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PubMed Search Mechanics Tips & Tricks. PubMed for Trainers, Fall 2011 U.S. National Library of Medicine (NLM) and NLM Training Center. Objectives. By the end of this session, you should understand: Some specific uses of PubMed search tags, including some common pitfalls.

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Pubmed search mechanics tips tricks

PubMed Search Mechanics Tips & Tricks

PubMed for Trainers, Fall 2011U.S. National Library of Medicine (NLM) and NLM Training Center


Objectives
Objectives

  • By the end of this session, you should understand:

    • Some specific uses of PubMed search tags, including some common pitfalls.

    • How to explore search field indexes.

    • How to combine searches using History.

PubMed for Trainers


Search tags
Search Tags

  • Search fields can be specified using search tags in a PubMed search.

  • The search term should appear before the search tag; e.g.:

    • lung [mh]

  • Search tags must be enclosed in square brackets

  • Using search tags will turn off Automatic Term Mapping (ATM)

PubMed for Trainers


Some commonly used or otherwise interesting search tags
Some Commonly Used or Otherwise Interesting Search Tags

  • MeSH Subheadings [sh]

  • Title [ti]

  • Title and abstract [tiab]

  • Text word [tw]

  • Author [au]

  • Affiliation [ad]

    A complete list can be found in PubMed Help (“Search Field Descriptions and Tags”): http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Search_Field_Descrip

PubMed for Trainers


Mesh subheadings sh
MeSH Subheadings [sh]

  • The [sh] search tag allows users to “free float” subheadings.

    • breast neoplasms[mh] AND trends[sh]

    • Automatic inclusion of narrower terms is turned off with the [sh:noexp] tag.

PubMed for Trainers


Homework review
Homework Review

  • Construct a PubMed search using tags for hypertension as a major topic and the subheading “toxicity” applied to any MeSH term.

PubMed for Trainers


Title ti
Title [ti]

  • [ti] can be used to search for words and numbers in the title field

    • The entire title is rarely included in the title index, therefore is rarely searchable as an unbroken string

    • Search using words or phrases from the title, e.g.,

      air pollution [ti] blood pressure [ti] traffic [ti]

PubMed for Trainers


Exercise
Exercise

Find an article with “outcome of triple negative breast cancer” in the title using search tags.

What is another way you could conduct this search in PubMed?

PubMed for Trainers


Title abstract tiab
Title/Abstract [tiab]

  • [tiab] can be used to search for words and numbers included in the title, abstract, and other abstract of a citation.

    • Note: If an article does not have a published English abstract, NLM does not create one.

  • [tiab] is often used by searchers to find topic-related keywords, however, it fails to find terms from the subject fields of PubMed records.

PubMed for Trainers


Homework review1
Homework Review

Examine the results for this PubMed search:

quality of life [majr] NOT quality of life [tiab]

What does this search show about potential weaknesses of searching only titles and abstracts?

PubMed for Trainers


Text word
Text word

  • Words and numbers that are searched with the Text Words [tw] field tags will be search in the following fields:

    • Title

    • Abstract

    • MeSH headings & subheadings

    • Publication Types

    • Other Terms field

    • Chemical Names of Substances

    • Secondary Source Identifier

    • Personal Name as Subject

PubMed for Trainers


Exercise1
Exercise

Compare the PubMed results for the following searches:

  • chikungunya [tiab]

  • chikungunya[tw]

PubMed for Trainers


Affiliation ad
Affiliation [ad]

  • PubMed citations only list the affiliation information for the first author of the article

  • The affiliation may include the institutional name and postal or e-mail address.

  • The affiliation data is as it appears in the original journal article. It is not standardized, therefore the same institution may appear in variant forms.

PubMed for Trainers


Homework review2
Homework Review

Try the following PubMed search:

buffalo [ad] AND jusko[au]

If you were trying to find all articles written by Jusko from the University at Buffalo, what is missing from your results?

PubMed for Trainers


Thought experiment
Thought Experiment

  • Can you search PubMed for all articles written by U.S.-based researchers?

PubMed for Trainers


Explore the indexes
Explore the Indexes

  • The Indexes are viewable on the PubMed Advanced Search page.

    • In the Search Builder select the field from the drop-down menu.

    • Type in the terms.

    • Click Show Index.

PubMed for Trainers


Explore the indexes example
Explore the Indexes example

Number of times the term appears in PubMed

PubMed for Trainers


Combine searches using history
Combine searches using History

  • Click the search number to see the options pop-up, or

  • Enter the search number (#3) in the search box to combine previous searches

PubMed for Trainers


Combine searches using history example
Combine searches using History example

PubMed for Trainers


Combine searches using history example1
Combine searches using History example

PubMed for Trainers


Exercise2
Exercise

  • Find references about the relationship between circadian rhythms and melatonin in humans. 

  • Find references about heart surgery. Notice how the term is mapped using Search details.

  • Using History, combine the heart surgery search with the previous search to find references about heart surgery, circadian rhythms and melatonin in humans.

PubMed for Trainers


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