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2006 NOVEMBER–DECEMBER; 353
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November 16, 2006 [posted]
December 01, 2006 [Sentence modified]

MEDLINE® Data Changes — 2007

this time of year the NLM Technical Bulletin traditionally includes information on changes made to MEDLINE® during annual National Library of Medicine® (NLM® ) maintenance known as Year-End Processing. This article collects in one place the notable data changes for 2007; mention of a topic may be linked to another article where details will be found. For information on how this maintenance affects the NLM schedule for adding indexed MEDLINE citations to PubMed®, see the article, MEDLINE®/PubMed® End-of-Year Activities. NLM Tech Bull. 2006 Sep-Oct;(352):e6.

A new Web page, National Library of Medicine (NLM) Annual MEDLINE/PubMed Year-End Processing Activities, provides background and examples about the typical changes that take place for MEDLINE citations during year-end processing.

MeSH® Vocabulary Updated for 2007

The MeSH Browser currently contains a link to the 2007 MeSH vocabulary. Searchers should consult the Browser to find MeSH headings of interest and to see these in relationship to other headings. The Browser contains MeSH Headings 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.

For highlights about 2007 MeSH see the article, What's New for 2007 MeSH, in this issue of the NLM Technical Bulletin.

PubMed's MeSH database and translation tables will be updated to reflect 2007 MeSH in mid-December when end-of-year activities are complete and the newly maintained MEDLINE data are available in PubMed.

Updated MeSH in MEDLINE Citations

MEDLINE citations with updated MeSH should be in PubMed in mid-December 2006. See the Changing a saved search section in PubMed Help for details on revising My NCBI stored searches.

The MeSH Section homepage provide links to descriptions of the different types of MeSH maintenance applied to MEDLINE citations. In addition to the information found in the Introduction to MeSH, 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. This information is helpful for those individuals or organizations who apply MeSH headings to their own application (such as indexing curricula guides) and want to keep those applications up-to-date with the new year of MeSH.

New MeSH Headings

This year 494 new MeSH Headings were added.

Typically, NLM does not retrospectively re-index MEDLINE citations with new MeSH Headings. Therefore, searching for a new MeSH term tagged with [mh] or [majr] effectively limits retrieval to citations indexed after the term was introduced. PubMed's Automatic Term Mapping (ATM) expands an untagged subject search to include both MeSH Term and Text Word(s), and may retrieve relevant citations indexed before the introduction of a new MeSH term.

A notable exception this year to the general rule of not retrospectively re-indexing MEDLINE citations with brand new concepts is Papillomavirus Vaccines, a new 2007 Category D heading shown below. The scientific importance of this topic prompted NLM to add this new heading to existing citations. Searching on Papillomavirus Vaccines will, therefore, retrieve citations indexed before the implementation of 2007 MeSH even though the History Note in the 2007 MeSH Browser shows 2007 as the date of introduction for this concept.

Brand New Concepts

Examples of new 2007 MeSH headings of special interest to searchers are highlighted below by Category to give you an idea of what is forthcoming. Be sure to use the link above to browse all of the new 2007 concepts.

Category A
Embryonic Stem Cells
Fetal Stem Cells
Adult Stem Cells
Please note that NLM indexing policy for these three new terms above dictates that if the article discusses transplantation of a specific type of stem cells, indexers shall index the specific stem cell with the subheading /transplantation. They will not coordinate with STEM CELL TRANSPLANTATION.
Blastocyst Inner Cell Mass [related to stem cells]
Category C
Cardiovascular Infections
Female Athlete Triad Syndrome
Lethargy
Stupor
Category D
Dengue Vaccines
Herpes Zoster Vaccines
Papillomavirus Vaccines
West Nile Virus Vaccines
Category G
DNA Breaks
DNA Breaks, Double-Stranded
DNA Breaks, Singly-Stranded
DNA Cleavage
DNA Degradation, Necrotic
DNA Fragmentation
DNA Mismatch Repair
Environmental Remediation
Extinction, Biological
Gene Regulatory Networks
Herbicide Resistance
Microsatellite Instability
Wetlands
Category J
Metal Nanoparticles
Nanocapsules
Nanocomposites
Nanoparticles
Nanowires
Category M
Infant, Extremely Low Birth Weight
[weight at birth is fewer than 1000 grams (2.2 lbs), regardless of gestational age]

Changes to MeSH Headings

This year, 120 MeSH Headings were either changed or deleted and replaced with more up-to-date terminology. During year-end processing, NLM updates MeSH headings on the MEDLINE citations.

