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; Pronephros; Serotonergic Neurons; Thymocytes; Torso; Wharton Jelly
Category B - Organisms: Agricultural Inoculants; Aliivibrio; Endophytes; Fibrobacteres; Merkel cell polyomavirus; Neanderthals; Planctomycetales; Verrucomicrobia
Category C - Diseases: Abnormal Karyotype; Accessory Nerve Injuries; Acute Pain; Aliivibrio Infections; Alternariosis; Breakthrough Pain; Cerebral Phaeohyphomycosis; Chronic Pain; Coinfection; Fusariosis; Hyalohyphomycosis; Hypoglossal Nerve Injuries; Intra-Abdominal Hypertension; Intraabdominal Infections; Lobomycosis; Masked Hypertension; Musculoskeletal Pain; Neoplasm Micrometastasis; Nociceptive Pain; Oculomotor Nerve Injuries; Olfactory Nerve Injuries; Otomycosis; Phaeohyphomycosis; Pott Puffy Tumor; Reproductive Tract Infections; Trichosporonosis; White Coat Hypertension
Category D - Chemicals and Drugs: Antibodies, Monoclonal, Humanized; Arthropod Proteins; Biological Control Agents; Biosimilar Pharmaceuticals; Biphasic Insulins; Brassinosteroids; 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; Insulins; Morpholinos; Polyketides; Polyphenols
Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment: Axenic Culture; Batch Cell Culture Techniques; Cell Engineering; Chemistry Techniques, Synthetic; Chemoradiotherapy; Chemoradiotherapy, Adjuvant; Consolidation Chemotherapy; Fertility Preservation; Functional Neuroimaging; Induction Chemotherapy; Maintenance Chemotherapy; Metabolic Engineering; Metastasectomy; Multiplex Polymerase Chain Reaction; Neoplasm Grading; Neuroimaging; 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: Carnivory; Herbivory; HIV Serosorting
Category G - Biological Sciences: Bays; Caves; Cell Cycle Checkpoints; Cellular Microenvironment; Clonal Evolution; Clonal Selection, Antigen-Mediated; Exome; G1 Phase Cell Cycle Checkpoints; G2 Phase Cell Cycle Checkpoints; Gene-Environment Interaction; Groundwater; Hydrothermal Vents; Karyotype; Lakes; M Phase Cell Cycle Checkpoints; Magnetic Fields; Magnetic Phenomena; Natural Springs; Oil and Gas Fields; Ponds; Pregnancy, Quadruplet; Pregnancy, Quintuplet; Pregnancy, Triplet; Pregnancy, Twin; Protein Interaction Maps; Reproductive Isolation; S Phase Cell Cycle Checkpoints; Telomere Homeostasis; Telomere Shortening; Transcriptome; 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: Pharmacovigilance; Social Media; Social Networking; Text Messaging
Category M - Named Groups: Emergency Responders; Firefighters; 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:

Biological Products to Biological Agents
The new heading, Biological Control Agents are organisms; however, they are not treed under Category B, but are treed in Category D under Biological Agents and in Category J under Agriculture.
Education of Mentally Retarded to Education of Intellectually Disabled
Laboratory Techniques and Procedures to Clinical Laboratory Techniques
- It is difficult to discriminate between Laboratory and Clinical Laboratory Techniques so in 2012 MeSH Laboratory Techniques and Procedures was deleted and replaced by Clinical Laboratory Techniques. This term is now treed under both Diagnostic Techniques and Procedures and Investigative Techniques.
Mental Retardation to Intellectual Disability
Mycobacteria, Atypical to Nontuberculous Mycobacteria
Mycobacterium Infections, Atypical to Mycobacterium Infections, Nontuberculous
Technology, Medical to Medical Laboratory Science
Vibrio fischeri to Aliivibrio fischeri; and Vibrio salmonicida to Aliivibrio salmonicida
- Both Aliivibrio fischeri and Aliiviobrio salmonicida are treed under Aliivibrio. The former terms were retained as Entry Terms.

