MEDLINE Data Changes - 2013

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 2013.

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 2012 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 2013

The MeSH Browser currently points to the 2013 MeSH vocabulary with a link to the 2012 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 2013 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 2013 MeSH, see the forthcoming article, What's New for 2013 MeSH.

The PubMed MeSH database and translation tables will also be updated to reflect 2013 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 2012. See Changing Saved Searches for details on revising My NCBI saved searches.

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 2013 changes should be available sometime in January 2013. 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

302 new MeSH Headings were added to MeSH in 2013.

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.

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 2013 concepts on the MeSH New Descriptors Web page.

Category A - Anatomy

Acellular Dermis

Madin Darby Canine Kidney Cells

MCF-7 Cells

Sf9 Cells

Category B - Organisms

Odonata

Acanthocheilonema

Category C – Diseases

[Editor's Note: The MeSH Heading Tropical Diseases has been deleted from 2013 MeSH. The MeSH Heading Tropical Medicine has reverted back to its 2012 MeSH content. New MeSH XML files with these changes are available for download. These changes are effective in the MeSH Browser.]

Binge Drinking

Maternal Death

Parental Death

Organophosphate Poisoning

Tropical Diseases

Category D - Chemicals and Drugs

Acid Sensing Ion Channel Blockers

Aminobenzoates

Cannabinoid Receptor Agonists

Cannabinoid Receptor Antagonists

Cannabinoid Receptor Modulators

Caspase Inhibitors

Endocannabinoids

Epithelial Sodium Channel Agonists

Epithelial Sodium Channel Blockers

Immobilized Nucleic Acids

Junctional Adhesion Molecule A

Junctional Adhesion Molecule B

Junctional Adhesion Molecule C

Junctional Adhesion Molecules

MARVEL Domain-Containing Proteins

Matrix Metalloproteinase Inhibitors

Myelin-Oligodendrocyte Glycoprotein

N-Terminal Acetyltransferases

Oligodendrocyte-Myelin Glycoprotein

Organofluorophosphonates

Organophosphonates

Organothiophosphates

Organothiophosphonates

Polycomb-Group Proteins

Proteasome Inhibitors

Receptors, Artificial

RNA, Long Untranslated

Single-Domain Antibodies

Sodium Channel Agonists

Tight Junction Proteins

Voltage-Gated Sodium Channel Agonists

Voltage-Gated Sodium Channel Blockers

Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment

Biopsy, Large-Core Needle

Brain-Computer Interfaces

Cardiac Catheters

Catheter Obstruction

Central Venous Catheters

Endoscopic Ultrasound-Guided Fine Needle Aspiration

Epidemiological Monitoring

Image-Guided Biopsy

Organ Dysfunction Scores

Percutaneous Coronary Intervention

Public Health Surveillance

Vascular Access Devices

Category F - Psychiatry and Psychology

Ageism

Homophobia

Racism

Sexism

Social Discrimination

Social Marginalization

Category G - Biological Sciences

Animal Distribution

Antioxidant Response Elements

Arterial Pressure

Atrial Pressure

AU Rich Elements

Epigenetic Repression

Estuaries

Immunoreceptor Tyrosine-Based Activation Motif

Immunoreceptor Tyrosine-Based Inhibition Motif

Islands

Mitochondrial Degradation

Mitochondrial Dynamics

Mitochondrial Turnover

Plant Development

Plant Dispersal

Re-Epithelialization

Transcription Elongation, Genetic

Transcription Initiation, Genetic

Transcription Termination, Genetic

Water Resources

Category H - Natural Sciences

Geography, Medical

Molecular Medicine

Category I - Anthropology, Education, Sociology and Social Phenomena

Human Migration

Medicalization

Category K - Humanities

Personal Narratives as Topic

Category J – Technology, Industry, and Agriculture

Breakfast

Food Quality

Inventions

Lunch

Meals

Snacks

Tobacco Products

Category L - Information Science

Databases, Chemical

Databases, Pharmaceutical

Literature Based Discovery

RxNorm

Category M - Named Groups

Inventors

Transgendered Persons

Category N - Health Care

Health Services for Transgendered Persons

Meaningful Use

Secondary Care

Solid Waste

Tertiary Care Centers

Tertiary Healthcare

Waste Water

Category V – Publication Characteristics

Personal Narratives

Changes to MeSH Headings

This year 56 MeSH Headings were either changed or deleted and replaced with more up-to-date terminology. During YEP, NLM updates MeSH headings on MEDLINE citations.