In addition to the replaced-by heading changes, year-end processing includes adjustments to MEDLINE citations to reflect 2007 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 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. Some examples follow.

These types of changes suggest the importance of routinely using PubMed's Details feature when searching to see how terms are mapped in the new year's vocabulary and then checking the MeSH Browser or PubMed's MeSH database for clarification.

Replaced heading; old heading deleted and not retained as entry term to new heading; adjustments to search strategies needed; further adjustments made to existing citations

Example:
In 2006 MeSH, the term Urogenital Diseases was in two trees under:
Urologic and Male Genital Diseases
Female Genital Diseases and Pregnancy Complications
In 2007 MeSH, the term Urogenital Diseases was deleted and replaced with:
Female Urogenital Diseases
The term Urologic and Male Genital Diseases was replaced with:
Male Urogenital Diseases

Citations previously indexed with Urogenital Diseases will be globally maintained to have this term replaced with the term Female Urogenital Diseases. Therefore, NLM will be processing additional tasks to insure that the citations properly have the correct MeSH heading Female Urogenital Diseases and/or Male Urogenital Diseases on them.

Example:
In 2007 MeSH, Tampons is being replaced with the heading Tampons, Surgical. Citations indexed to Tampons will get this new heading. NLM will be processing follow-up tasks to insure that citations which were related to Menstrual Hygiene Products will get that appropriate heading rather than the Tampons, Surgical heading.

Replaced heading; old heading deleted and not retained as entry term to new heading; adjustments to search strategies needed; no further adjustments made to existing citations beyond the replaced headings

Example:
In 2007, the MeSH heading Nutrition was split into two concepts:
Nutritional Sciences
Nutrition Physiology

A global change will replace Nutrition on previously indexed citations with the heading Nutrition Physiology. A similar change will happen for other Nutrition headings:

Adolescent Nutrition to Adolescent Nutrition Physiology
Animal Nutrition to Animal Nutrition Physiology
Child Nutrition to Child Nutrition Physiology
Infant Nutrition to Infant Nutrition Physiology
Maternal Nutrition to Maternal Nutrition Physiology
Prenatal Nutrition to Prenatal Nutrition Physiology


Nutritional Sciences (or its specifics) is to be used to index articles about nutrition as a specialty and/or about educational, historical, economic, and legislative aspects of nutrition.

Nutrition Physiology (or its specifics) is to be used to index articles about physiological, immunological and genetic aspects of nutrition.

Example:
Another example of a heading that has been deleted from the MeSH vocabulary is:
Interleukin 14

Citations that had Interleukin 14 on them will have this term replaced with the general term Interleukins.

Scope Note Change
Example:
A term whose scope note definition has changed for 2007 is:
Genes, MDR

In 2006 this term was restricted to mammalian cells (eukaryotes).
In 2007 the term's definition expanded to include prokaryotes as well as eukaryotes.

Entry Term Elevation
Example:
An entry term that has been elevated to a new MeSH heading is:
Pollen Tube

Pollen Tube had been an entry term to the MeSH heading Flowers. If Pollen Tube was used in saved searches, it retrieved citations indexed to Flowers. Now, for 2007, the meaning is more specific.

Retreeing
The position of headings in the MeSH Trees can change from year to year.

Example:
Vitamins is now in the J2 tree as well as the D27 tree for 2007 MeSH.

Other Notable MeSH Changes and Related Impact on Searching


Publication Type Change

All of the MeSH Category V terms previously identified as MeSH Headings (MH) will be identified as Publication Type (PT) values in the MEDLINE citations:

  1. [The following sentence was modified on December 1, 2006.]
    The V04 branch of six descriptors of which the five indented terms are used for indexing on journal citations:
    • Support of Research [V04]
      • Research Support, Non-U.S. Gov't [V04.124]
      • Research Support, U.S. Gov't, Non-P.H.S. [V04.249]
      • Research Support, U.S. Gov't, P.H.S. [V04.500]
      • Research Support, N.I.H., Extramural [V04.500.500]
      • Research Support, N.I.H., Intramural [V04.500.750]
  2. In Vitro [V03.500]
  3. Comparative Study [V03.250]
  4. English Abstract [V01.260]

Entry Combination Revisions

This year during year-end processing, NLM will again retrospectively replace certain MeSH heading/subheading combinations, known as entry combinations, with the appropriate precoordinated MeSH heading or other MeSH heading/subheading combination in MEDLINE citations. Searchers who get zero retrieval for a MeSH Heading/subheading combination may want to check the 2007 MeSH Browser for the heading to see if the Entry Combination information indicates a different term.

