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Open Data Driving Scholarly  Communications in 2020 Philip E. Bourne UCSD [email_address] 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
My Perspective is Drawn from Being: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Apologies in advance for the life sciences perspective
This Lecture will Try and Present All Aspects of this Perspective 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
But First: Why Open Data Are Important –  The Story of Meredith 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
Meredith got data the old fashioned way – she did not discover it in a broad and deep search she read the papers and bugged the authors Imagine what she could do if data were instantly discoverable, the value quantified in some way and more simply used 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
Some Thoughts as a Data Producer ,[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 On the Future of Genomic Data Science 11 February 2011:  vol. 331 no. 6018 728-729
Some Thoughts in Supporting Curation http://collections.plos.org/ploscompbiol/biocurators.php They really should to do  more to promote  themselves
Data Curation – The Process Can be Crazy ,[object Object],[object Object],Supporting Curation
The PDB Annotation/Validation Workflow Depositor Annotate Depositor Approval Validation Report Step 2 Step 3 Step 4 Step 1 ,[object Object],[object Object],Supporting Curation In the Future will a Biological Database Really be Different from a Biological Journal?  PLoS Comp. Biol. 1(3) e34 PDB  ID Distribution Site Archival Data Core  DB PDB  Entry Deposit Validate Corrections
Some Happy Thoughts as a Database Provider – The PDB ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
Some Happy Thoughts as a Database Provider Number of released entries Year We manage to handle  Increased volume and  complexity at a lesser cost Usage increases and the community broadens Database Provision Increasingly these define future funding, could it be the H-factor mistake for data?
Some History as a Data Provider ,[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
Some History as a Data Provider ,[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
Some Not so Happy Thoughts as a Database Provider ,[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
Trends Today as a Database Provider ,[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
Semantic Tagging & Widgets are a Powerful Tool to Integrate Data and Knowledge of that Data, But as Yet Not Used Much Will Widgets and Semantic Tagging Change Computational Biology?  PLoS Comp. Biol. 6(2) e1000673 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
Trends Today as a Database Provider ,[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
Example of  Interoperability: The Database View www.rcsb.org/pdb/explore/literature.do?structureId=1TIM BMC Bioinformatics 2010 11:220 Database Provision
Example of Interoperability – The Literature View From Anita de Waard, Elsevier  Database Provision
Literature Integration – The Dream ,[object Object],[object Object],[object Object],[object Object],1. A link brings up figures  from the paper 0. Full text of PLoS papers stored  in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results 4. The composite view has links to pertinent blocks  of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle PLoS Comp. Biol. 2005 1(3) e34 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
Catching our Breath… My Perspective is Drawn from Being: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
Perspective as a Data User ,[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User
Data/Institutional Repositories  ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User Innkeeper at the Roach Motel D. Salo 2008 http://muse.jhu.edu/journals/library_trends/v057/57.2.salo.html
Data/Institutional Repositories  ,[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User
Data and Journals ,[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User
Interim Solution:  Use the Traditional Reward System The Wikipedia Experiment – Topic Pages ,[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User
Catching our Breath… My Perspective is Drawn from Being: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
What Do I Want by 2020 or Earlier? ,[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User
What Do We Need to Do to Get There? A Data Registry? ,[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User
What Do We Need to Do to Get There? An App+ Store? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Data User
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Acknowledgements 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Funding Agencies:  NSF, NIGMS, DOE, NLM, NCI,  NCRR, NIBIB, NINDS, NIDDK

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Open Data Driven Scholarly Communication in 2020

  • 1. Open Data Driving Scholarly Communications in 2020 Philip E. Bourne UCSD [email_address] 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
  • 2.
  • 3. This Lecture will Try and Present All Aspects of this Perspective 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
  • 4. But First: Why Open Data Are Important – The Story of Meredith 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
  • 5. Meredith got data the old fashioned way – she did not discover it in a broad and deep search she read the papers and bugged the authors Imagine what she could do if data were instantly discoverable, the value quantified in some way and more simply used 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011
  • 6.
  • 7. Some Thoughts in Supporting Curation http://collections.plos.org/ploscompbiol/biocurators.php They really should to do more to promote themselves
  • 8.
  • 9.
  • 10.
  • 11. Some Happy Thoughts as a Database Provider Number of released entries Year We manage to handle Increased volume and complexity at a lesser cost Usage increases and the community broadens Database Provision Increasingly these define future funding, could it be the H-factor mistake for data?
  • 12.
  • 13.
  • 14.
  • 15.
  • 16. Semantic Tagging & Widgets are a Powerful Tool to Integrate Data and Knowledge of that Data, But as Yet Not Used Much Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comp. Biol. 6(2) e1000673 7th Int. Data Curation Conference Bristol UK Dec. 7, 2011 Database Provision
  • 17.
  • 18. Example of Interoperability: The Database View www.rcsb.org/pdb/explore/literature.do?structureId=1TIM BMC Bioinformatics 2010 11:220 Database Provision
  • 19. Example of Interoperability – The Literature View From Anita de Waard, Elsevier Database Provision
  • 20.
  • 21.
  • 22.
  • 23.
  • 24.
  • 25.
  • 26.
  • 27.
  • 28.
  • 29.
  • 30.
  • 31.