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Third-Party PubMed Tools

Third-Party PubMed Tools. Now that’s a horse of a different color…. Wisconsin Health Science Libraries Association September 21, 2012 Holly Ann Burt, MLIS, AHIP NN/LM GMR. Photo credit: dianecordell on flickr. Objectives. Participants will be able to:

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Third-Party PubMed Tools

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  1. Third-Party PubMedTools Now that’s a horse of a different color… Wisconsin Health Science Libraries Association September 21, 2012 Holly Ann Burt, MLIS, AHIP NN/LM GMR Photo credit: dianecordellon flickr

  2. Objectives Participants will be able to: • Use and teach others about the latest updates to PubMed.gov • Name and develop search strategies for at least three* third-party PubMed tools • Identify situations in which searching with a third-party tool would be beneficial • Stay current with new developments related to third-party PubMed tools

  3. Agenda • Introductions • What’s new with PubMed • The PubMed API • Case Studies • Group Exercises • Discussion Questions

  4. What’s New at NLM? • Disaster resources: • CHEMM, REMM and DIMRC • DIS Specialization • GeneEd - http://geneed.nlm.nih.gov/ • LiverTox- http://livertox.nih.gov/ • Searched 1.8 billion times in 2011 • MeSH turned 50 in 2010

  5. What’s New with PubMed?

  6. by the Numbers • More than 22 million article citations • More than 5,600 journals indexed • Goes back in time to the 1800’s • Earliest MEDLINE citation: 1902 • Earliest PubMed citation: 1809 • Searched 1.8 billion times in 2011 • MeSH turned 50 in 2010

  7. Updates Recent changes: • Filters navigation bar • Results by year • Images from PubMed Central • History and Search Builder in Advanced • My Bibliography accepts non-PubMed items

  8. Why Redesign? “While retaining the robust functionality, the interface was simplified to make it easier to use while promoting scientific discovery.” -NLM Technical Bulletin

  9. Keeping Current • PubMed New and Noteworthy • NLM Technical Bulletin • PUBMED-ALERTS@list.nih.gov • MEDLIB-L • NN/LM GMR Cornflower

  10. PubMed API

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

  12. API Resources • How Stuff Works: How APIs Work: http://tinyurl.com/27rw2kn • Explanation of APIs, using conferencing software as an example. • EntrexAJAX: http://entrezajax.appspot.com/ • A third-party derivative of NCBI’s EUtils designed for launching searches directly from the browser (improves speed)

  13. Alternatives SLIM v.2

  14. Case Studies

  15. Themes • Semantic searching • Visualization • Simplification

  16. Research Question • What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?

  17. eTBlast Developed by: Virginia Biometrics Institute Claim to fame: Analyzes large chunks of text http://etest.vbi.vt.edu/etblast3/

  18. eTBlast Search

  19. eTBlast Graphic Results

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

  21. Quertle Search page

  22. Quertle Results page

  23. Themes II • Semantic searching • Visualization • Simplification

  24. LigerCat Developed by: Biology of Aging project at Marine Biological Laboratory – Woods Hole Oceanographic Institution Library Claim to fame: Produces tag clouds based on MeSH headings http://ligercat.ubio.org/

  25. LigerCat search page Runs MeSH search directly in PubMed

  26. LigerCat results page

  27. PubAnatomy Developed by: National Center for Integrative Bioinformatics, University of Michigan Claim to fame: Maps the journal literature to brain anatomy and gene expression correlations http://www.ncibi.org/gateway/pubanatomy.html

  28. PubAnatomy Results

  29. Themes III • Semantic searching • Visualization • Simplification

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

  31. PubGet Search results

  32. PMInstant Developed by: Jonathan Bourman with Pubmed AJAX API Claim to fame: Fast. Very fast. Displays search results while you are still typing. http://pminstant.com/

  33. PMInstant Search Results

  34. Group Exercises

  35. Pick a card… In groups of 2 or 3, explore a third-party PubMed tool and prepare to report: • Developer(s) • Key features • When you’d use it • Negative aspects

  36. Discussion Questions

  37. Discussion Question I • What ideas from third-party developers should NCBI adopt for PubMed?

  38. Discussion Question II • Which third-party tool(s) are you likely to use again? In what circumstances?

  39. Discussion Question III • If you could offer NLM one piece of advice, what would it be?

  40. Thank you!

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