Here are the eighteen Entry Combinations new for 2007:

Previous MeSH Heading/Subheading
(Entry Combination)
Replaced Heading for 2007
Cell Nucleus/transplantation Nuclear Transfer Techniques
Edar-Associated Death Domain Protein/deficiency Ectodermal Dysplasia, Hypohidrotic, Autosomal Recessive
Keratin-1/deficiency Hyperkeratosis, Epidermolytic
Keratin-3/deficiency Corneal Dystrophy, Juvenile Epithelial of Meesmann
Keratin-4/deficiency Leukokeratosis, Hereditary Mucosal
Keratin-5/deficiency Epidermolysis Bullosa Simplex
Keratin-6/deficiency Pachyonychia Congenita
Keratin-9/deficiency Keratoderma, Palmoplantar, Epidermolytic
Keratin-10/deficiency Hyperkeratosis, Epidermolytic
Keratin-12/deficiency Corneal Dystrophy, Juvenile Epithelial of Meesmann
Keratin-13/deficiency Leukokeratosis, Hereditary Mucosal
Keratin-14/deficiency Epidermolysis Bullosa Simplex
Keratin-16/deficiency Pachyonychia Congenita
Keratin-17/deficiency Pachyonychia Congenita
Nails/abnormalities Nails, Malformed
PHEX Phosphate Regulating Neutral Endopeptidase/deficiency Hypophosphatemic Rickets, X-Linked Dominant
Transforming Growth Factor beta1/deficiency Camurati-Engelmann Syndrome
alpha-Galactosidase/deficiency Fabry Disease

Additional Changes to MEDLINE and OLDMEDLINE Data


1. OLDMEDLINE Status change

There are two changes. First the status tag [PubMed - OLDMEDLINE for pre1966] will be simplified to [PubMed - OLDMEDLINE]. The second change is for those OLDMEDLINE citations which have had their Old Term keyword mapping to MeSH completed, the PubMed citation status will be changed from [PubMed - OLDMEDLINE] to [PubMed - indexed for MEDLINE]. These records will be retrieved when limiting to the MEDLINE subset, or when searching medline [sb]. Searchers not interested in these older citations are advised to restrict their searches using the date range function within the Limits feature, or to set up a filter for publication date.

2. Partial Retraction notations

NLM is adding two fields to the MEDLINE citation: Partial retraction in and Partial retraction of. These fields are established as a means of distinguishing between a journal article that is retracted in whole (reflected by the use of the already existing Retraction of and Retraction in elements) versus one that is retracted in part (e.g., a cell line was contaminated but that didn't affect all results/conclusions of the paper). Partial retraction of contains the bibliographic reference of an article being partially retracted, and is present in the citation for the notice of partial retraction. Partial retraction in contains the bibliographic reference of the notice of partial retraction, and is present in the citation for the original paper.

Beginning in December 2006 NLM will begin to cite partial retractions. Older citations may be edited to use these new fields.

Partial Retraction
Summary Display: Partial retraction in:
Abstract/Citation Displays: Partial retraction in:
Partial retraction of:
MEDLINE Display: PRIN
PROF
Search phrase: haspartialretractionin
haspartialretractionof
XML names: PartialRetractionIn
PartialRetractionOf

3. Full Journal Title format change in MEDLINE citations

Some MEDLINE journal titles contain the general material designation (GMD), within brackets, as a part of the full journal title. NLM is removing the bracketed GMD from the journal titles during year-end processing. However, you may find this change reflected on some citations before the new system is available in mid-December. Generally this designation is the value [electronic resource]. With so many journals now available online the qualifier is not necessary for the journal title display. Ending periods are also being removed.

The following example shows how a full journal title with a GMD currently looks in the MEDLINE display in PubMed:

      JT — BMC bioinformatics [electronic resource].

After the title has been revised it will look like this:

      JT — BMC bioinformatics

The full journal title display in the Journals database will also change.

Additional Information

Consult the new Annual MEDLINE/PubMed Year-End Processing Activities Web page for information about:

Heading Mapped-To (HM) Maintenance
EC/RN Numbers (RN) and Name of Substance (NM)
Supplementary Concept Records (SCRs) Elevated to MeSH Headings
Pharmacological Actions (PA)

By Sara Tybaert
MEDLARS Management Section

Tybaert S. MEDLINE Data Changes — 2007. NLM Tech Bull. 2006 Nov-Dec; (353):e3.

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