Discussion of strategy with a financial analyst

Conducting Smarter PubMed Searches – Part 2

In my previous blog (you can read it here) I introduced you to basic search strategies to streamline your literature search on one of the most popular biomedical databases, PubMed. Sometimes, however, it can be useful to go beyond these simple methods of searching. Therefore, in today’s blog, I want to dig a bit deeper. Let’s look at some of the more advanced search features that PubMed has to offer.

Build your search using MeSH terms

  • What are MeSH terms? MeSH, or Medical Subject Headings, is the name of a controlled medical vocabulary used to uniformly and consistently index articles in PubMed. It consists of hierarchically structured terms that are designed to reflect the content of each catalogued record. MeSH terms are assigned by trained indexers – typically 10–12 terms per article
  • Why MeSH terms can be helpful to your search. MeSH terms can be particularly useful if your initial free text search retrieves no or not as many articles as you expected. Since authors often use different synonyms to describe the same terminology, a relevant article may elude your query if you fail to account for all possible analogues of your free text search term (eg, cancer can also be described as malignancy or neoplasm). Additionally, using free text search terms may retrieve articles where your keyword, while appearing in the abstract, is not the main focus of the paper. MeSH terms will help you address both of these issues
  • How do you determine the best MeSH terms for your search? MeSH terms and their definitions can be looked up in the MeSH database. Entering your keyword will present you with a selection of related MeSH terms. Clicking on a specific MeSH term will open a new page that includes a number of different features
    • A list of subheadings (diagnosis, treatment, etc) that can help you further focus your search
    • Clicking the “Restrict to MeSH major topic” box will make your MeSH term the major focus of the retrieved references
    • At the end of the page, you will find a hierarchical arrangement of terms related to the MeSH term you selected that can be included or excluded from your query
    • Once you have made your choices, click on “Add to search builder” and then “Search PubMed” on the left side of the page. Keep in mind: As with basic searching, Boolean operators can be used to combine different MeSH terms! Furthermore, MeSH terms can also be combined with other free text words or phrases to increase your search retrieval
  • One more tip: Should you find a perfect article of interest, look at the MeSH terms assigned to this reference by opening the MeSH terms link under the articles abstract. This may provide you with new useful terms for your next search!
  • Does this mean that you should use MeSH terms for all your searches? No. While MeSH terms can be very helpful, they also have their limitations; MeSH terms are not always available for each concept (eg, new and emerging technologies) or are not assigned to each record (eg, “ahead of print” articles that have not yet been indexed). Combining free text and MeSH terms is, therefore, often the best strategy!

Save useful searches and get automated alerts
PubMed provides access to a storage space as part of a free personal account called “My NCBI.” Searches saved to this account can be executed or adapted at a later time. Additionally, you can set email alerts for each of your queries that will be triggered should new results for a search be retrieved. Be sure that you specify the frequency of such alerts – the default is monthly, so you may miss out on updates for weeks if you don’t!

Use the “Clinical Queries” feature to quickly perform searches for clinical problems
Not much time to plan your search strategy? Use preprogrammed strategies, so called “Clinical Queries,” provided by PubMed that can help you filter your search by 3 clinical research areas

  1. Clinical study categories – this option can further be refined by therapy, diagnosis, etiology, prognosis, or clinical prediction guides
  2. Systematic reviews – helps you retrieve systematic reviews, meta-analyses, reviews of clinical, evidence-based medicine, consensus development conferences, or guidelines
  3. Medical genetics – finds articles related to medical genetics