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November 26, 2007 [posted]
November 28, 2007 [Editor's note added]
December 13, 2007 [updated]

MEDLINE® Data Changes — 2008

a t this time each 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 (YEP). This article collects, in one place, the notable data changes for 2008. Some topics 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 Year-End Processing (YEP) Activities. NLM Tech Bull. 2007 Sep-Oct;(358):e10.

This article links to two addtional resources: [link removed] Annual MEDLINE/PubMed Year-End Processing (YEP): Impact on Searching During Fall 2007 and [link removed] Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information which has examples for the typical changes that take place for MEDLINE citations during year-end processing.

MeSH® Vocabulary Updated for 2008

The MeSH Browser currently contains a link to the 2008 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 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.

This year, for the first time, the MeSH Tree Structures are available online in both PDF and HTML formats with all indented terms showing.

For highlights about 2008 MeSH see the forthcoming article, What's New for 2008 MeSH, in this issue of the NLM Technical Bulletin.

The PubMed MeSH database and translation tables will be updated to reflect 2008 MeSH in early 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 early December 2007. See the [link removed] Changing a saved search section in PubMed Help for details on revising My NCBI saved searches.

The MeSH Section homepage provides links to descriptions of MeSH maintenance. 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 using MeSH headings in 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 456 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'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. 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 2008 concepts on the MeSH New Descriptors Web page.

Category A
Embryonal Carcinoma Stem Cells
Cerebrum (with entry terms of Cerebral Hemispheres; Left Cerebral Hemisphere; Right Cerebral Hemisphere)
Muscle, Striated
Peritoneal Stomata (i.e., natural openings as contrasted with Surgical Stomas, i.e., artificial openings)

Category B
Four new specific strains of E. coli added and the tree revised:
Enterohemorrhagic Escherichia coli
Enteropathogenic Escherichia coli
Enterotoxigenic Escherichia coli
Shiga-Toxigenic Escherichia coli

Category C
There was a major reclassification and retreeing of the Leukemia and Lymphoma terms based on the International Classification of Diseases for Oncology, third edition (ICD-O-3). The following new headings were added:
Leukemia, Prolymphocytic, B-Cell
Leukemia, Large Granular Lymphocytic
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Precursor B-Cell Lymphoblastic Leukemia-Lymphoma
Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative
Leukemia, Myelomonocytic, Juvenile
Lymphoma, Extranodal NK-T-Cell
Lymphoma, Primary Cutaneous Anaplastic Large Cell
NOTE: Most of the "old headings" were retained in MeSH as entry terms except for following four:
Leukemia, CALLA-positive (index as Precursor B-Cell Lymphoblastic Leukemia-Lymphoma)
Leukemia, Null-cell (index as Precursor B-Cell Lymphoblastic Leukemia-Lymphoma)
Leukemia, Subleukemic (index as Leukemia)
Leukemia, T-Cell, HTLV-II-Associated (index as Leukemia, T-Cell)

[Editor's Note: The following paragraph was updated on December 13, 2007.]
There were also significant changes related to the Coronary Disease tree. It was retreed. Angina Pectoris is no longer treed under Coronary Disease. Coronary Disease, Angina Pectoris and the new heading Acute Coronary Syndrome are all at the same tree level for 2008. The following new terms were added to the Coronary Disease tree:
Coronary Artery Disease (with entry terms of Coronary Arteriosclerosis and Coronary Atherosclerosis)
Coronary Occlusion (do not confuse with Coronary Stenosis)
Acute Coronary Syndrome

Heart Failure (with entry term of Heart Failure, Congestive)
Heart Failure, Diastolic
Heart Failure, Systolic

Extensively Drug-Resistant Tuberculosis (not to be confused with Tuberculosis, Multidrug-Resistant)

Category D
Biomarkers, Pharmacological (use only in context of drug development, safety, or dosage determination)
Retinol-Binding Proteins, Cellular
Retinol-Binding Proteins, Plasma

Category E
All laser therapeutic techniques are now grouped under one general heading:
Laser Therapy (coordinate with disease term/surgery)
Angioplasty, Laser (coordinate with disease term/surgery)
Corneal Surgery, Laser (coordinate with disease term/surgery)
Laser Coagulation (coordinate with disease term/surgery)
Laser Therapy, Low-Level (coordinate with disease term/radiotherapy)
Lithotripsy, Laser (coordinate with disease term/therapy)

New specific laser terms:
Lasers, Dye
Lasers, Excimer
Lasers, Gas
Lasers, Semiconductor
Lasers, Solid-State

Category G

Category I
New headings were added for each NIH Institute. In the past there were only headings for National Institutes of Health (U.S.), National Institutes of Mental Health (U.S.) and National Library of Medicine (U.S.).
Peace Corps
United States Agency for International Development
United States Department of Homeland Security
United States Office of National Drug Control Policy

Category N
Blue Cross Blue Shield
Medicare Part D
Men’s Health
Minority Health
Medication Therapy Management (use only in context of insurance paying for drugs)

New Disaster-Related Headings
Disaster Medicine
Mass Casualty Incidents
Weapons of Mass Destruction
A new entry term of note for the MeSH term Civil Defense is Emergency Preparedness.

