How to get the most out of PubMed

Amit Sood, MDAmit Ghosh, MD

Mayo Clinic College of MedicineRochester, MN

* 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

EBM and Biomedical Databases

Constraints

Physician/Patient Preferences

Decision

Evidence

Decision

Types of Questions

BACKGROUND

FOREGROUND

MedicalStudent

AttendingResident

Background - How? When? Why? Who? What?

Foreground - Specific patient, specific problem, specific setting

Types of Evidence

Original Studies

Predigested Information

Types of Evidence

Original Studies

Predigested Information

• Individual Journals

• Searchable Databases

e.g. MedLine, EMBASE,

CINAHL, PsycINFO,

CANCERnet, SPORTDiscus,

PubMed

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

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

Basic PubMed Features

MEDLINE

Old MEDLINE

PubMed - inprocess

PubMed - assupplied bypublisher

Components of PubMed

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

Query Box

Features bar

Side bar

PubMed Homepage

Menu Bar

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

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

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

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

Stop Words

Framing the Question

The Three steps

Step 1 - Define the components of the question:• Population• Intervention• Comparison• Outcome

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.

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

Basic Search Concepts

Goals for Case #1

Limits Clipboard

Related ArticlesDetails

Display optionsHistory

• 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

Patient Acute Cholecystitis

Intervention Observation

Comparison Surgical management

Outcome Survival

Components of the question

Patient Acute Cholecystitis

Intervention Observation

Comparison Surgical management

Outcome Survival

Components of the question

Study design - Randomized Controlled Trial

Goals for Case #2

Single Citation Matcher

• 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

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

Goals for Case #3

Clinical Queries

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

Goals for Case #4

Tags

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

Using tags

• Can accomplish all the results with tags

• Include in [ ], spacing does not matter

• Commonly used tags:Journal title – [ta]Address of Author – [ad]Publication dates – [dp]Text word - [tw] Title search - [ti]

Author name - [au]

Using tags

Goals for Case #5

My NCBI

You are an expert on Cancer Related Fatigue and would like to remain updated with all the recent advances on this topic.

Case #5

• 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

Goals for Case #6

Bibliography Management

Software

You are an expert on Cancer Related Fatigue and would like to write a review article on this topic.

Case #6

Additional useful tips

Additional Useful tips

• Browser is too slow

• Saving your search ….. Fast

• Preview/Index

• Full text citations

• Additional useful ‘Limits’ options

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

Questions and Comments