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How to get the most out of PubMed
Amit Sood, MDAmit Ghosh, MD
Mayo Clinic College of MedicineRochester, MN
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* EBM and Biomedical Databases* Basic PubMed Features* Framing the Question* Basic Search Concepts* Single Citation Matcher * Clinical Queries * Tags * My NCBI (Cubby)* Bibliographic Management Software * Additional Useful Tips* Questions and Comments
Plan For Today’s Workshop
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EBM and Biomedical Databases
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Constraints
Physician/Patient Preferences
Decision
Evidence
Decision
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Types of Questions
BACKGROUND
FOREGROUND
MedicalStudent
AttendingResident
Background - How? When? Why? Who? What?
Foreground - Specific patient, specific problem, specific setting
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Types of Evidence
Original Studies
Predigested Information
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Types of Evidence
Original Studies
Predigested Information
• Individual Journals
• Searchable Databases
e.g. MedLine, EMBASE,
CINAHL, PsycINFO,
CANCERnet, SPORTDiscus,
PubMed
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Types of Evidence
Original Studies
Predigested Information
• Individual Journals
• Searchable Databases
e.g. MedLine, EMBASE,
CINAHL, PsycINFO,
CANCERnet, SPORTDiscus,
PubMed
Cochrane collaboration
ACP Journal Club
Clinical Practice guidelines
UpTodate
TRIP database
EBM reviews
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Types of Evidence
Original Studies
Predigested Information
• Individual Journals
• Searchable Databases
e.g. MedLine, EMBASE,
CINAHL, PsycINFO,
CANCERnet, SPORTDiscus,
PubMed
Cochrane collaboration
ACP Journal Club
Clinical Practice guidelines
UpTodate
TRIP database
EBM reviews
Search Engines
Ovid Entrez Medscape Healthgate NLM Gateway
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Basic PubMed Features
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MEDLINE
Old MEDLINE
PubMed - inprocess
PubMed - assupplied bypublisher
Components of PubMed
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Individual journals
NLM[PubMed - in process]
[PubMed – as supplied by publisher]
Medline [PubMed – indexed for Medline]
Few months
Accuracy check
MeSH terms assignment
How it works
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Query Box
Features bar
Side bar
PubMed Homepage
Menu Bar
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Medline Subject Headings = MeSH
• MeSH is NLM’s controlled vocabulary thesaurus
• MeSH terms are used to describe the subject of each article
• Arranged in alphabetic and hierarchical structure
• Automatic explosion - PubMed searches the MeSH term and also the narrower terms automatically
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All MeSH categories eg. Anatomy, Disease etc.
Subcategories eg. Infections
Disease groups eg. Bacterial infections
Subheadings eg. etiology, therapy
Individual diseases eg. UTI
MeSH Tree
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Automatic term mapping
Journals Translation Table
MeSH Translation Table
Phrase list
Search individually and combine the results
Search an unqualified term
Stops search at first match
Author index
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Boolean logic
• Represents relationships between entities
• AND, OR, and NOT
• Be cautious with using NOT
• Processed in a left to right sequence
• Can overcome this by including terms in parentheses
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Stop Words
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Framing the Question
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The Three steps
Step 1 - Define the components of the question:• Population• Intervention• Comparison• Outcome
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The Three steps
Step 1 - Define the components of the question:• Population• Intervention• Comparison• Outcome
Step 2 - Identify the study design that will answer the question.
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The Three steps
Step 1 - Define the components of the question:• Population• Intervention• Comparison• Outcome
Step 2 - Identify the study design that will answer the question.
Step 3 - Define the study types: Diagnosis; Prognosis; Therapy; Harm
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Basic Search Concepts
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Goals for Case #1
Limits Clipboard
Related ArticlesDetails
Display optionsHistory
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• 45 yo female with no past medical history• Presents with right upper quadrant abdominal pain and
fever• Mild leukocytosis, normal LFTs• Diagnosed with Acute Cholecystitis• Patient is advised surgery but opts for observation for a
few days• She seeks your advise as her Primary care physician
What is our well built clinical question ?
Case #1
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Patient Acute Cholecystitis
Intervention Observation
Comparison Surgical management
Outcome Survival
Components of the question
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Patient Acute Cholecystitis
Intervention Observation
Comparison Surgical management
Outcome Survival
Components of the question
Study design - Randomized Controlled Trial
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Goals for Case #2
Single Citation Matcher
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• A 55 yo male with advanced emphysema is seen for follow up. He quit smoking 2 years ago but has significant dyspnea at rest. He wants to know if he would be a candidate for lung volume reduction surgery
• You recall reading an abstract of an RCT published in 2003 in the NEJM and would like to quickly pull it up, while the patient waits in the office.
Case #2
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Single Citation Matcher
• Very useful tool to locate a citation about which all the details are not known
• Can be used to search multiple citations
• Range of dates should be entered separated by a colon - 1999:2001
• Batch citation matcher - mostly used by publishers
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Goals for Case #3
Clinical Queries
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Your research mentor invites you to write a book chapter on the adjuvant therapy of lung cancer, right when you are getting ready to submit your crucial NIH grant.
You do not want to say No, but would like to get it over with in the least amount of time possible!
Case #3
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Goals for Case #4
Tags
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You are interested in doing research on coronary artery disease at Harvard. Your colleague suggests you work with Dr. Eugene Braunwald. You have heard of him but are not sure how well published he is.
You would like to retrieve all the articles authored by Dr. E Braunwald from Harvard Medical School on Coronary Artery Disease that are published in the last 10-years.
Case #4
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Using tags
• Can accomplish all the results with tags
• Include in [ ], spacing does not matter
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• Commonly used tags:Journal title – [ta]Address of Author – [ad]Publication dates – [dp]Text word - [tw] Title search - [ti]
Author name - [au]
Using tags
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Goals for Case #5
My NCBI
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You are an expert on Cancer Related Fatigue and would like to remain updated with all the recent advances on this topic.
Case #5
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• Used to store search strategies
• Can look up all the new citations since last searched
• Can set up an email delivery of the new citations
• Can set up LinkOut and document delivery services preferences
Using My NCBI
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Goals for Case #6
Bibliography Management
Software
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You are an expert on Cancer Related Fatigue and would like to write a review article on this topic.
Case #6
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Additional useful tips
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Additional Useful tips
• Browser is too slow
• Saving your search ….. Fast
• Preview/Index
• Full text citations
• Additional useful ‘Limits’ options
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What we learnt today
* Introduction* Basic PubMed features: Homepage, MeSH database,
Boolean logic * Framing the Question: PICO format* Basic Search Concepts: Limits, Clipboard, Details,
History, Display options * Single Citation Matcher * Clinical Queries * Tags * My NCBI (Cubby)* Bibliographic Management Software * Additional Useful Tips
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Questions and Comments