Biomedical information retrieval using PubMed ®

Your money!

• Lunch Money - Rs 65• Stationary - Rs 31• Certificate - Rs 04

• Total - Rs 100

Instructions

• Use the computer as and when instructed to

• No other use of the computer is permitted during the workshop

Learning Objectives

By the end of this session, you should be able to:

• Understand how PubMed translates basic searches.

• Use MeSH and Limits to refine your search.

• Understand and use Boolean operators.

• Develop a search strategy.

• Download and email citations

You have to search a thesis topic on types of drug and diet therapy for skin cancer

Search the web to see what has been already done on this topic

Information Overload

Try PubMed ®

Looking at all the wrong places Retrieval of core information

How do I access PubMed?

Directly at: http://pubmed.com

Or, National Library of Medicine’s homepage: http://www.nlm.nih.gov

Copyright ©2006 AlphaMed Press

Vincent, B. et al. Oncologist 2006;11:243-251

Figure 1. Illustration of how information is stored in the MEDLINE database

Try PubMed

Avoid Stopwords

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Superfluous words

typesofandfor

What is a Search Strategy?

– A plan that helps you look for the information you need. • Search Strategy Tips

– Pick a search topic– Divide topic into concepts – Find words (keywords) or subject headings (MeSH) to

represent these concepts – Refine your search to dates, study groups, etc., as

appropriate. (Limits)– Combine concepts with Boolean (AND, OR, or NOT)

connectors

Types of drug and diet therapy for skin cancer

Patient population (Not defined)Intervention/therapy (Drug & Diet therapy)Comparison (Not applicable), and Outcome (Skin cancer)

• Find out the MeSH word for ‘Skin Cancer’

What is MeSH?

• MeSH – Medical Subject Headings• Controlled vocabulary terms

» Epistaxis, Brain Edema, Otitis Media, Myocardial Infarction

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Click MeSH Database12:14 AM

Select Limits

Click to apply limits.Search

Results are reducedfrom 4,224 to 64

Click Display Settings

Select Abstract and click Apply

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Selected results can also be sent to a clipboard area. Select Send to Clipboard from the dropdown menu.

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Building Blocks(Boolean Operators)

Always use in UPPERCASE12:14 AM

AND narrowsOR broadensNOT excludes

Copyright ©2006 AlphaMed Press

Vincent, B. et al. Oncologist 2006;11:243-251

Using the Boolean operator AND between search terms returns only records that contain all of the search terms

22,18770 2,790502,02152

Copyright ©2006 AlphaMed Press

Vincent, B. et al. Oncologist 2006;11:243-251

Using the Boolean operator OR between search terms returns all records that contain any of the search terms

Copyright ©2006 AlphaMed Press

Vincent, B. et al. Oncologist 2006;11:243-251

Using the Boolean operator NOT between search terms returns only records that contain the first search term and not the second

Default Functions of PubMed

• If no boolean between words, it assumes ‘AND’salmonella hamburger = salmonella AND

hamburger• If anything is written in WORD Alphabet (s) form, it assumes author gupta p shah d• If journal name or pubmed version is typed, it searches it only in

the journal gupta p shah d lancet

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Exercise 1

Impact of daily vs weekly supplementation of iron and folic acid on hemoglobin status

Impact of daily vs weekly supplementation of iron and folic acid on hemoglobin status

Exercise 2

• Use MeSH Database to build a strategy that will find citations to articles about Statistics of Measles Outbreak.

• Measles and Outbreak should be the major topics of the articles.

Exercise 3

Your supervisor asks you to find an article he read in JAMA or New England Journal of Medicine about “Virtual colonoscopy” written by Mitka M.

Exercise 4

• Find citations to articles about the ethics of kidney transplantation.

• Filter to review articles. • Select 5 items and add them to the Clipboard.• Go to the Clipboard and view the selected

items in Abstract format and email the citations to your account.

Where PubMed lacks?

Local, cultural scientific research Non-indexed journals

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Practice makes a man perfect