Third-Party Tools<br />Alison Aldrich, NN/LM PNR<br />
Objectives<br />Participants will be able to:<br />Use and teach others about the latest updates to PubMed.gov<br />Name a...
Agenda<br />Introductions<br />What’s new with PubMed<br />The PubMed API<br />Case Studies<br />Group Exercises<br />Disc...
What’s new with PubMed?<br />
by the Numbers<br />More than 20 million article citations<br />More than 5,000 journals indexed<br />Goes back in time to...
Year in Review<br />October 2009<br />
Year in Review<br />October 2009<br />
Year in Review<br />Key changes in the October 2009 redesign:<br />Tabs removed<br />Blue left navigation bar eliminated<b...
Year in Review<br />Why redesign?<br />“While retaining the robust functionality, the interface was simplified to make it ...
Year in Review<br />Key changes since the October 2009 redesign:<br />Some functions moved from Advanced Search to Limits<...
Keeping Current<br />PubMed New and Noteworthy<br />NLM Technical Bulletin<br />PUBMED-ALERTS@list.nih.gov<br />MEDLIB-L<b...
PubMed API<br />
Drive traffic to your data, not your website!<br />-David Hale, NIH<br /> your website!<br />PubMed API (eUtils)<br />API ...
Alternatives<br />SLIM v.2<br />
Case Studies<br />
Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
Research Question<br />What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?<br /...
eTBlast<br />Developed by:<br />Virginia Biometrics Institute <br />Claim to fame:<br />Analyzes large chunks of text<br /...
Developed by: <br />Biomedical informaticist Jeff Saffer & molecular toxicologist Vicki Burnett <br />Claim to fame:<br />...
Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
LigerCat<br />Developed by:<br />Biology of Aging project at Marine Biological Laboratory – Woods Hole Oceanographic Insti...
Runs MeSH search directly in PubMed<br />
PubAnatomy<br />Developed by:<br />National Center for Integrative Bioinformatics, University of Michigan<br />Claim to fa...
PubAnatomy<br />
Ali Baba<br />Developed by:<br />InstitutfürInformatik, Humboldt-Universität, Berlin<br />Claim to fame:<br />Graphically ...
Ali Baba<br />What are the risk factors of treating G6PD-deficient malaria patiens with primaquine?<br />
Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
Developed by:<br />A Boston clinical pathologist who founded PubGet, Inc. <br />Claim to fame:<br />Better than your libra...
PMInstant<br />Developed by:<br />Jonathan Bourman with Pubmed AJAX API<br />Claim to fame:<br />Fast. Very fast. Displays...
Group Exercises<br />
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...
Discussion Questions<br />
What ideas from third-party developers should NCBI adopt for PubMed?<br />
Which third-party tool(s) are you likely to use again? In what circumstances?<br />
If you could offer NLM one piece of advice, what would it be?<br />
Thank you and enjoy PNC!<br />Alison Aldrich, NN/LM PNR<br />206-221-3489<br />aldrich3@uw.edu<br />
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
MLA CE Course: Third-Party PubMed Tools
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MLA CE Course: Third-Party PubMed Tools

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As taught at the Washington Medical Librarians Association meeting, March 24, 2011 in Kenmore, Washington.

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  • http://www.flickr.com/photos/andy_roberts_uk/4760301573/in/photostream/ all rights reserved
  • * But we will cover at least 12
  • Introductions: State your name, workplace, how long you’ve been there, and an interesting search you’ve done
  • Ask: how many of you use the PubMed interface as the primary way you search Medline?A good source for the latest PubMed stats is: http://www.nlm.nih.gov/services/faqmed.html
  • Source: healthlinks.washington.edu
  • Source: healthlinks.washington.edu
  • Tabs were: Limits, Preview/Index, History, DetailsBlue left navigation bar included links to MeSH, Journals DB, Clinical QueriesDisplay Settings managed under one rollover instead of multiple buttonsBrief, Citation, and AbstractPlus formats are no longer available – a point of contentionUW Librarians produced a handy “Where has it gone?” list:http://healthlinks.washington.edu/howto/pubmed_changes_2009/---Advanced Search search builder example:JMLA [Journal] and pubmed[MeSH]Note that links to MeSH, Journals, Clinical Queries, Specialized Queries still below
  • A focus on end-user searching.
