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PubMed for Trainers, Fall 2011 U.S. National Library of Medicine (NLM) and NLM Training Center PubMed Search Mechanics Tips & Tricks

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Objectives Fall 2011 PubMed for Trainers 2 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.

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Search Tags Fall 2011 PubMed for Trainers 3 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)

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Some Commonly Used or Otherwise Interesting Search Tags Fall 2011 PubMed for Trainers 4 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 http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp. Search_Field_Descrip

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MeSH Subheadings [sh] Fall 2011 PubMed for Trainers 5 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.

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Exercise Fall 2011 PubMed for Trainers 6 Construct a search on how doctors are using cell phones to track epidemics. Hint: Use the subheading, epidemiology

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Homework Review Fall 2011 PubMed for Trainers 7 Construct a PubMed search using tags for hypertension as a major topic and the subheading toxicity applied to any MeSH term.

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Title [ti] Fall 2011 PubMed for Trainers 8 [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]

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Exercise Fall 2011 PubMed for Trainers 9 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?

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Title/Abstract [tiab] Fall 2011 PubMed for Trainers 10 [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.

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Homework Review Fall 2011 PubMed for Trainers 11 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?

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Text word Fall 2011 PubMed for Trainers 12 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

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Exercise Fall 2011 PubMed for Trainers 13 Compare the PubMed results for the following searches: chikungunya [tiab] chikungunya [tw]

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Affiliation [ad] Fall 2011 PubMed for Trainers 14 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.

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Homework Review Fall 2011 PubMed for Trainers 15 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?

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Thought Experiment Fall 2011 PubMed for Trainers 16 Can you search PubMed for all articles written by U.S.-based researchers?

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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. Fall 2011 PubMed for Trainers 17

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Explore the Indexes example Number of times the term appears in PubMed Fall 2011 PubMed for Trainers 18

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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 Fall 2011 PubMed for Trainers 19

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Combine searches using History example Fall 2011 PubMed for Trainers 20

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Combine searches using History example Fall 2011 PubMed for Trainers 21

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Exercise Fall 2011 PubMed for Trainers 22 1. Find references about the relationship between circadian rhythms and melatonin in humans. 2. Find references about heart surgery. Notice how the term is mapped using Search details. 3. Using History, combine the heart surgery search with the previous search to find references about heart surgery, circadian rhythms and melatonin in humans.