SCAIR spring 2019 Joakim Westerlund/Jenny Betmark / Isolina Ek Linköping University Library

1. BoostyoursearchrepertoireSources and strategies for structuredsearchingwith the exampleofPubMed SCAIR spring 2019 Joakim Westerlund/Jenny Betmark/Isolina Ek Linköping University Library

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

3. Grey literature / Gray literature "[Grey literature is] thatwhich is produced on all levelsofgovernment, academics, business and industry in print and electronic formats, butwhich is not controlled by commercialpublishers, i.e., where publishing is not the primaryactivityof the producingbody" . Joachim Schöpfel. Towards a Prague Definition of Grey Literature. Twelfth International Conference on Grey Literature: Transparency in Grey Literature. Grey Tech Approaches to High Tech Issues. Prague, 6-7 December 2010, CzechRepublic. pp.11-26

4. Grey literature / Gray literature For example DissertationsConference proceedingsPatentsUnpublishedmanuscriptsGuidelines Governmentdocuments Search for in Databases Searchengines Web pages Institutionalrepositories References in foundarticles Hand-searching Contact experts

5. https://liu.se/en/library

6. http://guide.bibl.liu.se/mvhEnglish

7. Finding dissertations • http://libris.kb.se/ • http://swepub.kb.se

8. Diva @ LiU – local repository • Local repository for student theses and research publications – many in full text • You can register your own publications – information available via ep.liu.se / Publish in Diva /

9. Findongoingtrials and systematicreviews • Clinical trials https://clinicaltrials.gov/ • Prospero https://www.crd.york.ac.uk/prospero/

10. Try yourself Find a dissertation (or somethingelse) relevant for you in Libris, SwePub OR Diva

11. Finding e-books and e-referencebooks

12. Evidencebased medicine - resources

13. SBU and CochraneLibrary

14. Try to find a relevant e-book/chapter in SpringerLink or another e-bookcollection Browseoneof the e-encyclopedias for information on yourtopic. Pleasehave a fewminutes to findevidence-based information or anythingelse in the subject guide, such as images, statistics or clinicaltrials. Try yourself

15. Agenda • PubMed - The first choice articledatabase in medicine • Content - quality and quantity • Indexingwith and findingMeSH terms • Search • CustomizePubMed • Save and workwith the result

16. 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 -

17. 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…” • Difference between MEDLINE, PubMed & PMC • https://www.nlm.nih.gov/bsd/difference.html

18. 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

19. Content… • Journal selection process in Medline • https://www.nlm.nih.gov/lstrc/jsel.html • How to include a journal in PMC • https://www.ncbi.nlm.nih.gov/pmc/pub/addjournal/ • Is a journal in Medline, in PMC - or in both?

20. PubMed and Predatory journals? • There is a debate on this that you should be aware of • One recent article and a response from NLM: • How predatory journals leak into PubMed • Andrea Manca, David Moher, Lucia Cugusi, ZeeviDvir, Franca Deriu • CMAJ Sep 2018, 190 (35) E1042-E1045; DOI:10.1503/cmaj.180154 • Response from NLM • Predatory journals will be discussed more later in the course. 

21. 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/bsd/difference.html

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

23. Whoareyou? • “One of the advantages of being disorganized is that one is always having surprising discoveries.” • “It's best to know what you are looking for before you look for it.” Winnie the Pooh (A.A.Milne)

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

27. Ownwork

28. Searching with blocks # 1: ms OR multiplesclerosis # 2: group AND (exercise OR training) # 3: experience OR experiences OR attitude OR attitudes OR satisfaction OR view # 4: #1 AND #2 AND #3

29. To limit: stem cell AND transplantation To expand: treatmentORtherapy To exclude: type 1 diabetes NOT type 2 diabetes  Caution! Boolean operators

30. Excluding animal studies What is the problem with: Diabetes NOT animals This is OK: Diabetes NOT (animals NOT humans)

31. Structured searches? Systematic searches? • Exhaustive and rigorous! • Narrow focus • All must be found • Sensitive (vs precise) • Objective and reproducible • Documentation, oftennessecary to update • Journal articles, butalsogreyliterature

32. SearchPubMed Free text searching MeSHsearching (Thesaurus/Subject term/Controlledvocabulary) Combining the Free text- and MeSH-search Documentingyoursearch Keepupdated

33. Test search and develop a searchstrategy • Free text terms (spellings, acronyms, synonyms) example: ageing/aging • Subjectheadings (PubMed MESH, Psycinfothesaurus) • Keyarticles

35. MeSH • 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 • MeSH database • Svensk MeSH – translation to/from Swedish • Previous indexing

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

37. How to findmoreMeSH 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) Reviews (http://dx.doi.org/10.1002/14651858.CD003980.pub2) Cochranegroups (https://tobacco.cochrane.org/resources/cochrane-tag-specialised-register) http://tinyurl.com/y2h8d8lc

39. PubMed – Automatic term mapping Group exercise               94 274 ("population groups"[MeSH Terms] OR ("population"[All Fields] AND "groups"[All Fields]) OR "population groups"[All Fields] OR "group"[All Fields]) AND ("exercise"[MeSH Terms] OR "exercise"[All Fields]) Group exercises              98 402 ("population groups"[MeSH Terms] OR ("population"[All Fields] AND "groups"[All Fields]) OR "population groups"[All Fields] OR "group"[All Fields]) AND ("exercise"[MeSH Terms] OR "exercise"[All Fields] OR "exercises"[All Fields] OR "exercisetherapy"[MeSH Terms] OR ("exercise"[All Fields] AND "therapy"[All Fields]) OR "exercisetherapy"[All Fields]) Group exercise*                  819 (groupexercise[All Fields] OR groupexercises[All Fields] "groupexercise"                 674 "groupexercise"[All Fields]

40. PubMed – Automatic term mapping Multiplesclerosis             83 136 "multiplesclerosis"[MeSH Terms] OR ("multiple"[All Fields] AND "sclerosis"[All Fields]) OR "multiplesclerosis"[All Fields] "Multiplesclerosis"            78 314 "multiplesclerosis"[All Fields] Multiplesclero*                  78 337 multiplesclerois[All Fields] OR multiplescleroses[All Fields] OR multiplesclerosi[All Fields] OR multiplesclerosing[All Fields] OR multiplesclerosis[All Fields] OR multiplesclerosis,[All Fields] OR multiplesclerosist[All Fields] OR multiplesclerotics[All Fields]

43. Phrasesearching in PubMed

44. Canpharmaceuticals cause hair loss?

45. Subheadings • Defines an aspectof a MeSH-term

47. Subheadings, cont… Searchthem via ”Advanced”-window chemicallyinduced[Subheading] adverse effects[Subheading] - - >  Prefer them this way - ”floating”! < - -  

48. Subheadings, cont.... Considerthemalso as a search term in theirown right, ie: psychology[Subheading] epidemiology[Subheading] surgery[Subheading]

49. Pharmaceuticals, drugs and chemicals MeSH-terms - > methotrexate Supplementary concept - > gemcitabine Pharmacologic actions -> Antirheumatic Agents, Immunosuppressive Agents… Explode a substancegroup A specificresource from NCBI aboutchemicalsubstances : • PubChem

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