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Searching Deeply for Data, Results and Tools What is Stopping Us?   Philip E. Bourne University of California San Diego [e...
Meredith    A story that celebrates all that open access has done and shows the promise for the future
That is the good news… Now let me tell you what I believe we need to do to make Meredith the rule rather than the exceptio...
The Research Enterprise Literature Data Methods
The Research Enterprise Without eScholarship http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/
Literature <ul><li>Meredith certainly benefited from the OA literature … </li></ul><ul><li>But we have a long way to go in...
Literature –  But First What is the Promise Shared Function Literature Data Methods Immunology Literature Cardiac Disease ...
Solution: We Need SciVerse™ like Developments Leveraging  OA Content <ul><li>A very clever idea – The App model </li></ul>...
Literature - PMC <ul><li>Problems </li></ul><ul><ul><li>Producers do not care enough </li></ul></ul><ul><ul><li>OA publish...
Solutions: Scientists As Advocates <ul><li>My knee jerk reaction – is this the best a bunch of great minds can come up wit...
Solution:  a) Play Upon a Scientist’s Guilt re The Reward System  b) Educate Evaluators The Right Thing To Do Reward P.E. ...
Solution:  Use the Traditional Reward System  in New Ways The Wikipedia Experiment – Topic Pages <ul><li>Identify areas of...
Problems Regarding Data <ul><li>Meredith got the data she needed in part by bugging authors – It should be easier </li></u...
Solutions Regarding Data <ul><li>There are some wonderful resources out there (e.g., Entrez from the NLM) – copy them </li...
Problems Regarding Methods <ul><li>Meredith had to use a “trial’ license of Mathematica </li></ul><ul><li>I cant easily re...
Solutions Regarding Methods <ul><li>Meredith was able to get computer cycles for free in the cloud </li></ul><ul><li>There...
Summary – Creating More Merediths <ul><li>OA groups to keep doing what they are doing and support leveraging the content a...
General References <ul><li>What Do I Want from the Publisher of the Future PLoS Comp Biol  6(5): e1000787 </li></ul><ul><l...
References to Exemplars <ul><li>Semantic Biochemical Journal - 2010: Using  Utopia </li></ul><ul><li>Article of the Future...
Thank You! [email_address]
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Searching Deeply for Data, Results and Tools- What is Stopping Us?

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Searching Deeply for Data, Results and Tools- What is Stopping Us?