Additonal Tree for the MeSH Heading: Access to Information

In the past Access to Information was treed only under the Category I tree for Privacy. Now it is located in two trees: Category I Privacy and Category L Publishing.

MeSH Heading/Publication Type Pairs

For 2008 MeSH there was a major revision of Publication Types (PT) and corresponding subject descriptors (MeSH Headings). The goal of this revision was to make clear the distinction between the descriptors that are "about" certain topics/subjects and the Publication Types that identify the form of the information presented. The change to the MeSH Headings was to add the phrase "as Topic" to the end of the headings. For example, the revised descriptor "Clinical Trials as Topic" would be used to retrieve articles about design, methodology, economics, etc. of clinical trials, while the Publication Type "Clinical Trial" should be used to retrieve original reports of the conduct or result of a specific clinical trial. In summary, there is no change to indexing policy as to when to assign a MeSH Heading versus a Publication Type (only the preferred form of the terms has changed).

The following are revised MeSH Headings that correspond to the Publication Types used for journal article indexing:

Bibliography as Topic
Biography as Topic
Clinical Trials as Topic
Clinical Trials, Phase I as Topic
Clinical Trials, Phase II as Topic
Clinical Trials, Phase III as Topic
Clinical Trials, Phase IV as Topic
Congresses as Topic
Consensus Development Conferences as Topic
Consensus Development Conferences, NIH as Topic
Controlled Clinical Trials as Topic
Correspondence as Topic
Dictionaries as Topic
Directories as Topic
Duplicate Publication as Topic
Evaluation Studies as Topic
Government Publications as Topic
Guidelines as Topic
Interviews as Topic
Legislation as Topic
Meta-Analysis as Topic
Multicenter Studies as Topic
Patient Education as Topic
Practice Guidelines as Topic
Randomized Controlled Trials as Topic
Retraction of Publication as Topic
Review Literature as Topic
Twin Studies as Topic
Validation Studies as Topic (New for 2008)

Publication Type Change

For 2008 all publication type terms in MeSH will lose the bracketed rubric "[Publication Type]" at the end of the term name. Example: Clinical Trial [Publication Type]. This change is of note if a user is in the MeSH Browser, but, it will not mean a change to either the display or the searching of MEDLINE citations in PubMed because the publication type rubric was never carried as part of the term name in citation data.

New Publication Types

For 2008 MeSH two new publication types have been added to the vocabulary and will be used on MEDLINE citations:

1. Interactive Tutorial
Interactive Tutorial describes items published online and consisting primarily of non-narrative text, such as a video recording or other interactive content in which the sequence of content presented depends upon interaction from the user. The only narrative text may be the abstract; otherwise there is little or no "traditional" narrative text.

Examples are:

This new publication type will not be applied if a video or other interactive content is only a part of the supplemental or other minor portion of a published article.

In the near future, NLM will apply this new PT retrospectively to existing citations that qualify. When used, no other PT is assigned. Even though treed under Review [pt], the number of references, if they exist, will not be counted nor appear in the MEDLINE citation.

2. Introductory Journal Article
Introductory Journal Article describes prefatory summaries or introductions to a special issue or a section of a journal devoted to a specific topic. Prior to 2008, introductions were not cited if they merely served to summarize each article that followed, or if the introduction did not include substantive, original content. However, the policy for a citation in MEDLINE still requires that the introductory or prefatory texts must discuss scholarly or scientific subject matter; texts that only thank contributors, acknowledge financial or organizational support, or the like are not cited in MEDLINE.

If the title of the text states "Editorial Introduction" or "Editorial Preface" or other variations of "editorial," then Editorial [pt] is applied in addition to Introductory Journal Article [pt].

Even if an introductory article has cited references, these items are not considered to be Review [pt]. Comment linkages to the specific articles discussed will not be made.

Changes to MeSH Headings

This year 334 MeSH Headings were either changed or deleted and replaced with more up-to-date terminology. During YEP, NLM updates MeSH headings on MEDLINE citations.

