PubMed Searching Workshop


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Workshop given to first year MD students at McGill University, October 2012

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  • Let the class answer this question on their own, then show them the answers. Note: if you want to find out how many citations are in PubMed on the day of the class, run a search for all[sb]
  • Read the question, and then ask them to search it. After they have done the search, ask volunteers how many results they got ask students to look at the abstracts—are the articles about Acquired Immunodeficiency Syndrome? Note: most of the results are about “hearing aids” and not AIDS. Check the search details box to show class how PubMed interprets your search.
  • Show the students this record. Point out how MeSH headings were used to describe it. Link to the mesh heading for Hearing Loss/ – show that it explodesGo back to the citationLink to the mesh heading for AIDS – show that it does not explodePoint out that we can use MeSH and the MeSH database to improve our searching. Demonstrate the search using MeSH and the PubMed Search Builder:(”Hearing Loss"[Mesh]) AND "Acquired Immunodeficiency Syndrome"[Mesh] = 42 results
  • Do a little test of the class to make sure they know which terms explode
  • Ask the class to find the MeSH terms for these concepts.Note: St. John’s Wort maps to Hypericum (does not explode)Upper extremity maps to the same term (explodes)When they are done – ask the class which term exploded.
  • Use of SubheadingsAsk the class: What concepts do we have here? Click to underline chronic fatigue syndrome (CFS) and causes. Explain that subheadings are used with MeSH terms to further describe a particular aspect of a MeSH concept,such as "etiology" or ”drug therapy”.Explain that each MeSH term has a predefined list of subheadings which may be used with it.You may select one, several or all the applicable subheadings for your MeSH term. BEST PRACTICE: use one or two only.Demonstrate > Look up the MeSH term for CFS > point out the “subheadings” link to define each subheading. Point out the heading for therapy. Does not include drug therapy, diet therapy, radiotherapy, and surgeryRun the search > "Fatigue Syndrome, Chronic/etiology"[Mesh] = 1751 results (still a lot!)
  • Using AND to narrow a searchAsk: What are the main ideas of this question? Animation: Chronic fatigue and causes still there—now add a third oneDemonstrate using the PubMed search builder to add two terms using ANDPoint out that Multiple Sclerosis explodes, ask if they may want to turn that function off? Why? Why not? Point out: logic of using the etiology subheading with CFS (and not MS). ("Fatigue Syndrome, Chronic/etiology"[Mesh]) AND "Multiple Sclerosis"[Mesh] = 43 results
  • FiltersWhat are the concepts? Tamoxifen, breast cancer. Then talk about filters, older patient, etc. ("Breast Neoplasms/drug therapy"[Mesh]) AND "Tamoxifen"[Mesh]If filter for Ages does not appear: Show additional filters > select AgesAges will now appear as one of the possible filtersFilter to 65 and older = 2159 Still a lot! So use another limitFilter to Review = 109 Explain how could use language, years , Publication typeProblematic filters: sex, text availabilityIMPORTANT: MENTION THAT YOU HAVE TO TURN FILTERS OFF BEFORE STARTING A NEW SEARCH
  • ("Diabetes Mellitus, Type 2/prevention and control"[Mesh]) AND "Patient Education as Topic"[Mesh]Filters: Aged 65+Note: have the students find the concepts independently. Demo the search when they are done. IMPORTANT -Note: point out options to send yourself the search strategy (email without selecting any checkboxes next to citations)Note: point out options to send yourself citations (email after selected the checkboxes next to chosen articles)
  • Concepts in this slide: Using subheadings Using AND Relevancy of results Practicing for the assignmentThis question is most like their assignment, so have them practice as if it were their assignment= have them email a relevant article to themselves and the search strategyDon’t explode here b/c Fatty Liver, alcoholic/ is narrow term for Fatty Liver/Trick Non-alcoholic fatty liver maps to a supplementary concept record. Link to Fatty Liver to get the correct MeSH heading.
  • PubMed Searching Workshop

    1. 1. LIFE SCIENCES LIBRARY PubMed WorkshopBasis of Medicine Unit 2October 2012
    2. 2. What do you know about PubMed? “Unfiltered” information tool – contains individual studies Good for answering foreground questions Produced by the U.S. National Library of Medicine Funded by U.S. taxpayers Open for anyone to use Contains over 22 million citations (as of Oct 1)
    3. 3. ObjectivesBy the end of this PubMed workshop, you will beable to construct an effective search and locatearticles using:1. MeSH headings2. MeSH subheadings3. AND operator4. PubMed filters5. Publishers’ links or “Find it @ McGill” links
    4. 4. Give it a tryYou’re preparing for a class on disabilitiesimpacting people living with AIDS. Find articlesin PubMed on hearing loss for people with AIDS.
    5. 5. What is MeSH?
    6. 6. Which Subject Heading Explodes?A. Bird Diseases B. Neutropenia
    7. 7. Practice finding MeSH terms  St. John’s Wort  Upper extremity
    8. 8. Using subheadingsYou observe a patient with chronic fatiguesyndrome, and you want to know more about theresearch on possible causes
    9. 9. Narrowing the searchYou observe a patient with multiple sclerosissuffering from chronic fatigue syndrome. Findarticles on possible causes of chronic fatigue in MS.
    10. 10. Using FiltersSara is a 70 year old patient with breast cancer. Youare wondering about the use of tamoxifen for thispatient. Find articles discussing the use of tamoxifenin older breast cancer patients.
    11. 11. Putting it all togetherYou’re working in a community clinic and have seenmany older adults at risk for developing type 2diabetes. As a research project, you want to test theeffectiveness of a patient education program foradults 65 years and older to prevent this disease.Find out if any similar projects have been reported inthe literature.
    12. 12. Assignment PrepGeorge is a 40 year old obese man diagnosed withnon-alcoholic fatty liver disease. You would like tosee if diet therapy is an option for him.
    13. 13. Assignment Three questions based on one case scenario To be completed individually Due by 5 pm on October 30, 2012 Submitted to Dean’s office, 6th Floor of McIntyre Questions? Contact Robin Featherstone