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 November 30, 2004 [posted]
December 3, 2004 [sentences added]
December 27, 2004 [note updated]
December 27, 2004 [note updated]
December 27, 2004 [note updated]
 
 
 MEDLINE® Data Changes - 2005
 
 

[Editor's Note: Gathered here are links to other NLM Technical Bulletin articles or technical notes that have supporting detail referred to in this article. Additional links are also embedded in this article at the appropriate places.]

MEDLINE®/PubMed® End-of-Year Activities. NLM Tech Bull. 2004 Sep-Oct;(340):e4.

2005 MeSH® Changes to Hominidae and the Check Tag Human; Resulting PubMed and NLM Catalog Change to Search for Animals. NLM Tech Bull. 2004 Nov-Dec;(341):e6.

What's New for 2005 MeSH®. NLM Tech Bull. 2004 Nov-Dec;(341):e8.

[Added December 27, 2003]
2005 MeSH® Information Added to MeSH Home Page. Technical Notes. NLM Tech Bull. 2004 Nov-Dec;(341):e1.

drop cap letter for t 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. This article attempts to collect in one place the notable data changes for 2005; mention of a topic may be linked to another article where details will be found. 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. NLM Tech Bull. 2004 Sep-Oct;(340):e4.

MeSH® Vocabulary Updated for 2005
The MeSH Browser currently contains 2005 MeSH vocabulary with a link to 2004 MeSH. Searchers should consult the Browser to find MeSH headings of interest and to see these in relationship to other headings. The Browser displays MeSH records, including the scope notes, annotations, entry terms, history notes, allowable qualifiers (subheadings), previous headings, etc. for MeSH headings along with subheading records and Supplementary Concept Records (SCRs) for substances that are not MeSH headings. It also provides links to relevant sections of the NLM Indexing Manual.

For highlights about 2005 MeSH see the article What's New for 2005 MeSH®, NLM Tech Bull. 2004 Nov-Dec; (341); e8 in this issue of the NLM Technical Bulletin.

It is expected that PubMed's MeSH database and translation tables will be updated to reflect 2005 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 2004. See the article, Hands-On: Revising PubMed® Cubby Stored Searches. NLM Tech Bull. 2001 Nov-Dec;(323):e10 for details on changing Cubby stored searches to reflect changes in MeSH.

New MeSH Headings
This year 487 new MeSH Headings were added.

In general, 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.

For example, a new MeSH term, Acanthoma, has been introduced for 2005 MeSH. A PubMed query on November 22, 2004 for acanthoma unqualified yields 251 citations, of which 206 have already been indexed; none of these 206 will have the new MeSH heading added. Searchers may wish to include headings previously used to index these new concepts in addition to the text word retrieval that PubMed will automatically add to an unqualified strategy. For Acanthoma, the previous indexing was Skin Neoplasms (1965-2004), as seen in the 2005 MeSH Browser.

In some cases, NLM does adjust citations retrospectively for new concepts. For example, for 2005 the MeSH heading Seals was deleted and all occurrences of that term were replaced by the MeSH heading Seals, Earless. Additional maintenance tasks are being performed to find those citations previously indexed with Seals that should not have Seals, Earless but should have that term replaced with one of the following new MeSH headings as appropriate: Fur Seals or Sea Lions, which are also members of the suborder Pinnipedia along with Seals, Earless and Walruses. The string "Seals" no longer occurs in 2005 MeSH because the word is ambiguous. Any searches containing the term "Seals" 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.

[Editor's Note updated on December 27, 2004: A list of new MeSH Headings for 2005 can be found at: http://www.nlm.nih.gov/mesh/introduction2005.html.]

Changes to MeSH Headings
This year 192 MeSH Headings were replaced with more up-to-date terminology. During year-end processing, NLM updates MeSH headings on the MEDLINE citations.

For example, this year the old MeSH Heading Myocardial Diseases has been changed to Cardiomyopathies. The MeSH term Myocardial Diseases on MEDLINE citations indexed from 1966-2004 will all be changed to Cardiomyopathies. The old version of the heading has been retained as an entry term to the new heading, so no adjustments to searching are necessary.

