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  November 26, 2003 [posted]
December 23, 2003 [updated], [editor's note], [editor's note]

 
 
  MEDLINE® Data Changes - 2004
 
 

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

What's New for 2004 MeSH®. NLM Tech Bull. 2003 Nov-Dec;(335):e3.

2004 MeSH Changes to the Category B Organisms Tree and the Check Tag Animal. NLM Tech Bull. 2003 Sep-Oct;(334):e5.

Heading Mapped-to Maintenance: for Supplementary Concept Records' Names of Substance. NLM Tech Bull. 2003 Nov-Dec;(335):e4.

Case Report [mh] Replaced by Case Reports[pt]. Technical Notes. NLM Tech Bull. 2003 Nov-Dec;(335):e1.

Status Tags on PubMed® Citations. Technical Notes. NLM Tech Bull. 2003 Nov-Dec;(335):e1.

[Added December 23, 2003]
2004 MeSH® Information Added to MeSH Home Page. Technical Notes. NLM Tech Bull. 2003 Nov-Dec;(335):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 2004; 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. 2003 Sep-Oct;(334):e7., in the September-October 2003 issue of the NLM Technical Bulletin.

MeSH Vocabulary Updated for 2004
The MeSH Browser currently contains 2004 MeSH with a link to 2003 MeSH. Searchers should consult this Browser to find descriptors of interest and to see these in relationship to other descriptors. The Browser displays MeSH records, including the scope notes, annotations, entry vocabulary, history notes, allowable qualifiers (subheadings), 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 2004 MeSH see the article, What's New for 2004 MeSH®. NLM Tech Bull. 2003 Nov-Dec;(335):e3., in this issue of the NLM Technical Bulletin.

It is expected that PubMed's MeSH database and translation tables will be updated to reflect 2004 MeSH in early December 2003 when end-of-year activities are complete and the newly maintained MEDLINE is available via PubMed.

Updated MeSH in MEDLINE Citations
MEDLINE citations with updated MeSH should be in PubMed in early December 2003. See the article, Hands-On: Revising PubMed® Cubby Stored Searches. NLM Tech Bull. 2001 Nov-Dec;(323):e10.NLM Tech Bull. 2003 Nov-Dec;(335):e3., in the November-December 2001 issue of the NLM Technical Bulletin for details on changing Cubby stored searches to reflect changes in MeSH.

New MeSH Headings
This year 666 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 qualified as [mh] or [majr] 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, Malnutrition, has been introduced for 2004 MeSH. A PubMed query on November 26, 2003 for malnutrition unqualified yields 129,776 citations, of which 128,769 have already been indexed; none of these 128,769 citations 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 Malnutrition, the previous indexing was Nutrition Disorders.

[Editor's Note added December 23, 2003:
A list of new MeSH Headings for 2004 can be found at:
http://www.nlm.nih.gov/mesh/introduction2004.html.]

Changes to MeSH Headings
This year 109 MeSH Headings were replaced with more up-to-date terminology. During year-end processing, NLM makes the changes in the MeSH headings on the MEDLINE citations.

For example, this year the old MeSH Heading Progestational Hormones has been changed to Progestins in 2004 MeSH. The MeSH term Progestational Hormones on MEDLINE citations indexed from 1966-2003 will all be changed to Progestins. The old version of the heading has been retained as an entry term to the new heading, so no adjustments to searching are necessary, unless you want your text word portion to use the more up-to-date vocabulary.

Another example is the deletion of the MeSH heading Anabolic Steroids from 2004 MeSH. All occurrences of that term in MEDLINE citations will be replaced by the new MeSH heading, Anabolic Agents. In this case, the old version of the heading has not been retained as an entry term to the new heading, so adjustments to searching and stored searches are needed.

Beyond the replaced-by heading changes, year-end processing includes additional adjustments to MEDLINE citations to reflect the 2004 MeSH vocabulary and enhance retrieval. 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.

Remember that the mapping of "old" headings and/or see references (entry terms) can also change. For example, Blacks was a 2003 MeSH Heading. Blacks has become a see reference in 2004 to the new heading African Continental Ancestry Group. As a result, the search term Blacks will still retrieve postings, but those hits are not necessarily the exact equivalent of what was retrieved before. In 2004, the old concept of Blacks is now represented by the preferred term of African Americans, which is treed under the African Continental Ancestry Group. (See also Ethnic Groups and Geographic Origins below.)

Here is a summary list of 2003 MeSH headings that were replaced by another heading yet the 2003 string maps to yet another heading for 2004.

