How to search the medical literature on the net
Samir Haffar M.D.
Associate Professor of Gastroenterology
My students are dismayed when I say to them
“Half of what you are taught as medical students
will in 10 years have been sh...
Background questions
• Sometimes
Involve a single fact such as:
“What is the causative agent of Chagas disease?”
“What is ...
Searching background questions
Easy to search
• Standard textbooks such as Harrison, Nelson….
• Innovative electronic text...
Textbooks
Textbooks may be a useful source of information
on “background” questions but:
• May provide biased advice
• Rap...
• Very popular with generalists, specialists, & house staff
– Ease of use
– Comprehensiveness
– Inclusion of disease-orien...
• Questions that provide the evidentiary basis for specific
clinical decisions
• Best structured using the framework of:
-...
What is the best evidence?
• The best evidence is the evidence most likely to
provide an unbiased view of the truth
• Bias...
Level of evidence
Oxford Centre of EBM
Levels of
evidence
Bias
Bias
Bias
Bias
Bias
Bias
Validity/StrengthofInference
Example of PICO/PIO Concept
• 70-year-old man with PUD & stable angina tt by low-
dose aspirin, statin, ACE inhibitor & ni...
Key components of your clinical question
PICO
P
I
C
O
Patient Elderly patient with aspirin-associated PU
Intervention Clop...
Formulation of the relevant question
In a elderly patient with aspirin-associated PU,
is clopidogrel more effective than P...
The amount of medical literature
0
500000
1000000
1500000
2000000
2500000
Biomedical MEDLINE Trials Diagnostic
MedicalArti...
How can I find what I am searching for?
• Interface to MEDLINE (NLM*) & easiest way to use it
• From 1950 to date
• 19 million articles as of November 2009
• Grow...
Annual addition of articles to PubMed
50 years ago Majority of research not published in English
Currently Almost 90% of a...
PubMed tutorial
• Side bar of the PubMed entry page
• Quite detailed tutorial program
• Takes about 2 hours to go right th...
PubMed Tutorials
http://www.ncbi.nlm.nih.gov/
MeSH Database
Text word & MeSH term*
• Text word
Any word or phrase in the title or abstract of an article
• MeSH terms
Vocabulary used ...
Tree structure of MeSH in PubMed
The „explode‟ (exp) feature of tree structure allows to
capture entire subtree of MeSH* t...
Alternative spellings & misspellings
(a) hemorrhage American spelling
[Mesh term]
(b) haemorrhage British spelling
(c) hem...
Boolean operator ‘OR’
After its creator George Boole
Akobeng AK. Arch Dis Child 2005 ; 90 : 837 – 840.
Akobeng AK. Arch Dis Child 2005 ; 90 : 837 – 840.
Boolean operator ‘AND’
After its creator George Boole
Akobeng AK. Arch Dis Child 2005 ; 90 : 837 – 840.
Boolean operator ‘NOT’
After its creator George Boole
Boolean search
After its creator George Boole
Boolean operators Meaning
Peptic ulcer OR Hemorrhage
Peptic ulcer AND Hemorr...
‘Wildcards’
malig* means malignancy
malignant
malign
but not malunion
malaligned
etc
PubMed command – 1
Command What it does?
OR Finds articles containing either of specified words
Ex: child OR adolescent
AN...
PubMed command – 2
Command What it does?
*
Truncation
Acts as a wildcard indicating any further letters
Ex: child * = (chi...
PubMed translation of query into search terms
PICO Element Search terms for PubMed
P Elderly patient
Peptic ulcer
Limit to...
PubMed Clinical Queries
• Search faster & more relevant articles
• Category
Etiology, dg, therapy, prognosis, clinical pre...
PubMed Clinical Queries
PubMed Clinical Queries
N Engl J Med 2005 ; 352 : 238 – 44.
Clopidogrel vs aspirin & esomeprazole
Difference 7.9 % points
95 % CI: 3.4 – 12.4
P = ...
Aspirin plus esomeprazole was superior to
clopidogrel in the prevention of recurrent
ulcer bleeding.
How to improve your PubMed search?
• “Related Articles” link
• Select another set of terms & try again
• “AbstractPlus” fo...
Related articles link
“Limits” link
“Limits” link
Question type & study design
Study DesignQuestion
Intervention RCT
Incidence & prognosis Cohort study
Prevalence Cross-sec...
