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Third-Party Tools Third-Party PubMed Tools Now that’s a horse of a different color… Wisconsin Health Science Libraries Association September 21, 2012 Holly.

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Presentation on theme: "Third-Party Tools Third-Party PubMed Tools Now that’s a horse of a different color… Wisconsin Health Science Libraries Association September 21, 2012 Holly."— Presentation transcript:

1 Third-Party 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 flickrdianecordell

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 Disaster resources: ◦ CHEMM, REMM and DIMRC ◦ DIS Specialization GeneEd - LiverTox - Searched 1.8 billion times in 2011 MeSH turned 50 in 2010 What’s New at NLM?

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 AdvancedAdvanced 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 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: ◦ Explanation of APIs, using conferencing software as an example. Entrex AJAX: ◦ 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

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™

21 Quertle Search page

22 Quertle Results page

23 Themes 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

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

28 PubAnatomy Results

29 Themes 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

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.

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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