In-Depth Database Tutorial: PubMed

Locating Controlled Vocabulary (MeSH term) for your concepts

• MeSH (Medical Subject Headings) is NLM’s controlled vocabulary of biomedical terms used to describe the subject of each journal article in MEDLINE. These are a standardized set of terms that are used to bring consistency to the searching process. In total, there are approximately 26,000 terms, and they are updated annually to reflect changes in medicine and medical terminology. Using MeSH terms helps account for variations in language, acronyms, and British vs. American English.

• MeSH can be searched from a NCBI interface. To access this database from the UD version of PubMed home screen, select the following link pictured below (labeled "MeSH Database"). Note that it is important to start from UD's custom homepage so that you can access full-text results.

• Within the current configuration of PubMed, this link takes users to the MeSH database that has the appearance of the old (pre-2020) PubMed interface. This difference is normal, and the two systems are fully integrated with one another. The page that opens should look like the following screen-shot. In the search box at the top of the page, enter a term for your first concept (in this case, the drug "Atorvastatin") and then click "Search":

• Your search will either take you directly to a MeSH term, or it will provide you with a list of options. If you do get a list of options, simply select the one that best fits your concept by clicking on the title of the term. It should open page like the one for Atorvastatin pictured here:

Aside: Important notes to keep in mind when using MeSH terms*

*The search on Atorvastatin will resume at the end of this subsection and in the Keywords section.

Before moving forward with the above search, it is important to note a few things about MeSH terms and the important information provided with a single MeSH entry.

• MeSH Terms are arranged hierarchically by subject categories with more specific terms arranged beneath broader terms. MeSH terms in PubMed automatically include the more specific MeSH terms in a search. MeSH hierarchies can be viewed towards the bottom of each individual MeSH entry page.

• The following shows the tree for Atorvastatin. Note that there are no terms beneath Atorvastatin. This means that no narrower terms will get searched when MeSH term Atorvastatin is search. If, however, "Heptanoic Acids" was searched as a MeSH term, it would default to searching for the MeSH term Atorvastatin, as well as searching for results with the MeSH terms "Fluvastatin" and "Heptanoates" (as pictured in the second MeSH hierarchy below). This default setting is known as "Automatically exploding" the MeSH term. It helps with locating results that are related to your topic. That being said, at times, exploding can make your search too general. 

• Choosing to focus (also referred to as “not exploding”) will only search for your chosen MeSH term. Terms are chosen by MeSH indexers to be the primary focus of an individual article. Command to search: [Mesh:noexp] will only find the term specified, not the terms beneath it (for example: “Heptanoic Acids”[Mesh: noexp] only finds records indexed with Heptanoic Acids, not Fluvastatin, Heptanoates, or Atorvastatin). In addition to this command, you can check box labled, "Do not include MeSH terms found below this term in the MeSH hierarchy" in the MeSH record, as pictured here:

• Searching for “major headings” will narrow your search to only find MeSH terms listed as a major topic of an article. Command to search: [majr] (e.g. “Atorvastatin”[majr] will find articles with Atorvastatin as a major topic). Within individual article records, major topic MeSH terms will have an asterisks (e.g. Atorvastatin*), while non-major topics will not have one. As seen in the screen-capture above, the check box labeled "Restrict to MeSH Major Topic" can be selected to achieve this same command

• Subheadings: MeSH can be made more specific by the addition of  subheadings such as "therapy" and "prevention and control." Note that using subheadings is a double-edged sword because it can limit your results significantly and prove unnecessary when searching with multiple concepts. By default, all subheadings are automatically included when you search for an individual MeSH term because they all form a narrower subsection of the initial term (i.e. "Atorvastatin/administration and dosage"[Mesh]  is a narrow set of results contained with the broad set of results retrieved by searching "Atorvastatin"[MeSH]).

  • When in the MeSH record, add subheadings by clicking on the boxes next to the desired subheadings (as seen in the above screenshot). 

  • As with MeSH terms, PubMed search results, by default, include the more specific terms arranged beneath broader terms for the MeSH term and also includes the more specific terms arranged beneath broader Subheadings.

Adding MeSH terms to the search box

• The MeSH term for Atorvastatin can be directly searched within the PubMed databases from the MeSH page for the concept. 
• Once you've decided on how you want to configure the MeSH term (explode vs. not-explode, major heading, subheadings, etc), simply click on the button towards the upper-right side of the screen labeled "Add to search builder" (as pictured in the following screen-capture)

• After you click this button, the term should populate the PubMed Search Builder box (as pictured above). In this case, clicking the button caused the text "Atorvastatin"[Mesh] to populate the search box.

• Additional note about MeSH/Subheading Combinations: You can manually add subheadings in the search box by using the format MeSH Term/Subheading, e.g. neoplasms/diet therapy. You can also use the two letter abbreviation for subheadings rather than typing out the full phrase, e.g. neoplasms/dh. Click here for the abbreviations of other MeSH subheadings. (https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.mesh_subheadings/). Warning: Adding too many subheadings may lead to missing important articles. For a MeSH/Subheading combination, only one Subheading at a time may be directly attached to a MeSH term. For example, a search of hypertension with the subheadings diagnosis or drug therapy will appear as hypertension/diagnosis or hypertension/drug therapy.

• Before running this search in PubMed, you will first need to add keywords to the search strategy, as shown in the following section ("Sample Search Step 2: Keywords"). Do not close the MeSH search page because the following steps will show you how to add keywords directly to the PubMed Search Builder box within the MeSH entry page.