MEDLINE® Data Changes 2009
Other pertinent articles: |
What's New for 2009 MeSH
MEDLINE/PubMed Year-End Processing Activities
2009 MeSH Now Available
MEDLINE Data Changes 2009
PubMed Notes 2009
Newly Maintained MEDLINE for 2009 MeSH Now Available in PubMed
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 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:
- 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
Replaced-by Heading for 2009
|Acid Ceramidase/deficiency||Farber Lipogranulomatosis|
|Coproporphyrinogen Oxidase/deficiency||Coproporphyria, Hereditary|
|Electromagnetic Fields/therapeutic use||Magnetic Field Therapy|
|Heart Ventricles/physiology||Ventricular Function|
|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®.
Tybaert S. MEDLINE® Data Changes 2009. NLM Tech Bull. 2008 Nov-Dec (365):e14.