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December 05, 2008 [posted]

MEDLINE® Data Changes — 2009

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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 2009. 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 2008 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 2009

The MeSH Browser currently includes a link to the 2009 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.

The MeSH Section homepage provides links under "All About MeSH" to the Introduction of 2009 MeSH and under "Obtaining MeSH" to download electronic copies.

The MeSH Tree Structures are also available online in both PDF and HTML formats with all indented terms showing.

For highlights about 2009 MeSH see the article, What's New for 2009 MeSH.

The PubMed MeSH database and translation tables will also be updated to reflect 2009 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 citations with updated MeSH will be in PubMed in mid-December 2008. See the Changing Saved Searches Quick Tour 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 2009 changes should be available sometime in January 2009. 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 year of MeSH.

New MeSH Headings

This year 446 new MeSH Headings were added.

Typically, NLM does not retrospectively re-index MEDLINE citations with new MeSH Heading concepts. Therefore, searching 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 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 2009 concepts on the MeSH New Descriptors Web page.

Category A - Anatomy
Venous Valves
Granulocyte-Macrophage Progenitor Cells
Immunological Synapses
Megakaryocyte Progenitor Cells
Megakaryocyte-Erythroid Progenitor Cells
Monocyte-Macrophage Precursor Cells
Natural Killer T-Cells (treed under T-Lymphocytes)
Stem Cell Niche
Hepatic Stellate Cells
Category B - Organisms
Rats, Transgenic
Methicillin-Resistant Staphylococcus aureus (indexers will also add Staphylococcal Infections or specifics and/or Methicillin Resistance, if discussed)
Salt-Tolerant Plants (many new Fungi headings were added (B05))
Category C - Diseases
Lung Injury
Acute Lung Injury
Ventilator-Induced Lung Injury
Failed Back Surgery Syndrome
Pancreatitis, Graft
Primary Graft Dysfunction
Morgellons Disease
Category D - Chemicals and Drugs
Prescription Drugs (do not confuse with Drug Prescriptions)
Viscoelastic Substances
Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment
Early Detection of Cancer
Magnetic Field Therapy
Uterine Artery Embolization
Ablation Techniques
Endometrial Ablation Techniques
Comparative Genomic Hybridization
Gene Knock-In Techniques
Gene Knockdown Techniques
Gene Knockout Techniques
Genome-Wide Association Study
Category F - Psychiatry and Psychology
Illness Behavior
Medication Adherence
Wandering Behavior
Category G - Biological Sciences
Light Signal Transduction
Rod-Cone Interaction
Plant Root Nodulation
Category H - Natural Sciences
Evidence-Based Dentistry
Evidence-Based Emergency Medicine
Evidence-Based Nursing
Evidence-Based Practice
Infectious Disease Medicine
Integrative Medicine
Wilderness Medicine
Category I - Anthropology, Education, Sociology and Social Phenomena
Medicine, Korean Traditional
National Institute of Neurological Disorders and Stroke
Resistance Training
Category K - Humanities
Afghan Campaign 2001-
Category L - Information Science
Journal Impact Factor
Category M - Named Groups
Drug Users
Osteopathic Physicians
Young Adult (new check tag; defined as a person between 19 and 24 years of age)
Category N - Health Care
Moving and Lifting Patients
Electronic Prescribing
Hospitals, Isolation
Clinical Governance (not limited to the United Kingdom)
New subcategory N06 (Environment and Public Health)
Bhopal Accidental Release
Biohazard Release
Chemical Hazard Release
Extreme Cold
Extreme Heat
Infectious Disease Incubation Period
Lot Quality Assurance Sampling
Multilevel Analysis
Secondary Prevention
Seveso Accidental Release
Structure Collapse
Sverdlovsk Accidental Release
Tertiary Prevention
Category Z - Geographicals
Cape Verde
New Orleans

Changes to MeSH Headings

This year 149 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 to citations of particular interest include:

Other changes that affect searching include:

In addition to the replaced-by heading changes, YEP includes other adjustments to MEDLINE citations to reflect 2009 MeSH vocabulary and to enhance search retrieval. These follow-on adjustments are largely the adding of more MeSH headings or Supplementary Concept Record Names of Substances (NM) 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 2009 is Phototransduction being split into Vision, Ocular and Light Signal Transduction.

