Table of Contents: 2016 NOVEMBER–DECEMBER No. 413
Tybaert S. MEDLINE Data Changes — 2017. NLM Tech Bull. 2016 Nov-Dec;(413):e4a.
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 2017:
The MeSH Browser currently points to the 2017 MeSH vocabulary with a link to the 2016 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 2017 MeSH from links on the MeSH homepage:
The MeSH Tree Structures are available online under the Changes to 2017 MeSH Hierarchy section on the download page.
For highlights about 2017 MeSH, see What's New for 2017 MeSH.
The PubMed MeSH database and translation tables will be updated to reflect 2017 MeSH in mid-December when YEP activities are complete and the newly maintained MEDLINE data are available in PubMed.
MEDLINE records with updated MeSH are anticipated to be in PubMed in mid-December 2016. See "Modifying a Saved Search Strategy" for details on revising My NCBI saved searches.
This year 77 MeSH headings were either changed or deleted and replaced with more up-to-date terminology. During YEP, NLM updates MeSH headings on MEDLINE citations.
629 new MeSH headings, including two new Publication Types, were added to MeSH in 2017.
All of the new 2017 concepts are available in PDF format, New Headings with Scope Notes, Annotations and Tree Locations.
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.
Brain Injuries, Traumatic: Promoted to a MeSH heading. Previously an Entry Term to Brain Injuries. Note that Mild Traumatic Brain Injury was added as an Entry Term to Brain Concussion. Both MeSH headings are children to Brain Injuries.
SCR Protein Terms: A number of protein terms were promoted to MeSH terms in 2017. An example is the 2016 SCR record for lumican. For 2017 lumican was promoted to a MeSH heading. At the same time, three new SCR records were created for the specific species and all three new SCRs were mapped to the new MeSH heading Lumican:
Molecular Sequence Data: The indexing policy has changed. Between 1988-2016 this term was indexed for articles that contained:
Starting with 2017 MeSH indexing, Molecular Sequence Data will only be indexed for general articles about sequence data.
Postoperative Complications: The indexing policy has changed. This term will be added unstarred to prospective citations that are indexed with any Surgical Procedures, Operative/adverse effects heading as an aid to searchers. The policy change was not applied retrospectively to existing indexed citations.
Disease headings: The indexing policy was clarified to coordinate with either Humans or Animals, as appropriate to the article. If not specified in the article, then indexers will add Humans, based on a review of existing citations that guided this recommendation.
Animal Diseases: A MeSH Scope Note was added: Diseases that occur in VERTEBRATE animals. By indexing policy, this heading:
Multimodal Imaging: Note the new specific terms for 2017:
Adult Stem Cells: This term has a new MeSH Scope Note. Some Entry Terms were removed. Selected related headings are:
Peripheral Blood Stem Cells: The MeSH Scope Note: Hematopoietic stem cells found in peripheral blood circulation. Note that Peripheral Stem Cells is an Entry Term to Peripheral Blood Stem Cells.
Immunogenicity, Vaccine and Vaccine Potency: The emphasis of Vaccine Potency is on the dose. Sometimes both headings may be used to cover the general and specific concepts.
Immunotherapy: Indexing policy on when to use /drug therapy or /therapy on the disease term:
Persons and Professions: Forty-one new headings were added to the M Tree.
Network Meta-Analysis: Indexing policy is to coordinate with Meta-Analysis [Publication Type] if pertinent.
Protein Domains: Many new headings were added to the G2 Tree.
Two new Publication Types, Calendars and Study Guide, are available for catalogers but will not be used by MEDLINE indexers.
In order to improve indexing consistency and efficiency and to make MEDLINE searching easier and more straightforward, a new subheading, diagnostic imaging, was added.
Three existing subheadings were deleted and replaced by the new subheading, /diagnostic imaging.
Additional reasons for these changes are:
Indexing policy for the new subheading /diagnostic imaging is:
Examples:
1. Multimodal imaging in detection of pancreatic cancer.
| 2016 Indexing | 2017 Indexing |
| PANCREATIC NEOPLASMS / *diagnosis | PANCREATIC NEOPLASMS / *diagnostic imaging |
| MULTIMODAL IMAGING | MULTIMODAL IMAGING |
2. Automatic 3D motion estimation of left ventricle from C-arm rotational angiocardiography using a prior motion model and learning based boundary detector.
| 2016 Indexing | 2017 Indexing |
| VENTRICULAR DYSFUNCTION, LEFT / *radiography | VENTRICULAR DYSFUNCTION, LEFT / *diagnostic imaging |
| HEART VENTRICLES / *radiography | HEART VENTRICLES / *diagnostic imaging |
| ANGIOCARDIOGRAPHY / *methods | ANGIOCARDIOGRAPHY / *methods |
| IMAGING, THREE-DIMENSIONAL | IMAGING, THREE-DIMENSIONAL |
3. PET imaging of prostate cancer.
| 2016 Indexing | 2017 Indexing |
| PROSTATIC NEOPLASMS / *radionuclide imaging | PROSTATIC NEOPLASMS / *diagnostic imaging |
| POSITRON-EMISSION TOMOGRAPHY | POSITRON-EMISSION TOMOGRAPHY |
4. Color Doppler sonography for evaluation of portal venous system in hepatocellular carcinoma.
| 2016 Indexing | 2017 Indexing |
| CARCINOMA, HEPATOCELLULAR / *ultrasonography | CARCINOMA, HEPATOCELLULAR / *diagnostic imaging |
| LIVER NEOPLASMS / *ultrasonography | LIVER NEOPLASMS / *diagnostic imaging |
| PORTAL VEIN / *ultrasonography | PORTAL VEIN / *diagnostic imaging |
| ULTRASONOGRAPHY, DOPPLER, COLOR | ULTRASONOGRAPHY, DOPPLER, COLOR |
5. Quality of reporting noninferiority/similarity in research studies of diagnostic imaging.
| Indexing: No Change |
| BIOMEDICAL RESEARCH |
| DIAGNOSTIC IMAGING / *standards |
See MeSH Tree Changes for 2017 for a complete list of the MeSH heading tree hierarchy changes in PDF format.