  • Links on Resources handouthttps://list.nih.gov/archives/pubmed-alerts.html
  • The National Center for Biotechnology Information (NCBI) makes a huge amount of information available for free to the world. The way they make it accessible to people is through the PubMed interface. They also make it available to machines, and one of the ways they do that is through the Entrez Utilities API. eUtils have been available since 2002. This particular kind of API is called a web service. Here’s how it works:A programmer writes some software that constructs a URL that is going to be a request for information.The software sends the URL to the web servers at NCBINCBI sends back a response in the form of xmlThe software knows how to handle that xml and display it“To access these data, a piece of software first posts an eUtils URL to NCBI, then retrieves the results of this posting, after which it processes the data as required. The software can thus use any computer language that can send a URL to the eUtils server and interpret the XML response; examples of such languages are Perl, Python, Java, and C++. Combining eUtils components to form customized data pipelines within these applications is a powerful approach to data manipulation.”-- from http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework&amp;part=eutilsDavid Hale explaining how open data fuels creativity and innovation, using NLM’s Pillbox as an example:http://blip.tv/file/4110607Pillbox is a partnership between NLM and the FDA
  • How to find out about them? Under Additional Resources on your handout:-David Rothman’s blog-VCU LibGuideHow to decide which to cover?Still functional w/ some evidence of continued development – should be obvious who the developers areDo something unique as compared to PubMed interfaceBonus points if described recently in the journal literature
  • Pass out Bingo cards
  • Semantic search – incorporates extra indexing or algorithms to better understand the searcher’s intent
  • Current developers: Virginia Biometrics Institute, a lab @ VA Tech, and formerly @ UT Southwestern. Harold Garner is the PI.Good for entering: abstracts, paragraphs even from unpublished works, PICO statements*error in URL on handout – add /etblast3/
  • Saffer and Burnett worked at Pacific Northwest National Laboratory
  • Produces graphs or diagrams of search results
  • An alternativeMeSH browserSlow for searches retrieving a lot of results.
  • From PubAnatomy user guide: http://www.ncibi.org/gateway/pdf/docs/PubAnatomy%20User%20Guide.pdfFrom PubAnatomy user guide: http://www.ncibi.org/gateway/pdf/docs/PubAnatomy%20User%20Guide.pdfSearches keywords, genes, and keywords+genesSupports BooleanSources: PubMed,EntrezGene, Allen Brain AtlasBreaks out for you:CitationsGenes in those citationsMeSH termsAuthorsDiseases InteractionsImagesContext-sensitive menus (right click on just about anything)Can export to citation manager, but what is a pl file?Can export to ExcelOpen an account to save search history
  • Search terms entered as:primaquine malaria g6pd deficiencyRequires a download and JavaLow number of max results could be a problem, but you can create a graph from related articlesArrows when a directional relationship can be detected
  • Fewer options in the interface with the goal of being easy to use
  • PubGetvitamin D AND multiple sclerosisSupports Boolean; AND by defaultPubMed: 322 overall; 245 UW onlinePubGet: 411 overall; 162 PDFs onlyOrange box shows exactly what the deal is w/ the PDFAdvanced search – like single citation matcher but no autocompleteCan buy PDFs from multiple sources with a PayPal accountFirefox plugin to download full-text in batchesEmail PDF function sends recipient a link to the .pdf – it works if they have accessAutomatic export to RefWorks; for EndNote and similar, download as RIS formatPaperPlanebookmarklet – Search in PubMed interface, then click on abstract screen to let PubGet find the PDF (must allow pop-ups)PubGet Mobile – test with http://www.testiphone.com/CAN’T FIGURE OUT HOW TO SAVE ACROSS LOGINS OR WHAT AN INDIVIDUAL ACCOUNT MAKES POSSIBLE
  • Pubget’s mobile siteNot an appWorks with any device capable of viewing/storing PDFs
  • Example search (somewhat slowly): diabetic complicationsPractical utility?
