Table of Contents: 2015 NOVEMBER–DECEMBER No. 407
Tybaert S. MEDLINE Data Changes — 2016. NLM Tech Bull. 2015 Nov-Dec;(407):e8.
This article collects the notable data changes made to MEDLINE during annual National Library of Medicine (NLM) maintenance known as Year-End Processing (YEP) for 2016:
The MeSH Browser currently points to the 2016 MeSH vocabulary with a link to the 2015 MeSH Vocabulary. Searchers should consult the Browser to find MeSH Headings of interest and their relationships to other headings. The Browser contains MeSH Heading records that may include scope notes, annotations, entry terms, history notes, allowable qualifiers (subheadings), previous indexing and other information. It also includes Subheading records and Supplementary Concept Records (SCRs) for substances and diseases that are not MeSH Headings.
You can download MeSH from the MeSH homepage:
The MeSH Tree Structures are available online in PDF format with all indented terms showing.
For highlights about 2016 MeSH, see the article, What's New for 2016 MeSH.
The PubMed MeSH database and translation tables will be updated to reflect 2016 MeSH in mid-December when YEP activities are complete and the newly maintained MEDLINE data are available in PubMed.
MEDLINE records with updated MeSH will be in PubMed in mid-December 2015. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.
434 new MeSH Headings were added to MeSH in 2016. Four new Publication Types were added.
Typically, NLM does not retrospectively re-index MEDLINE citations with new MeSH Heading concepts. Therefore, searching PubMed for a new MeSH term tagged with [mh] or [majr] effectively limits retrieval to citations indexed after the term was introduced. PubMed Automatic Term Mapping (ATM) expands an untagged subject search to include both MeSH Terms and All Fields index terms 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 for a particular concept before the new MeSH Heading was introduced.
This year 66 MeSH Headings were either changed or deleted and replaced with more up-to-date terminology. During YEP, NLM updates MeSH Headings on MEDLINE citations.
Examples of new MeSH headings that may be of special interest to searchers are highlighted below by Category. All of the new 2016 concepts are available as a PDF, New MeSH Headings for 2016. Note that headings listed below may be treed in more than one category.
Changes of particular interest include:
MeSH Publication Types
|2015 MeSH V03 TREE||2016 MeSH V03 TREE|
Note: Indexers will assign Clinical Study [PT] only if the authors use "clinical study" and if there are no indications that the study is either a "clinical trial" or "observational study."
In order to improve indexing consistency and efficiency and to make MEDLINE searching easier and more straightforward, the subheading diagnostic use was deleted from MeSH.
To cover the concept of Diagnostic Use related to diseases, search:
To cover the concept of Diagnostic Use related to clinical/physiological conditions, search:
To cover the general concept of the diagnostic use of substances, search:
Extensive changes were made to MeSH 2016 Tree structures. In cases where a term was treed at two levels within the same subtree one of the tree positions was eliminated. For example:
In other cases, terms were regrouped into new tree categories. For example:
Additional information on these changes can be found in the MeSH Tree Changes: Uncle vs. Nephew Projects section of the What's New for 2016 MeSH article.
The Index Section undertook several projects related to updating the Annotation element that contains instructions for the indexer and cataloger in the MeSH Browser. These instructions are helpful for searchers, too. The projects are ongoing. Some examples of changes include:
1. Hormones, Hormone Substitutes, and Hormone Antagonists
|MeSH Heading||Hormones, Hormone Substitutes, and Hormone Antagonists||Hormones, Hormone Substitutes, and Hormone Antagonists|
|Annotation||used for searching: indexers and catalogers apply specifics||used for searching; INDEXER: Do not use; CATALOGER: Do not use|
|Annotation||barium enema: coordinate with BARIUM SULFATE / diag use, not BARIUM||barium enema: coordinate with BARIUM SULFATE, not BARIUM|
|Annotation||GEN;NIM; DF: CYTODIAG||general or unspecified; prefer specifics|
|Annotation||GEN; coord with specific organism /infection heading (IM) or other cause (IM); viral encephalitis = ENCEPHALITIS, VIRAL unless ENCEPHALITIS, ARBOVIRUS but see note there; ENCEPHALOMYELITIS & specifics & SUBACUTE SCLEROSING PANENCEPHALITIS (see note there) are also available; DF: ENCEPH||general, note specifics particularly INFECTIOUS ENCEPHALITIS and ENCEPHALITIS, VIRAL|
|Annotation||caused by Francisella tularensis (formerly Pasteurella tularensis)||coordinate with TICK_BORNE DISEASES if pertinent|
|Scope Note||A plague-like disease of rodents, transmissible to man. It is caused by FRANCISELLA TULARENSIS and is characterized by fever, chills, headache, backache, and weakness.||A plague-like disease of rodents, transmissible to man. It is caused by FRANCISELLA TULARENSIS and is characterized by fever, chills, headache, backache, and weakness.|
Of note to searchers: remember that this coordination applies to 2016 forward indexing and was not adjusted retrospectively; for comprehensive searching on Tick-Borne Diseases, you may want to OR Tularemia to your search (even though not all cases of Tularemia are "caused by tick vectors").
