Third-Party PubMed Tools
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Third-Party
Tools
Now that’s a horse of a different color…
Photo credit: dianecordell on flickr
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Agenda
start
end
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Agenda
1
Introductions
end
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Agenda
1
Introductions
2
PubMed
end
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Agenda
1
Introductions
2
PubMed
3
APIs
end
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Agenda
1
Introductions
2
PubMed
3
APIs
4Case Studies
end
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Agenda
1
Introductions
2
PubMed
3
APIs
4Case Studies
5
Group Projects
end
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Agenda
1
Introductions
2
PubMed
3
APIs
4Case Studies
5
Group Projects
Discussion
end6
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Agenda
end1
Introductions
2
PubMed
3
APIs
4Case Studies
5
Group Projects
6 7Discussion
Evaluation
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By you will be able to…
• Describe the history of end-user access to MEDLINE
• 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
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HOW WE GOT HEREA brief history of end-user access to MEDLINE
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1897:First volume of Index Medicus published.
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1964:MEDLARS became operational
Computer room at the National Library of Medicine, 1960s
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1971:MEDLINE (“MEDLARS online”) provides online access to a subset of references
Texas Instruments Silent 700 with Acoustic Coupler
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1986:Health professionals started running their own searches with PC-based Grateful Med
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1997:PubMed is born!
Free Web-based access to MEDLINE
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1997:PubMed is born!
Free Web-based access to MEDLINE
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Today
• 20 million article citations and counting
• More than 5,000journals indexed
• Goes back in time to the 1940’s
• Searched 1.6 billiontimes in 2010
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2002:NLM says “take our data, too!”
Entrez Programming Utilities (Eutils) introduced
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Drive traffic to your data, not your website!
-David Hale, NIHyour website!
PubMed API (eUtils)
• API = Application Programming Interface
• Makes data available for use in other programs or interfaces
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Alternatives
SLIM v.2
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Agenda
1
Introductions
2
PubMed
3
APIs
4Case Studies
end
You are
here
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CASE STUDIES
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Themes
• Relevance
• Visualization
• Mobile access
• Simplification
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Research Question
• What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?
http://pubmed.gov
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eTBlast
Developed by:
Virginia Biometrics Institute
Claim to fame:
Analyzes large chunks of text
http://etest.vbi.vt.edu/etblast3/
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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/
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Themes
• Relevance
• Visualization
• Mobile Access
• Simplification
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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/
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Runs MeSHsearch directly in PubMed
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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
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PubAnatomy
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Ali Baba
Developed by:Institut für Informatik, Humboldt-Universität,
Berlin
Claim to fame:Graphically summarizes search results to reveal
relationships and associations
http://alibaba.informatik.hu-berlin.de/
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Ali Baba
What are the risk factors of treating G6PD-
deficient malaria patienswith primaquine?
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Themes
• Semantic searching
• Visualization
• Mobile Access
• Simplification
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PubMed Mobile Beta
Developed by:
National Center for Biotechnology Information, National Library of Medicine
Claim to fame:
Simplified access to basic PubMed features
http://www.ncbi.nlm.nih.gov/m/pubmed/
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PubMed Mobile Beta
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PubMed for Handhelds
Developed by:
Lister Hill Center, National Library of Medicine
Claim to fame:
Unique search options - PICO, askMEDLINE, disease associations
http://pubmedhh.nlm.nih.gov/
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PubMed for Handhelds
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PubMed Mobile (Android)
Developed by:
CRinUS
Claim to fame:
The best PubMed app for Android so far
http://www.cyrket.com/p/android/com.bim.pubmed/
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PubMed CLIP (iPhone)
Developed by:
Groupnet Corporation
Claim to fame:
Lots of options for saving and sharing references.
http://www.groupnet.co.jp/products/pubmedclip/en/
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Themes
• Semantic searching
• Visualization
• Mobile Access
• Simplification
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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/
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iPubMed
Developed by:
Researchers at the University of California, Irvine and Tsinghua University, China
Claim to fame:
Fast, fuzzy searches.
http://ipubmed.ics.uci.edu/
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GROUP EXERCISES
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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
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DISCUSSION QUESTIONS
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What ideas from third-party developers should NCBI adopt for PubMed?
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Which third-party tool(s) are you likely to use again? In what circumstances?
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Thank you!
Alison Aldrich
NN/LM PNR
http://nnlm.gov/pnr
(800) 338-7657