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2016 MeSH Highlights: Questions and Answers

Below are answers to your questions about the Medical Subject Headings (MeSH), asked during the 2016 MeSH Highlights Webinar and during the #medlibs twitter chat on February 4, 2016. We've attempted to categorize them by subject area.

MeSH Development - MEDLINE Indexing - PubMed Searching - MeSH and Cataloging - MeSH Data and Downloading - Publication Types - Training

MeSH Development

  1. Q: How are the MeSH terms and categories derived?
    A: The driving force behind MeSH development is the biomedical literature, itself. The vocabulary is developed in response to the needs of indexers and catalogers to describe concepts being discussed in the literature. In addition, new MeSH terms are suggested by users. Terms are created with the judgment and expertise of the MeSH staff, in cooperation with Indexing, Cataloging, History of Medicine, and the MEDLARS Management Section at NLM. 
  2. Q: How are entry terms selected and when are they added?
    A: We primarily select terms based upon term requests from users for new vocabulary. Every year we get many suggestions for individual terms. In addition we get general requests for additional terminology to reflect topical areas that are not well represented in MeSH. The Entry terms are added when we revise MeSH, annually.
  3. Q: How many entry terms are in the MeSH vocabulary?
    A: In 2016 MeSH there are 681,505 Entry terms (ETs), including ETs for Descriptors, Subheadings, Publication Types and Supplementary Concepts.
  4. Q: Is relevancy towards access to information as there is a movement of using more social tagging and less subject heading controls. What is the future of MeSH headings?
    A: That's a great question, but one we can probably not intelligently address in a quick Q&A.  Perhaps this would be a good topic for a panel discussion at a medical library or informatics conference.
  5. Q: do you regularly analyze author-supplied keywords, and do some data-mining on them, to see if they suggest new MeSH terms...?
    A: Our system is more pragmatic than keyword analysis. Our indexers and catalogers require vocabulary to describe the significant concepts discussed in the literature, so indexers and catalogers can immediately tell us when the vocabulary is missing a concept. We also respond to user requests.
  6. Q: interested in hearing the reasons behind why some MeSH were deleted
    A: There can be a few reasons. For example, sometimes a Heading is ambiguous (what exactly does “Tropical Disease” mean?). Sometimes a heading is merged with another heading (e.g., Black Pepper was merged with Piper nigrum).
  7. Q: How do I find concepts that are similar but just nuanced enough to be different?
    A: Exploring MeSH using the MeSH Database can be a great way to find concepts for searching. Look for siblings or close neighbors in a MeSH tree, or look for "See Also" references in the MeSH Database record. "See Also" references are especially useful because those typically go across trees rather than up/down trees. 
  8. Q: How often are mid-year changes to MeSH done (e.g., the recent addition of Zika Virus terms)?
    A: There have been about 12 mid-year changes to MeSH since 1977. They are not common.
  9. Q: What is being done regarding ethnicity subjects to support health care disparities research/concerns?
    A: Every year MeSH staff selects topics of current interest to review in addition to our usual responsive monitoring of the biomedical literature. We will consider studying the vocabulary surrounding health care disparities in a future review. We appreciate the suggestion.
  10. Q: Why was the diagnostic use (DU) subheading (qualifier) removed?
    A: The proper application of the diagnostic use subheading was unclear, and therefore was inconsistently used by indexers. It was also redundant, for example, in describing the diagnostic use of chemicals. The subheading /diagnosis is used with the disease term and a specific diagnostic test is included in the MEDLINE record (e.g., Colonic Neoplasms/diagnosis and Colonoscopy would be added to a record in addition to the term Indigo Carmine when describing that substance’s diagnostic use).
  11. Q: Why is gabapentin a supplementary concept instead of a regular MeSH?
    A: The vast majority of chemicals in MeSH exist as supplementary concepts. These records are created on a daily basis by Index Section Chemists who make around 5,000 of them a year. Each year we try to a promote a good number of the most important compounds from Supplementary Concepts to Descriptor Classes. If you see something we overlooked like gabapentin please put in a MeSH request and we will look into it.

In addition to the above questions we received a number of specific requests for MeSH changes. To make sure your idea gets reviewed and put into the MeSH workflow we ask that you enter it into our request system. If for some reason we don't agree to do it we will let you know.

