The document discusses third-party tools that provide alternative interfaces for searching PubMed. It begins with a brief history of access to MEDLINE and the development of PubMed and its APIs. The bulk of the document describes several case studies of third-party tools, grouping them according to themes like semantic searching, visualization, mobile access, and simplification. It concludes with exercises for groups to explore different tools in more depth and discussion questions about adopting ideas from third parties or circumstances for using various tools.

1. Now that’s a horse of a different color…Third-Party ToolsPhoto credit: dianecordellon flickr

2. Agendastartend

3. AgendaIntroductions1end

4. AgendaIntroductions12endPubMed

5. AgendaIntroductionsAPIs123endPubMed

6. AgendaIntroductionsAPIs1234endCase StudiesPubMed

7. AgendaIntroductionsGroup ProjectsAPIs12345endCase StudiesPubMed

8. AgendaIntroductionsGroup ProjectsAPIs123456endCase StudiesDiscussionPubMed

9. AgendaIntroductionsGroup ProjectsAPIsEvaluation1234567endCase StudiesDiscussionPubMed

10. By you will be able to…Describe the history of end-user access to MEDLINEName and develop search strategies for at least three* third-party PubMed toolsIdentify situations in which searching with a third-party tool would be beneficialStay current with new developments related to third-party PubMed tools

11. How we got hereA brief history of end-user access to MEDLINE

12. 1897: First volume of Index Medicuspublished.

13. 1964:MEDLARS became operationalComputer room at the National Library of Medicine, 1960s

14. 1971:MEDLINE (“MEDLARS online”) provides online access to a subset of referencesTexas Instruments Silent 700 with Acoustic Coupler

15. 1986:Health professionals started running their own searches with PC-based Grateful Med

16. 1997:PubMed is born! Free Web-based access to MEDLINE

17. 1997:PubMed is born! Free Web-based access to MEDLINE

18. Today20 million article citations and countingMore than 5,000 journals indexedGoes back in time to the 1940’sSearched 1.6 billion times in 2010

19. 2002:NLM says “take our data, too!” Entrez Programming Utilities (Eutils) introduced

20. Drive traffic to your data, not your website!-David Hale, NIH your website!PubMed API (eUtils)API = Application Programming InterfaceMakes data available for use in other programs or interfaces

21. AlternativesSLIM v.2

22. AgendaIntroductionsYou are hereAPIs1234endCase StudiesPubMed

23. Case Studies

24. ThemesRelevanceVisualizationMobile accessSimplification

25. Research QuestionWhat is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?http://pubmed.gov

26. eTBlastDeveloped by:Virginia Biometrics Institute Claim to fame:Analyzes large chunks of texthttp://etest.vbi.vt.edu/etblast3/

30. Developed by: Biomedical informaticist Jeff Saffer & molecular toxicologist Vicki Burnett Claim to fame:Search results based on relationships; Power Terms™http://www.quertle.info/v2/

33. ThemesRelevanceVisualizationMobile AccessSimplification

34. LigerCatDeveloped by:Biology of Aging project at Marine Biological Laboratory – Woods Hole Oceanographic Institution LibraryClaim to fame:Produces tag clouds based on MeSH headingshttp://ligercat.ubio.org/

35. Runs MeSH search directly in PubMed

37. PubAnatomyDeveloped by:National Center for Integrative Bioinformatics, University of MichiganClaim to fame:Maps the journal literature to brain anatomy and gene expression correlationshttp://www.ncibi.org/gateway/pubanatomy.html

38. PubAnatomy

39. Ali BabaDeveloped by:InstitutfürInformatik, Humboldt-Universität, BerlinClaim to fame:Graphically summarizes search results to reveal relationships and associationshttp://alibaba.informatik.hu-berlin.de/

40. Ali BabaWhat are the risk factors of treating G6PD-deficient malaria patiens with primaquine?

41. ThemesSemantic searchingVisualizationMobile AccessSimplification

42. PubMed Mobile BetaDeveloped by:National Center for Biotechnology Information, National Library of MedicineClaim to fame:Simplified access to basic PubMed featureshttp://www.ncbi.nlm.nih.gov/m/pubmed/

43. PubMed Mobile Beta

44. PubMed for HandheldsNOTDeveloped by:Lister Hill Center, National Library of MedicineClaim to fame:Unique search options - PICO, askMEDLINE, disease associationshttp://pubmedhh.nlm.nih.gov/

45. PubMed for Handhelds

46. PubMed Mobile (Android)Developed by:CRinUSClaim to fame:The best PubMed app for Android so farhttp://www.cyrket.com/p/android/com.bim.pubmed/

47. PubMed CLIP (iPhone)Developed by:Groupnet CorporationClaim to fame:Lots of options for saving and sharing references.http://www.groupnet.co.jp/products/pubmedclip/en/

48. ThemesSemantic searchingVisualizationMobile AccessSimplification

49. Developed by:A Boston clinical pathologist who founded PubGet, Inc. Claim to fame:Better than your library’s link resolver at retrieving PDFshttp://pubget.com/

52. iPubMedDeveloped by:Researchers at the University of California, Irvine and Tsinghua University, ChinaClaim to fame:Fast, fuzzy searches.http://ipubmed.ics.uci.edu/

54. Group Exercises

55. Pick a card…In groups of 2 or 3, explore a third-party PubMed tool and prepare to report:Developer(s)Key featuresWhen you’d use itNegative aspects

56. Discussion Questions

57. What ideas from third-party developers should NCBI adopt for PubMed?

58. Which third-party tool(s) are you likely to use again? In what circumstances?

59. Thank you!Alison AldrichNN/LM PNRhttp://nnlm.gov/pnr(800) 338-7657aldrich3@uw.edu