How many questions can doctors answer each day?
64 residents in 2 hospitals
401 consultations
280 questions (2 for 3 patie...
1- Ask
2- Acquire
4- Apply
5- Assess
Patient
dilemma
Principles
of EBP
Evidence alone does not
decide – combine with other...
50,000 articles/yr
from 120 journals
~3,000 articles/yr
meet critical appraisal
& content criteria
(94% noise reduction)
M...
High quality/relevant data – Pearls
Glasziou P, Del Mar C. Evidence based practice workbook.
Blackwell Publishing, 2nd edi...
High quality/relevant data
Pearls
If not valid No value
If not relevant No value
Steps
– Answerable question
– Search
– Appraise
– Apply
EBM & Systematic Review
Find a systematic review
Steps
– Answerabl...
Limitations of evidence
• Evidence simply doesn‟t exist
• Some of what is available
Not easily accessible
Not clinically r...
Learning through play
• Try all “buttons”
• Make lots of “mistakes”
• Have fun
Thank You
How to search the medical litterature on the net?
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How to search the medical litterature on the net?

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  • Dismayed: يفزع
  • Hemophagocytic syndrome:Can masquerade as cirrhosis with ascites.These patients have fever, jaundice, and hepatosplenomegaly, usually in the setting of lymphoma or leukemia.Reference: de Kerguenec C, Hillaire S, Molinie V, Gardin C, Degott C, Erlinger S, Valla D. Hepatic manifestations of hemophagocytic syndrome: a study of 30 cases. Am J Gastroenterol 2001;96:852– 857.
  • (1/3 of medical litterature)
  • The logrank test The most popular method of comparing the survival of groups, which takes the whole follow up period into account.The logrank test is used to test the null hypothesis that there is no difference between the populations in the probability of an event (here a death) at any time point.The analysis is based on the times of events (here recurrence ulcer bleeding deaths).If a survival time is censored, that individual is considered to be at risk of dying in the month of the censoring but not in subsequent weeks. This way of handling censored observations is the same as for the Kaplan-Meier survival curve.Because the logrank test is purely a test of significance it cannot provide an estimate of the size of the difference between the groups or a confidence interval. For these we must make some assumptions about the data. Common methods use the hazard ratio, including the Cox proportional hazards model, which we shall describe in a future Statistics Note.
  • MeSH:The National Library of Medicine’s controlled vocabulary used for indexing articles for MEDLINE/PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminologies for the same concepts.
  • Pearls: لؤلؤةThe quality of most published information is very poor: Most published information is irrelevant and/or the methods are not good. Finding the high-quality evidence is like trying to sip pure water from a hose pumping dirty water, or looking for ‘rare pearls’.
  • How to search the medical litterature on the net?

    1. 1. How to search the medical literature on the net Samir Haffar M.D. Associate Professor of Gastroenterology
    2. 2. My students are dismayed when I say to them “Half of what you are taught as medical students will in 10 years have been shown to be wrong. And the trouble is, none of your teachers knows which half.” Dr Sydney Burwell Dean of Harvard Medical School
    3. 3. Background questions • Sometimes Involve a single fact such as: “What is the causative agent of Chagas disease?” “What is the hemophagocytic syndrome? ” • Often Involve much more information such as: “How do I insert a jugular venous central line?”
