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Advanced PubMed searching

Advanced PubMed searching. Marisa Conte meese@umich.edu. Topics. Clinical queries and other tools Search construction: controlled vocabulary and Boolean searching Advanced search and limits Managing results: export citations, save searches and collections, customize retrieval. Tour.

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Advanced PubMed searching

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  1. Advanced PubMedsearching Marisa Conte meese@umich.edu

  2. Topics • Clinical queries and other tools • Search construction: controlled vocabulary and Boolean searching • Advanced search and limits • Managing results: export citations, save searches and collections, customize retrieval

  3. Tour

  4. Clinical queries

  5. Special queries and subjects

  6. Single citation matcher

  7. Search construction • Identify relevant concepts, including controlled vocabulary • Combine concepts w/ appropriate Boolean logic • Use special features or limits to refine results

  8. Identifying concepts Medical Subject Headings (MeSH)

  9. Search construction: Concept building • Identify major concepts • Identify preferred terms for concepts (including subheadings if relevant) • Identify synonyms for major concepts

  10. Review: Keywords vs. controlled vocabulary Keywords Controlled vocabularies

  11. Search construction: Vocabulary Keywords Controlled vocabularies • What are they? • Literal search • Looks for occurrences of words • When to use? • Current topics • Difficult-to-describe concepts • No vocabulary exists in database • Examples • Drug names (Lipitor, Prozac) • Slang • Concepts (Swine flu, oil spill)

  12. Search construction: Vocabulary Keywords Controlled vocabularies • What are they? • Set of words or phrases used to describe concepts • Dictionary of accepted terms for a database • When to use? • Searching a database that uses one • Examples • MeSH (Medical Subject Headings) • EMTREE (Embase)

  13. MeSH entry - pathology

  14. Subheading: pathology

  15. Shortcuts to MeSH • ‘Search details’ from results screen • View MeSH indexing from relevant citations • Use Advanced search > ‘Search builder’ feature with MeSH dropdown selected

  16. Identify MeSH terms: Use ‘Search details’

  17. Details

  18. ID MeSH: Citation indexing

  19. Identify MeSH: Search builder

  20. Searching MeSH from PubMed

  21. MeSH database • Identify MeSH headings • Entry terms can suggest keywords for comprehensive searches • Hierarchy view can help identify more relevant (broader/more focused) terms • Subheadings can help refine search • Focus on specific application of MeSH: eg bronchiolitis/drug therapy • Search builder exports MeSH term to PubMed

  22. Question 1: • Does Epstein Barr virus cause a chronic hepatitis, in particular one that resembles autoimmune hepatitis? • Try: keyword search • Try: Clinical queries, using etiology as a filter • Try: MeSH (+/- keywords) • Epstein-Barr virus infections [mh] AND hepatitis, autoimmune [mh]

  23. Results 1

  24. Combining concepts

  25. Review: Boolean Logic Concept 1 Child Children Adolescent Teenager Concept 2 Obesity Obese Overweight BMI Concept 3 Mortality Premature death OR OR OR AND AND OR OR OR OR

  26. Combining concepts - searchline • Use parentheses to group related concepts • Capitalize Boolean operators

  27. Combining concepts – search builder

  28. Combining concepts – search history

  29. Question 2 • What are the cytologic features that distinguish a high grade intraductal pancreatic mucinous neoplasm (IPMN) from a low grade neoplasm? • Identify key terms: intraductal papillary mucinous neoplasm [tiab]; carcinoma, pancreatic ductal [mh]; cytodiagnosis [mh]; cytology [tiab] OR cytologic [tiab] • Combine concepts

  30. Refining results

  31. What do I do when I get … Too many results? Not enough results? Remove limits Add keywords or MeSH terms to improve recall Use related citations to identify other relevant concepts • Use MeSH and/or subheadings to refine concept definition • Restrict keywords to title and/or abstract • Use limits – date, publication type, etc. • Use special features – clinical queries or topic-specific queries

  32. Search construction: Techniques • Limits – use sparingly (language, age, publication type)

  33. Clipboard

  34. Clipboard

  35. managing results MyNCBI

  36. Set up account • Click myNCBI in upper right corner • Click ‘Register for an account’ • Complete registration screen (including email address) • Confirm email sent to account

  37. My NCBI homepage

  38. Manage results Email, export to EndNote, save as Collection

  39. Save search, set search alerts Save search URL, save search to MyNCBI

  40. Save search via link

  41. Save search from history

  42. Set preferences and filters Customize PubMed

  43. Setting preferences

  44. PubMed filters

  45. Questions? meese@umich.edu

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