Internal Database Training: PubMed

Overview

• PubMed = Index and Abstracts + includes PubMed Central
  • Pub = free public access
  • Med = MEDLINE database that PubMed searches
  • Government Resource
    • Part of the National Center for Biotechnology Information (NCBI)
    • NCBI is part of the National Library of Medicine (NLM)
    • NLM is under the National Institutes of Health (NIH)
  • Contains:
    • 33+ million citations for biomedical literature from MEDLINE, life science journals, and online books.
    • Citations may include links to full text content from PubMed Central and publisher web sites.
    • If full text is available it's either because:
      • it's in PubMed Central
      • it falls under NIH mandate for sharing funded research within 12 months
      • open access journal/publisher
      • syncing with Forsyth Library database subscriptions (on campus)
  • Does not contain: information about meeting abstracts, conference proceedings, dissertations, patents, or websites.
• PubMed Central = Full Text
  • Contains:
    • 6 Million full text articles
• Overview
  • ADVANCED tool for health sciences
    • MeSH headings and subheadings
    • Automatic Term Mapping (ATM) using 3 translation tables)
  • accessible to clinicians, scientists, researchers, consumer health and anyone since it's NLM/.gov
  • LOTS of support documentation - hours of CE, 4 hour long workshops
    • (ex. Preprints: Accelerating Research - 60 min)
    • See full list in the Online Training link to the right

• Creating an Account
  • Transitioning to 3rd party logins (@mail.fhsu Gmail works; Microsoft outlook @fhsu.edu login won't)
  • ​The National Center for Biotechnology Information (NCBI) maintains TONS of biology-related resources in addition to PubMed.
  • If you find yourself using PubMed frequently, or other NCBI resources, it might be useful to register for an account. 
  • Similar benefits - saving searches, setting alerts, etc.
• Filters, Cite, & Share Tools
  • Filters: Article Type, Language, Publication Date (expand graphic)
  • Citation options: APA, MLA, AMA, NLM
  • Share: twitter, FB, permalink
• Article Detail Page
  • hyperlinked author names to find more works by them
  • abstract + keywords
  • similar articles
  • cited by
  • publication type
  • MeSH terms

Searching

• Advanced Search
  • clicking "AND" adds your field and terms to the query box
  • Lots of fields
  • Autocomplete for many fields (ex. journal)
  • If at all possible identify most appropriate MeSH terms and use them in your query
  • Click "search" to see results or "Add to history" to stay on the advanced search page and see the number of results with that query
    • Search history can help you combine several previous searches using Boolean operators
• Example
  • Topic: Flu Vaccine for People with Egg Allergies
  • Basic Search "flu vaccine and egg allergy" = 169 results
  • MeSH search "flu vaccine" brings up MeSH term "Influenza Vaccines" to reveal definition, subheadings, entry terms, and placement in MeSH tree structure
    • allergy to a vaccine would be "Adverse Effects" 
    • Check the box and click "Add to Search Builder" on the right side
  • MeSH search "egg allergy brings up MeSH term "Egg Hypersensitivity"
    • Click "Add to Search Builder" on right side
    • When ready, click "Search PubMed"
  • MeSH searching "Influenza Vaccines/adverse effects"[Mesh]) AND "Egg Hypersensitivity"[Mesh] = 47 results

What are MeSH Terms?

National Library of Medicine (NLM) indexers examine articles and assign the most specific MeSH headings, subheadings, and terms that describe the concepts discussed in the article

• MeSH Headings - MeSH stands for Medical Subject Headings.  
  • List of standard terms added by indexers to the article record to help improve search results.
  • The indexer assigns as many MeSH headings as appropriate to cover the topics of the article (generally 5 to 15).
    • If there is no specific heading for a concept, the indexer will use the closest, general heading available.
  • When PubMed searches a MeSH term, it will automatically include narrower terms in the search, if applicable.
• Subheadings - further describe a particular aspect of a MeSH concept
• Terms -  reflect the characteristics of the group being studied
  • Ex: the age group, human or other animal, male or female

MeSH Database

MeSH controlled vocabulary is setup in a hierarchical tree structure. You can search for MeSH terms for your search by going to MeSH database in PubMed from the PubMed homepage or at: ncbi.nlm.nih.gov/mesh/.  The MeSH database allows you to:

• View the definition of a the MeSH term
• Select a broader or narrower MeSH term from a tree structure
• Access a list of subheadings of the MeSH term
• Restrict your search to articles where the term is the major focus of articles
• Click "Add to Search Builder" if you want to select a MeSH term or subheading to your query and continue searching the database for other MeSH terms to define your research question

What This Means When Searching

In your search query, MeSH terms are automatically mapped to the most specific term and included in your search.

Pros:

• working with a carefully maintained (annually updated) controlled vocabulary
• MeSH database gets you familiar with the preferred medical vocabulary and terminology quickly
• subject searching
• knowing MeSH terms will help not only with searching PubMed, but other databases as well

Cons:

• Not all PubMed articles are indexed with MeSH terms
• Newer articles can take weeks for processing to get MeSH terms added
  • *This is changing as of Jan 2022, PubMed is transitioning to automated MeSH indexing of MEDLINE citations in PubMed. Automated indexing will provide users with timely access to MeSH indexed metadata and allow NLM to scale MeSH indexing for MEDLINE to the volume of published biomedical literature. Human indexers have been and will continue to be involved in the refinement of automated indexing algorithms and will play a significant role in the quality assurance approaches for automated indexing.​
• Therefore, only searching with MeSH terms can limit your results

(Content adapted from UNC Health Sciences Library and NLM PubMed Tutorial)