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SCAIR autumn 2018-10-19/JB Medical library Linköping University Library

Boost your search repertoire Sources and strategies for structured searching with the example of PubMed. SCAIR autumn 2018-10-19/JB Medical library Linköping University Library.

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SCAIR autumn 2018-10-19/JB Medical library Linköping University Library

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  1. BoostyoursearchrepertoireSources and strategies for structuredsearchingwith the exampleofPubMed SCAIR autumn 2018-10-19/JB Medical library Linköping University Library

  2. The SmorgasbordUsefulsources: E-books, dissertations, EBM, PubMedCreating structuredsearchstrategies (with a focus on PubMed)

  3. Dissertations and other Swedish research Libris: National search service withtitlesheld by research libraries Diva LiU: Localrepository for student theses and research publications

  4. Exercise Find a dissertation (or somethingelse) relevant for you in Libris, SwePub OR Diva http://libris.kb.se/ http://swepub.kb.se liu.diva-portal.org/

  5. Subject guide

  6. Findongoingtrials and systematicreviews • Clinicaltrials.gov • Prospero: https://www.crd.york.ac.uk/PROSPERO/

  7. Finding e-bookcollections and e-referencebooks

  8. Evidencebased medicine - resources

  9. For example: Try to find a relevant e-book/chapter in SpringerLink or another e-bookcollection Browseoneof the e-encyclopedias for information on yourtopic. OR just havefewminutes to findevidence-based information or anythingelse in the subject guide, such as images, statistics or clinicaltrialsthatmightinterestyou. Exercise: diveinto the subject guide

  10. Joakim Westerlund • PubMed - The first choice articledatabase in medicine • Content - quality and quantity • Indexingwith and findingMeSH terms • CustomizePubMed • Save and workwith the result

  11. PubMedHistory • Index Medicus, printed index 1879- • MEDLINE is the primary content and the premier database to journal articles, launched 1960s’ • Publishers Medline – databaseofbibliographic information, produced by National Libraryof Medicine, USA , introduced 1996 – • Inclusionofolder stuff, nowcovering 1946 - • PubMed Central, PMC - a free archive for full-text biomedical and life sciences journal articles, launched 2000 -

  12. Joakim Westerlund PubMed and MEDLINE • Medline: • ”…citations from more than 5,600 scholarly journals…considers the quality of the scientific content of a journal…theadded value of using the NLM controlled vocabulary, Medical Subject Headings (MeSH)…” • PubMed: • “…include the MEDLINE database…In-process citations…citations to articles that are out-of-scope… pre-1966 citations…some additional life sciences journals that submit full text to PMC…booksavailable on the NCBI Bookshelf…” • Differencebetween MEDLINE, PubMed & PMC • https://www.nlm.nih.gov/pubs/factsheets/dif_med_pub.html

  13. Joakim Westerlund Different status for citations in PubMed • [PubMed - as supplied by publisher] • – search: publisher[sb], link • [PubMed - in process] • – search: inprocess[sb], link • [Indexed for MEDLINE] • – search: medline[sb], link • [PubMed] • – search: pubmednotmedline[sb], link • PubMed citation status • https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.status_subsets/?report=objectonly

  14. Joakim Westerlund Content… • Journals currentlyindexed in Medline • https://www.ncbi.nlm.nih.gov/nlmcatalog?term=currentlyindexed%5BAll%5D • Journal selection process in Medline • https://www.nlm.nih.gov/pubs/factsheets/jsel.html

  15. Joakim Westerlund In conclusion… “In conclusion, PubMed citations come from MEDLINE indexed journals, journals/manuscripts deposited in PMC, and NCBI Bookshelf. […] If you limit your PubMed search to MeSH controlled vocabulary or the MEDLINE subset, you will see only MEDLINE citations in your results.” https://www.nlm.nih.gov/pubs/factsheets/dif_med_pub.html

  16. Part 2 Creating structuredsearchstrategies(with a focus on PubMed)

  17. Structured or narrative? Exhaustive and rigorous! All must be found Objective and reproducible Documentation Sensitivity (vs precision) https://libguides.uwf.edu/c.php?g=215131&p=5145952

  18. Structured information searching: 1. What? • Formulatequestion, keyconcepts, terminology, synonyms, inclusion/exclusioncriteria 2. Where? • Whichdatabase/s? 3. How? • Truncation, phrases, boolean operators, subjectheadings/ free text, searchstrategy • Scopingsearchfirst, thenanalyze and changeifneededbefore final search 4. Documentation

  19. Formulatequestion • How do patients withmultiplesclerosisexperiencegroupexercise? • Howcanmesenchymalstem cells differentiate in vitro to insulin producing cells for the treatmentof diabetes?​

