PubMed: Biomedical Literature Database

• Introduction to PubMed with Lauren Atkins, the College of Pharmacy liaison librarian at the UF Health Science Center libraries

What is PubMed?

• PubMed is a bibliographic database produced by the National Library of Medicine (NLM), a division of the National Institutes of Health (NIH)
• It contains over 30 million citations for biomedical literature from Medline and life science journals and also includes online books
• Covers subjects such as medicine, pharmacy, biomedical sciences, and nursing
• Medline is a database from NLM and NIH containing 25 million references to journal articles in life sciences, mainly concentrating on biomedicine
• Medline articles are tagged with Medical Subject Headings (MeSH)
• Searching PubMed includes searching Medline
• PubMed is useful for finding journal articles, systematic reviews, clinical trials, and clinical evidence-based guidelines, so it is the primary database for research

Why use PubMed over Google?

• Google is useful for exploring topics and finding keywords, but it has limited scope and content, and the information found may not be trustworthy or peer-reviewed
• PubMed provides access to high-quality, trustworthy research to support evidence-based care and research

How to access PubMed

• Access PubMed through the UF Health Science Center library homepage (Library.Health.UFL.edu) to authenticate as a UF user and access UF's subscriptions
• On-campus access is through Library.Health.UFL.edu, then Quick Links, then Databases, and then PubMed
• Authenticating as a UF user provides access to articles via the "Find It at UF" button, providing access to the PDF without payment
• Off-campus access is available via two options
• VPN (Virtual Private Network): Software for longer research sessions; download and install instructions available via UF IT
• UF proxy server: For quick access to databases, books, and electronic journals
• For help with VPN or easy proxy, reach out to the Health Science Center library staff, and for issues with VPN software, contact UF IT

Basic Search in PubMed

• Creating a search strategy for a research question
• Helpful searching tips
• Conducting a search in PubMed
• Understanding search results in PubMed
• Applying additional filters to refine a search
• Example research question: Is clonidine effective in the treatment of ADHD in adolescents?
• Break down the research question into searchable concepts
• The drug (clonidine)
• The condition (attention deficit hyperactivity disorder or ADHD)
• The population (adolescents)

Searching Tips

• Boolean operators
• AND: Combines concepts
• OR: combines similar terms or concepts
• NOT: Omits a concept from the search (use sparingly)
• Quotes: Use quotes to search for a specific phrase
• Asterisk (): A truncation symbol, finds variations of a word (e.g., adolescent will search for adolescent and adolescents)
• Example search query: clonidine AND ("attention deficit hyperactivity disorder" OR ADHD) AND adolescent*
• Be cautious when using "NOT" to avoid accidentally omitting relevant articles

Conducting a Search in PubMed

• Paste the search query into PubMed
• Search terms are bolded in the search results
• Consider the number of results
• Too many results mean it should be more specific
• Too few results mean it should be broadened
• Filters on the left refine the search
• Restrict by year, text availability, article type (clinical trial, meta-analysis, systematic reviews)
• Restrict it by publication date range, language, and species
• Adding additional filters
• Including clinical trial phases, species, languages, and age ranges
• Caution when using age range filters, as they may miss articles that do not specify numeric age
• Searching terms in the title/abstract field
• Use [TIAB] or "title abstract" after search terms
• Including keywords in the title or abstract will refine the search to relevant articles

Medical Subject Headings (MeSH) in PubMed

• MeSH is a controlled vocabulary used to index articles in PubMed
• Using MeSH terms creates comprehensive and accurate search queries
• MeSH terms are found in PubMed's MeSH database and MeSH-indexed articles
• Combine MeSH terms with keywords to include both indexed articles and newer, unindexed articles
• Access the MeSH database via PubMed.gov under "Explore"
• The MeSH record shows the description of the term, subheadings, entry terms, pharmacological action, and the MeSH tree
• The MeSH tree shows where the term fits within the broader MeSH structure
• Add MeSH terms to a PubMed search query by copying from the MeSH database and combining with relevant keywords in parentheses

How to add MeSH terms

• Example: (clonidine[MeSH] OR Catapres) AND ("attention deficit disorder with hyperactivity"[MeSH] OR ADHD) AND (adolescent[MeSH] OR teen*)
• Find additional MeSH terms by looking at articles' tagged MeSH terms
• Click on a MeSH term in an article to search it in PubMed or MeSH, or add it to the search query

Searching for Pharmacological Actions in PubMed

• Pharmacological action is the pharmacologic effect of a drug or chemical
• Every drug and chemical MeSH heading has defined pharmacological action headings
• Antirheumatic Agents [Pharmacological Action] searches for all drugs and chemicals known as anti-rheumatic agents
• Example research question: What antihypertensive drugs are effective in the treatment of ADHD in adolescents?
• The new search concept includes antihypertensive drugs
• Find pharmacological actions in the MeSH database
• Note that pharmacoaction terms include MeSH terms and supplementary concepts but not keywords
• Example: "Antihypertensive Agents"[Pharmacological Action] AND ("attention deficit disorder with hyperactivity"[MeSH] OR ADHD) AND (adolescent[MeSH] OR teen*)

Exporting Citations from PubMed into EndNote

• EndNote is a citation management software system
• It is free for UF students, faculty, and staff, for collecting, editing, managing, and formatting citations
• Other options are Mendeley, Zotero, F1000, and Sciwheel (now Sciwheel)
• To export citations for PubMed to EndNote web, select the citations, click "Send to," and then "Citation Manager"
• Select "Create File" to download the selected citations
• In EndNote Web, go to "Collect," then "Import References"
• Choose the file, select "PubMed" as the import filter, and import
• To insert citations into Word, download and install the "Cite While You Write" option for your computer
• In Word, select the EndNote tab, insert the citation, and the in-text citation and bibliography will be generated