Skip to Main Content

Biology 3210: Molecular Biology: PubMed/Medline (NLM)

A class guide for Biology 3210, Molecular Biology.

Search PubMed @ UofL

Provider:  U.S. National Library of Medicine

Coverage: pre-1966 to present

Full-text: None -- links out to full-text found in online repositories

Abstracts: Some

What is PubMed?

 

PubMed is an index to scholarly articles in the biomedical and life sciences.  It is developed and maintained by the National Center for Biotechnology Information (NCBI) and the U.S. National Library of Medicine (NLM).

What does PubMed index?

PubMed contains all the journal citations indexed in MEDLINE, the NLM's journal citation database (more than 20 million references in 5600 journals).  In addition, it includes:

  • in-process citations that are being reviewed for quality control and indexing in MEDLINE
  • citations to articles deemed out-of-scope for MEDLINE
  • citations to pre-prints (articles accepted for publication in a MEDLINE indexed journal but not yet published)
  • citations supplied by publishers to journals that pre-date the date a journal was selected for inclusion in MEDLINE
  • pre-1966 citations not yet updated for inclusion in MEDLINE
  • citations to some additional (i.e., non-MEDLINE) journals in the life sciences where full-text is deposited to the NLM
  • citations to manuscripts  of articles published by researchers funded by the National Institutes of Health (NIH).
  • citations to books and chapters of books accessible through the NCBI.1

PubMed includes abstracts to the literature being indexed.  It also provides links to full-text articles deposited to the National Library of Medicine, articles freely accessible via the Web (called "open access") and, when used through the Library's homepage, it will also display the   button in order to find journal articles within the universe of resources accessible through the University of Lethbridge. 

Why might you want to use PubMed?

You should choose PubMed when you wish to:

  • survey the literature in the biomedical and life sciences fields.
  • find and possibly access articles accepted for publication but not yet published.

 1. Source:  http://www.nlm.nih.gov/pubs/factsheets/dif_med_pub.html

 

PubMed Search Functionality

Keyword Searching

Keyword searching, using terms you, as a user, are familiar with, is the usual first approach to any database.  This is called searching using natural language.  Searching by keyword will always return something of use to the user.  In this regard, the search is rewarding.  However, keyword searching, generally returns more references to articles than one can actually manage to review for their relevance. 

A successful search should return 25-30 references.  The specificity of scientific terms may mean that keyword searching find you exactly what you are looking for--or, maybe not.  A good approach is to look at a few of the references to see if they are what you are looking for.  If they are, then examine the subject headings for the record and search according to subject heading (see below) OR combine your keyword search with a field search (see below) to narrow your results.  Both strategies will increase the specificity of your search.

Subject Searching

Subject searching is a form of searching using a controlled vocabulary where a limited number of of pre-defined terms are assigned to the reference based on an analysis of the content of the article being indexed.  When you find the correct subject heading, the search returns fewer but definitely relevant articles regardless of whether they contain particular key words.

PubMed uses MeSH as its controlled vocabulary.  MeSH stands for Medical Subject Headings.  The MeSH headings applied to the Wilson & McNaugton (1994) example paper appear to the right.

To learn more about searching using MeSH headings, check out this video tutorial from the folks at NLM.

Field Searching

Field searching allows you to search specific fields within the citation.  A list of fields that can be searched appear to the right.

Field searching is available through the Advanced Search function of PubMed.  To search specific fields, use the pull down menu in Advanced Search search-builder and then enter your search term.  If you already know the fields you wish to search, you can enter them directly into the search box.  Examples of field searching include:

tatsuno[Author] --- to search all articles authored by Tatsuno.

or

tatsuno, masami[Author] --- to search all articles authored specifically by Masami Tatsuno

or

lethbridge[Affiliation] -- to search for articles where the authors were affiliated with the University of Lethbridge at the time of publication.

 or

Neurons/physiology[Mesh] -- to find articles that discuss the physiology of neurons as categorized by the MeSH.

Using Boolean Operators:  AND, OR, and NOT

 Boolean operators can be used in the Advanced Search option of PubMed as part of the Search Builder.

Truncation and Wildcards

Truncation and wildcards are not available in PubMed.

Limiters

Once you have retrieved a list of references, you may want to refine the search by limiters or facets or, as they are known in PubMed, filters.  Examples of PubMed filters include article type, publication dates, species studied, etc.

These filters can be pre-set by using the Manage Filters function through your MyNCBI account.

 

Tools in PubMed

 

 

 

Registering for a MyNCBI account is free.  MyNCBI allows you to:

  • save searches
  • receive automatic email alerts based on your saved searches
  • set your preferred display format
  • set up pre-formated search filters (see: Manage Filters)
  • highlight search terms
  • review last 6 months' activity, searches and citations

The following video provides a nice overview of MyNCBI.

  

 

Exporting and Emailing Citations

As with many databases, PubMed allows you to email citations to yourself or others.  [See the SEND TO option in the upper right hand corner.]  As well it allows you to save the citations you find to a citation manager such as Endnote.