December 27, 2005 [Editor's note added]
MEDLINE® Data Changes - 2006
[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.]
2006 MeSH® Now Available. NLM Tech Bull. 2005 Sep-Oct;(346):e1.
MEDLINE® PubMed® End-of-Year Activities. NLM Tech Bull. 2005 Sep-Oct;(346):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.
PubMed® Notes 2006. NLM Tech Bull. 2005 Nov-Dec;(347):e11.
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 attempts to collect in one place the notable data changes for 2006; 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® and for two indexing policy changes, see the article, MEDLINE/PubMed End-of-Year Activities. NLM Tech Bull. 2005 Sep-Oct;(346):e4.
MeSH® Vocabulary Updated for 2006
The MeSH Browser currently contains a link to the 2006 MeSH vocabulary. 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 2006 MeSH see the article, What's New for 2006 MeSH, coming soon in this issue of the NLM Technical Bulletin.
It is expected that PubMed's MeSH database and translation tables will be updated to reflect 2006 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 2005. See the article, Hands-On: Revising PubMed Cubby Stored Searches. NLM Tech Bull. 2001 Nov-Dec;(323):e10. for details on revising My NCBI stored searches to reflect changes in MeSH.
New MeSH Headings
This year 933 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. For example, a new MeSH term, Abdominal Fat, has been introduced for 2006 MeSH. A PubMed query on October 3, 2005 for abdominal fat without any search tags yields 5,774 citations, of which 5,573 have already been indexed; none of these 5,573 will have the new MeSH heading added. Searchers may wish to include headings previously used to index these concepts in addition to the text words PubMed may use to supplement a strategy. For Abdominal Fat, the previous indexing was Adipose Tissue (1966-2005), as seen in the 2006 MeSH Browser (see Figure 1).
Changes to MeSH Headings
This year 188 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 Fetal Anoxia has been changed to Fetal Hypoxia (see Figure 2). The MeSH term Fetal Anoxia on MEDLINE citations indexed from 1975-2005 will all be changed to Fetal Hypoxia. The old version of the heading has been retained as an entry term to the new heading, so no adjustments to searching are necessary. Notice that the History Note uses a 2-date convention, i.e.: 2006(1975). The first date is when the current preferred value, Fetal Hypoxia, was introduced to MeSH while the second date in parentheses is when the concept was introduced to MeSH. A search using the current value will retrieve citations indexed back through the date in the parentheses (regardless of what the terminology was over the years).
Another example is the deletion of the MeSH Heading Antibiotics, Peptide from 2006 MeSH. All occurrences of that term on MEDLINE citations will be replaced by the new MeSH heading Anti-Bacterial Agents. In this case, the old heading has not been retained as an entry term to the new heading, so adjustments to searching and saved searches are needed.
Yet another example of a change is the deletion of the broad term Anti-Allergic and Respiratory System Agents in 2006 MeSH as a result of an extensive review this year of the MeSH D Category. This term is not being replaced by a new term in 2006 MeSH. However, there are no MEDLINE citations indexed to this term so the change will not affect searching retrieval.
In addition to the replaced-by heading changes, year-end processing includes adjustments to MEDLINE citations to reflect 2006 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. An example of a MeSH heading adjustment for 2006 is the heading Rats which has been redefined more broadly to include species in addition to Rattus norvegicus. A maintenance task is being performed to find those citations not indexed with Rats that now qualify under the new definition. We will add Rats to these citations.
Note also that the mapping of "old" headings and/or entry terms can also change. For example, Gene Fusion was a 2005 MeSH Heading. In 2006 this same term now exists as a different MeSH Vocabulary record because its meaning has changed. All occurrences of Gene Fusion in MEDLINE citations will be replaced with Artificial Gene Fusion. A search of Gene Fusion in 2006 will still retrieve citations, but they are not necessarily the exact equivalent of what was retrieved before. Please read the 2006 definitions of Artificial Gene Fusion and Gene Fusion to determine which heading is now appropriate for your search.