In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2016 MeSH vocabulary and to enhance search retrieval. These follow-on adjustments are largely the adding of more MeSH Headings or Supplementary Concept Record Names 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. An example for 2016 MeSH is the clarification of the ambiguous word biogenesis. The single 2015 MeSH Heading Biogenesis was replaced by two 2016 MeSH Headings – Organelle Biogenesis and Origin of Life. NLM has adjusted the citations so that the appropriate new heading replaced the single old heading.
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 the PubMed Details feature when searching to see how terms are mapped with the new year's vocabulary and then checking the MeSH Browser or the MeSH database for clarification. Additional information is also available in the article, Skill Kit: The Effects of Year End Processing (YEP) on Saved Searches or RSS Feeds.
This year during YEP, NLM will again retrospectively replace certain MeSH heading/subheading combinations, known as Entry Combinations, with the new precoordinated MeSH heading. If you get no retrieval for a MeSH Heading/subheading combination check the heading in the 2016 MeSH Browser to see if the Entry Combination information indicates a different term.
There are eight new Entry Combinations for 2016.
|Previous MeSH Heading/Subheading
|Replaced-by Heading for 2016|
|Adenylyl Cyclases/antagonists & inhibitors||Adenylyl Cyclase Inhibitors|
|Cholestenone 5 alpha-Reductase/analogs & derivatives||5-alpha Reductase Inhibitors|
|Lacrimal Duct Obstruction/surgery||Dacryocystorhinostomy|
|Microchip Analytical Procedures/instrumentation||Lab-On-A-Chip Devices|
|Orexin Receptors/antagonists & inhibitors||Orexin Receptor Antagonists|
|Placenta/growth & development||Placentation|
|Poly(ADP-ribose) Polymerases/antagonists & inhibitors||Poly(ADP-ribose) Polymerase Inhibitors|
|Ultrasonic Waves/therapy||Ultrasonic Therapy|
In October 2015, NLM added 233 new labels to the list of structured abstract labels. This brings the total of vetted and mapped labels to 3,032. The new 2015 file can be found at: https://structuredabstracts.nlm.nih.gov/Downloads/Structured-Abstracts-Labels-102615.txt.
Additional information is found in the article, Structured Abstracts in MEDLINE: Newly Identified and Mapped Labels Available.
In the fall of 2015, NLM processed all OLDMEDLINE citations using a form of the Medical Text Indexer software modified specifically for this subset of MEDLINE data in order to add additional MeSH Headings and complete a project that mapped OLDMEDLINE Other Term (OT) subject headings to MeSH Headings. The result of this project was that all OLDMEDLINE citations now have at least one MeSH Heading and were, therefore, converted to MEDLINE status. The over 2 million jsubsetom citations updated via this process will be included in the baseline export of citations for MEDLINE data licensees and will be available in PubMed in mid-December. Due to the extremely large number of citations modified, these citations were not marked with a Date Last Revised (LR) in order to speed the processing of the updates.
In August of 2015, NLM processed updates to 3,308 MEDLINE journals for changes to diacritics in the journal title (the JT element seen in the MEDLINE display in PubMed). This work affected over 2 million MEDLINE/PubMed citations. The revised citations were held in the NLM Data Creation and Maintenance System until mid-December when 2016 baseline files for MEDLINE data licensees are exported and MEDLINE/PubMed citations maintained with 2016 MeSH are made available in PubMed. Due to the large volume of citations affected, these citations were not marked with a Date Last Revised (LR) in order to speed the processing of the updates.
During September and October 2015, NLM processed two MEDLINE Country of Publication [PL] clean-up projects:
On August 11, 2015, NLM updated the PubMed Title/Abstract [tiab] index to include publisher-provided Author Keywords which are part of the MEDLINE citations.
MEDLARS Management Section