  1. 1. Searching Deeply for Data, Results and Tools What is Stopping Us?   Philip E. Bourne University of California San Diego [email_address] http://www.sdsc.edu/ pb Relevant Work from Us: http ://www.sdsc.edu/pb/SummaryScholarComm. pdf http://www.slideshare.net/pebourne/?? Berlin-9 Nov. 9, 2011
  2. 2. Meredith A story that celebrates all that open access has done and shows the promise for the future
  3. 3. That is the good news… Now let me tell you what I believe we need to do to make Meredith the rule rather than the exception Disclaimer: My viewpoint is that of a computational biologist
  4. 4. The Research Enterprise Literature Data Methods
  5. 5. The Research Enterprise Without eScholarship http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/
  6. 6. Literature <ul><li>Meredith certainly benefited from the OA literature … </li></ul><ul><li>But we have a long way to go in several respects </li></ul>PubMed Central Contents Nov 8, 2011 PubMed Contents Nov 8, 2011 Literature Data Methods
  7. 7. Literature – But First What is the Promise Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature
  8. 8. Solution: We Need SciVerse™ like Developments Leveraging OA Content <ul><li>A very clever idea – The App model </li></ul><ul><li>Leverage content </li></ul><ul><li>Provide an open API </li></ul><ul><li>Get the community to do all the work </li></ul><ul><li>Drive folks to buy content </li></ul><ul><li>Problem: </li></ul><ul><ul><li>OA does not have the resources </li></ul></ul><ul><ul><li>OA + CA is more compelling </li></ul></ul><ul><li>Solution: </li></ul><ul><ul><li>More developers </li></ul></ul><ul><ul><li>Federal and Foundation support to leverage OA content </li></ul></ul>Literature Data Methods
  9. 9. Literature - PMC <ul><li>Problems </li></ul><ul><ul><li>Producers do not care enough </li></ul></ul><ul><ul><li>OA publishers are not aware enough – I cant even reliably parse the PMC license records to know what I can access </li></ul></ul><ul><li>Solutions </li></ul><ul><ul><li>Continue to advocate </li></ul></ul><ul><ul><li>Raise awareness and establish consistency so that history does not repeat itself </li></ul></ul>Literature Data Methods <ul><li>Advocacy </li></ul><ul><li>Follow-on to Beyond the PDF </li></ul><ul><li>https://sites.google.com/site/beyondthepdf/ </li></ul><ul><li>Force11 www.force11.org </li></ul>
  10. 10. Solutions: Scientists As Advocates <ul><li>My knee jerk reaction – is this the best a bunch of great minds can come up with! </li></ul><ul><li>My more thoughtful reaction – every little bit helps – it will broaden awareness of the value of OA like nothing else </li></ul>Literature Data Methods
  11. 11. Solution: a) Play Upon a Scientist’s Guilt re The Reward System b) Educate Evaluators The Right Thing To Do Reward P.E. Bourne 2011 Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comp. Biol . 7(1) e1002001
  12. 12. Solution: Use the Traditional Reward System in New Ways The Wikipedia Experiment – Topic Pages <ul><li>Identify areas of Wikipedia that relate to the journal that are missing of stubs </li></ul><ul><li>Develop a Wikipedia page in the sandbox </li></ul><ul><li>Have a Topic Page Editor review the page </li></ul><ul><li>Publish the copy of record with associated rewards </li></ul><ul><li>Release the living version into Wikipedia </li></ul>Literature Data Methods
  13. 13. Problems Regarding Data <ul><li>Meredith got the data she needed in part by bugging authors – It should be easier </li></ul><ul><li>There is a long tail of data which is lost </li></ul><ul><li>Institutional repositories are too institutional </li></ul><ul><li>Journals are passing the buck </li></ul><ul><li>We are heading towards the same issues with data repositories as we have with publishers </li></ul>Literature Data Methods Disclaimer: My viewpoint is that of a computational biologist
  14. 14. Solutions Regarding Data <ul><li>There are some wonderful resources out there (e.g., Entrez from the NLM) – copy them </li></ul><ul><li>We need data repositories working together now </li></ul><ul><li>We need more than a DOI – we need metadata catalogs for data so we can deep search and rank </li></ul><ul><li>Data needs to be recognized as a publication </li></ul>Literature Data Methods Disclaimer: My viewpoint is that of a computational biologist
  15. 15. Problems Regarding Methods <ul><li>Meredith had to use a “trial’ license of Mathematica </li></ul><ul><li>I cant easily reproduce my own research </li></ul><ul><li>There is little reward for providing access to methods </li></ul>Literature Data Methods Disclaimer: My viewpoint is that of a computational biologist
  16. 16. Solutions Regarding Methods <ul><li>Meredith was able to get computer cycles for free in the cloud </li></ul><ul><li>There are workflow systems out there but they are yet to become mainstream </li></ul><ul><li>We need modular Evernote like solutions </li></ul><ul><li>Mendeley is a piece of the puzzle </li></ul>Literature Data Methods Taverna Wings
  17. 17. Summary – Creating More Merediths <ul><li>OA groups to keep doing what they are doing and support leveraging the content as part of the research enterprise </li></ul><ul><li>Advocacy </li></ul><ul><ul><li>More initiatives like the Hargreaves data mining proposal </li></ul></ul><ul><ul><li>Funders now have data sharing policies, next is methods sharing </li></ul></ul><ul><li>Funding for collaboration, standards, OA killer apps </li></ul>
  18. 18. General References <ul><li>What Do I Want from the Publisher of the Future PLoS Comp Biol 6(5): e1000787 </li></ul><ul><li>Fourth Paradigm: Data Intensive Scientific Discovery http://research.microsoft.com/enus/ collaboration/fourthparadigm/ </li></ul>
  19. 19. References to Exemplars <ul><li>Semantic Biochemical Journal - 2010: Using Utopia </li></ul><ul><li>Article of the Future, Cell, 2009: </li></ul><ul><li>Prospect, Royal Society of Chemistry, 2009: </li></ul><ul><li>Adventures in Semantic Publishing, Oxford U, 2009 : </li></ul><ul><li>The Structured Digital Abstract, Seringhaus/Gerstein, 2008 </li></ul><ul><li>CWA Nanopublications – 2010 </li></ul><ul><li>https://sites.google.com/site/beyondthepdf / </li></ul><ul><li>https://sites.google.com/site/futureofresearchcommunications / </li></ul><ul><li>http://www.force11.org </li></ul>
  20. 20. Thank You! [email_address]

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