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.
Other Notable MeSH Changes and Related Impact on Searching
Publication Type Change
Review of Reported Cases [Publication Type] and Review, Multicase [Publication Type] and Review, Tutorial [Publication Type] are deleted in 2006 MeSH and replaced by Review [Publication Type]. All three terms are being retained as entry terms to Review [Publication Type].
This consolidation of the Review publication types is a continuation of work that was begun in 2005 MeSH. Last year both Review, Academic [Publication Type] and Review Literature [Publication Type] became entry terms to Review [Publication Type]. These three additional changes for 2006 MeSH are completing the conversion to the general, multipurpose Review [Publication Type].
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 (e.g., the combination Hypothyroidism/congenital was changed to Congenital Hypothyroidism and the combination Serotonin Plasma Transport Proteins/antagonists & inhibitors was changed to Serotonin Uptake Inhibitors). Searchers who get zero retrieval for a MeSH Heading/subheading combination may want to check the 2006 MeSH Browser for the heading to see if the subheading has an Entry Combination that can be used for searching. Here is what the 2006 MeSH Browser looks like for the Hypothyroidism example:
|congenital: Congenital Hypothyroidism|
Here are the 16 Entry Combinations new for 2006:
|Previous MeSH Heading/subheading||Replaced Heading for 2006|
|Skin Diseases, Parasitic/drug therapy||Antiparasitic Agents|
|Tubulin/antagonists & inhibitors||Tubulin Modulators|
|Sodium Chloride Symporters/antagonists & inhibitors||Sodium Chloride Symporter Inhibitors|
|Serotonin Plasma Membrane Transporter Proteins/antagonists & inhibitors||Serotonin Uptake Inhibitors|
|Complement C1 Inhibitor Protein/deficiency||Angioneurotic Edema|
|Protoporphyrinogen Oxidase/deficiency||Porphyria, Variegate|
|Cyclooxygenase 1/antagonists & inhibitors||Cyclooxygenase Inhibitors|
|Cyclooxygenase 2/antagonists & inhibitors||Cyclooxygenase 2 Inhibitors|
|Xeroderma Pigmentosum Group A Protein/deficiency||Xeroderma Pigmentosum|
|Von Hippel-Lindau Tumor Suppressor Protein/deficiency||Hippel-Lindau Disease|
|Fragile X Mental Retardation Protein/deficiency||Fragile X Syndrome|
|Lysosomal-Associated Membrane Protein 2/deficiency||Glycogen Storage Disease Type IIb|
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 that MeSH Heading 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 2006 MeSH also include Enzyme Commission (EC) Nomenclature and Chemical Abstracts Service (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 933 new MeSH headings previously existed as an SCR, e.g., alpha Catenin. Such promotions of an SCR to MeSH Heading status will show a History Note (HN) with two dates. For alpha Catenin, the HN is 2006 (1991). This means the current form of the preferred MeSH Heading was introduced for 2006 MeSH but the concept has been in the MeSH vocabulary since 1991 and the current MeSH Heading will retrieve citations back through 1991 (the period of time during which indexers originally assigned the concept as an SCR).
Pharmacological Action (PA)
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].
For 2006, Vitamins is a new Pharmacologic Action. This means that most of its children, i.e., the specific vitamin MeSH headings like Vitamin A or Ascorbic Acid (which is Vitamin C) have been removed from the vitamins MeSH tree. Now when an article discusses Ascorbic Acid as a vitamin, the indexer will choose the MeSH Heading Ascorbic Acid and also coordinate with the MeSH Heading Vitamins to describe that chemical's pharmacologic action. If you want to search for all vitamins in 2006 forward, then be sure to enter Vitamins without a search tag so that you will retrieve the older citations that were not indexed with the MeSH Heading Vitamins in the past (because the specific vitamins were treed under that parent and the parent term was not also added following the policy to index to the most specific concept). Citations indexed prior to 2006 are retrieved by the [pa] portion of the translated search strategy when the search term is not tagged.