Another example is the deletion of the MeSH Heading Adenoviruses, Bovine from 2005 MeSH. All occurrences of that term on MEDLINE citations will be replaced by the new MeSH heading Mastadenovirus. In this case, the old heading has not been retained as an entry term to the new heading, so adjustments to searching and stored searches are needed.

The MeSH Heading check tags reflecting grant support have been changed for 2005 as follows:
2004: Support, Non-U.S. Gov't
2005: Research Support, Non-U.S. Gov't

2004: Support, U.S. Gov't, P.H.S.
2005: Research Support, U.S. Gov't, P.H.S.

2004: Support, U.S. Gov't, Non-P.H.S.
2005: Research Support, U.S. Gov't. Non-P.H.S.

Beyond the replaced-by heading changes, year-end processing includes additional adjustments to MEDLINE citations to reflect 2005 MeSH vocabulary and 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 2 or more specific concepts.

Note also that the mapping of "old" headings and/or entry terms can also change. For example, Guided Tissue Regeneration was a 2004 MeSH Heading. In 2005 this same term now exists as a different MeSH Vocabulary record. All occurrences of Guided Tissue Regeneration in MEDLINE citations will be replaced with Guided Tissue Regeneration, Periodontal. A search of Guided Tissue Regeneration will still retrieve postings, but those hits are not necessarily the exact equivalent of what was retrieved before.

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

[Editor's Note updated on December 27, 2004: A list of MeSH Headings changed or deleted for 2005 is available at: http://www.nlm.nih.gov/mesh/introduction2005.html.]

Other Notable MeSH Changes and Related Impact on Searching

Human to Humans
The MeSH term Human changed to a new heading Humans with B01.150.900.649.801.400.350.400 as its tree number. See [Humans TB article] for important details that affect searching.

Publication Type Change
Review, Academic [Publication Type] and Review, Literature [Publication Type] are deleted in 2005 MeSH and replaced by Review [Publication Type]. Both Review, Academic [pt] and Review, Literature [pt] are being retained as entry terms to Review [Publication Type].

Entry Combination Revisions
This year during year-end processing, NLM will retrospectively again 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 (e.g., The combination Labor Pain/prevention & control was changed to Analgesia, Obstetrical and the combination Fetus/injuries was changed to Prenatal Injuries). Searchers who get zero retrieval for a MeSH Heading/subheading combination may want to check the 2005 MeSH Browser for the heading to see if the subheading has an Entry Combination that can be used for searching. Here is what the 2005 MeSH Browser looks like for the Labor Pain example:

MeSH Heading Labor Pain
Entry Combination prevention & control:Analgesia, Obstetrical


Here are the 17 Entry Combinations new for 2005:

Previous MeSH Heading/subheading Replaced Heading for 2005
Aromatase/antagonists & inhibitors Aromatase Inhibitors
Coproporphyrinogen Oxidase/deficiency Porphyrias, Hepatics
Diabetes Mellitus/complications Diabetes Complications
Embryo/growth & development Embryonic Development
Embryo/injuries Prenatal Injuries
Embryo, Nonmammalian/growth & development Embryonic Development
Ferrochelatase/deficiency Protoporphyria, Erythropoietic
Fetus/growth & development Fetal Development
Fetus/injuries Prenatal Injuries
Hydroxymethylbilane Synthase/deficiency Porphyria, Acute Intermittent
Labor Pain/prevention & control Analgesia, Obstetrical
Peptides/biosynthesis Peptide Biosynthesis
Protein Kinases/antagonists & inhibitors Protein Kinase Inhibitors
Proteins/biosynthesis Peptide Biosynthesis
Receptors, Leukotriene/antagonists & inhibitors Leukotriene Antagonists
Receptor, Angiotensin, Type 1/antagonists & inhibitors Angiotensin II Type 1 Receptor Blockers
Uroporphyrinogen III Synthetase/deficiency Porphyria, Erythropoietic

Heading Mapped-To (HM) Maintenance
This year NLM will again perform maintenance to add the current HM value as a MeSH Heading for every SCR (Supplementary Concept Record) Name of Substance in a MEDLINE citation, whenever the current value is absent. For more information on Heading Mapped-to Maintenance, please see the article, Heading Mapped-to Maintenance: for Supplementary Concept Records' Names of Substance. NLM Tech Bull. 2003 Nov-Dec;(335):e4.