2003 Heading 2004 Replaced-by-Heading 2003 Heading is a See Reference or a Redefined 2004 Heading
Animals Animal Population Groups Animals
Blacks African Americans African Ancestry Continental Group
Cytochrome a Cytochrome a Group Cytochromes a
Cytochrome b Cytochrome b Group Cytochromes b
Cytochrome c Cytochrome c Group Cyrochromes c
Mannosidosis alpha-Mannosidosis Mannosidase Deficiency Diseases
Mosses Bryopsida Bryophyta
Pneumocystis carinii Pneumocystis Pneumocystis carinii [redefined MH]
Tonometry Tonometry, Ocular Manometry

In addition to "old" MeSH headings becoming entry terms to a different MeSH heading, see references can be moved to a different heading as well. For example, Sphagnum was a see reference to Mosses in 2003, but moved to become a see reference to Sphagnopsida for 2004.

These types of changes suggest searchers should routinely use the Details button in PubMed to see how terms are mapped in the new year's vocabulary and then check the MeSH Browser for clarification.

[Editor's Note added December 23, 2003:
Lists of MeSH Headings changed or deleted for 2004 can be found at:
http://www.nlm.nih.gov/mesh/introduction2004.html.]

Other Notable MeSH Changes and Related Impact on Searching

Animal to Animals
The 2003 MeSH Heading Animals will be changed to Animal Population Groups and will retain a second-level position in the MeSH Category B Tree hierarchy. The MeSH term Animal will be changed to a new heading Animals with B1 as its tree number. See 2004 MeSH Changes to the Category B Organisms Tree and the Check Tag Animal. NLM Tech Bull. 2003 Sep-Oct;(334):e5. for details.

Age Group MeSH Heading Change
For 2004, one change was made in the Age Groups. Middle Aged replaces Middle Age; the latter term remains an entry term and the tree structure has not changed. The Ages pull-down menu in the PubMed Limits function remains the same. There is no impact for searchers.

MeSH Heading to Publication Type Change: Case Report
The MeSH Heading Case Report will be removed from all MEDLINE citations and will be replaced with the publication type Case Reports. See Case Report [mh] Replaced by Case Reports[pt]. Technical Notes. NLM Tech Bull. 2003 Nov-Dec;(335):e1. for details.

Broadened Definition for /toxicity
For 2004, the definition of the /toxicity subheading has been broadened to include exposure to environmental agents. No changes were made to existing MEDLINE citations. See What's New for 2004 MeSH®. NLM Tech Bull. 2003 Nov-Dec;(335):e3. for details.

Ethnic Groups and Geographic Origins
The MeSH term Racial Stocks and its four children (Australoid Race, Caucasoid Race, Mongoloid Race, and Negroid Race) have been deleted from MeSH in 2004. A new heading, Continental Population Groups, has been created with new indentions that emphasize geography. Ethnic Groups is a sibling to the new Continental Population Groups.

Indexers will now be indexing to the geographic origins. To accommodate this change in policy, the following edits were made in MeSH headings on MEDLINE citations:

2003 Heading 2004 Replaced-by-Heading
Aborigines Oceanic Ancestry Group
Australoid Race Oceanic Ancestry Group
Blacks African Americans
Caucasoid Race European Continental Ancestry Group
Eskimos Inuits
Mongoloid Race Asian Continental Ancestry Group
Negroid Race African Continental Ancestry Group
Racial Stocks Continental Population Groups
Whites European Continental Ancestry Group

Some additional edits were also made. For example, citations that were indexed to Blacks that were also indexed to countries other than the United States had the new MeSH heading African Continental Ancestry Group added as well.

Entry Combination Revisions
This year during year-end processing, NLM again replaced 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 Lymphatic Vessels/growth & development was changed to Lymphangiogenesis and the combination Bone Marrow Cells/transplantation was changed to Bone Marrow Transplantation). Searchers who get zero retrieval on a MeSH heading/subheading combination may want to check the 2004 MeSH Browser for that heading to see if that subheading is listed as an Entry Combination and what the appropriate equivalent is for searching. Here is what the MeSH Browser looks like for the Bone Marrow Cells example:

MeSH Heading Bone Marrow Cells
Entry Combination transplantation:Bone Marrow Transplantation

Heading Mapped-To (HM) Maintenance
This year NLM performed maintenance to add the current HM value as an MeSH Heading for every SCR (Supplementary Concept Record) Name of Substance in a MEDLINE citation, whenever the current value was 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 2004 MeSH also cover Enzyme Commission (EC) Nomenclature and CAS Registry Number data, including Substance Name [NM]. These affect not only the MeSH chemical concepts in Category D, but the Supplementary Concept Records as well. The corresponding changes were made to 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.

