent(s) with no subheadings

To cover the concept of Diagnostic Use related to clinical/physiological conditions, search:

• organ or process terms with appropriate subheadings
• the specific diagnostic technique
• the specific chemical(s) or physical agent(s) with no subheadings

To cover the general concept of the diagnostic use of substances, search:

• the MeSH Heading Diagnostic Uses of Chemicals

MeSH Tree Changes

Extensive changes were made to MeSH 2016 Tree structures. In cases where a term was treed at two levels within the same subtree one of the tree positions was eliminated. For example:

• Conjunctivitis, Acute Hemorrhagic was removed as a child of Coxsackievirus Infections but retained as a sibling of Coxsackievirus Infections.

In other cases, terms were regrouped into new tree categories. For example:

• Armed Conflicts gathers all the specific wars in one Category I tree. Treeing of specific wars in Category K was retained.
• Diet, Food, and Nutrition was added as a new Category G tree where MeSH terms for beverages, foods, and nutrition are gathered. The original treeing in Category J was retained. MeSH terms for specific fruits and vegetables are now treed only in Category B – Plants.

Additional information on these changes can be found in the MeSH Tree Changes: Uncle vs. Nephew Projects section of the What's New for 2016 MeSH article.

MeSH Annotation Projects

The Index Section undertook several projects related to updating the Annotation element that contains instructions for the indexer and cataloger in the MeSH Browser. These instructions are helpful for searchers, too. The projects are ongoing. Some examples of changes include:

1. Hormones, Hormone Substitutes, and Hormone Antagonists

• Standardized wording for indexer and cataloger usage placed at the end of the Annotation.

	2015	2016
MeSH Heading	Hormones, Hormone Substitutes, and Hormone Antagonists	Hormones, Hormone Substitutes, and Hormone Antagonists
Annotation	used for searching: indexers and catalogers apply specifics	used for searching; INDEXER: Do not use; CATALOGER: Do not use

2. Enema

• Updating content to reflect revisions of indexing policy, such as the removal of mention of diagnostic use.

	2015	2016
MeSH Heading	Enema	Enema
Annotation	barium enema: coordinate with BARIUM SULFATE / diag use, not BARIUM	barium enema: coordinate with BARIUM SULFATE, not BARIUM

3. Cytodiagnosis

• Simplified wording to remove jargon such as GEN (means "general") and NIM (means "Not Index Medicus" — usually not starred as the main point of the article) and DF (means "Data Form" abbreviation).

	2015	2016
MeSH Heading	Cytodiagnosis	Cytodiagnosis
Annotation	GEN;NIM; DF: CYTODIAG	general or unspecified; prefer specifics

4. Encephalitis

• Adding information to note specifics that are new terms, such as drawing attention to the new heading Encephalitis, Viral.

	2015	2016
MeSH Heading	Encephalitis	Encephalitis
Annotation	GEN; coord with specific organism /infection heading (IM) or other cause (IM); viral encephalitis = ENCEPHALITIS, VIRAL unless ENCEPHALITIS, ARBOVIRUS but see note there; ENCEPHALOMYELITIS & specifics & SUBACUTE SCLEROSING PANENCEPHALITIS (see note there) are also available; DF: ENCEPH	general, note specifics particularly INFECTIOUS ENCEPHALITIS and ENCEPHALITIS, VIRAL

5. Tularemia

• Removing redundant information found elsewhere in the MeSH Browser record. For example, this 2015 annotation has been deleted in the 2016 MeSH Browser because the information is in the Scope Note.

• Adding coordination rules that address the indexing policy related to the extensive retreeing project. For example, this 2016 annotation guides indexers to add Tick-Borne Diseases when appropriate now that Tularemia is no longer treed under Tick-Borne Diseases.