Changes of particular interest include:

• The Organophophorus Compounds tree was revised in order to simplify the tree structure; compounds that have similar functions and structures were grouped together. Phosphonic Acids was deleted and replaced on citations with the heading Organophosphonates. Phosphonic Acids is retained as an Entry Term; however, it maps not to the replaced by heading, Organophosphonates, but rather to a different heading, Phosphorous Acids.
• The Carboxylic Acids tree was revised to improve consistency of treeing.
• New Cannabinoid Receptors Modulator terms were created. The term Endocannabinoids was removed from the D27 category (Hormones, Neurotransmitter agents). It is treed now under the structural category – Fatty Acids (D10) and has a new scope note.

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2013 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 Type (PT) for 2013

Personal Narratives was reintroduced as a new Publication Type. The publication type will be used for accounts of personal experiences. Users may recall that in 2011 Personal Narratives did exist as a Publication Type but in 2012 it was replaced by the publication type Autobiography. In 2013 MeSH, Personal Narratives and Autobiography are separate publication types and both available for use.

Notable MeSH Changes and Related Impact on Searching

• The 2012 term Gene Therapy is now an Entry Term for the heading Genetic Therapy.
• These new headings were previously entry terms to Prejudice. For 2013, they are treed under Prejudice:
  • Ageism
  • Homophobia
  • Racism
  • Sexism
• Geography, Medical is the discipline. Previously it was an entry term for Geography.
• Molecular Medicine is the discipline. Techniques include Molecular Targeted Therapy and Molecular Diagnostic Techniques.

Do not confuse:

• Atrial Pressure with Arterial Pressure
• Brain-Computer Interfaces with User-Computer Interface
• MARVEL Domain-Containing Proteins with Tight Junction Proteins
• Maternal Death with Maternal Mortality
• Mitochondrial Turnover with Mitochondrial Degradation or Mitochondrial Dynamics
• Myelin-Oligodendrocyte Glycoprotein with Oligodendrocyte-Myelin Glycoprotein or with Myelin-Associated Glycoprotein
• N-Terminal Acetyltransferases with Amino-Acid N-Acetyltransferase
• Single-Domain Antibodies with Single-Chain Antibodies
• The Entry Term, Percutaneous Coronary Revascularization for the heading Percutaneous Coronary Intervention with Myocardial Revascularization.

 

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 2013 MeSH Browser to see if the Entry Combination information indicates a different term.

There are 98 new Entry Combinations for 2013 listed in a separate table.

Additional Changes to MEDLINE and OLDMEDLINE Data:

Author Reply to a published letter

Beginning with 2013 publication year, NLM is instituting a substantive change in the MEDLINE citations policy for indicating an author reply to a published letter. Until now, the MEDLINE citation policy for indicating an author reply to a published letter, when published in the same journal issue, called for the insertion of "discussion" or "author reply" in the pagination field of the MEDLINE citation for the letter. A separate citation for the author reply was not created. If an author reply to a letter was published later, in a separate issue, the author reply was treated as a regular comment, and a separate citation was created. Under the new policy, a separate citation is now created for an author reply no matter the issue in which it is published. For more information on this policy change, see the article, Author Replies to Comments to be Cited Separately in MEDLINE/PubMed.

ELocationID

In October 2012 NLM implemented a new process whereby if a publisher provides a doi in the ArticleId element in their publisher XML submission, and did not also supply data in the ELocationID field, then we will copy that data into the MEDLINE ELocationID field in the MEDLINE citation. Retrospectively, we followed this same process and copied the doi data from ArticleId to ELocationID, if no other data existed in the ELocationID field, for citations from 2008 forward. 2008 was the year when NLM introduced the ELocationID field.

Grants

The Grant Number Information Found in the GR Field in the MEDLINE/PubMed Web page has been updated to include new two-letter grant codes and their associated organization abbreviations. There is also a change for one of the organization name acronyms.

