1.Third-Party Tools
Alison Aldrich, NN/LM PNR

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
Whats new with PubMed
The PubMed API
Case Studies
Group Exercises
Discussion Questions
4. Whats new with PubMed?
5. by the Numbers
More than 20 million article citations
More than 5,000 journals indexed
Goes back in time to the 1940s
Searched 1.3 billion times in 2009
MeSH turns 50
6. Year in Review
October 2009
7. Year in Review
October 2009
8. Year in Review
Key changes in the October 2009 redesign:
Tabs removed
Blue left navigation bar eliminated
Functions moved to Advanced Search
Display options consolidated
Discovery ads added to right column
9. Year in Review
Why redesign?
While retaining the robust functionality, the interface was simplified to make it easier to use while promoting scientific discovery.
-NLM Technical Bulletin
10. Year in Review
Key changes since the October 2009 redesign:
Some functions moved from Advanced Search to Limits
Updates to Search Builder tool
More flexibility in e-mail formats
Details stays on the right
Updates to Clinical Queries
http://pubmed.gov
11. Keeping Current
PubMed New and Noteworthy
NLM Technical Bulletin
PUBMED-ALERTS@list.nih.gov
MEDLIB-L
NN/LM PNR Dragonfly
12. PubMed API
13. Drive traffic to your data, not your website!
-David Hale, NIH
your website!
PubMed API (eUtils)
API = Application Programming Interface
Makes data available for use in other programs or interfaces
14. Alternatives
SLIM v.2
15. Case Studies
16. Themes
Semantic searching
Visualization
Simplification
17. Research Question
What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?
http://pubmed.gov
18. eTBlast
Developed by:
Virginia Biometrics Institute
Claim to fame:
Analyzes large chunks of text
http://etest.vbi.vt.edu/etblast3/
19. 20. 21. 22. 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/
23. 24. 25. Themes
Semantic searching
Visualization
Simplification
26. 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/
27. Runs MeSH search directly in PubMed
28. 29. 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
30. PubAnatomy
31. Ali Baba
Developed by:
InstitutfrInformatik, Humboldt-Universitt, Berlin
Claim to fame:
Graphically summarizes search results to reveal relationships and associations
http://alibaba.informatik.hu-berlin.de/
32. Ali Baba
What are the risk factors of treating G6PD-deficient malaria patiens with primaquine?
33. Themes
Semantic searching
Visualization
Simplification
34. Developed by:
A Boston clinical pathologist who founded PubGet, Inc.
Claim to fame:
Better than your librarys link resolver at retrieving PDFs
http://pubget.com/
35. 36. 37. 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/
38. 39. Group Exercises
40. Pick a card
In groups of 2 or 3, explore a third-party PubMed tool and prepare to report:
Developer(s)
Key features
When youd use it
Negative aspects
41. Discussion Questions
42. What ideas from third-party developers should NCBI adopt for PubMed?
43. Which third-party tool(s) are you likely to use again? In what circumstances?
44. If you could offer NLM one piece of advice, what would it be?
45. Thank you and enjoy PNC!
Alison Aldrich, NN/LM PNR
206-221-3489
aldrich3@uw.edu