Patient Safety Orientation : 3 - Orientation to Citation DBs, PubMed & MeSH , & MYNCBI

 1. Read about "citation databases," "controlled vocabulary," and "subject headings"

The building block of many databases, including PubMed, is the citation record. The PubMed database is essentially a compilation of citation records.  Web of Science, EMBASE, and Academic Search Complete are examples of other "citation databases" (also known as "bibliographic databases").

Citation records describe the title, authorship, and other publication information related to an article or book as an aid to users in locating the material in full-text.

Additionally, many citation records contain the abstracts of articles in order to help researchers decide quickly if the article is actually relevant. In the same way that title and author information are part of the searchable fields in a citation record, so is the abstract information. Each of these fields may be searched alone or in a combination. A simple keyword search usually searches all available fields in the citation record, depending on the database. 

Many citation databases use “controlled vocabulary” to index records according to subjects. Controlled vocabulary begins as an authoritative list of standardized terms, which a database uses to organize records by subject or another meaningful concept. Using controlled vocabulary ensures that a subject will be consistently described across all the citation records in the database.

Subject headings or indexing terms are prime examples of controlled vocabulary that describe what an article is "about" in a concise manner. They are placed in special searchable fields in the citation record and researchers can limit their search results to only those records containing defined subject headings.  

Subject headings or indexing terms are usually made available in a browseable thesaurus. The thesaurus will often contain "entry terms" that will map to the official subject heading. For example, the subject heading in a database might be automobile. Terms like "car", "passenger vehicle", "sedan", or "my ride" would be entry terms. When the searcher puts any of these entry terms into the search box, the entry term will be automatically mapped to the subject heading "automobile". Thus, the all the records tagged (indexed) with the subject heading automobile will be retrieved by searching for the entry term "car".   Another example of a subject heading with entry terms might involve the generic name for a drug as the subject heading and entry terms that include all the brand names for the drug.   Be aware that the list of entry terms may be missing or incomplete. So, while entry terms can be helpful, it is always better to find the actual subject term in the thesaurus. When entry terms are present in the thesaurus or subject heading record, they can be used to expand a keyword search string.

Subject headings used in the PubMed database are called MeSH headings. MeSH stands for Medical Subject Headings (see box below). These headings are applied to the citation record by a subject expert at the National Library of Medicine who reads the article and decides what the article is "about".  Sometimes dozens of MeSH terms are applied to a record because the same article addresses many subjects of interest to diverse researchers.

MeSH subject headings can be looked up by searching the MeSH database. Note, searching the MeSH database is different from searching PubMed. The MeSH database is a compilation of MeSH records that provide information on subject headings (MeSH terms). Once you have looked up the MeSH terms in the MeSH database, you can copy them into the PubMed search box to search the PubMed database of citations.  

Many major databases have arranged their subject headings in a hierarchical fashion. In the MeSH database, this hierarchy is called the "MeSH tree". By using a hierarchical organization of subject headings, the searcher can select a level of specificity, ranging from broad concepts (e.g., Rodentia meaning Rodents) to narrow concepts (e.g., Mice).

Be aware that the process of indexing records with subject headings is not perfect and subject headings may change over time.   Also, note that controlled vocabulary varies by database and a concept may be called by terms in different databases. One database may use "car" as its official subject heading, while another will use "automobile".  Even inside the same database, there may be some degree of variation in the ways a subject term will be applied. Expert searchers often check the subject headings (MeSH terms) associated with articles to discover the variations in indexing similar or closely related concepts. The more you know about subject headings, the more powerful you will become as a searcher!

2. View this brief tutorial to learn about the general concept of controlled vocabulary. The Wellington Medical and Health Sciences Library created this 3 minute video:http://www.youtube.com/watch?v=aDR3VjwXvEo

3. See an additional video on controlled vocabularies has been prepared by the University of Washington librarian's (approx. 6 minutes):http://www.youtube.com/watch?v=pHh8ud5zsvg

1. Read more about MeSH

     Me dical

    S ubject

    H eading

MeSH is the controlled vocabulary used by the National Library of Medicine in their PubMed/Medline database. MeSH searching is subject searching as opposed to keyword searching. Subject searching helps us focus precisely on the most relevant articles and discard articles where a keyword might appear incidentally, but does not truly match the focus of the search.