  20. Keyconcepts • How do patients withmultiplesclerosisexperiencegroupexercise? • Howcanmesenchymalstem cells differentiatein vitro to insulin producing cells for the treatmentofdiabetes?​

  21. Terminology and synonyms

  22. Inclusion/exclusioncriteria (eligibility) Examples: • Participants (age, sample size, gender etc) • Articles only in English • Randomized studies • Humans • 2015-

  23. Searching in blocks Search no 1: ms OR multiplesclerosis Search no 2: group AND (exercise OR training) Search no 3: experience OR attitude OR satisfaction OR view Search no 4: #1 AND #2 AND #3

  24. Exercise • Formulateyoursearchquestion • Identifykeyconcepts (use PICO ifapplicable) • Note down some terms youknowregardingtheseconcepts • Alsoconsideriftherearecertaincriteriayoufindimportant (inclusion/exclusioncriteria) Examples: Age, gender, typeofstudy, studysize, timerange, outcomemeasure etc. • Test search in PubMed and revisesearchstrategyifneeded

  25. Joakim Westerlund Subjectheadings • MeSH - thesaurus/controlledvocabulary for subjectanalysis, annuallyupdated, approx. 27 000 concepts • Arranged in a hierarchical categorized manner/tree structure – arm › hand › finger • (Youcanturnthissearch option off) • ”subheadings” for a morespecificsearch • ”Major Topics” for focusing on the mostimportantMeSH-terms • MeSHdatabase: https://www.ncbi.nlm.nih.gov/mesh • Svensk MeSH – translation to/from Swedish

  26. Joakim Westerlund Canpharmaceuticals cause hair loss?

  27. Joakim Westerlund Subheadings • Defines an aspectof a MeSH-term

  28. Joakim Westerlund How to findmore relevant MeSH terms PubReMiner (http://hgserver2.amc.nl/cgi-bin/miner/miner2.cgi) MeSH on Demand (https://www.nlm.nih.gov/mesh/MeSHonDemand.html) Yale MeSHAnalyzer (http://mesh.med.yale.edu/) Search strings (http://pubmedsearches.blogspot.se) https://tinyurl.com/mmkkb9n

  29. Joakim Westerlund Pharmaceuticals, drugs and chemicals MeSH-terms - > methotrexate Supplementaryconcept - > gemcitabine Pharmacologic actions -> Antirheumatic Agents, Immunosuppressive Agents… Explode a substancegroup CAS-number A specificresource from NCBI aboutchemicalsubstances : • PubChem

  30. ExerciseTest MeSHDatabase and/or Svensk MeSHTry to findsome relevant MeSH-terms for yourtopic!

  31. Joakim Westerlund Workingwith the result clipboard – save referencesduringyoursearch session (will be lostaftereighthours) e-mail –sendreferences order – order articles comment - PubMedCommons create alert, save yoursearches etc – create an My NCBI account

  32. Joakim Westerlund NCBI Account • BibliographyFavorites • Save yoursearches, set alerts, etc • CustomizePubMed! • Filters • Subject – search terms • Properties – ages, publicationtypes, subsets, etc • NCBI Site preferences

  33. Joakim Westerlund Exercise Create a search strategy in PubMed for your topic. Try to use both free text terms (consider spellings, acronyms, synonyms) AND subject headings (MeSH) Document your PubMed adjusted search strategy in a word document and/or save the search in your “My NCBI account”.

  34. 2. Whichdatabases? • PubMed • Citation databases: Scopus, Web of Science, Google Scholar • Othersubject/topicspecificdatabases: Cinahl, PsycINFO etc. • Searchengines, indexes: Google scholar, UniSearch • Cochrane, SBU • Grey literature

  35. Reflect a minute on whatdatabasesthatmight be ofinterest to you! • Writethem down in the form

  36. Search tips – depends on database Don’tusethese in PubMed: • Truncationdeaf* -> specifydeaf, deafness, or more • Phrasesearching ”hearing impairment” -> useAdvancedsearch Index list • Proximity operators are not applicable in PubMed • egg NEAR/2 allergy(Web of science) • egg W/2 allergy(Scopus)

  37. To limit: ”stem cell” AND transplantation To expand: treatmentORtherapy To exclude: ”type 1 diabetes” NOT ” type 2 diabetes”  Caution! Boolean operators ”stem cell” AND (treatment OR therap*)

  38. Joakim Westerlund Document and edit the search in Word Copy the searchinto Word Edit the search in Word Paste it back intoPubMed - - > And, please, be precise with the parentheses! < - -

  39. Joakim Westerlund A ”final” strategy? Almost never! Youcanalmostalwaysimproveyoursearch… Iteration, - time and patience

  40. Joakim Westerlund Searchstrategies - Peer Review PRESS • Peer Review on Electronic SearchStrategies • 10.1016/j.jclinepi.2016.01.021

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