Pharmacological Action (PA) for Supplementary Concept Records:
As a reminder, a new policy, effective August 2002, calls for adding PAs to new or existing SCRs only if the following three criteria are met:

  • there must be more than 20 citations discussing the Pharmacological Action being exhibited by that drug;
  • there must be 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 (10%) on that drug accounts for those effects.

Please see the article, Pharmacologic Action Headings: PubMed®. NLM Tech Bull. 2003 Jul-Aug;(333):e6., that describes recent changes to PubMed where a Pharmacologic Action index is available. 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].

Expansion of Trees
MeSH Trees were expanded from 9 to 11 levels this year. There is one 11-level heading:

Sex Chromatin A11.284.430.106.279.345.190.160.180.383.800  

An example of a 10-level heading is:

Trypanosoma lewisi B01.500.841.750.443.950.450.868.887.410 

Maintenance to Citations Created by the Kennedy Institute of Ethics
Other maintenance is being done to citations created by the Kennedy Institute of Ethics (KIE) to add the MeSH Headings Human or Animals where appropriate. Prior to NLM's re-invention of its Data Creation and Maintenance System (DCMS) in 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 Changes to MEDLINE Data

Deletion of the MEDLINE UI
NLM has completed the transition to using the PMID as the only unique identifier for MEDLINE and OLDMEDLINE citations. The MEDLINE UI (Unique Identifier) is no longer exported to PubMed or to licensees, nor is it searchable or displayable in PubMed effective with the 2004 data reload. A MEDLINE/PMID Matcher is available at to assist users who need help in translating from the MEDLINE UI to the PMID. [8/24/2010: The link to the MEDLINE/PMID Matcher was removed because it is no longer available.]

Identification of Clinical Trials in MEDLINE
For the tenth year, NLM continued to work with the Cochrane Collaboration to enhance the identification of clinical trials in MEDLINE. During 2003, "Randomized Controlled Trial" or "Controlled Clinical Trial" Publication Types, along with their parent Publication Type of Clinical Trial, were added to over 1,900 MEDLINE citations identified by the Cochrane Collaboration. The updated MEDLINE citations have been available in PubMed since late October.

2-way Links for Published Erratum [PT]
Older citations with the publication type Published Erratum [PT] now have a link back to the citation for the original paper, and that citation links forward to the citation for the published erratum. Originally, NLM was making the 2-way links only for errata published since the year 2000; now over 900 citations with Published Erratum, regardless of the publication date, have 2-way links. See the Abstract or Citation display for PMID 1952033 as an example.

Remember that most published errata are themselves not indexable items; rather, NLM annotates the original citation with the "Erratum in:" information, but there is no citation to which to link. In those cases where the published erratum had additional substantive information that also warranted a citation, there are now 2-way links between the erratum notice and the original paper's citation.

New Status Value: In Data Review
Starting after the new PubMed system comes up in early December, users viewing the MEDLINE format display may see a new Status value. The new value, "in data review," will indicate that this citation was released to PubMed after issue level bibliographic data verification only (meaning that the journal, date of publication, volume, and issue are all correct). The citation remains "in data review" for verification of the citation level elements, notably authors, article title, and abstract. Once the citation level verification has been completed for every citation in an issue, those citations are re-released to PubMed carrying a Status value of "in process."

Only publisher-supplied citations will go through this second release as an in process level citation; citations created via keyboarding or scanning and optical character recognition at NLM are quality-controlled for all data elements before being sent to PubMed the first time. This change in procedure for publisher-supplied citations is being done to shorten the time before corrections appear in PubMed and are available to licensees. Before, "in process" citations were released only once after undergoing issue level data verification and corrections to other data elements were not made public in PubMed until the citations were completely processed with MeSH headings assigned. Now these citations will be released a second time after citation level verification and in advance of full MeSH indexing being completed.

The summary display of PubMed will use the same PubMed label of [PubMed - in process] for both the "in data review" and "in process" status values. The MEDLINE display format shows the citation's actual status value. The value "in data review" means that NLM has not completed its review of the citation level data elements. NLM may also make further edits to citations with the value "in process" as staff continue to review citations while they are being indexed with MeSH.

Please see Status Tags on PubMed® Citations. Technical Notes. NLM Tech Bull. 2003 Nov-Dec;(335):e1. for details on the various PubMed display labels and how to search for their corresponding subsets.

Sara Tybaert
and
Jane Rosov
MEDLARS Management Section

black line separting article from citation

Tybaert S and Rosov J. MEDLINE Data Changes - 2004. NLM Tech Bull. 2003 Nov-Dec;(335):e6.

 


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