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MLA CE Course: Third-Party PubMed Tools

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As taught at the Washington Medical Librarians Association meeting, March 24, 2011 in Kenmore, Washington.

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MLA CE Course: Third-Party PubMed Tools

  1. 1. Third-Party Tools<br />Alison Aldrich, NN/LM PNR<br />
  2. 2. Objectives<br />Participants will be able to:<br />Use and teach others about the latest updates to PubMed.gov<br />Name and develop search strategies for at least three* third-party PubMed tools<br />Identify situations in which searching with a third-party tool would be beneficial<br />Stay current with new developments related to third-party PubMed tools<br />
  3. 3. Agenda<br />Introductions<br />What’s new with PubMed<br />The PubMed API<br />Case Studies<br />Group Exercises<br />Discussion Questions<br />
  4. 4. What’s new with PubMed?<br />
  5. 5. by the Numbers<br />More than 20 million article citations<br />More than 5,000 journals indexed<br />Goes back in time to the 1940’s<br />Searched 1.3 billion times in 2009<br />MeSH turns 50<br />
  6. 6. Year in Review<br />October 2009<br />
  7. 7. Year in Review<br />October 2009<br />
  8. 8. Year in Review<br />Key changes in the October 2009 redesign:<br />Tabs removed<br />Blue left navigation bar eliminated<br />Functions moved to Advanced Search<br />Display options consolidated<br />Discovery “ads” added to right column<br />
  9. 9. Year in Review<br />Why redesign?<br />“While retaining the robust functionality, the interface was simplified to make it easier to use while promoting scientific discovery.”<br />-NLM Technical Bulletin<br />
  10. 10. Year in Review<br />Key changes since the October 2009 redesign:<br />Some functions moved from Advanced Search to Limits<br />Updates to Search Builder tool<br />More flexibility in e-mail formats<br />Details stays on the right<br />Updates to Clinical Queries<br />http://pubmed.gov<br />
  11. 11. Keeping Current<br />PubMed New and Noteworthy<br />NLM Technical Bulletin<br />PUBMED-ALERTS@list.nih.gov<br />MEDLIB-L<br />NN/LM PNR Dragonfly<br />
  12. 12. PubMed API<br />
  13. 13. Drive traffic to your data, not your website!<br />-David Hale, NIH<br /> your website!<br />PubMed API (eUtils)<br />API = Application Programming Interface<br />Makes data available for use in other programs or interfaces<br />
  14. 14. Alternatives<br />SLIM v.2<br />
  15. 15. Case Studies<br />
  16. 16. Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
  17. 17. Research Question<br />What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?<br />http://pubmed.gov<br />
  18. 18. eTBlast<br />Developed by:<br />Virginia Biometrics Institute <br />Claim to fame:<br />Analyzes large chunks of text<br />http://etest.vbi.vt.edu/etblast3/<br />
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  22. 22. Developed by: <br />Biomedical informaticist Jeff Saffer & molecular toxicologist Vicki Burnett <br />Claim to fame:<br />Search results based on relationships; <br />Power Terms™<br />http://www.quertle.info/v2/<br />
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  24. 24.
  25. 25. Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
  26. 26. LigerCat<br />Developed by:<br />Biology of Aging project at Marine Biological Laboratory – Woods Hole Oceanographic Institution Library<br />Claim to fame:<br />Produces tag clouds based on MeSH headings<br />http://ligercat.ubio.org/<br />
  27. 27. Runs MeSH search directly in PubMed<br />
  28. 28.
  29. 29. PubAnatomy<br />Developed by:<br />National Center for Integrative Bioinformatics, University of Michigan<br />Claim to fame:<br />Maps the journal literature to brain anatomy and gene expression correlations<br />http://www.ncibi.org/gateway/pubanatomy.html<br />
  30. 30. PubAnatomy<br />
  31. 31. Ali Baba<br />Developed by:<br />InstitutfürInformatik, Humboldt-Universität, Berlin<br />Claim to fame:<br />Graphically summarizes search results to reveal relationships and associations<br />http://alibaba.informatik.hu-berlin.de/<br />
  32. 32. Ali Baba<br />What are the risk factors of treating G6PD-deficient malaria patiens with primaquine?<br />
  33. 33. Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
  34. 34. Developed by:<br />A Boston clinical pathologist who founded PubGet, Inc. <br />Claim to fame:<br />Better than your library’s link resolver at retrieving PDFs<br />http://pubget.com/<br />
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  37. 37. PMInstant<br />Developed by:<br />Jonathan Bourman with Pubmed AJAX API<br />Claim to fame:<br />Fast. Very fast. Displays search results while you are still typing.<br />http://pminstant.com/<br />
  38. 38.
  39. 39. Group Exercises<br />
  40. 40. Pick a card…<br />In groups of 2 or 3, explore a third-party PubMed tool and prepare to report:<br />Developer(s)<br />Key features<br />When you’d use it<br />Negative aspects<br />
  41. 41. Discussion Questions<br />
  42. 42. What ideas from third-party developers should NCBI adopt for PubMed?<br />
  43. 43. Which third-party tool(s) are you likely to use again? In what circumstances?<br />
  44. 44. If you could offer NLM one piece of advice, what would it be?<br />
  45. 45. Thank you and enjoy PNC!<br />Alison Aldrich, NN/LM PNR<br />206-221-3489<br />aldrich3@uw.edu<br />

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