How to Conduct a Systematic Search in PubMed


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  • Robin Note: Talk about problems searching PubMed; talk about keyword/text word searching. Mention that Medline is our preferred database for conducting a systematic review
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  • Gen High sensitivity/recall Well documented: Information allows search to be replicated and/or updated Sensitivity is often at the expense of precision: Sensitivity is the proportion of all useful articles that are retrieved; precision is the proportion of all retrieved articles that are useful
  • Gen Systematic reviews: Importance of writing a protocol, having a draft before consulting a librarian
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  • Gen Background versus foreground questions; background: What are the clinical features of rheumatoid arthritis? What types of biologics are used to treat rheumatoid arthritis?
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  • Gen Biologics: If this is too broad or vague, consider being specific about the biologic therapies you are considering and naming them: this is a method to make your search more targeted Types of questions (domains): Etiology [RCT, cohort, case-control] Therapy [RCT] Prognosis [cohort] Harm [cohort, case-control] Diagnosis [cross-sectional, case-control] Economic [cost-effectiveness analysis, etc.]
  • Robin What is MeSH?
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  • Gen: Go to PubMed, examine article, show them where MeSH are You can find your target articles in a multitude of ways: Google Scholar, a quick and dirty PubMed search, an article someone recommended to you…
  • Gen For the purpose of this exercise, we ’re not being completely systematic, but this is the groundwork for a systematic search
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  • Do first step in the search… (1.) "Arthritis, Rheumatoid"[Mesh:NoExp] (2.) "rheumatoid arthritis"[Title/Abstract] (3.) 1 OR 2 Then let them do the next concept on their own
  • Robin Activity: let them do second and third concept searches, then demo for them
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  • Gen Problem: no information about RefWorks on this page! But workshops include RefWorks now
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  • Robin Flow of information through the different phases of a systematic review.
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  • Robin Describe liaison model, where to find info about liaison librarians by subject/specialty
  • How to Conduct a Systematic Search in PubMed

    1. 1. How to Conduct a Systematic Search in PubMedRobin Featherstone, MLIS Genevieve Gore, MLISLiaison Librarian (Medicine) Liaison Librarian (Medicine)Life Sciences Library Life Sciences Library Slides:
    2. 2. ObjectivesBy the end of today’s class, you will be able to:3.Identify subject headings using the MeSHDatabase4.Construct a search strategy5.Run your search using the PubMed AdvancedSearch Builder6.Contact a librarian for help
    3. 3. What’s a Systematic Review? A review of a clearly formulated question that uses systematic and explicit methods to identify, select, and critically appraise relevant research, and to collect and analyse data from the studies that are included in the review.From: Cochrane Collaboration (2012). Glossary: Systematic Review. Accessed Jan 6, 2011:
    4. 4. Flow of Information Through the Different Phases of a Systematic ReviewFrom: 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.pmed1000097
    5. 5. What’s a Systematic Search? Systematic reviews of interventions require a thorough, objective and reproducible search of a range of sources to identify as many relevant studies as possible (within resource limits).From: Cochrane Handbook (2012). Section 6: Searching for Studies . Accessed Jan 9, 2011:
    6. 6. How to Find Articles1. Develop a research question2. Develop a search strategy3. Run the search in PubMed4. Apply filters5. Export references to a citation manager
    7. 7. Develop a Research Question
    8. 8. ScenarioYou’re applying for a grant to support yourresearch on infections in arthritis patientsThink of a question related to this topic...
    9. 9. How questions influence search results High = lots of articles Broad QuestionsRetrieval(# of searchresults) Narrow Questions Low = very few articles Low = mostly High = directly irrelevant articles Relevancy relevant articles
    10. 10. Possible QuestionsBroad:• What is the prevalence of infections in arthritis patients?Narrow:• What is the risk of respiratory infections for rheumatoid arthritis patients treated with biologics?Very Narrow:• What is the rate of Caplan Syndrome for asbestos workers in Northern Quebec between 1985 and 2005?
    11. 11. Develop a Search Strategy
    12. 12. Step-by-Step1. 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 terms
    13. 13. Identify ConceptsWhich concepts are contained in the question:What is the risk of respiratory infections forrheumatoid arthritis patients treated with biologics?
    14. 14. Develop a PICOPopulation P Patients with rheumatoid arthritisInterventionor Exposure I BiologicsComparison COutcome orendpoint O Risk of respiratory infections Type of question?
    15. 15. What is MeSH?
