searching pubmed and medline

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Post on 07-May-2015



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Workshop developed to teach MLIS students how to effectively search for evidence-based medical information through Ovid-Medline and PubMed.


  • 1.Accessing Medline- A Workshop in PubMed and Medline-OVID Group members: Vivian, Bridget, Ashley, and Kristen B

2. Today's Workshop 1. Learning Objectives (Kristen) 2. Medline (Kristen) 3. Literature Review (Ashley) 4. PubMed (Bridget) 5. PubMed-NCBI (Bridget) 6. Medline-OVID (Vivian) 7. Medline-OVID - My Workspace (Vivian) 8. Class Activity 3. Learning Objectives 1. Comparison of how MeSH maps natural language differently between PubMed and Medline- Ovid 2. Understand how to save, share, and combine search strategies and auto-alerts for PubMed and Medline-OVID 3. Understand how to export citations into RefWorks from PubMed and Medline-OVID 4. Medline Premier, comprehensive biomedical database in the United States Updated daily 5500 biomedicine and life science journals in nearly 40 languages English abstracts are including for more than 80% of the records Full text coverage: 1948-Present Number of records: 18000000+ 5. Literature Review Allison JJ, Kiefe CI, Weissman NW, Carter J, Centor RM. The art and science of searching Medline to answer clinical questions. Intl J of Technology Assessment in Health Care. 1999; 15 (2): 281-296. Delwiche, FA. Searching Medline via Pubmed. Clinical Laboratory Science. 2008; 21 (1): 35-41. De Groote, SL. PubMed, Internet Grateful Med, and Ovid: A comparison of three Medline internet interfaces. Medical Reference Services Quarterly. 2000; 19 (4): 1-13. Gault LV, Shultz MS, Davies KJ. Variations in medical subject headings (MeSH) mapping: From the natural language of patron terms to the controlled vocabulary of mapped lists. J Med Libr Assoc. 2002; 90 (2): 173-180. Katchamart W, Faulkner A, Feldman B, Tomlinson G, Bombardier C. PubMed had a higher sensitivity than Ovid-Medline in the search for systematic reviews. J of Clinical Epidemiology. 2011; 64 (7): 805-807. 6. Lit Review Findings Usability and User Preference of Ovid vs. PubMed Effectiveness of search tool dependant on users familiarity with it Functionality (use of Boolean operators, truncations and proximity searching) Variations in how Ovid and PubMed map free language onto MeSH Sensitivity of PubMed vs. Ovid in retrieving all relevant articles Use of Filters 7. User Preference Thiele RH, Poiro NC, Scalzo DC, Nemergut EC. Speed, accuracy and confidence in Google, Ovid, PubMed, and UpToDate: Results of a randomised trial. Postgrad Med J. 2010; 86: 459-465. Google 45% PubMed 25% Ovid 4% UptoDate 26% 8. Variations in MeSH Mapping Gault LV, Shultz MS, Davies KJ. Variations in medical subject headings (MeSH) mapping: From the natural language of patron terms to the controlled vocabulary of mapped lists. J Med Libr Assoc. 2002; 90 (2): 173-180. Cannot assume symmetrical retrieval from MeSH in different systems Pubmed and Ovid provide methods for suggesting mesh, but methods are varying 9. SensitivityKatchamart W, Faulkner A, Feldman B, Tomlinson G, Bombardier C. PubMed had a higher sensitivity than Ovid-Medline in the search for systematic reviews. J of Clinical Epidemiology. 2011; 64 (7): 805-807. PubMed has higher sensitivity than Ovid The Study: PubMed found more results for each concept - rheumatoid arthritis, MTX and randomized control trials 18 eligible articles were selected, Ovid had 10. Limits and FiltersWinchester DE, Bavry AA. Limitations of the MEDLINE database in constructing meta-analyses. Ann Intern Med. 2010; 153: 347-8 When search limits are used, researchers miss important and relevant records Only limits that can be safely used are dates and language those not based on MeSH Applying search limits is not an integral part of search strategy - well executed searches benefit from limits when they are applied post hoc to remove unwanted documents 11. Tips and Tricks Revealed in Lit Review 1. Use both MeSH and free text words to limit Eg. search "trial" as free-text in the abstract filed in addition to MeSH 1. Use synonyms and truncation 1. Don't actively limit but use double negation Eg. (NOT (Animals [MeSH] NOT Humans [MeSH])) - ensures no non-indexed human studies are missed 12. PubMed - Introduction What is PubMed? Types of Citations Advanced Search Builder Automatic Term Mapping MeSH Subheadings (Qualifiers) Search Field Descriptions & Tags Filters Features (Single Citation Matcher, Clinical Queries & My NCBI) 13. PubMed - What Is It? Free access to MEDLINE Links to full-text articles in PubMed Central, publisher web sites, and other related resources Over 22 million citations Developed & maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine 14. PubMed - Type of Citations PubMed - as supplied