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Third-Party
PubMedTools
Now that’s a horse of a different color…
Wisconsin Health Science Libraries Association
September 21, 2012
Holly Ann Burt, MLIS, AHIPNN/LM GMR
Photo credit: dianecordell on flickr
Objectives
Participants will be able to:Use and teach others about the latest
updates to PubMed.govName 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
Agenda
IntroductionsWhat’s new with PubMedThe PubMed APICase StudiesGroup ExercisesDiscussion Questions
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
2011MeSH turned 50 in 2010
What’s New at NLM?
What’s New with PubMed?
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
Updates
Recent changes:Filters navigation barResults by year Images from PubMed CentralHistory and Search Builder in
Advanced My Bibliography accepts non-
PubMed items
Why Redesign?
“While retaining the robust functionality, the interface was simplified to make it easier to use while promoting scientific discovery.”
-NLM Technical Bulletin
Keeping CurrentPubMed New and NoteworthyNLM Technical [email protected]/LM GMR Cornflower
PubMed API
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!
API Resources
How Stuff Works: How APIs Work: http://tinyurl.com/27rw2kn◦Explanation of APIs, using
conferencing software as an example.Entrex AJAX: http
://entrezajax.appspot.com/ ◦A third-party derivative of NCBI’s
EUtils designed for launching searches directly from the browser (improves speed)
Alternatives
SLIM v.2
Case Studies
ThemesSemantic searchingVisualizationSimplification
Research Question
What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?
eTBlast
Developed by:Virginia Biometrics Institute
Claim to fame:Analyzes large chunks of text
http://etest.vbi.vt.edu/etblast3/
eTBlast Search
eTBlast Graphic Results
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/
Quertle Search page
Quertle Results page
Themes IISemantic searchingVisualizationSimplification
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/
LigerCat search page
Runs MeSH search directly in PubMed
LigerCat results page
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
PubAnatomy Results
Themes IIISemantic searchingVisualizationSimplification
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/
PubGet Search results
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/
PMInstant Search Results
Group Exercises
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
Discussion Questions
Discussion Question IWhat ideas from third-party
developers should NCBI adopt for PubMed?
Discussion Question IIWhich third-party tool(s) are you
likely to use again? In what circumstances?
Discussion Question IIIIf you could offer NLM one piece
of advice, what would it be?
Thank you!