MEDLINE Indexing

  1. Q: Indexers to assign Clinical Study [PT] only if authors use "clinical study" & if no indications that study is either "clinical trial" or "observational study." Please expand about 'indications'? What should publishers be clear about for indexers?
    A: Authors may use the words “clinical study” (often in the title), but indexers assign the more specific Publication Types Clinical Trial or Observational Study according to the information in the full text of the article (usually in the Abstract, Introduction or Materials and Methods). If the author describes the study for example as “random,” “phase II,” “observational study,” “clinical intervention study,” “randomized trial,“ “randomized intervention,” etc., indexers will identify the study as a Clinical Trial (or specific) or Observational Study.
    If the author uses the words “clinical study” and there is no further specification, the article will be indexed with Clinical Study[PT].

    Publishers  can assist  indexers by  instructing authors to use  language that  clearly identifies the type of study in  their article  (Clinical Study, Clinical Trial or specifics, or Observational Study). It is particularly helpful if this information is included in the article abstract and/or study design/methods section.

PubMed Searching 

  1. Q: Am I correct that the Entry terms are synonyms[sic] for the MeSH term?  So using the MeSH term will get all of the articles indexed with MeSH term of course, but also those articles with those entry terms (free language)? 
    A: Entry terms are used by systems like PubMed to pull the MeSH term(s) into your search. In PubMed, the term you used for searching is included in the search, but not any other Entry Terms that may be associated with the MeSH Heading. All relevant indexed records will be retrieved by the preferred MeSH heading.
  2. Q: to clarify if there was a MeSH term previously used, but now is a synonym, and a new MeSH terms is used in its place, PubMed DOES update all the records, taking all the old MeSH (now synonym) off and puts the new term on. AM I understanding correctly?
    A: In cases where a MeSH heading is replaced and the new heading is synonymous with the old, MEDLINE is updated so that the old term is replaced with the new term in all relevant MEDLINE records. We go into other possibilities during our class, Advanced PubMed: Tips Tricks and Tools: MeSH. Please join us!

  3. Q: just a clarification on entry terms why do we not see "irregular heartbeat" as an entry term listed  on the Arrhythmias, Cardiac" entry terms
    A: During the Webinar, we accidentally used a term from the Unified Medical Language System (UMLS) that maps to MeSH instead of a MeSH Entry term. Vocabulary from the UMLS is integrated into the PubMed search in a "mapping file," adding synonyms to enhance PubMed retrieval. The terms from the UMLS work just like Entry Terms, mapping to the preferred MeSH Heading. We apologize for the confusion.
  4. Q: would like to be able to select multiple pub types at the same time when limiting a search!­
    A: You can select multiple publication types from the filters menu in PubMed, but we're assuming that you mean you'd like to combine them with an AND instead of OR, which is how the filters currently work. We are happy to share your suggestion with the PubMed developers. To reach them directly, use the Write to the Help Desk link from the bottom of any PubMed page.
  5. Q: I wish you would go back to the old method of showing all the filters on one page. Hiding them is very confusing to occasional users and is challenging to teach.­
    A:  We are happy to share your suggestion with the PubMed developers. To reach them directly, use the Write to the Help Desk link from the bottom of any PubMed page.

MeSH and Cataloging

  1. Q: With the MeSH tree changes, have classification numbers [for books] changed as well?  Is there a list of these somewhere?
    A: The updated NLM Classification will be released in April 2016 with a section on class numbers added and cancelled and there is an accompanying Technical Bulletin article detailing all the changes.  The Classification Team reviews the new MeSH vocabulary each year to determine if there is an impact on the Classification. This evaluation is going on now and some class numbers may be updated to reflect the new trees.
  2. Q: I thought I read somewhere that some subheadings are going to be broken apart from Main Headings - I think this is mainly for cataloging, not searching. But can you elaborate on where this is headed? 
    A: The initial call for comments concerning the proposal to discontinue artificially reconstructed subjects strings is found at /pubs/techbull/mj15/mj15_cataloging_unstringing_survey.html

    The official announcement about our decision to implement this policy is found at /pubs/techbull/so15/so15_cataloging_unstringing_subject_heading.html

    EXAMPLE

    OLD DISPLAY ON DISTRIBUTED RECORDS
    Subject strings created for distribution:
    650 12 $a Acquired Immunodeficiency Syndrome $x ethnology $z Africa $v Congresses
    650 12 $a Acquired Immunodeficiency Syndrome $x ethnology $z Caribbean Region $v Congresses
    650 22 $a Cross Cultural Comparison $z Africa $v Congresses
    650 22 $a Cross Cultural Comparison $z Caribbean Region $v Congresses
    650 22 $a Health Policy $z Africa $v Congresses
    650 22 $a Health Policy $z Caribbean Region $v Congresses

