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Now that’s a horse of a different color…<br />Third-Party Tools<br />Photo credit: dianecordellon flickr<br />

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Agenda<br />start<br />end<br />

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Agenda<br />Introductions<br />1<br />end<br />

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Agenda<br />Introductions<br />1<br />2<br />end<br />PubMed<br />

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Agenda<br />Introductions<br />APIs<br />1<br />2<br />3<br />end<br />PubMed<br />

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Agenda<br />Introductions<br />APIs<br />1<br />2<br />3<br />4<br />end<br />Case Studies<br />PubMed<br />

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Agenda<br />Introductions<br />Group Projects<br />APIs<br />1<br />2<br />3<br />4<br />5<br />end<br />Case Studies<br />PubMed<br />

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Agenda<br />Introductions<br />Group Projects<br />APIs<br />1<br />2<br />3<br />4<br />5<br />6<br />end<br />Case Studies<br />Discussion<br />PubMed<br />

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Agenda<br />Introductions<br />Group Projects<br />APIs<br />Evaluation<br />1<br />2<br />3<br />4<br />5<br />6<br />7<br />end<br />Case Studies<br />Discussion<br />PubMed<br />

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By you will be able to…<br />Describe the history of end-user access to MEDLINE<br />Name and develop search strategies for at least three* third-party PubMed tools<br />Identify situations in which searching with a third-party tool would be beneficial<br />Stay current with new developments related to third-party PubMed tools<br />

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How we got here<br />A brief history of end-user access to MEDLINE<br />

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1897: <br />First volume of Index Medicuspublished.<br />

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1964:<br />MEDLARS became operational<br />Computer room at the National Library of Medicine, 1960s<br />

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1971:<br />MEDLINE (“MEDLARS online”) provides online access to a subset of references<br />Texas Instruments Silent 700 with Acoustic Coupler<br />

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1986:<br />Health professionals started running their own searches with PC-based Grateful Med<br />

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1997:<br />PubMed is born! <br />Free Web-based access to MEDLINE<br />

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1997:<br />PubMed is born! <br />Free Web-based access to MEDLINE<br />

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Today<br />20 million article citations and counting<br />More than 5,000 journals indexed<br />Goes back in time to the 1940’s<br />Searched 1.6 billion times in 2010<br />

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2002:<br />NLM says “take our data, too!” <br />Entrez Programming Utilities (Eutils) introduced<br />

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

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Alternatives<br />SLIM v.2<br />

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Agenda<br />Introductions<br />You are here<br />APIs<br />1<br />2<br />3<br />4<br />end<br />Case Studies<br />PubMed<br />

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Case Studies<br />

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Themes<br />Relevance<br />Visualization<br />Mobile access<br />Simplification<br />

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Research Question<br />What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?<br />http://pubmed.gov<br />

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

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Developed by: <br />Biomedical informaticist Jeff Saffer & molecular toxicologist Vicki Burnett <br />Claim to fame:<br />Search results based on relationships; <br />Power Terms™<br />http://www.quertle.info/v2/<br />

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Themes<br />Relevance<br />Visualization<br />Mobile Access<br />Simplification<br />

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

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Runs MeSH search directly in PubMed<br />

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

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PubAnatomy<br />

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Ali Baba<br />Developed by:<br />InstitutfürInformatik, Humboldt-Universität, Berlin<br />Claim to fame:<br />Graphically summarizes search results to reveal relationships and associations<br />http://alibaba.informatik.hu-berlin.de/<br />

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Ali Baba<br />What are the risk factors of treating G6PD-deficient malaria patiens with primaquine?<br />

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Themes<br />Semantic searching<br />Visualization<br />Mobile Access<br />Simplification<br />

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PubMed Mobile Beta<br />Developed by:<br />National Center for Biotechnology Information, National Library of Medicine<br />Claim to fame:<br />Simplified access to basic PubMed features<br />http://www.ncbi.nlm.nih.gov/m/pubmed/<br />

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PubMed Mobile Beta<br />

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PubMed for Handhelds<br />NOT<br />Developed by:<br />Lister Hill Center, National Library of Medicine<br />Claim to fame:<br />Unique search options - PICO, askMEDLINE, disease associations<br />http://pubmedhh.nlm.nih.gov/<br />

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PubMed for Handhelds<br />

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PubMed Mobile (Android)<br />Developed by:<br />CRinUS<br />Claim to fame:<br />The best PubMed app for Android so far<br />http://www.cyrket.com/p/android/com.bim.pubmed/<br />

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PubMed CLIP (iPhone)<br />Developed by:<br />Groupnet Corporation<br />Claim to fame:<br />Lots of options for saving and sharing references.<br />http://www.groupnet.co.jp/products/pubmedclip/en/<br />

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Themes<br />Semantic searching<br />Visualization<br />Mobile Access<br />Simplification<br />

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

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iPubMed<br />Developed by:<br />Researchers at the University of California, Irvine and Tsinghua University, China<br />Claim to fame:<br />Fast, fuzzy searches.<br />http://ipubmed.ics.uci.edu/<br />

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Group Exercises<br />

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

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Discussion Questions<br />

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What ideas from third-party developers should NCBI adopt for PubMed?<br />

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Which third-party tool(s) are you likely to use again? In what circumstances?<br />

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Thank you!<br />Alison Aldrich<br />NN/LM PNR<br />http://nnlm.gov/pnr<br />(800) 338-7657<br />aldrich3@uw.edu<br />