Be aware that there is some delay in indexing PubMed articles. So if you want the latest articles, you will need to use keywords in addition to MeSH terms. Also, be aware that a small percentage of articles are never indexed with MeSH and must always be retrieved through keyword searching. By the third month post-publication, about 75% of articles have been indexed. However, it may take as long as 3 years for all articles to be indexed, depending on the place of publication and other factors.

A number of PubMed users don't realize how important MeSH is because many keyword searches automatically map to MeSH (remember entry terms). Automatic mapping to MeSH occurs when keywords are either identical to MeSH terms or "entry terms". Thus, a searcher can enter an entry term into the PubMed search box and the database will automatically translate the search into a string that includes the entry term plus the MeSH term.

For example, if you do a keyword search on "Rodents", the PubMed search engine automatically maps you to the MeSH term "Rodentia" and includes it in the search string together with the keyword "Rodents". A quick look in the "details box" on your search page will tell you exactly how your keyword search was translated by the PubMed search engine. If a MeSH term does not exist for your keyword, then no translation is made and you must generate all the words that might be related to this concept on your own. 

MeSH is especially important when a keyword has many meanings - for example, consider the term, "Nursing".  There are over 80 concepts related to the word "Nursing" included in the MeSH thesaurus. If you enter "Nursing" into the PubMed search box, you will retrieve every citation indexed with any of the 80+ MeSH concepts associated with the term "Nursing". If you want to retrieve only the citations related to "Breast feeding", you must select the MeSH term related to "Breast feeding". Go to the MeSH database and enter the term "Nursing" into the search box. The MeSH database will retrieve many MeSH terms that relate to the concept "Nursing".

MeSH searching allows users to further limit retrieval by applying the "Major Concepts" and other subheadings limits. These limiters should be used carefully since indexing is not always precise. If the expert indexer did not identify the concept as a "Major Concept" and you ask for this level of precision, you may miss articles that you might consider quite relevant. Many articles may be relevant, although they are indexed only at the basic level of MeSH and not the "Major Concept" level. 

MeSH searching is also useful in cases where a  high level or "parent" MeSH term has numerous subordinate terms or "children". These subordinate or "child" terms beneath the broad, high level "parent" terms are automatically included in  a search by the "explode" function.  For example, the MeSH term "Health Services Research" has numerous children (and grandchildren) who will automatically be entered into a search string by the internal PubMed query translator. Note, you have an option to choose not to explode a parent terms. In the case of "Health Services Research"[Mesh], the internal translator will add in children or subordinate Mesh terms including "Health Care Surveys"[Mesh], "Health Services Needs and Demand"[Mesh], etc. Searching "Health Services Research"[Mesh] with the explosion turned off reduces the number of retrievals by approximately 90% (in this case, over several hundred thousand results). In some cases, the explosion of the terms is quite beneficial because you want to include the concepts related to the subordinate terms, but in other cases you want to turn off the explosion function and exclude the child concepts.  

Be aware that if you do keyword only searching, you will not benefit from the subordinate concepts listed in the MeSH hierarchy. Explosion only occurs when a MeSH term is used. .

Be aware that many concepts to not exist in the MeSH database or exist in a way you might not expect. For example, MeSH does not contain the term, "Service-learning", a concept which will retrieve over 500 citations when used as a keyword.

2. View these brief introduction to the MeSH database of subject headings: http://www.youtube.com/watch?v=nF_oQNtnbuQ  and  http://www.youtube.com/watch?v=uyF8uQY9wys

3. Take the self-paced online tutorial "Medical Subject Headings (MeSH®) in MEDLINE®/PubMed®: A Tutorial" at http://www.nlm.nih.gov/bsd/disted/meshtutorial/introduction/index.html

4. Examine the following pdf, which provides you with printable information about using MeSH and PubMed help: http://nnlm.gov/training/resources/meshtri.pdf