MEDLINE Data Changes - 2003

his 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. For information on how this maintenance affects NLM's schedule for adding indexed MEDLINE citations to PubMed^® , see the article, MEDLINE^® /PubMed^® End-of-Year Activities in the September-October 2002 issue of the NLM Technical Bulletin.

What changes will I see?

• The annual update to Medical Subject Headings (MeSH^®), NLM's controlled vocabulary used for subject indexing and retrieval
• Updated MeSH in MEDLINE citations to reflect changes in MeSH vocabulary including entry combination revisions
• Other changes to data in MEDLINE citations including identification of Clinical Trial and Publication Types

Annual Update to Medical Subject Headings: 2003 MeSH
The MeSH Section's MeSH Browser currently contains 2003 MeSH with a link to 2002 MeSH. Searchers should consult the MeSH Section's MeSH Browser to find descriptors of interest and to see these in relationship to other descriptors. The Browser displays virtually complete MeSH records, including the scope notes, annotations, entry vocabulary, history notes, allowable qualifiers (subheadings), etc. It also provides links to relevant sections of the NLM Indexing Manual. For details about 2003 MeSH see the article What's New for 2003 MeSH^® in this issue of the NLM Technical Bulletin. It is expected that PubMed's MeSH Browser and translation tables will be updated to reflect 2003 MeSH on November 26, 2002 when end-of-year activities are complete and the newly maintained MEDLINE is available via PubMed.

Updated MeSH in MEDLINE Citations

Updated MeSH may begin to appear on MEDLINE citations on November 26. See the article, Hands-On: Revising PubMed^® Cubby Stored Searches, in the November-December 2001 issue of the NLM Technical Bulletin for details on changing Cubby stored searches to reflect changes in MeSH.

• Changes to MeSH Headings
  During year-end processing, MeSH Headings in MEDLINE citations are updated to reflect changes in 2003 MeSH.

  For example, this year the old MeSH Heading Pineal Body has been changed to Pineal Gland in 2003 MeSH. MEDLINE citations indexed from 1966-2002 containing the MeSH term Pineal Body will all be changed to Pineal Gland. Another example is the deletion of the MeSH heading Actinobacteria Group in 2003 MeSH and all occurrences of that term in MEDLINE replaced by the new MeSH heading, Actinobacteria.

  Remember that the mapping of see references can also change. For example last year, "Allspice" was removed as, "See Rosales." Since 2002, it has been "See Pimenta" which has the History note of "2002; use Rosales 1998-2001, use SPICES 1993-1997."

  The bulk of the MeSH changes will be in place in PubMed on November 26. Additional changes to MEDLINE citations to reflect the 2003 MeSH vocabulary and enhance retrieval are expected to appear in PubMed during the following week(s). These follow-on adjustments are largely the adding of more MeSH headings or supplementary concept record Names of Substances (NM) to help refine retrieval. In some cases, the changes clarify areas where a single concept existed before but it is now represented by 2 or more specific concepts such as happened wtih the old heading Shrimp (see below).

• New MeSH Headings
  Please see highlights in What's New for 2003 MeSH^®. NLM Tech Bull. 2002 Nov-Dec;(329):e5.

  One new subheading, ethics, has been created. The Scope Note for "ethics" states that this new subheading will be "used with techniques and activities for discussion and analysis with respect to human and social values. The MeSH Heading Ethics is reserved for articles on ethics as a field of study."