In addition to the replaced-by heading changes, year-end processing includes adjustments to MEDLINE citations to reflect 2008 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. Some examples follow.

Replaced-by heading; old heading retained as entry term to another heading; adjustments made to existing citations beyond the replaced headings

In 2008 the MeSH Heading "Embryo" was replaced by the MeSH Heading "Embryo, Mammalian." "Embryo" was retained as an Entry Term in MeSH, but it now maps to Embryonic Structures which is a parent term to both Embryo, Mammalian and Embryo, Nonmammalian. This mapping will ensure a comprehensive explosion in PubMed.

NLM performed additional maintenance on existing citations for three scenarios:

  1. Changed Embryo, Mammalian to Embryo, Nonmammalian when there is evidence in the citation that the species is nonmammalian.
  2. Added Embryo, Nonmammalian when there is evidence that both mammal and non-mammal embryos are discussed.
  3. Added Embryo, Nonmammalian when there is no evidence as to what species is discussed.

Replacing a MeSH Heading with a different MeSH Heading does not change the major status or the subheadings applied. However, if a MeSH Heading is added to a citation it is added without subheadings. The major emphasis (starred heading) is applied.

Replaced-by heading: old heading is deleted and is not retained in MeSH, new term is an SCR

In 2008 the MeSH Heading "Gene Products, vpu" is replaced by the Supplementary Concept Record, "vpu protein, Human immunodeficiency virus 1." In other words, search this "old" MeSH Heading as: vpu protein, Human immunodeficiency virus 1 [nm]

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 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 the MeSH Database for clarification.

Other Notable MeSH Changes and Related Impact on Searching

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 heading in the 2008 MeSH Browser to see if the Entry Combination information indicates a different term.

Here are the eleven Entry Combinations new for 2008:

Previous MeSH Heading/Subheading
(Entry Combination)
Replaced-by Heading for 2008
Face/transplantation Facial Transplantation
Lasers/therapeutic use Laser Therapy
Refractive Errors/surgery Refractive Surgical Procedures
Complement C1 Inhibitor Protein/deficiency Angioedema, Hereditary
Atrial Septum/abnormalities Heart Septal Defects, Atrial
Ventricular Septum/abnormalities Heart Septal Defects, Ventricular
Endocardial Cushions/abnormalities Endocardial Cushion Defects
Hexosaminidase B/deficiency Sandhoff Disease
beta-Hexosaminidase alpha Chain/deficiency Tay-Sachs Disease
beta-Hexosaminidase beta Chain/deficiency Sandhoff Disease
Von Ebner Glands/radiography Sialography

Pharmacological Action

Two new Pharmacological Action [PA] terms for 2008 are:

Additional Changes to MEDLINE and OLDMEDLINE Data

1. Two new fields are being added to the MEDLINE citation starting in 2008

2. Investigator List (Collaborators)
The Investigator field in the MEDLINE citation will begin to be used for MEDLINE/PubMed in the 2008 production year to contain personal names of individuals (e.g., collaborators and investigators) who are not authors but rather are listed in the paper as members of a collective/corporate group that is an author of the paper. The personal names in this list will not be associated with the specific collective/corporate group author in which they are listed in the paper. The names will be listed in the order in which they are published; the same name listed multiple times will be repeated because NLM can not make assumptions as to whether those names are the same person.

Prior to 2008 production year Investigator data only appears on citation data created or maintained by our past collaborating data producer, the National Aeronautics and Space Administration (NASA). NASA used the data to identify NASA funded principal investigator(s) who conducted the research discussed in the article cited (but are not necessarily the authors).

3. Grant Number (GR) Field
Several changes are being made to the Grant Number (GR) field. Please see the forthcoming article, More Changes to Grant Number Information, in this issue of the NLM Technical Bulletin. [Editor's Note: This article was published on November 28, 2007.]

4. Update on most recent identification of Clinical Trials in MEDLINE records:
In September 2006 NLM, working with the Cochrane Collaboration, maintained over 4,000 citations to enhance or correct the identification of clinical trials as a Publication Type in MEDLINE. This large set of data changes included two years worth of changes (2004 and 2005). Data for 2006 and 2007 have not yet been received from the Cochrane Collaboration.

Additional Information

Consult the Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information Web page, especially the Recurring Annual Changes and References sections.

By Sara Tybaert
MEDLARS Management Section

Tybaert S. MEDLINE Data Changes — 2008. NLM Tech Bull. 2007 Nov-Dec; (359):e6.

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