Non-Medical Public and Private Facilities [J03]: This new tree was introduced for 2017 MeSH and gathers about 40 MeSH headings in one spot. Most of these headings remain in their original tree locations as well. Note that there are no children for Private Facilities or Public Facilities. Indexing policy is to coordinate with these headings only when the specific type of facility is discussed. Indexers will not try to determine if a facility is private or public.
Examples:
Phenomena and Processes [G]: This tree was reorganized.
For 2016 MeSH:
For 2017 MeSH:
Subheading Tree Modifications for 2017
The /diagnosis tree was modified (see Figure 1).
Figure 1: The subheading tree modifications for /diagnosis.
Figure 2: The subheading tree modification for /pathology in the anatomy & histology tree.
In addition to changes and deletions of MeSH terms on MEDLINE citations, YEP includes other adjustments to reflect 2017 MeSH vocabulary and enhance search retrieval. These follow-on adjustments are largely to add additional MeSH headings or Supplementary Concept Record Names to citations in order to help searchers refine retrieval. In some cases, the changes clarify areas where a single concept existed before, but is now represented by two or more specific concepts.
Examples for 2017 MeSH include the following:
Examples for 2017 MeSH include the following:
When one of these deleted subheadings was replaced with /diagnostic imaging, a MeSH heading for the specific diagnostic technique was added to the citations, if the specific technique or one of its children was not already on the citation:
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 2017 MeSH Browser to see if the Entry Combination information indicates a different term.
There are 12 new Entry Combinations for 2017.
| Previous MeSH Heading/Subheading (Entry Combination) |
Replaced-by Heading for 2017 |
| Anterior Cruciate Ligament/injuries | Anterior Cruciate Ligament Injuries |
| Cardiovascular Diseases/rehabilitation | Cardiac Rehabilitation |
| Fascia/surgery | Fasciotomy |
| Growth Plate/injuries | Salter-Harris Fractures |
| In Vivo Dosimetry/instrumentation | Radiation Dosimeters |
| Menisci, Tibial/injuries | Tibial Meniscus Injuries |
| Myocardium/diagnostic imaging | Heart/diagnostic imaging |
| Peripheral Blood Stem Cells/transplantation | Peripheral Blood Stem Cell Transplantation |
| Rotator Cuff/injuries | Rotator Cuff Injuries |
| School Teachers/education | Teacher Training |
| Shoulder/injuries | Shoulder Injuries |
| Stroke/rehabilitation | Stroke Rehabilitation |
The new MeSH Browser was launched on November 16, 2016. For more information see New MeSH Browser Available.
In October 2016, NLM transitioned from one Data Creation and Maintenance System (DCMS) to two separate systems, the PubMed Data Management System (PMDM) and the Indexing Management System (IMS). This change will separate citation creation and bibliographic data maintenance (PMDM) from assigning MeSH indexing vocabulary (IMS). The new systems facilitate improvements to citation and indexing workflows. To read more about the new model for managing journal citation data in PubMed see MEDLINE/PubMed Production Improvements Underway.
In October 2016, NLM launched newly redesigned Data Distribution Program Web pages. For an explanation for the changes to the Web pages see Changes to the NLM Data Distribution Program. In conjunction with these changes NLM discontinued the license requirement for obtaining MEDLINE/PubMed citations and switched to a "Terms and Conditions" agreement.
The FTP data file exports are now in a new location as explained on the revised Web pages.
NLM is implementing a new consolidated DTD (Document Type Definition) for users of the FTP server and the E-utilities API. More information will be available in a forthcoming article.
The algorithm that creates the journal title name in the NLM Catalog was revised to omit the statement of responsibility (data in the 245 $c) from the journal title name. Data in the MARC 245 $a, $b, $n and $p is still included in the journal title name.
For example (see Figure 3):
Figure 3: Updated journal title name in the NLM Catalog.
This change impacted approximately 540,000 citations in approximately 9,000 PubMed titles.
1. Partial Retractions Policy Change
In September 2016, NLM announced a policy change for citing Partial Retractions. For more information see Partial Retractions: NLM Policy Change.
3. Conflict of Interest (COI) Statement
NLM is adding a conflict of interest statement as provided by the publisher. Sometime in 2017, journal citations will contain conflict of interest statements for the article as submitted by the publisher.
The corresponding tag for the MEDLINE display is COI.
4. Authors Who Contribute Equally
In 2017 NLM will implement a method for publishers to indicate when authors "contributed equally" to a journal article. We do not have a target date yet for when publishers will be able to begin submitting these data.
The corresponding tag using 2 letters in the MEDLINE display will be CE.
The contributed equally designation will also appear in the Summary (text) display and the Abstract display.
Please see MEDLINE Celebrates Its 45th Anniversary for fun highlights of the changes in the world since MEDLINE launched in 1971.
By
Sara Tybaert
MEDLARS Management Section
MEDLINE Data Changes — 2017