December 02, 2010 [posted]

MEDLINE® Data Changes — 2011

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 2011. 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 2010 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 2011

The MeSH Browser currently includes a link to the 2011 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 2011 MeSH, for diseases that are not MeSH Headings.

The MeSH Section homepage provides a link under "All About MeSH" to the Introduction of 2011 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 2011 MeSH see What's New for 2011 MeSH.

The PubMed MeSH database and translation tables will also be updated to reflect 2011 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 2010. 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 2011 changes should be available sometime in January 2011. 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

573 new MeSH Headings were added to MeSH in 2011.

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 2011 concepts on the MeSH New Descriptors Web page.

Category A - Anatomy: Animal Fins; Arthropod Antennae; Chromosomal Puffs; Chromosomes, Insect; Nematocyst; Neural Stem Cells; Polytene Chromosome; Sensilla
Category B - Organisms: Aquatic Organisms; Hermaphroditic Organisms; Influenza A Virus, H10N7 Subtype; Influenza A Virus, H7N1 Subtype; Influenza A Virus, H7N2 Subtype; Influenza A Virus, H7N3 Subtype; Introduced Species; Livestock; Mice, 129 Strain; Pets
Category C - Diseases: Acute Kidney Injury; Anastomotic Leak; Asymptomatic Diseases; Asymptomatic Infections; Conducted Energy Weapon Injuries; Diabetic Cardiomyopathies; Digital Dermatitis; Intraoperative Awareness; Neglected Diseases; Out-of-Hospital Cardiac Arrest; Peripheral Arterial Disease; Post-Exercise Hypotension
Category D - Chemicals and Drugs: Antibodies, Monoclonal, Murine-Derived; Asymptomatic Diseases; Asymptomatic Infections; Bleaching Agents; Calcimimetic Agents; Cerumenolytic Agents; Counterfeit Drugs; Hair Bleaching Agents; Hygroscopic Agents; Iridoid Glucosides; Iridoid Glycosides; Lipid Regulating Agents; Nonsteroidal Anti-Androgens; Plasma Gases; Peptidomimetics
Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment: Argon Plasma Coagulation; Bloodless Medical and Surgical Procedures; Diagnostic Self Evaluation; DNA Contamination; Drug Repositioning; Drug Substitution; Enzyme Therapy; Fiducial Markers; Inappropriate Prescribing; Ischemic Postconditioning; Lost to Follow-Up; Medication Reconciliation; Mesotherapy; Molecular Targeted Therapy; Natural Orifice Endoscopic Surgery; Operative Blood Salvage; Opiate Substitution Treatment; Perioperative Period; Self Report; Serum Bactericidal Antibody Assay; Sex Reassignment Procedures; Sex Reassignment Surgery
Category F - Psychiatry and Psychology: Bullying; Catastrophization; Drug-Seeking Behavior
Category G - Biological Sciences: Bacterial Load; Bacterial Secretion Systems; Carbon Cycle; Carbon Footprint; Catabolite Repression; Cell-in-Cell Formation; Circadian Clocks; Cold-Shock Response; Cytophagocytosis; El Nino-Southern Oscillation; Emperipolesis; Entosis; Host Specificity; Microbial Consortia; Nitrogen Cycle; Peripartum Period; Plant Immunity; Seed Dispersal; Seed Dormancy; Self-Fertilization; Spinal Cord Regeneration; Stem Cell Research; Transcellular Cell Migration; Virus Uncoating; Water Cycle
Category H - Natural Sciences: Epigenomics; General Practice; Neuropsychiatry; Orthognathic Surgery; Stem Cell Research
Category I - Anthropology, Education, Sociology and Social Phenomena: Gross Domestic Product; Social Participation; Test Taking Skills
Category J – Technology, Industry, and Agriculture: Agricultural Irrigation; Food, Organic; Molecular Farming; Organic Agriculture; Synbiotics; Weed Control
Category L - Information Science: Information Literacy; Molecular Sequence Annotation
Category M - Named Groups: Doulas; General Practitioners; Physicians, Primary Care
Category N - Health Care: Electronic Waste; Environmental Policy; Epidemics; Food Safety; For-Profit Insurance Plans; Not-For-Profit Insurance Plans; Informed Consent By Minors; Pandemics; Patient Protection and Affordable Care Act; Recycling; United States Department of Defense
Category Z - Geographicals: Black Sea; Confederate States of America

Changes to MeSH Headings

This year 71 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:

The Algae tree was disassembled because it was determined that the MeSH Heading "Algae" was not a useful concept in a taxonomic-based hierarchy. For 2011 MeSH, Algae is being deleted and its children distributed among the appropriate eukaryotic trees.

Specific 'algae' are retained as Entry Terms (ET) for the following descriptors:

Treed under Plants and coordinated as appropriate with Plant DNA; Plant RNA; or Plant Proteins:

            Chlorophyta
                ET: Algae, Green
            Rhodophyta
                ET: Algae, Red

Treed under Eukaryota and coordinated as appropriate with DNA; RNA; or Proteins:

            Phaeophyta
                ET: Algae, Brown
            Chrysophyta
                ET: Algae, Golden-Brown

The following MeSH Headings will no longer be used for indexing, in light of the Algae tree being disassembled:

Algal Proteins

Algal DNA

Algal RNA

Livestock and Pets are now separate descriptors treed under Animals, Domestic. Note that Livestock excludes Poultry.
Hermaphroditism and Pseudohermaphroditism are replaced with the MeSH Heading: Disorders of Sex Development. Hermaphroditism and Pseudohermaphroditism are Entry Terms for this heading.
Hermaphroditism, True was replaced with the heading Ovotesticular Disorders of Sex Development. Hermaphroditism, True is an Entry Term for this heading.

