December 05, 2008 [posted]

MEDLINE® Data Changes — 2009

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

Microvessels

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

Myxobolus

Myxozoa

Placozoa

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

Viscosupplements

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

Stalking

Wandering Behavior

Category G - Biological Sciences

Light Signal Transduction

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

Cemeteries

Cremation

Medicine, Korean Traditional

National Institute of Neurological Disorders and Stroke

Resistance Training

Sunbathing

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

Prescriptions

Electronic Prescribing

Hospitals, Isolation

Clinical Governance (not limited to the United Kingdom)

Telenursing

New subcategory N06 (Environment and Public Health)

Bhopal Accidental Release

Biohazard Release

Biosurveillance

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

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:

Both Disease Transmission and Disease Transmission, Horizontal are now Disease Transmission, Infectious.
Phototransduction is now Vision, Ocular which covers events happening in the eye. For plants or micro-organisms or non-image forming, non-visual phototransduction (happening in the brain or pituitary gland) use Light Signal Transduction.
Stress, previously in Category C - Diseases, was changed to Stress, Physiological in Category G - Biological Sciences. It may now be used with micro-organisms, plants, and invertebrates.
Take note of the reorganized Categories G - Biological Sciences and H - Natural Sciences as described in the What's New for 2009 MeSH article.

Other changes that affect searching include:

Metazoa is a new Entry Term to Animals.
The subheading /genetics is now allowed for Category C - Diseases.
Neoplasms, Multiple Primary has a revised scope note that now permits these neoplasms to be histologically the same or different (previously they had to be different).
Myelodysplasia was an Entry Term to Neural Tube Defects; now the Entry Term is Spinal Cord Myelodysplasia to reduce confusion with Myelodysplastic Syndromes (a bone marrow formation defect).
The Entry Term Patient Non-Compliance was moved from Treatment Refusal to Patient Compliance. This parallels the Entry Term Medication Non-Adherence on Medication Adherence.
Disasters: The old heading Natural Disasters was deleted and replaced by Disasters. Many Entry Terms from the old Natural Disasters heading, e.g., Tornadoes, were elevated to stand-alone MeSH Headings plus new events, such as Structure Collapse, were added. Specific events are no longer treed under Disasters. If the article discusses an event as being a disaster, indexers will coordinate with the heading Disasters and the specific geographic location.

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

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.
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.
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.
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.
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.
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.