    4. 4. Searching background questions Easy to search • Standard textbooks such as Harrison, Nelson…. • Innovative electronic texts such as UpToDate • Some companies group collections of textbooks MDConsult http://www.mdconsult.com/ Stat!Ref http:// www.statref.com/ • Entry of single concept such as disease or diagnostic test
    5. 5. Textbooks Textbooks may be a useful source of information on “background” questions but: • May provide biased advice • Rapidly become out of date
    6. 6. • Very popular with generalists, specialists, & house staff – Ease of use – Comprehensiveness – Inclusion of disease-oriented formation • Provides recommendations (guidelines) for clinicians
    7. 7. • Questions that provide the evidentiary basis for specific clinical decisions • Best structured using the framework of: - Patient - Intervention - Comparison (if relevant) - Outcomes Foreground questions PICO/PIO
    8. 8. What is the best evidence? • The best evidence is the evidence most likely to provide an unbiased view of the truth • Bias is difference between study results & truth • Of course, we can never know the truth, but we can try to come as close as possible by performing & using well-designed & well executed studies
    9. 9. Level of evidence Oxford Centre of EBM Levels of evidence Bias Bias Bias Bias Bias Bias Validity/StrengthofInference
    10. 10. Example of PICO/PIO Concept • 70-year-old man with PUD & stable angina tt by low- dose aspirin, statin, ACE inhibitor & nitrates as needed • The patient developed recently an UGI bleeding UGI endoscopy revealed no ulcer & biopsy was – for HP • You wonder if clopidogrel is more effective than the association of PPI & asipirin for recurrent PU bleeding
    11. 11. Key components of your clinical question PICO P I C O Patient Elderly patient with aspirin-associated PU Intervention Clopidogrel Comparaison PPI + Aspirin Outcome Recurrent PU bleeding Good question should have 3 or 4 components
    12. 12. Formulation of the relevant question In a elderly patient with aspirin-associated PU, is clopidogrel more effective than PPI & aspirin to prevent recurrence of PU bleeding?
    13. 13. The amount of medical literature 0 500000 1000000 1500000 2000000 2500000 Biomedical MEDLINE Trials Diagnostic MedicalArticlesperYear 5,000 per day 1,500 per day 95 per day 55 per day Glasziou P, Del Mar C. Evidence based practice workbook. Blackwell Publishing, 2nd edition, 2007. So much evidence, so little time
    14. 14. How can I find what I am searching for?
    15. 15. • Interface to MEDLINE (NLM*) & easiest way to use it • From 1950 to date • 19 million articles as of November 2009 • Growing at rate of 700 000 articles/year • ≈ 5 000 indexed journals • > 70 million search done each month • Search terms by topics, authors or journal Free on the Internet since the mid-1990s * US NLM: United States National Library of Medicine
    16. 16. Annual addition of articles to PubMed 50 years ago Majority of research not published in English Currently Almost 90% of articles published in English
    17. 17. PubMed tutorial • Side bar of the PubMed entry page • Quite detailed tutorial program • Takes about 2 hours to go right through • Very helpful
    18. 18. PubMed Tutorials http://www.ncbi.nlm.nih.gov/
    19. 19. MeSH Database
    20. 20. Text word & MeSH term* • Text word Any word or phrase in the title or abstract of an article • MeSH terms Vocabulary used to index all MEDLINE articles • Example: “hemorrhage” [Text Word] “haemorrhage” [Text Word] “hemorrhage” [MeSH Terms] * MeSH: Medical Subject Headings in PubMed
    21. 21. Tree structure of MeSH in PubMed The „explode‟ (exp) feature of tree structure allows to capture entire subtree of MeSH* terms within single word One of 3 MeSH categories of peptic ulcer * MeSH: Medical Subject Headings in PubMed
    22. 22. Alternative spellings & misspellings (a) hemorrhage American spelling [Mesh term] (b) haemorrhage British spelling (c) hemorhage Misspelling (d) haemorhage Misspelling
    23. 23. Boolean operator ‘OR’ After its creator George Boole Akobeng AK. Arch Dis Child 2005 ; 90 : 837 – 840.