EC/RN Numbers (RN) and Name of Substance (NM)
Changes in 2005 MeSH also cover Enzyme Commission (EC) Nomenclature and CAS Registry Number data, including Substance Name (NM). These not only affect the MeSH chemical concepts in Category D, but the Supplementary Concept Records as well. The corresponding changes will be made to the MEDLINE citations during year-end processing.

Supplementary Concept Records (SCRs) Elevated to MeSH Headings
For general information on SCRs 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 Some of the 487 new MeSH headings previously existed as an SCR, e.g., Luteolin.

Pharmacological Action (PA) for Supplementary Concept Records
As a reminder, NLM policy, effective August 2002, calls for adding Pharmacological Action terms to new or existing Supplementary Concept Records in the MeSH Browser if the following three criteria are met:

  • There are more than 20 citations in PubMed discussing the Pharmacological Action being exhibited by that drug;
  • There is substantial evidence that the Pharmacological Action is in effect in humans (i.e., the drug is used clinically); and
  • A reasonable proportion of the literature (greater than or equal to 10%) on that drug accounts for those effects.

Please see the article Pharmacologic Action Headings: PubMed®. NLM Tech Bull. 2003 Jul-Aug;(333):e6 which describes Pharmacologic Action terms. If you enter a MeSH Term that is also a Pharmacologic Action Term, PubMed will search the term as [MH], [PA], or [TW], e.g., platelet aggregation inhibitors will automatically map to: platelet aggregation inhibitors [mh] OR platelet aggregation inhibitors [pa] OR platelet aggregation inhibitors [tw].

Maintenance to Citations by the Kennedy Institute of Ethics
Other maintenance is being done to citations created by the Kennedy Institute of Ethics (KIE) to complete the process, begun last year, to add the MeSH Headings Humans or Animals where appropriate to KIE-created records. Prior to late 2000, it was not KIE practice to index with these headings. However, now that KIE-created citations are part of regular MEDLINE processing, KIE follows NLM indexing practice on the use of these headings to improve retrieval for searches on bioethical topics.

Other maintenance tasks for KIE citations will remove century keywords that correspond to the MeSH century headings. For any of these citations that do not already include the MeSH century term, the appropriate MeSH term will be added.

Transliteration of Title for Cyrillic Language Articles Ceases in 2005
The titles of articles from journals published in Cyrillic languages such as Russian, Ukrainian and Bulgarian will no longer be transliterated into the Roman alphabet for MEDLINE. This has always been the MEDLINE policy for journals published in Oriental languages, such as Chinese, Japanese and Korean. Transliteration is labor intensive and the value of transliterations has dwindled, so an extension of the policy to Cyrillic languages is appropriate at this time. Title transliterations did appear in the author section of Index Medicus; transliterations do not appear in most PubMed citation displays, and it is not possible to query PubMed using text words from the Transliterated/Vernacular Title [TT] field.

The new policy for Cyrillic will begin with journals published in 2005. Author names will continue to be transliterated and article titles will, of course, continue to be translated into English.

Identification of Clinical Trials in MEDLINE
NLM expects to work with the Cochrane Collaboration again this year to enhance the identification of clinical trials in MEDLINE. This year, however, the work will not be completed until after the 2005 version of PubMed is introduced. NLM will announce when the records affected by this collaborative effort are revised in PubMed.

Other Changes to MEDLINE Data
Starting after the new PubMed system comes up mid-December there are several changes to PubMed's display formats. They are as follows:

1. Status Values: MEDLINE and OLDMEDLINE
There is a change to the Status Value (STAT) format present in the MEDLINE display option: records in "MEDLINE" status are the approximately 13 million records that are complete with MeSH headings and chemical substance names, and have completed all of NLM's quality assurance/validation programs. This category of records previously had the Status "Completed" in the MEDLINE display. The PubMed Summary display format for this category of records will continue to include the citation status tag [PubMed - indexed for MEDLINE]. For further information see the article Status Tags On PubMed® Citations. Technical Notes. NLM Tech Bull. 2003 Nov-Dec;(335):e1.

