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November 29, 2011 [posted]

MEDLINE Data Changes — 2012

At this time each year the NLM Technical Bulletin traditionally includes information about changes made to MEDLINE® during annual National Library of Medicine® (NLM®) maintenance known as Year-End Processing (YEP). This article collects, in one place, the notable data changes for 2012. Some topics may be linked to another article where details will be found. 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 2011 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 2012

The MeSH Browser currently includes 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 that are not MeSH Headings, and, for the first time for 2012 MeSH, for diseases that are not MeSH Headings.

The MeSH Section homepage provides a link under "All About MeSH" to the Introduction of 2012 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 2012 MeSH, see the forthcoming article, What's New for 2012 MeSH.

The PubMed MeSH database and translation tables will also be updated to reflect 2012 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 2011. 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 2012 changes should be available sometime in January 2012. 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

454 new MeSH Headings were added to MeSH in 2012.

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 2012 concepts on the MeSH New Descriptors Web page.

Category A - Anatomy
Acinar Cells
Adrenergic Neurons
Animal Shells
B-Lymphocytes, Regulatory
Cholinergic Neurons
Corneal Keratocytes
Dopaminergic Neurons
GABAergic Neuron
Head Kidney
Human Umbilical Vein Endothelial Cells
Imaginal Discs
Mesenchymal Stromal Cells
Mirror Neurons
Plant Cells
Serotonergic Neurons
Wharton Jelly
Category B - Organisms
Agricultural Inoculants
Merkel cell polyomavirus
Category C - Diseases
Abnormal Karyotype
Accessory Nerve Injuries
Acute Pain
Aliivibrio Infections
Breakthrough Pain
Cerebral Phaeohyphomycosis
Chronic Pain
Hypoglossal Nerve Injuries
Intra-Abdominal Hypertension
Intraabdominal Infections
Masked Hypertension
Musculoskeletal Pain
Neoplasm Micrometastasis
Nociceptive Pain
Oculomotor Nerve Injuries
Olfactory Nerve Injuries
Pott Puffy Tumor
Reproductive Tract Infections
White Coat Hypertension
Category D - Chemicals and Drugs
Antibodies, Monoclonal, Humanized
Arthropod Proteins
Biological Control Agents
Biosimilar Pharmaceuticals
Biphasic Insulins
Chlorophyll Binding Proteins
Chloroplast Proteins
HLA...Antigens (numerous subtypes)
Insulin Aspart
Insulin Lispro
Insulin, Lente
Insulin, Regular, Human
Insulin, Regular, Pork
Insulin, Short-Acting
Insulin, Ultralente
Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment
Axenic Culture
Batch Cell Culture Techniques
Cell Engineering
Chemistry Techniques, Synthetic
Chemoradiotherapy, Adjuvant
Consolidation Chemotherapy
Fertility Preservation
Functional Neuroimaging
Induction Chemotherapy
Maintenance Chemotherapy
Metabolic Engineering
Multiplex Polymerase Chain Reaction
Neoplasm Grading
Organ Sparing Treatments
Parasite Load
Primary Cell Culture
Real-Time Polymerase Chain Reaction
Solid-Phase Synthesis Techniques
Therapy with Helminths
Ultrasonic Surgical Procedures
Category F - Psychiatry and Psychology
HIV Serosorting
Category G - Biological Sciences
Cell Cycle Checkpoints
Cellular Microenvironment
Clonal Evolution
Clonal Selection, Antigen-Mediated
G1 Phase Cell Cycle Checkpoints
G2 Phase Cell Cycle Checkpoints
Gene-Environment Interaction
Hydrothermal Vents
M Phase Cell Cycle Checkpoints
Magnetic Fields
Magnetic Phenomena
Natural Springs
Oil and Gas Fields
Pregnancy, Quadruplet
Pregnancy, Quintuplet
Pregnancy, Triplet
Pregnancy, Twin
Protein Interaction Maps
Reproductive Isolation
S Phase Cell Cycle Checkpoints
Telomere Homeostasis
Telomere Shortening
V(D)J Recombination
Water Wells
Category H - Natural Sciences
HapMap Project
Plant Pathology
Category I - Anthropology, Education, Sociology and Social Phenomena
Anthropology, Medical
Category J – Technology, Industry, and Agriculture
Calcifying Nanoparticles
Drinking Water
Energy Drinks
Category K - Humanities
Germ Theory of Disease
Hygiene Hypothesis
Category L - Information Science
Social Media
Social Networking
Text Messaging
Category M - Named Groups
Emergency Responders
Laboratory Personnel
Category N - Health Care
Accountable Care Organizations
Disease Eradication
Emergency Shelter
Gas, Natural
Geothermal Energy
Patient Safety
Petroleum Pollution
Renewable Energy
Reproductive Health
Category Z - Geographicals
Gulf of Mexico
Holy Roman Empire

Changes to MeSH Headings

This year 57 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 2012 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.

For example in 2012, MeSH Headings for individual Recombinant Proteins will no longer be created. Existing MeSH Headings were either deleted or moved to Supplementary Concept Records (SCRs). The Recombinant aspect of the concepts was lost when these MeSH Headings were changed:

In order to retain the Recombinant aspect of the concepts, we ran a task that also added the MeSH Heading Recombinant Proteins to these citations.

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.

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 2011 MeSH Browser to see if the Entry Combination information indicates a different term.

There are 29 new Entry Combinations for 2012 listed in a separate table.

Additional Changes to MEDLINE and OLDMEDLINE Data

Cites Data
In the fall of 2011, NLM updated the cites data to MEDLINE citations. We added 4.46 million new or changed cites. This update added to the initial cites data we loaded in 2009 and updated in 2010. There are now about 36 million cites. Currently, NLM is adding cites data on a regular ongoing basis.

Cites data contain PMIDs and source data for items in the bibliography or list of references at the end of an article that is deposited in PubMed Central® (PMC) and whose citation record is in the NLM Data Creation and Maintenance System (DCMS). It is possible for a citation to be present in the list of references and yet the PMID is not included in the Cites list because it is not present in the DCMS.

Structured Abstracts

In late summer 2011, NLM added 189 new labels to the list of structured abstract labels. This brings the total of vetted and mapped labels to 1,645.

PubMed Notes

(Previously, this was a separate article in the November-December issue of the NLM Technical Bulletin.)

During this past year two new indexes were announced in PubMed Help:
Completion Date [DCOM] — The date NLM completed all quality control and MeSH indexing of the citation.
Modification Date [LR] — The date on which the citation was last revised.

By Sara Tybaert
MEDLARS Management Section

Tybaert S. MEDLINE Data Changes — 2012. NLM Tech Bull. 2011 Nov-Dec;(383):e6a.

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