    24. 24. Akobeng AK. Arch Dis Child 2005 ; 90 : 837 – 840. Boolean operator ‘AND’ After its creator George Boole
    25. 25. Akobeng AK. Arch Dis Child 2005 ; 90 : 837 – 840. Boolean operator ‘NOT’ After its creator George Boole
    26. 26. Boolean search After its creator George Boole Boolean operators Meaning Peptic ulcer OR Hemorrhage Peptic ulcer AND Hemorrhage Peptic ulcer NOT Hemorrhage
    27. 27. ‘Wildcards’ malig* means malignancy malignant malign but not malunion malaligned etc
    28. 28. PubMed command – 1 Command What it does? OR Finds articles containing either of specified words Ex: child OR adolescent AND Finds articles containing both specified words Ex: child AND adolescent NOT Excludes articles containing the specified word Ex: child NOT adolescent Glasziou P, Del Mar C. Evidence based practice workbook. Blackwell Publishing, 2nd edition, 2007. Limits Articles restricted in several ways by: date, language, age, … ( ) Use parentheses to group words Ex: (colorectal cancer) AND (screen AND mortality)
    29. 29. PubMed command – 2 Command What it does? * Truncation Acts as a wildcard indicating any further letters Ex: child * = (child OR childs OR children OR childhood) Glasziou P, Del Mar C. Evidence based practice workbook. Blackwell Publishing, 2nd edition, 2007. [ti] Finds articles with the word in title Ex: ulcer [ti] = find article with the word ulcer in title [so] or so Find articles from a specific source Ex: ulcer AND BMJ [so] = finds articles on ulcer in BMJ MeSH Controlled vocabulary keywords used in also in Cochrane Often useful to use both MeSH heading & text words
    30. 30. PubMed translation of query into search terms PICO Element Search terms for PubMed P Elderly patient Peptic ulcer Limit to “aged: 65+ years” “peptic ulcer” [MeSH term] I Clopidogrel “clopidogrel” [MeSH term] C PPI Aspirin “proton pump inhibitors” [MeSH term] “aspirin” [MeSH term] O Recurrence Peptic ulcer bleeding “recurrence” [MeSH term] “peptic ulcer hemorrhage” [MeSH term] Other RCT Limit to “randomized controlled trial”
    31. 31. PubMed Clinical Queries • Search faster & more relevant articles • Category Etiology, dg, therapy, prognosis, clinical prediction guides • Search Narrow specific search Broad sensitive search
    32. 32. PubMed Clinical Queries
    33. 33. PubMed Clinical Queries
    34. 34. N Engl J Med 2005 ; 352 : 238 – 44. Clopidogrel vs aspirin & esomeprazole Difference 7.9 % points 95 % CI: 3.4 – 12.4 P = 0.001 by log-rank test
    35. 35. Aspirin plus esomeprazole was superior to clopidogrel in the prevention of recurrent ulcer bleeding.
    36. 36. How to improve your PubMed search? • “Related Articles” link • Select another set of terms & try again • “AbstractPlus” format • “Limits” link: sex, age, language, RCT,… • “MeSH” terms: Medical Subject Headings
    37. 37. Related articles link
    38. 38. “Limits” link
    39. 39. “Limits” link
    40. 40. Question type & study design Study DesignQuestion Intervention RCT Incidence & prognosis Cohort study Prevalence Cross-sectional study Etiology & risk factors Cohort or case-control Diagnosis Cross-sectional study In each case, SR of all available studies better than individual study
    41. 41. How many questions can doctors answer each day? 64 residents in 2 hospitals 401 consultations 280 questions (2 for 3 patients) 80 answers (29%) Sources of answers: – Textbooks (31%) – Articles (21%) – Consultants (17%) Green ML et al. Am J Med 2000;109:218–233. Residents 103 GPs Questions collected over 2.5 d 1101 questions 702 answers (64%) Sources of answers: – Available print – Human resources – Literature search: 2 answers Ely JW et al. BMJ 1999;319: 358–361. GPs
    42. 42. 1- Ask 2- Acquire 4- Apply 5- Assess Patient dilemma Principles of EBP Evidence alone does not decide – combine with other knowledge & values 3- Appraise Hierarchy of evidence 5 A
    43. 43. 50,000 articles/yr from 120 journals ~3,000 articles/yr meet critical appraisal & content criteria (94% noise reduction) McMaster PLUS project – First level Critical appraisal filters  Valid  Ready for clinical attention Health Information Research Unit – McMaster University – Canada
    44. 44. High quality/relevant data – Pearls Glasziou P, Del Mar C. Evidence based practice workbook. Blackwell Publishing, 2nd edition, 2007. Finding high-quality evidence like searching for „rare pearls‟
    45. 45. High quality/relevant data Pearls If not valid No value If not relevant No value
    46. 46. Steps – Answerable question – Search – Appraise – Apply EBM & Systematic Review Find a systematic review Steps – Answerable question – Search ++++ – Appraise x 2 – Synthesize – Apply Time: 6 months – Team 2 000 articles This patient dies Systematic reviewEBM Time: 90 seconds < 20 articles This patient survives
    47. 47. Limitations of evidence • Evidence simply doesn‟t exist • Some of what is available Not easily accessible Not clinically relevant Not of good quality Not applicable to your patient It takes time to develop high quality evidence & more time to get it to publication
    48. 48. Learning through play • Try all “buttons” • Make lots of “mistakes” • Have fun
    49. 49. Thank You

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