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Table of Contents: 2012 NOVEMBER–DECEMBER No. 389

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MEDLINE Data Changes — 2013

Tybaert S. MEDLINE Data Changes — 2013. NLM Tech Bull. 2012 Nov-Dec;(389):e4a.

2012 November 30 [posted]
2012 December 11 [Editor's note added] [Editor's note added]
Other pertinent articles:

A New System of Registry Number Identifiers for Chemicals in the MeSH Database

Author Replies to Comments to be Cited Separately in MEDLINE/PubMed

MEDLINE/PubMed Year-End Processing Activities

2013 MeSH Now Available

Cataloging News — 2013

dotMEDLINE Data Changes — 2013

What's New for 2013 MeSH

Newly Maintained MEDLINE for 2013 MeSH Now Available in PubMed

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:

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

Do not confuse:

 

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).

Screen capture of a PubMed search of a UNII code using the RN field tag.
Figure 1: PubMed search of a UNII using the RN field tag.

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.

By Sara Tybaert
MEDLARS Management Section

NLM Technical Bulletin National Library of Medicine National Institutes of Health