  New headings related to bioethical concepts include:
  Anonymous Testing
  Posthumous Conception
  Embryo Research
  Fetal Research
  Research Embryo Creation
  Retrospective Moral Judgement
  Ethics Consultation
  Codes of Ethics
  Ethics, Research
  Moral Development
  

  New chromosomes MeSH headings include:
  Chromosomes, Human, X
  Chromosomes, Human, Y
  Chromosomes, Mammalian
  Chromosomes, Plant
  Multipotent Stem Cells
  Pluripotent Stem Cells
  Totipotent Stem Cells
  

  There are many new plant terms including:
  Flowering Tops
  Flowers
  

  Additional bacteria headings include:
  Leptospira interrogans serovar australis
  Leptospira interrogans serovar autumnalis
  Leptospira interrogans serovar canicola
  Leptospira interrogans serovar hebdomadis
  Leptospira interrogans serovar icterohaemorrhagiae
  Leptospira interrogans serovar Pomona
  Neisseria meningitidis, Serogroup A
  Neisseria meningitidis, Serogroup B
  Neisseria meningitidis, Serogroup C
  Neisseria meningitidis, Serogroup W-135
  Neisseria meningitidis, Serogroup Y
  Vibrio Cholerae O1 (letter O, not number zero)
  Vibrio Cholerae O139 (letter O, not number zero)
  

  Other new headings are: Ephrins (with 8 specific ephrins); Integrin Alpha Chains (with 15 specifics); and Integrin Beta Chains (with 2 specifics).

  Generally, NLM does not retrospectively index MEDLINE citations with new MeSH Headings. Therefore, searching for a new MeSH Term qualified as [MeSH Term] or [Major MeSH Topic] effectively limits retrieval to citations indexed after the term was introduced. An unqualified subject search in PubMed expands a search by including both MeSH Term and Text Words, and may retrieve relevant citations indexed before the introduction of a new MeSH Term.

  For example, a new MeSH term, "Echinacea" was introduced in 2000 MeSH. A PubMed query on November 13, 2002 for echinacea qualified as [MH] yields 92 citations indexed from 2000 to date. A simple, unqualified PubMed query for echinacea yields 208 citations, many of which were indexed prior to 2002.

• Other MeSH Changes
  The MeSH heading Shrimp was deleted and all occurrences of that term were replaced by the MeSH heading, Decapoda (Crustacea). Additional, maintenance tasks are being performed to find those citations previously indexed with Shrimp that should not have Decapoda (Crustacea) but should have that term replaced with one of the following new MeSH headings as appropriate: Palaemonidae, Pandalidae or Penaeidae which are all specific families of shrimp. The string "Shrimp" no longer occurs in MeSH because the word is ambiguous. Any searches containing the term "Shrimp" will no longer map to a MeSH heading and should be revised. This is one example of a deleted heading. Please consult the MeSH Browser/MeSH Pages for others.

  The MeSH heading Delivery is deleted as a MeSH heading in 2003 but not deleted from the 2003 MeSH vocabulary because it has a new status as entry term for the new MeSH heading Delivery, Obstetric. Maintenance tasks were performed to replace the MeSH heading Delivery with the new MeSH heading Delivery, Obstetric but the old term may still be used in searching PubMed for the concept. (Note: Entry terms in the MeSH vocabulary provide greater ease of use and accessibility to MeSH. They are synonyms, near-synonyms, abbreviations, alternate spellings, and other alternate forms that may be more familiar or easier to type. Generally, entry vocabulary may be used interchangeably with preferred descriptors for searching of PubMed.)

• Age Group MeSH Heading Tree Changes:
  For 2003, two major changes were made in the Age Groups tree. First, Adolescent replaces Adolescence; the former term remains an entry term. Second, both Adolescent and the Infant branch were pulled out of the Child branch and made "siblings" to Child. The Ages pull-down menu in the PubMed Limits function will be adjusted so that retrieval for All Child remains as in the past (i.e., 0-18 years) to accommodate retrieval for the age groups Adolescent and Child. However, if the MeSH heading, Child is used in a search, retrieval will be restricted to Child and Child, Preschool and not Adolescent nor any of the Infant headings. This may also have a major effect on stored searches using Child.
  
