Searching Deeply for Data, Results and Tools- What is Stopping Us?
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Philip Bourne summarizes challenges facing open access to scientific literature, data, and methods, and proposes solutions to address them. Specifically, he notes that (1) open access literature has further progress needed, (2) data sharing faces issues around accessibility and standardization, and (3) methods reproducibility could be improved. His proposed solutions include advocating for open access, leveraging existing open resources, promoting data and methods sharing policies, and funding collaboration around standards and applications.
![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](https://image.slidesharecdn.com/berlin-9-111108222402-phpapp02/85/Searching-Deeply-for-Data-Results-and-Tools-What-is-Stopping-Us-1-320.jpg)
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Searching Deeply for Data, Results and Tools- What is Stopping Us?
- 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. Meredith A story that celebrates all that open access has done and shows the promise for the future
- 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. The Research Enterprise Literature Data Methods
- 5. The Research Enterprise Without eScholarship http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/
- 6. Literature Meredith certainly benefited from the OA literature … But we have a long way to go in several respects PubMed Central Contents Nov 8, 2011 PubMed Contents Nov 8, 2011 Literature Data Methods
- 7. Literature – But First What is the Promise Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature
- 8. Solution: We Need SciVerse™ like Developments Leveraging OA Content A very clever idea – The App model Leverage content Provide an open API Get the community to do all the work Drive folks to buy content Problem: OA does not have the resources OA + CA is more compelling Solution: More developers Federal and Foundation support to leverage OA content Literature Data Methods
- 9. Literature - PMC Problems Producers do not care enough OA publishers are not aware enough – I cant even reliably parse the PMC license records to know what I can access Solutions Continue to advocate Raise awareness and establish consistency so that history does not repeat itself Literature Data Methods Advocacy Follow-on to Beyond the PDF https://sites.google.com/site/beyondthepdf/ Force11 www.force11.org
- 10. Solutions: Scientists As Advocates My knee jerk reaction – is this the best a bunch of great minds can come up with! My more thoughtful reaction – every little bit helps – it will broaden awareness of the value of OA like nothing else Literature Data Methods
- 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. Solution: Use the Traditional Reward System in New Ways The Wikipedia Experiment – Topic Pages Identify areas of Wikipedia that relate to the journal that are missing of stubs Develop a Wikipedia page in the sandbox Have a Topic Page Editor review the page Publish the copy of record with associated rewards Release the living version into Wikipedia Literature Data Methods
- 13. Problems Regarding Data Meredith got the data she needed in part by bugging authors – It should be easier There is a long tail of data which is lost Institutional repositories are too institutional Journals are passing the buck We are heading towards the same issues with data repositories as we have with publishers Literature Data Methods Disclaimer: My viewpoint is that of a computational biologist
- 14. Solutions Regarding Data There are some wonderful resources out there (e.g., Entrez from the NLM) – copy them We need data repositories working together now We need more than a DOI – we need metadata catalogs for data so we can deep search and rank Data needs to be recognized as a publication Literature Data Methods Disclaimer: My viewpoint is that of a computational biologist
- 15. Problems Regarding Methods Meredith had to use a “trial’ license of Mathematica I cant easily reproduce my own research There is little reward for providing access to methods Literature Data Methods Disclaimer: My viewpoint is that of a computational biologist
- 16. Solutions Regarding Methods Meredith was able to get computer cycles for free in the cloud There are workflow systems out there but they are yet to become mainstream We need modular Evernote like solutions Mendeley is a piece of the puzzle Literature Data Methods Taverna Wings
- 17. Summary – Creating More Merediths OA groups to keep doing what they are doing and support leveraging the content as part of the research enterprise Advocacy More initiatives like the Hargreaves data mining proposal Funders now have data sharing policies, next is methods sharing Funding for collaboration, standards, OA killer apps
- 18. General References What Do I Want from the Publisher of the Future PLoS Comp Biol 6(5): e1000787 Fourth Paradigm: Data Intensive Scientific Discovery http://research.microsoft.com/enus/ collaboration/fourthparadigm/
- 19. References to Exemplars Semantic Biochemical Journal - 2010: Using Utopia Article of the Future, Cell, 2009: Prospect, Royal Society of Chemistry, 2009: Adventures in Semantic Publishing, Oxford U, 2009 : The Structured Digital Abstract, Seringhaus/Gerstein, 2008 CWA Nanopublications – 2010 https://sites.google.com/site/beyondthepdf / https://sites.google.com/site/futureofresearchcommunications / http://www.force11.org