In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2011 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) for chemicals 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 2011 MeSH is the changing of Disorders of Sex Development to Sex Determination Processes on appropriate 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.

New and changed Publication Types (PT) for 2011

For 2011, indexers will begin using a new Publication Type, Video-Audio Media for MEDLINE citations.

Also in 2011, MeSH changed two other publication types:

Instruction was replaced by Instructional Films and Videos (This PT is not used on MEDLINE citations. It is used only in cataloging)

Personal Narratives was replaced by Autobiography

Related to this Publication Type change above, there was a MeSH Heading change where Autobiography was replaced by Autobiography as Topic. Autobiography was previously used by indexers for both articles about the subject of autobiographies as well as articles that were themselves autobiographies. Following up on this, during Year-End Processing NLM identified citations within the MEDLINE set which were changed to the MeSH Heading Autobiography as Topic that were really the Publication Type meaning. For these citations, the MeSH Heading was deleted and the new Publication Type was added.

While not to be used for indexing or cataloging, searchers will find these two new Publication Types useful to collect all indented PTs in the automatic explosions:

Electronic Supplementary Materials
- Video-Audio Media
  - Interactive Tutorial
  - Webcasts

Research Support, U.S. Government
- Research Support, American Recovery and Reinvestment Act
- Research Support, U.S. Gov't, Non-P.H.S.
  - Research Support, U.S. Gov't, P.H.S.
  - Research Support, N.I.H., Extramural
  - Research Support, N.I.H., Intramural

Notable MeSH Changes and Related Impact on Searching

Acute Kidney Injury is not to be used for traumatic kidney injury which is indexed as Kidney/injuries.

For Counterfeit Drugs, if the meaning of the article is the action of counterfeiting, then indexers will coordinate with the MeSH Heading, Fraud.

Stem Cell Research is used in the sense of a specialty heading (which includes the topics of ethical, legal, moral, social, or religious aspects); it is not to be used routinely for research involving stem cells.

Note the introduction of Supplementary Concept Records (SCR) for diseases. About 3,000 diseases were added as SCRs in addition to 880 existing MeSH Headings that were enhanced with Entry Terms as the NLM MeSH Section incorporated terminology provided by the NIH Office of Rare Diseases. All SCR diseases are mapped to a MeSH Heading, e.g.:

: SCR Disease: Anders' syndrome; MeSH Heading map: Adiposis Dolorosa

That is, all citations for articles indexed with Anders' syndrome will also be indexed with the MeSH Heading, Adiposis Dolorosa. See the forthcoming article, PubMed Notes – 2011, for PubMed searching and display of Supplementary Concept diseases.

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 96 new Entry Combinations new for 2011 listed in a separate table.

Additional Changes to MEDLINE and OLDMEDLINE Data

Number of References
Effective October 1, 2010 NLM discontinued the practice of including the number of bibliographic references listed in articles cited in MEDLINE. NLM had included the number of references (displayed in the PubMed MEDLINE format as RF) for the following Publication Types:

Review

Consensus Development Conference

Consensus Development Conference, NIH

Interactive Tutorial

Meta-Analysis

This change in policy is prospective only; we will not remove number of references data from existing citations.
MEDLINE Character Set
Effective in September 2010, NLM now accepts for newly created MEDLINE citations any UTF-8 character in the Latin (Roman) and Greek scripts as well as mathematical and other symbols commonly found in biomedical literature. Other scripts such as Chinese, Japanese or Korean are not supported. For more details see the article, MEDLINE® Character Set Expansion.
Structured Abstracts
With the export of the baseline files after YEP to licensees, the journal citations identified as "Structured Abstracts" will have their author abstracts physically divided into segments. Abstracts not defined as Structured will export as they always have done.
Versioning Information
In order to accommodate a new model of publishing referred to as versioning, whereby multiple versions of the same online article are released in order to support the rapid prototyping of research, NLM will, beginning with the 2011 production year, create an individual citation for each article’s version and associate the versions via new attributes for the MEDLINECitation and PMID elements. This redesign is in anticipation of this new publication model; only a few journals have been identified that may use this model. One example is the journal, PLoS Currents.
Disease Supplementary Concept Records
Currently NLM exports MeSH SCR chemical and drug terms (class 1) and protocol terms (class 2) in the MEDLINE ChemicalList fields. Beginning with 2011 NLM will export Protocol and Disease terms (SCR classes 2 and 3) in the new SupplMeshList fields, leaving only class 1 (true chemical terms) in the ChemicalList.
Geographic MeSH Terms
Beginning with 2011 NLM will separate out MeSH geographic terms from other MeSH descriptors by use of a Type attribute in the MEDLINE DTD.
Cites Data
In the fall of 2010 NLM processed files to add new or changed cites data to MEDLINE citations. We added 5.5 million cites. This update added to the initial cites load we received in the fall of 2009. There are now about 32 million cites on about 1,297,000 citations.

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.
Article Title Ending Punctuation
In October 2010 NLM maintained over 4 million citations to bring the ending punctuation for non-English language citation article titles in line with the current bibliographic standard. All non-English citations now end with a period outside the closing bracket in the article title field. No Last Revision Date was added to these citations because of the large number involved.

By Sara Tybaert
MEDLARS Management Section

Tybaert S. MEDLINE® Data Changes — 2011. NLM Tech Bull. 2010 Nov-Dec;(377):e12a.