  
• MeSH policy on Supplementary Concept Records (SCR) for proteins:
  Creation of new SCRs for proteins is now limited to 11 model organisms that are considered to represent adequately a variety of classes commonly used in the medical literature. As a reminder, SCRs are controlled terms for names of substances discussed in articles and may also be used for searching in PubMed. In the past, an SCR was created for all sequenced proteins. Since most organisms are now sequenced, this list of SCRs has grown unwieldy and out of proportion with approximately 27,500 protein SCRs mapping to approximately 2,500 MeSH headings. New protein SCRs, therefore, are now limited to model organisms and those of biomedical significance. Currently the list includes the following 11 model organisms: Human, Rat, Mouse, Xenopus, Zebrafish, Drosophila, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Eschericia coli. Other model organisms may be added in the future. Examples of biomedically important proteins are: Proteins used as drugs/vaccines, implicated (mutated, quantitative difference) as biological markers in disease, proteins from pathogens, unusual enzymes, allergens, antigens, venoms, and toxins.

  The general format for a protein SCR now is "protein name, organism name." Examples are:

  1. for a model organism protein: E2L3 protein, Arabidopsis
  2. for a non-model organism protein with medical significance: NorA protein, Staphylococcus.

  Articles using non-model organism proteins will be indexed using the appropriate MeSH heading protein class and coordinated with the MeSH heading for the organism as well as having the SCR name of substance in the Substance Name [NM] field.

  In addition, MeSH headings for non-model, organism-specific proteins will not be created unless they are considered biomedically important such as proteins used as drugs and proteins related to diseases. New protein terms, either Descriptors or Supplementary Concept Records, will be qualified with the name of the organism from which the protein was isolated.

• Pharmacological Action (PA) for Supplementary Concept Records:
  A new policy has been established for PAs so that only well-established PAs will be included on new and existing SCRs. In the past, a PA would be added to new or existing SCRs based on information about the Pharmacological Action for that concept appearing in only one article. The new policy, effective August 2002, calls for adding PAs to new or existing SCRs only if the following three criteria are met:
  
  
  1. there must be more than 20 citations discussing the Pharmacological Action being exhibited by that drug;
  2. there must be substantial evidence that the Pharmacological Action is in effect in humans (i.e., it is used clinically); and
  3. a reasonable proportion of the literature (10%) on that drug account for those effects.

  As a result, more than 35,000 PAs were deleted from SCRs for 2003. The remaining SCR PAs follow the above rules.

Other Changes to MEDLINE Data

• Identification of Clinical Trials in MEDLINE
  For the ninth year, NLM continued to work with the Cochrane Collaboration to enhance the identification of clinical trials in MEDLINE. During 2002, "Randomized Controlled Trial" or "Controlled Clinical Trial" Publication Types were added to over 2800 MEDLINE citations identified by the Cochrane Collaboration. The updated MEDLINE citations will be available in the 2003 PubMed system.
  
  
• Entry Combination Revisions
  An entry combination (EC) is an explicit illegal MeSH heading/subheading. These are "illegal" because the concept has been replaced with a precoordinated MeSH heading. This year during year-end processing, NLM again replaced ECs newly established for 2003 MeSH with the legal, precoordinated MeSH heading in MEDLINE citations (e.g., the illegal combination Nervous System/injuries was changed to Trauma, Nervous System and the illegal combination Stem Cells/transplantation was changed to Stem Cell Transplantation).
  
  
• Supplementary Concept Records Elevated to MeSH Headings
  For information on supplementary concept records elevated to MeSH heading status see the article, Changes in the Treatment of Chemical Data in MEDLINE� Citations. NLM Tech Bull. 2001 Nov-Dec;(323):e7.
  
  
• Miscellaneous Changes and Corrections
  Other maintenance is being done to citations created by the Kennedy Institute of Ethics to reflect the completion of the integration of the Bioethics Thesaurus with MeSH.

By Jane Rosov
MEDLARS Management Section

Rosov J. MEDLINE® Data Changes - 2003. NLM Tech Bull. 2002 Nov-Dec;(329):e4.