  • Depending on time, allow 15 – 30 minutesCards:PubMed on Tap (uses iPad or an iPhone)HubMedNovoseekMEDSUMSLIM v.2 GoPubMed
  • MLA CE Course: Third-Party PubMed Tools

    1. 1. Third-Party Tools<br />Alison Aldrich, NN/LM PNR<br />
    2. 2. Objectives<br />Participants will be able to:<br />Use and teach others about the latest updates to PubMed.gov<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 />
    3. 3. Agenda<br />Introductions<br />What’s new with PubMed<br />The PubMed API<br />Case Studies<br />Group Exercises<br />Discussion Questions<br />
    4. 4. What’s new with PubMed?<br />
    5. 5. by the Numbers<br />More than 20 million article citations<br />More than 5,000 journals indexed<br />Goes back in time to the 1940’s<br />Searched 1.3 billion times in 2009<br />MeSH turns 50<br />
    6. 6. Year in Review<br />October 2009<br />
    7. 7. Year in Review<br />October 2009<br />
    8. 8. Year in Review<br />Key changes in the October 2009 redesign:<br />Tabs removed<br />Blue left navigation bar eliminated<br />Functions moved to Advanced Search<br />Display options consolidated<br />Discovery “ads” added to right column<br />
    9. 9. Year in Review<br />Why redesign?<br />“While retaining the robust functionality, the interface was simplified to make it easier to use while promoting scientific discovery.”<br />-NLM Technical Bulletin<br />
    10. 10. Year in Review<br />Key changes since the October 2009 redesign:<br />Some functions moved from Advanced Search to Limits<br />Updates to Search Builder tool<br />More flexibility in e-mail formats<br />Details stays on the right<br />Updates to Clinical Queries<br />http://pubmed.gov<br />
    11. 11. Keeping Current<br />PubMed New and Noteworthy<br />NLM Technical Bulletin<br />PUBMED-ALERTS@list.nih.gov<br />MEDLIB-L<br />NN/LM PNR Dragonfly<br />
    12. 12. PubMed API<br />
    13. 13. 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 />
    14. 14. Alternatives<br />SLIM v.2<br />
    15. 15. Case Studies<br />
    16. 16. Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
    17. 17. Research Question<br />What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?<br />http://pubmed.gov<br />
    18. 18. 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 />
    19. 19.
    20. 20.
    21. 21.
    22. 22. 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 />
    23. 23.
    24. 24.
    25. 25. Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
    26. 26. 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 />
    27. 27. Runs MeSH search directly in PubMed<br />
    28. 28.
    29. 29. 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 />
    30. 30. PubAnatomy<br />
    31. 31. 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 />
    32. 32. Ali Baba<br />What are the risk factors of treating G6PD-deficient malaria patiens with primaquine?<br />
    33. 33. Themes<br />Semantic searching<br />Visualization<br />Simplification<br />
    34. 34. 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 />
    35. 35.
    36. 36.
    37. 37. PMInstant<br />Developed by:<br />Jonathan Bourman with Pubmed AJAX API<br />Claim to fame:<br />Fast. Very fast. Displays search results while you are still typing.<br />http://pminstant.com/<br />
    38. 38.
    39. 39. Group Exercises<br />
    40. 40. 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 />
    41. 41. Discussion Questions<br />
    42. 42. What ideas from third-party developers should NCBI adopt for PubMed?<br />
    43. 43. Which third-party tool(s) are you likely to use again? In what circumstances?<br />
    44. 44. If you could offer NLM one piece of advice, what would it be?<br />
    45. 45. Thank you and enjoy PNC!<br />Alison Aldrich, NN/LM PNR<br />206-221-3489<br />aldrich3@uw.edu<br />
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