    NEW DISPLAY ON DISTRIBUTED RECORDS (NOW SAME AS IN NLM DATABASES)
    650 12 $a Acquired Immunodeficiency Syndrome $x ethnology
    650 22 $a Cross Cultural Comparison
    650 22 $a Health Policy
    651 _2 $a Africa $x ethnology
    651 _2 $a Caribbean Region $b ethnology
    655 _2 $a Congresses
  3. Q: What the new deconstruction means - just geographics and publication types or eventually all subheadings? How to adapt.   
    A: Only Geographics and Publication types are being separated.  Topical subheadings will remain with the main headings, just as they do in the NLM Catalog.
  4. Q: More information on the changes in MeSH Structure in OCLC and for authority control vendors.  
    A: Catalogers in other libraries that use MeSH are encouraged to follow NLM practice in assigning their subjects. Under no circumstances should a library edit a record in OCLC to re-create a string and remove the 651 and 655 fields. Any desired editing should be done only in your local catalog. After January 2016, libraries will be required to establish medical subjects in a deconstructed format in OCLC. OCLC will be updating all records in their database with 650 fields with a second indicator of 2 to follow the new NLM practice. NLM is working with authority vendors to provide guidance on how local catalogs can be updated.

MeSH Data and Downloading

  1. Q: Is the vocabulary available for download? If so, in what formats?
    A: MeSH is freely available in XML and ASCII and MeSH/MARC formats. See the MeSH homepage for further instructions. We are now also offering a beta version of MeSH in RDF. See Medical Subject Headings (MeSH) RDF Linked Data (beta).
  2. Q: who is the best person to contact for discussing tree numbers?  We have a text mining project that is using them.­
    A:  Please contact the MeSH staff via the NLM Contact form at Contact NLM. You may enter "Attn: MeSH Staff" to facilitate proper routing.
  3. Q: We use Sierra (III product) and cannot load MeSH authority records. Are there plans to make this possible? 
    A: We at NLM do our best to provide our data in standard formats that can be widely used (e.g., XML, ASCII, MARC). We cannot customize our systems for proprietary needs. Please work with your software provider or vendor and explain your needs for NLM data.
  4. Q: How do you find and search Supplementary Concepts in PQD?
    A: NLM doesn't support a product by the name of PQD. Please contact the producer of the product, directly. If the company needs information on using MeSH or the UMLS, please have them contact us via the NLM Contact form at Contact NLM.

Publication Types

  1. Q: Details please on the new "blog" publication type? To what blogs is this applied?
    A:  This publication type will be used by cataloging for blogs that are being archived by NLM. It is not being used for MEDLINE. You can read the scope note on the MeSH record: https://www.ncbi.nlm.nih.gov/mesh/2010023

  2. Q: What is the specific difference between retraction of publication and retracted publication?
    A: Retracted Publication: This is the publication that is retracted. 
    Retraction of Publication: This is the published retraction statement/notice that announces a publication is retracted. 

    NLM does not remove the citation for a retracted article, but updates the citation to indicate it has been retracted. The citation for the original article is indexed as Retracted Publication [PT] and is linked to the citation for the published retraction notice. For example see: https://www.ncbi.nlm.nih.gov/pubmed/26617705.

    The citation for the published retraction statement is indexed as Retraction of Publication [PT], and NLM makes a reciprocal link between the published retraction statement and the retracted article. For example see: https://www.ncbi.nlm.nih.gov/pubmed/26722610.

    For more information, please see the Fact Sheet: Errata, Retractions, Partial Retractions, Corrected and Republished Articles, Duplicate Publications, Comments (including Author Replies), Updates, Patient Summaries, and Republished (Reprinted) Articles Policy for MEDLINE

Training

  1. Q: Will the changes in MeSH be reflected in the PubMed tutorials or are the tutorials designed in such a way that annual updates to MeSH don't impact the content of the tutorials?
    A:  We review our NLM training materials after the MeSH updates in January and February. We try to pick examples that will last for several years at least, but occasionally we find we need to make adjustments. You can see the review date of all of our training materials in the lower right of the Web page. For example, the online tutorial "Using Medical Subject Headings (MeSH®) in Cataloging" has been fully revised for 2016 and should be available online shortly. It includes clear instructions on where Geographical terms and Publication Types should be recorded in a MARC environment, but we would not include that information in the MeSH scope notes. The MEDLINE Indexing Online Training Course is in the process of being updated with 2016 MeSH. The updates should be live by the end of February 2016.