OLDMEDLINE records will display "OLDMEDLINE" in the STAT field in PubMed. Previously, like the MEDLINE records discussed above, OLDMEDLINE records had the Status value "Completed." OLDMEDLINE records also contain the value OM in the SB (journal/citation subset) tag in the MEDLINE display format. The PubMed summary display format for this category of records will continue to include the citation status tag [PubMed - OLDMEDLINE for Pre1966].

2. Display of Corrected Author Names
Starting in 2005, all PubMed display formats, except the XML format, will display only correct (valid) author names. In the XML format, author names that were originally incorrectly spelled in the journal and subsequently corrected by a publisher's erratum notice will be identified by the XML tag Author ValidYN="N" (for not valid name). All other author names, including the subsequent entry of a corrected author name, will be identified by the tag Author ValidYN="Y" (for valid name) in the XML display.

For those who may appreciate a reminder, here is some background on corrections to Author Names in MEDLINE citations: When a journal publisher issues a published erratum correcting the journal's original spelling of an author's name in a citation, NLM adds the correct spelling of the author's name to the author list in the MEDLINE record and retains the old misspelled name. NLM now flags the originally incorrectly spelled name in the PubMed XML display format so it can be identified as an incorrect entry that has subsequently been corrected.

Please note that both the correct and incorrect names will be included in the PubMed Author index and, therefore, will be searchable in PubMed. So, if an incorrect author name is searched, PubMed will retrieve citations displaying the correct spelling of the name. The incorrect name will no longer show in the listed authors, but the note field will continue to indicate the author name correction. See Figure 1 below.

 
2004 Summary Display of Citation with Incorrect Author:

Iancovici-Kidon M, Sthoeger D, Abrahamov A, Wolach B, Beutler E, Gelbart T, Barak Y, Volach B.
A new exon 9 glucose-6-phosphate dehydrogenase mutation (G6PD "Rehovot") in a Jewish Ethiopian family with variable phenotypes.
Blood Cells Mol Dis. 2000 Dec;26(6):567-71. Erratum in: Blood Cells Mol Dis 2001 Jan-Feb;27(1):351. Volach B [corrected to Wolach B].
PMID: 11112389 [PubMed - indexed for MEDLINE]

2005 Summary Display -- incorrect author suppressed:

Iancovici-Kidon M, Sthoeger D, Abrahamov A, Wolach B, Beutler E, Gelbart T, Barak Y.
A new exon 9 glucose-6-phosphate dehydrogenase mutation (G6PD "Rehovot") in a Jewish Ethiopian family with variable phenotypes.
Blood Cells Mol Dis. 2000 Dec;26(6):567-71. Erratum in: Blood Cells Mol Dis 2001 Jan-Feb;27(1):351. Volach B [corrected to Wolach B].
PMID: 11112389 [PubMed - indexed for MEDLINE]
Figure 1 - Comparison of citation with incorrect author and with incorrect author suppressed.

3. Publishing Model
Information pertaining to the article's "model of publishing" will now be carried in PubMed. A new field displayable only in the MEDLINE and XML formats will indicate if the article cited is published in print only, print followed by electronic, electronic only, or electronic followed by print. The field is PUBM in the MEDLINE display (and Article PubModel=" " in the XML display) and may contain the value Print, Print-Electronic, Electronic, or Electronic-Print. This may help in processing of interlibrary loans.

Please note: This publishing model information is largely derived from what the publisher supplies to NLM; there are some older citations to electronic-only articles that are labeled as "Print" because the publisher submitted them that way. (NLM policy requires a specific publication date be recorded for citations identified as "Electronic." Those citations that can not provide a specific date (to the day) will be labeled as "Print." [added December 3, 2004]) It may not be feasible to correct these. NLM is making every effort to work with publishers to get the correct setting for new citations.



By Sara Tybaert
and
Jane Rosov
MEDLARS Management Section

black line separting article from citation

Tybaert S, Rosov J. MEDLINE® Data Changes - 2005. NLM Tech Bull. 2004 Nov-Dec;(341):e9.

 


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