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 in 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.

Indexing Policy for New Young Adult Check Tag

Young Adult is a new check tag for 2009 indexing forward. It will not be applied to citations retrospectively. NLM follows the U.S. Census definition of ages 19-24. This age range overlaps with the existing check tag Adult which is defined as the ages 19-44. Indexing policy is as follows:

If the article describes persons aged 19-24 only, we will use Young Adult check tag "Age 19-24" only.
If the article describes persons aged 25-44 only, we will use Adult check tag "Age 19-44" only.
If the article describes persons aged 19-44, we will use both Young Adult and Adult check tags "Age 19-24" and "Age 19-44."

Publication Type Indexing Policy Change

For 2009, NLM will begin using the Publication Type "Portraits" for MEDLINE indexing. In the past, NLM indexed to the MeSH Heading "Portraits as Topic." During YEP, NLM will revise, as appropriate, those citations with the MeSH Heading, "Portraits as Topic," to delete the MeSH Heading and add the Publication Type "Portraits."

Notable MeSH Changes and Related Impact on Searching

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 2009 MeSH Browser to see if the Entry Combination information indicates a different term.

Below are the eleven Entry Combinations new for 2009:

Previous MeSH Heading/Subheading
(Entry Combination)

Replaced-by Heading for 2009

Acid Ceramidase/deficiency Farber Lipogranulomatosis
Aspartylglucosylaminase/deficiency Aspartylglucosaminuria
Coproporphyrinogen Oxidase/deficiency Coproporphyria, Hereditary
Electromagnetic Fields/therapeutic use Magnetic Field Therapy
Heart Ventricles/physiology Ventricular Function
Lung/injuries Lung Injury
Patient Care/nursing Nursing Care
Ryanodine Receptor Calcium Release Channel/agonists Calcium Channel Agonists
Ryanodine Receptor Calcium Release Channel/antagonists & inhibitors Calcium Channel Blockers
SOX9 Transcription Factor/deficiency Campomelic Dysplasia
Survival of Motor Neuron 1 Protein/deficiency Spinal Muscular Atrophies of Childhood

For 2009 the Entry Combination: Disease/genetics which generated the heading Genetic Diseases, Inborn has been removed.

Additional Changes to MEDLINE and OLDMEDLINE Data

  1. One new field is being added to the MEDLINE citation starting in 2009:
    Country will now be a separate element in the Grant series of elements. Previously the country of the granting agency resided as part of the value found in the Agency element of the XML.
  2. Agency data within the Grant field:
    The Agency field within the Grant List will reflect the agency's hierarchical structure from lower to higher entity, when known. For example the old agency value of NCI will be NCI NIH HHS for 2009 meaning National Cancer Institute, National Institutes of Health, Department of Health and Human Services.
  3. Investigator List (Collaborators):
    The Investigator field in the MEDLINE citation now includes a Valid_YN attribute in the XML format. This allows NLM to correct an investigator name that was published incorrectly and retain both the correct and incorrect names for searching in PubMed.
  4. Other Abstract field - new valid value for type of abstracts:
    A new value, "Publisher," has been added as a valid value for the type of abstracts in the Other Abstract field.
  5. Other ID - a new valid value for source of Other ID:
    A new value, "NLM," has been added for the source of Other ID data. This value will be used for the PMCID and manuscript identifier data which will reside in the Other ID field starting with the 2009 PubMed system.
  6. PMCID data in Other ID field:
    Starting with the 2009 PubMed system users will see PMCID data in the Other ID field. In addition to the PMCID number, the Other ID will also have NIHMS (NIH Manuscript System), UKMS (United Kingdom Manuscript System), HALMS (the French Manuscript System), and HHMIMS (Howard Hughes Medical Institute Manuscript System) numbers. In some cases the data may contain a date in parentheses following the number. This date represents the embargo date after which the full text will be available in PubMed Central®.

By Sara Tybaert
MEDLARS Management Section

Tybaert S. MEDLINE® Data Changes — 2009. NLM Tech Bull. 2008 Nov-Dec (365):e14.

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