	2015	2016
MeSH Heading	Tularemia	Tularemia
Annotation	caused by Francisella tularensis (formerly Pasteurella tularensis)	coordinate with TICK_BORNE DISEASES if pertinent
Scope Note	A plague-like disease of rodents, transmissible to man. It is caused by FRANCISELLA TULARENSIS and is characterized by fever, chills, headache, backache, and weakness.	A plague-like disease of rodents, transmissible to man. It is caused by FRANCISELLA TULARENSIS and is characterized by fever, chills, headache, backache, and weakness.

Of note to searchers: remember that this coordination applies to 2016 forward indexing and was not adjusted retrospectively; for comprehensive searching on Tick-Borne Diseases, you may want to OR Tularemia to your search (even though not all cases of Tularemia are "caused by tick vectors").

Do not confuse:

• RNAi Therapeutics with RNA Interference
• Cell Plasticity with Neuronal Plasticity

Other Changes: One MeSH Concept Split into Two

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2016 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. An example for 2016 MeSH is the clarification of the ambiguous word biogenesis. The single 2015 MeSH Heading Biogenesis was replaced by two 2016 MeSH Headings – Organelle Biogenesis and Origin of Life. NLM has adjusted the citations so that the appropriate new heading replaced the single old heading.

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 2016 MeSH Browser to see if the Entry Combination information indicates a different term.

There are eight new Entry Combinations for 2016.

Previous MeSH Heading/Subheading (Entry Combination)	Replaced-by Heading for 2016
Adenylyl Cyclases/antagonists & inhibitors	Adenylyl Cyclase Inhibitors
Cholestenone 5 alpha-Reductase/analogs & derivatives	5-alpha Reductase Inhibitors
Lacrimal Duct Obstruction/surgery	Dacryocystorhinostomy
Microchip Analytical Procedures/instrumentation	Lab-On-A-Chip Devices
Orexin Receptors/antagonists & inhibitors	Orexin Receptor Antagonists
Placenta/growth & development	Placentation
Poly(ADP-ribose) Polymerases/antagonists & inhibitors	Poly(ADP-ribose) Polymerase Inhibitors
Ultrasonic Waves/therapy	Ultrasonic Therapy

Structured Abstracts

In October 2015, NLM added 233 new labels to the list of structured abstract labels. This brings the total of vetted and mapped labels to 3,032. The new 2015 file can be found at: https://structuredabstracts.nlm.nih.gov/Downloads/Structured-Abstracts-Labels-102615.txt.

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

OLDMEDLINE MeSH Mapping

In the fall of 2015, NLM processed all OLDMEDLINE citations using a form of the Medical Text Indexer software modified specifically for this subset of MEDLINE data in order to add additional MeSH Headings and complete a project that mapped OLDMEDLINE Other Term (OT) subject headings to MeSH Headings. The result of this project was that all OLDMEDLINE citations now have at least one MeSH Heading and were, therefore, converted to MEDLINE status. The over 2 million jsubsetom citations updated via this process will be included in the baseline export of citations for MEDLINE data licensees and will be available in PubMed in mid-December. Due to the extremely large number of citations modified, these citations were not marked with a Date Last Revised (LR) in order to speed the processing of the updates.

MEDLINE Journal Title Updates

In August of 2015, NLM processed updates to 3,308 MEDLINE journals for changes to diacritics in the journal title (the JT element seen in the MEDLINE display in PubMed). This work affected over 2 million MEDLINE/PubMed citations. The revised citations were held in the NLM Data Creation and Maintenance System until mid-December when 2016 baseline files for MEDLINE data licensees are exported and MEDLINE/PubMed citations maintained with 2016 MeSH are made available in PubMed. Due to the large volume of citations affected, these citations were not marked with a Date Last Revised (LR) in order to speed the processing of the updates.

MEDLINE Country of Publication

During September and October 2015, NLM processed two MEDLINE Country of Publication [PL] clean-up projects:

• typographical errors and name variants were corrected
• updated the value "Unknown" with the Country value found in LocatorPlus

PubMed Notes

On August 11, 2015, NLM updated the PubMed Title/Abstract [tiab] index to include publisher-provided Author Keywords which are part of the MEDLINE citations.