by publisher PubMed - in process PudMed - indexed for MEDLINE PubMed PubMed - OLDMEDLINE 15. PubMed - Example: 16. May miss non-indexed papers or "wrongly indexed" papers if only MeSH is used Use both MeSH terms AND keywords, including synonyms, related terms, variant endings and spellings PubMed - Comprehensive Searching 17. PubMed - Advanced Search Builder Choose a field (if you like) Run Search Combine search strings Isolate concepts 18. PubMed - Automatic Term Mapping (ATM) Maps keywords to MeSH headings, journal titles or author names Splits phrases apart and searches each term separately and combines them Parts of a search can be removed and/or added and rerun 19. PubMed - Keep in Mind... PubMed ignores Stopwords (i.e. because, regarding, mostly, however, each, etc.) List of Stopwords: ble/pubmedhelp.T43/?report=objectonly 20. PubMed - Use with Caution... Phrase searching is possible with "double quotations" *Warning: Using truncation or quotations will automatically turn off mapping and MeSH term explosion (try to use in addition by combining with OR) 21. Use the MeSH database to find a suitable term and "Add to Search Builder", then run your search in PubMed PubMed - Wrong Term Mapped? 22. PubMed - MeSH Search Tags (Qualifiers) [mh] To search a MeSH heading [majr] To search a MeSH heading that is a major topic of an article 23. PubMed - Warning: Warning: Using only MeSH subject terms excludes in-process & publisher-supplied citations & others that do not (or do not yet) include MeSH subject terms 24. PubMed - MeSH Search Tags No Exploding Turn-off automatic explosion by adding :noexp i.e. [mh: noexp] [majr: noexp] Terms will automatically explode 25. PubMed - MeSH Subheadings Want to Get More Specific?Add MeSH Subheadings (also called Qualifiers) by adding a slash and typing in the Qualifier's name or the Qualifier's abbreviation i.e. eye/injuries [majr] or eye/in [majr] *case and spacing don't matter *cannot turn off the explode feature for a subheading 26. PubMed - Subheadings cont'd List of Subheadings: pubmedhelp.T41/ Subheading Definitions: Qualifier Hierarchies: 27. PubMed - Search Field Descriptions/Tags List of PubMed Data Element Field Descriptions: e/pubmedhelp.T44/?report=objectonly Limits your search 28. PubMed - Author Field i.e. austin j [au] Will automatically truncate. To stop this, add quotations i.e. "austin je" [au] 29. PubMed - Date Field To search for a specific date, use this format: YYYY/MM/DD [date field] *month and year are optional 30. PubMed - Date Field cont'd... Date Field Date ranges can be entered with a colon i.e., 2004:2006 Comprehensive searches for a full year i.e., 2000:2000 (will retrieve citations with a different print and electronic year of publication) Searching by date FAQ: 31. PubMed - Filters Select filter (left side of screen) Click on "Show Additional Filters" if necessary *Filters will remain for all subsequent searches unless they are cleared 32. PubMed - Single Citation Matcher Enter the information you have to fill in the blanks Click go 33. PubMed - Clinical Queries A search interface to find citations in the areas of: Clinical Study Categories: Find citations corresponding to a specific clinical study category. Systematic Reviews: Find citations for systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, and guidelines. Medical Genetics: Find citations related to various topics in medical genetics. 34. PubMed - My NCBI Need to register (free!) 35. PubMed - My NCBI: User Preferences Some include: Link options Email options Display highlighted terms Single Citation Display 36. PubMed - My NCBI: Filtering Options Can customize your own filter and name it 37. PubMed - My NCBI:Save Search Strategy & Alert Setup Max number of saved searches is 100 per user-name Saved searches cannot be edited Limited to one email address per account *related articles cannot be saved; date and date ranges are 38. PubMed - RefWorks Refresher In PubMed... 1) Mark appropriate records in your search 2) Add to Clipboard (from "Send to" menu) 3) Display the Clipboard contents 4) Change "Display Settings" to Medline format 5) Select and Copy all of the text 39. PubMed - RefWorks Refresher Cont'd In RefWorks.... 6) Select References > Import 7) Select NLM PubMed from the Import Filter drop down menu 8) PubMed will appear automatically as the database 9) Click on the From Text link 10) Paste text into the box 11) Click IMPORT 40. Medline-OVID Uses OvidSP - their flagship research platform More than 2500 ebooks and collections, including archive collections of critical historical materials, as well as publisher and topical collections Over 1300 premium, peer-reviews journals, including dozens of journal collections Over 100 bibliographic and full-text databases Disciplines: Medicine, Nursing & Health Professions, Behavioural Sciences, Basic Science, Humanities & Technology