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:

Colony-Stimulating Factors, Recombinant was replaced by Colony-Stimulating Factors.
Erythropoietin, Recombinant was replaced by Erythropoietin.
Granulocyte Colony Stimulating Factor, Recombinant was replaced by Granulocyte Colony-Stimulating Factor.
Granulocyte Macrophage Colony-Stimulating Factors, Recombinant was replaced by Granulocyte-Macrophage Colony-Stimulating Factor.
Interferon Type I, Recombinant was replaced by Interferon Type I.
Interferon-gamma, Recombinant was replaced by Interferon-gamma.

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

Anthropology, Medical is the discipline (almost always starred for the main point). When it's not starred, it's used to indicate studies.
Biosimilar Pharmaceuticals is often referred to in British usage as Follow-on Pharmaceuticals.
Chemoradiotherapy and Chemoradiotherapy, Adjuvant: for treatment aspects search with the subheading therapy, not radiotherapy.
Coinfection will not be starred as the main point because the specific infection will be starred.
Entry Terms for "Effects" were added to some Category D27 terms. For example: Anabolic Agents got the new Entry Term: Anabolic Effects. In this case Anabolic Effects is only used for the anabolic effect of a chemical. Anabolic Effects should not be used for the anabolic effect of exercise.
Germ Theory of Disease is mostly for historical articles.
Long non-coding RNAs (long untranslated RNAs) are indexed with RNA, Untranslated.
Magnets are the subject; Magnetic Fields are the force; Magnetics is the discipline.
Medical Laboratory Science is the discipline. Biomedical Technology is the use of technology in medicine.
For 2012, these headings are treed only in Category M (Named Persons):
- Quadruplets
- Quintuplets
- Triplets
- Twins
These new headings are treed only in Category G (Biological Sciences) so it is now possible to distinguish the person from the pregnancy:
- Pregnancy, Quadruplet
- Pregnancy, Quintuplet
- Pregnancy, Triplet
- Pregnancy, Twin
Neanderthals are not defined as humans.
Plant Cells is for general use only: searchers should prefer the specific plant heading with the subheading cytology.
Plant Pathology is the discipline; use Plant Diseases for diseases in plants, or Plants/microbiology for bacteria or fungi in plants or Plants/virology for viruses in plants.
Reproductive Health used to be an Entry Term to Reproductive Medicine, which is the discipline.
Social Networking is individuals; Facebook gets searched here. Social Networks, which is an Entry Term to Social Support, are psychosocial support systems. Social Media are platforms. YouTube is searched as Video Recording. Twitter Messaging is an Entry Term to Blogging.
Sound is now treed under Radiation, Non-Ionizing and has these Entry Terms: Sonic Radiation and Ultrasound Radiation.
Transcriptome was previously an Entry Term to Gene Expression Profiling.
Torso does not have an Entry Term for Trunk because trunk can also refer to other anatomical structures such as nerves.

Do not confuse:

Adrenergic Neurons with Adrenergic Fibers
Antibodies, Monoclonal, Humanized with Antibodies, Monoclonal, Murine-Derived
Clonal Evolution with Clonal Selection, Antigen-Mediated
Cholinergic Neurons with Cholinergic Fibers
Holy Roman Empire with Roman World or with Rome
HIV Serosorting with HIV Seropositivity or HIV Seroprevalence
Laboratory Personnel with Medical Laboratory Personnel
Mesenchymal Stromal Cells with Mesenchymal Stem Cells
Neoplasm Grading (degree of malignancy expressed in Arabic numbers) with Neoplasm Staging (degree of spreading expressed in Roman numerals)
Pott Puffy Tumor with Pott Disease which is an Entry Term to Tuberculosis, Spinal
Reproductive Isolation with Fertility Preservation
Social Networking with Social Networks which is an Entry Term to Social Support

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.