Abbreviation (Full Name)
BLRD VA (Biomedical Laboratory Research and Development)
CSP VA (Cooperative Studies Program)
CSRD VA (Clinical Science Research and Development)
European Research Council
HSRD VA (Health Services Research and Development)
NCATS NIH HHS (National Center for Advancing Translational Sciences)
ORD VA (Office Research and Development)
ORIP NIH HHS (Office of Research Infrastructure Programs)
PCORI (Patient-Centered Outcomes Research Institute)
RRD VA (Rehabilitation Research and Development)
VA (Veterans Affairs)

Old Abbreviation (Full Name)	New Abbreviation (Full Name)
CDC (Office of the Director, Centers for Disease Control and Prevention)	ODCDC (Office of the Director, CDC)

Beginning in October 2012 NLM is able to carry Veterans Affairs (VA) and Patient-Assisted Outcomes Research Institute (PCORI) funding information for citations, when that information has been deposited in the NIH Manuscript Submissions (NIHMS) system.

Starting in November 2012 NLM is able to add European Research Council funding information. The European Research Council is a multi-national organization so NLM is using the value "International" as the country designator in the grant field. As with the VA and PCORI grant information, the European Research Council funding information is derived only from deposits in the NIHMS system.

Users may search for these new organizations using the abbreviation qualified by the [gr] search tag, e.g.:

VA [gr]

PCORI [gr]

European Research Council [gr]

Identifier

The NameID field was created in 2010; its name was changed this year to Identifier. To date this field has not yet been used. Identifier is intended to contain a unique identifier associated with the author, corporate author or investigator name. The value in the Identifier attribute Source (for example, ORCID) designates the organizational authority that established the unique identifier. MEDLINE/PubMed citations may include Identifier element and its attribute Source, if supplied by the publisher.

OtherAbstract

Starting with the 2013 system, NLM will start indicating abstracts not in MEDLINE/PubMed but available from the publisher’s Web site.

Some background: English-language author abstracts are taken directly from the published article and included in the Abstract field. If the article does not have a published abstract, the National Library of Medicine does not create one. However, some publishers create additional non-English-language abstracts.

These other abstracts, and the language they are in, can now be indicated in the Other Abstract field. Although the MEDLINE citation will not carry the text of this non-English abstract, the Other Abstract field will carry a standard phrase. This phrase will provide the indication of the availability of this abstract and its language on the publisher site. For example: "Abstract available in Portuguese and Spanish from the publisher."

Registry Number

[Editor's Note: MEDLINE citations only contain the Registry Number (RN) field. MEDLINE citations do not contain the Related Registry (RR) number field. However, data in the Related Registry number field of a MeSH Record can be searched in PubMed using the RN field tag. This is similar to the way that Entry Terms to MeSH Headings are not contained in the MEDLINE citation, but they can be searched in PubMed. Both Registry Numbers and Related Registry numbers are in the RN index.]

Beginning with 2013 MeSH, the Unique Ingredient Identifiers (UNIIs) from the Food and Drug Administration (FDA) Substance Registration System are included in the MeSH Supplementary Concept Record (SCR). In MeSH, the UNIIs serve as a new system of unique identifiers supplementing existing Chemical Abstracts Service (CAS) registry numbers and Enzyme Commission (EC) numbers.

Initially, the UNIIs are added to MeSH SCRs for chemicals with structures. The UNIIs are included in the Registry Number (RN) field. MeSH SCRs have only one RN field. If a UNII is added to a MeSH record with an existing CAS Registry Number or EC number in the RN field, the CAS Registry Number or EC number is moved to the Related Registry (RR) number field. MeSH SCRs can have multiple RR fields. For more information on the UNIIs, see the article, A New System of Registry Number Identifiers for Chemicals in the MeSH Database.

UNIIs will be searchable in PubMed using the RN field tag (see Figure 1).

In PubMed, UNIIs will be displayed only in the MEDLINE format with the RN field tag.

RN – Y92OUS2H9B (benphothiamine)

Structured Abstracts

In the fall of 2012, NLM added 304 new labels to the list of structured abstract labels. This brings the total of vetted and mapped labels to 1,949.