Other Changes to MEDLINE and OLDMEDLINE 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. MEDLINE records will include the Full Serial Title and the International Organization for Standardization (ISO) Abbreviation. The full journal title (taken from NLM's cataloging data following NLM's rules for how to compile a serial name) will be exported and displayed in the XML Title field. In the MEDLINE format, the JT tag is used for display.
The ISO Abbreviation field will be used to export NLM's version of the journal title ISO Abbreviation. These NLM ISO Abbreviations are constructed to assist NCBI in linking GenBank to PubMed and do not necessarily conform to the ISO standard. Less than one-third of the journals covered in MEDLINE carry NLM's NCBI version of the ISO Abbreviation in their catalog record and approximately one-fifth of all journals ever covered in MEDLINE carry it. An example is:
ISOAbbreviation: Am. J. Physiol., Cell Physiol. (note the comma and periods following the abbreviated words) that corresponds to the MEDLINE TA: Am J Physiol Cell Physiol.
The ISO abbreviation will only display in the XML display.
2. OLDMEDLINE citations may contain current MeSH Terms. NLM has begun an OLDMEDLINE keyword-to-MeSH Heading mapping project. OLDMEDLINE keywords are the original subject headings assigned to the citations when they appeared in the print indexes from which the OLDMEDLINE data came. This project maps those terms to the current MeSH vocabulary. When the new PubMed system comes up in mid-December, NLM estimates that approximately 92% of the OLDMEDLINE citations will have at least one MeSH Heading (86% of the keywords will be mapped). Additional work on this project will continue. [Editor's Note: See the OLDMEDLINE description for more information.]
3. Republished articles will begin to be cited in 2006. Background: Since 1987, NLM has cited corrected and republished articles. Here is a summary of how this information is treated in PubMed as of 2005:
|Corrected and Republished|
|Abstract/Citation Displays:||Corrected and republished in:
Corrected and republished from:
"Corrected and republished in:" cites the final, correct version of an article while "Corrected and republished from:" cites the original article that was subsequently republished in corrected form.
Please note that even though some of the element names are in shortened format, these data represent articles that have been corrected in some way and then republished, typically in the same journal.
For journal issues published effective 2006 forward, NLM will be citing articles that are republished in other journals so that users have additional access to the same information (perhaps one indexed journal is not available to a certain user to access, but another indexed journal is). This new policy applies if there is an explicit indication that the article is being republished or reprinted, even if it is being republished in an abridged or different version from the original. This condition is separate and distinct from articles that are corrected and republished.
In order to clarify the difference, changes will be made to the PubMed display and searching of the existing corrected and republished elements as well as introducing the new elements for the republished, but not corrected, articles as follows for 2006:
|Corrected and Republished Article Citations||Republished Article Citations|
|Abstract/ Citation Displays:||Corrected and republished in:
Corrected and republished from:
| Republished in:
|MEDLINE Display:|| CRI
|Search phrase:|| hascorrectedrepublishedin
|XML names:|| RepublishedIn
Please note that we are reusing some of the conventions for the new set of elements that had been previously associated with the corrected and republished set of elements.
4. Type of ISSN (Electronic vs. Print) - Beginning with the mid-December system the ISSN field in the MEDLINE display will have a qualifier that follows the ISSN data which will state whether it is for the print or the electronic version ISSN of the journal. This information also appears in the XML format as a qualifier on the ISSN element.
5. Cited Medium (Internet vs. Print) - Cited Medium, a qualifier on the Journal Issue field (only in the XML display) will indicate whether a citation was processed by NLM using the electronic or the print version of the journal.
Tybaert S. MEDLINE® Data Changes - 2006. NLM Tech Bull. 2005 Nov-Dec;(347):e7.