    16. 16. Which Subject Heading Explodes?A. Bird Diseases B. Neutropenia
    17. 17. Identify Subject HeadingsWhat are MeSH headings for these concepts? Rheumatoid Respiratory Biologics Arthritis InfectionAdd appropriate subject headings to yourworksheet
    18. 18. Find MeSH Using a Target Article
    19. 19. Search Strategy Concept #1 Concept #2 Concept #3 AND AND "Arthritis, "Respiratory Tract Rheumatoid"[Mesh: "Biological Agents"[Mesh] Infections"[Mesh]Subject OR NoExp]Headings OR “Biological Therapy”[Mesh]Text ORWords OR OR Blank worksheets:
    20. 20. BREAK – 10 mins
    21. 21. Next: Identify Text WordsWhy?2.Not all citations have subject headings3.Indexers are only humans (they makemistakes)
    22. 22. Search Strategy Concept #1 AND Concept #2 AND Concept #3 "Arthritis, "Respiratory Tract "Biological Agents"[Mesh]Subject OR Rheumatoid"[Mesh:NoExp] Infections"[Mesh]Headings “Biological Therapy”[Mesh] ORText "rheumatoid arthritis"[Title/ “chest biologics[Title/Abstract]Words Abstract] infection”[Title/Abstract] OR “chest infections”[Title/ OR Abstract] "lung "biological agent"[Title/Abstract] infection"[Title/Abstract] OR "biological OR "lung agents"[Title/Abstract] infections"[Title/Abstract] OR
    23. 23. PRISMA Checklist for Reporting Systematic Reviews #7) Describe all information sources (e.g. databases with dates of coverage, contact with study authors to identify additional studies) in the search and date last searched. #8) Present full electronic search strategy for at least one database, including any limits used, such that it could be repeated.From: PRISMA Statement for Reporting Systematic Reviews (2012). PRISMA Checklist. Accessed Jan 10, 2011:
    24. 24. Run the search
    25. 25. PubMed Advanced Search Builder
    26. 26. How to Search• Start with your first concept – Search for the subject headings first – Then search text words – Combine these synonymous searches with OR using your search history• Repeat for your second, third, and subsequent concepts• Finally, combine large search results set with AND
    27. 27. How to SearchConcept 1 Concept 2Search #1 = Search #6 =Search #2 = Search #7 =Search #3 = Search #8 =Search #4 = Search #9 =Search #5 = #1 OR #2 OR #3 OR #4 Search #10 = #6 OR #7 OR #8 OR #9 Search #11 = #5 AND #10 Results
    28. 28. Demo
    29. 29. Search Strategy Concept #1 Concept #2 Concept #3 AND ANDSubjectHeadings "Arthritis, Rheumatoid“ "Respiratory Tract "Biological Agents"[Mesh] [Mesh:NoExp] Infections"[Mesh] OR “Biological Therapy”[Mesh] ORTextWords "rheumatoid “chest biologics[Title/Abstract] arthritis"[Title/Abstract] infection”[Title/Abstract] OR OR “chest "lung infections”[Title/Abstract] "biological infection"[Title/Abstract] agent"[Title/Abstract] OR OR OR "lung infections"[Title/ "biological Abstract] agents"[Title/Abstract]
    30. 30. Applying filters
    31. 31. Example Filters1. Date of publication – only studies conducted between 2005 and 20102. Participants or subjects – only children 6 to 12 years of age3. Publication language – only materials written in English or French4. Research design – only clinical trials
    32. 32. Apply FiltersApply to your combined search result set: – English & French Language – Publication Year: 2001 – Current
    33. 33. Available to McGill students, faculty, staff. Export References to a Citation Manager Available to McGill students, faculty, staff.Information and workshops:
    34. 34. Citation ManagersWhat 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:
    35. 35. Next steps
    36. 36. Moving to EMBASE• Retain as much of your original strategy as possible• Recognize that subject headings will be different (or non-existent)• Keep track of your search terms using new worksheets
    37. 37. Next stepsFrom: 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.pmed1000097
    38. 38. Recap• How would you describe a systematic search?• To find your subject headings, use ________• To run your search in PubMed, use the _______
    39. 39. Where to go for Help Robin Featherstone Genevieve Gore Liaison Librarian Liaison LibrarianLife Sciences Library, Life Sciences Library, McGill University McGill University 514-398-4475 ext. 514-398-3472 09844
    40. 40. ResourcesSystematic review guidelines:Cochrane Handbook for Systematic Reviews of Interventions (Preferred Reporting Items of Systematic Reviews and Meta-Analyses) Reviews: CRD’s Guidance for Undertaking Reviews in Health Care!SSL!/WebHelp/SysRev3.htmIOM (Institute of Medicine). Finding what works in health care: Standards forSystematic Reviews Reviews: A Guide to Library Resources at McGill management:Getting help with EndNote
    41. 41. QuestionsRobin Featherstone, MLIS Genevieve Gore, MLISLiaison Librarian (Medicine) Liaison Librarian (Medicine) Slides:
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