Clinical Epidemiology - Systematic PubMed Searching Workshop

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Presentation slides from a clinical epidemiology searching workshop given at McGill University on June 5th, 2013.

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Clinical Epidemiology - Systematic PubMed Searching Workshop

  1. 1. Robin Featherstone, MLISLiaison Librarian (Medicine)Life Sciences LibraryHow to Conduct a SystematicSearch in PubMedHow to Conduct a SystematicSearch in PubMedGenevieve Gore, MLISLiaison Librarian (Medicine)Life Sciences LibrarySlides: http://www.slideshare.net/featherr
  2. 2. ObjectivesObjectivesBy the end of today’s class, you will be able to:1.Identify subject headings using the MeSHDatabase2.Construct a search strategy3.Run your search using the PubMed AdvancedSearch Builder
  3. 3. A review of a clearly formulated question thatuses systematic and explicit methods to identify,select, and critically appraise relevant research,and to collect and analyse data from the studiesthat are included in the review.From: Cochrane Collaboration (2012). Glossary: Systematic Review. Accessed Jun 4, 2013: http://www.cochrane.org/glossary/5#term423What’s a Systematic Review?What’s a Systematic Review?
  4. 4. From: Moher D, Liberati A, Tetzlaff J, Altman DG, The PRISMA Group (2009). Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement. PLoS Med 6(6): e1000097. doi:10.1371/journal.pmed1000097Flow of Information Through the Different Phases of aSystematic ReviewFlow of Information Through the Different Phases of aSystematic Review
  5. 5. Systematic reviews of interventions require athorough, objective and reproducible search of arange of sources to identify as many relevantstudies as possible (within resource limits).From: Cochrane Handbook (2012). Section 6: Searching for Studies. Accessed Jun 4, 2013: http://www.cochrane-handbook.org/What’s a Systematic Search?What’s a Systematic Search?
  6. 6. #7) Describe all information sources (e.g.databases with dates of coverage, contact withstudy authors to identify additional studies) inthe search and date last searched.#8) Present full electronic search strategy for atleast one database, including any limits used,such that it could be repeated.PRISMA Checklist for Reporting Systematic ReviewsPRISMA Checklist for Reporting Systematic ReviewsFrom: PRISMA Statement for Reporting Systematic Reviews (2012). PRISMA Checklist. Accessed Jan 10, 2011: http://www.prisma-statement.org/
  7. 7. 1. Develop a research question2. Identify databases, search engines, trialregistries, etc. in which to run your search3. Develop a search strategy4. Run the search in your first database5. Apply filters6. Export references to a citation manager7. Translate and run the search in yoursubsequent databasesHow to Find ArticlesHow to Find Articles
  8. 8. Develop a Research Question
  9. 9. You’re applying for a grant to support yourresearch on infections in arthritis patientsThink of a question related to this topic...ScenarioScenario
  10. 10. RelevancyRetrieval(# of searchresults)BroadQuestionsNarrowQuestionsHigh =lots ofarticlesLow =very fewarticlesHigh = directlyrelevant articlesLow = mostlyirrelevant articlesHow questions influence search resultsHow questions influence search results
  11. 11. Broad:• What is the prevalence of infections in arthritispatients?Narrow:• What is the risk of tuberculosis for rheumatoid arthritispatients treated with TNF alpha antagonists?Very Narrow:• What is the rate of Caplan Syndrome for asbestosworkers in Northern Quebec between 1985 and 2005?Possible QuestionsPossible Questions
  12. 12. Decide Where to SearchDecide Where to Search• Consult library subject guideshttp://www.mcgill.ca/library/library-findinfo/subjects/health• Talk to a librarian
  13. 13. Develop a Search Strategy
  14. 14. 1. Break your question into concepts2. Identify subject headings for each concept3. Identify text words for each concept• Tips:– Use a “target article” to help identify search terms– Use a worksheet to keep track of your termsStep-by-StepStep-by-Step
  15. 15. Which concepts are contained in the question:What is the risk of tuberculosis forrheumatoid arthritis patients treated withTNF alpha antagonists?Break into PICO ConceptsBreak into PICO Concepts
  16. 16. PICOPICOPICOPatients with rheumatoid arthritisTNF alpha antagonistsRisk of tuberculosisPopulationInterventionor ExposureComparisonOutcome orendpoint
  17. 17. What is MeSH?
  18. 18. A. Bird Diseases B. NeutropeniaWhich Subject Heading Explodes?Which Subject Heading Explodes?
  19. 19. Identify MeSH terms for your three conceptsand add to your strategy worksheet.Identify Subject HeadingsIdentify Subject HeadingsPICOPatients with rheumatoid arthritisTNF alpha antagonistsRisk of tuberculosis
  20. 20. AND ANDOR"Arthritis, Rheumatoid"[Mesh]"Tumor Necrosis Factor-alpha"[Mesh]"Tuberculosis"[Mesh]OR"Mycobacteriumtuberculosis"[Mesh]ORORORConcept #1 Concept #2 Concept #3SubjectHeadingsTextWordsSearch StrategySearch Strategy
  21. 21. BREAK – 15 mins
  22. 22. Why?1.Not all citations have subject headings2.Indexers are only human (they make mistakes)Next: Identify Text WordsNext: Identify Text Words
  23. 23. AND ANDOR"Arthritis, Rheumatoid"[Mesh]"Tumor Necrosis Factor-alpha"[Mesh]"Tuberculosis"[Mesh]OR"Mycobacteriumtuberculosis"[Mesh]OR"rheumatoid arthritis"[tw] “tumor necrosis factor alpha”[tw]OR "tumour necrosis factoralpha"[tw] OR “tumor necrosisfactor a”[tw] OR "tumour necrosisfactor a"[tw ]tuberculosis[tw]OR“TNF A”[tw] OR “TNF alpha”[tw]OR TNFA[tw] OR TNFalpha[tw]OREtanercept[tw] OR Infliximab[tw] OR Adalimumab[tw]Concept #1 Concept #2 Concept #3SubjectHeadingsTextWordsSearch StrategySearch Strategy
  24. 24. • Start with your first concept– Search for the subject headings first– Then search text words– Combine these synonymous searches with ORusing your search history• Repeat for your second, third, and subsequentconcepts• Finally, combine large search results set withANDHow to SearchHow to Search
  25. 25. Search #2 =Search #3 =Search #4 =Search #5 = #1 OR #2 OR #3 OR #4Search #1 =Concept 1Search #6 =Search #7 =Search #8 =Search #9 =Concept 2Search #10 = #6 OR #7 OR #8 OR #9Search #11 = #5 AND #10ResultsHow to SearchHow to Search
  26. 26. PubMed Advanced Search BuilderPubMed Advanced Search Builder
  27. 27. Run the search
  28. 28. AND ANDOR"Arthritis, Rheumatoid"[Mesh]"Tumor Necrosis Factor-alpha"[Mesh]"Tuberculosis"[Mesh]OR"Mycobacteriumtuberculosis"[Mesh]OR"rheumatoid arthritis"[tw] “tumor necrosis factor alpha”[tw]OR "tumour necrosis factoralpha"[tw] OR “tumor necrosisfactor a”[tw] OR "tumour necrosisfactor a"[tw]tuberculosis[tw]OR“TNF A”[tw] OR “TNF alpha”[tw]OR TNFA[tw] OR TNFalpha[tw]OREtanercept[tw] ORInfliximab[tw] ORAdalimumab[tw]Concept #1 Concept #2 Concept #3SubjectHeadingsTextWordsSearch StrategySearch Strategy
  29. 29. Applying filters
  30. 30. Example Filters - BasicExample Filters - BasicCommon PubMed filters:1.Date of publication– only studies conducted between 2000 and 20131.Publication language– only materials written in English or French
  31. 31. Apply to your combined search result set:– English and French LanguagePractice: Apply Basic FiltersPractice: Apply Basic Filters
  32. 32. Sample:•Cochrane Highly Sensitive Search Strategy foridentifying randomized trials in MEDLINE(PubMed format)Advanced FiltersAdvanced Filters
  33. 33. Practice: Advanced FilterPractice: Advanced FilterAdd this line to your search history:•[#of your final search set] NOT (Animals[mesh]NOT Humans[mesh])What does this advanced filter do? Why not justuse the basic PubMed filter for human studies?
  34. 34. Export References to a CitationManagerAvailable to McGill students, faculty, staff.Available to McGill students, faculty, staff.
  35. 35. What they do:– Identify and remove duplicate references– Format your bibliography– Organize references into groups– Share your references with colleagues– Automatically find full-text articles– Provide location for article screeningInformation and workshops:http://www.mcgill.ca/library/library-using/citationsoftwareCitation ManagersCitation Managers
  36. 36. Next steps
  37. 37. • Retain as much of your original strategy aspossible• Recognize that subject headings will bedifferent (or non-existent)• Keep track of your search terms using newworksheetsMoving to Other DatabasesMoving to Other Databases
  38. 38. From: Moher D, Liberati A, Tetzlaff J, Altman DG, The PRISMA Group (2009). Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement. PLoS Med 6(6): e1000097. doi:10.1371/journal.pmed1000097Next stepsNext steps
  39. 39. • A systematic search strategy is _____• To find databases, use _____• PubMed will automatically _____ your MeSH terms• To search in PubMed’s title and abstract fields, use_____Summary QuizSummary Quiz
  40. 40. Where to go for HelpWhere to go for HelpRobin FeatherstoneLiaison LibrarianLife Sciences Library,McGill University514-398-4475ext. 09844robin.featherstone@mcgill.caAnesthesia, Cardiology, Dermatology,Endocrinology & Metabolism,Gastroenterology, Hematology, InternalMedicine, Medical Education, Nephrology,Neurology & Neurosurgery, Obstetrics &Gynecology, Oncology, Ophthalmology,Orthopedics, Otolaryngology, RespiratoryMedicine, Surgery,Undergraduate Medicine, UrologyGenevieve GoreLiaison LibrarianLife Sciences Library,McGill University514-398-3472genevieve.gore@mcgill.caEpidemiology, Biostatistics ,& OccupationalHealth, Family Medicine, InfectiousDiseases, Pediatrics, Public Health
  41. 41. ResourcesResourcesSystematic review guidelines:Cochrane Handbook for Systematic Reviews of Interventionshttp://www.cochrane-handbook.org/PRISMA (Preferred Reporting Items of Systematic Reviews and Meta-Analyses)http://www.prisma-statement.org/statement.htmSystematic Reviews: CRD’s Guidance for Undertaking Reviews in Health Carehttp://www.york.ac.uk/inst/crd/SysRev/!SSL!/WebHelp/SysRev3.htmIOM (Institute of Medicine). Finding what works in health care: Standards forSystematic Reviewshttp://www.iom.edu/Reports/2011/Finding-What-Works-in-Health-Care-Standards-for-Systematic-Reviews.aspxSystematic Reviews: A Guide to Library Resources at McGillhttp://wikisites.mcgill.ca/systematicreview/index.php/Main_PageCitation management:Getting help with EndNotehttp://www.mcgill.ca/library/library-using/citationsoftware/endnote/help
  42. 42. QuestionsQuestions

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