future of data sharing
Post on 24-Jan-2015
711 Views
Preview:
DESCRIPTION
TRANSCRIPT
Physician Scientist Careeer Development
The Future of Data Sharing Platforms in Academic Medicine
A Basic Science Perspective
Philip E. BourneUniversity of California
San Diego
pbourne@ucsd.edu
Nov. 4, 2010
http://www.slideshare.net/pebourne/jim-gray-award-lecture
Physician Scientist Careeer Development
Why Am I Here?• I am a practicing basic life scientist who is concerned about the
speed of dissemination and level of comprehension in an eScience world
• I am fortunate enough to have a major biological resource (the Protein Data Bank) and a major biological journal (PLoS Computational Biology) as my playground for experimenting how we might do better
• It is your engagement that will facilitate change
• I believe your ability to embrace these changes will impact your career
Nov. 4, 2010
Physician Scientist Careeer Development
The Scientific Process is Too Slow to Respond to a Crisis – Either Global or Personal
Nov. 4, 2010Motivation
http://knol.google.com/k/plos-currents-influenza#
By the time the paper is published we could all be dead
* http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm
Jan. 2008 Jan. 2009 Jan. 2010Jul. 2009Jul. 2008 Jul. 2010
1RUZ: 1918 H1 Hemagglutinin
Structure Summary page activity forH1N1 Influenza related structures
3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir
In a time of crisis the need for fast access to accurate data and any knowledge ofthat data are paramount
MotivationNov. 4, 2010
Physician Scientist Careeer Development
If that is not enough…
For some people the scientific process may be too slow to save their life
Nov. 4, 2010Motivation
Physician Scientist Careeer Development
Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma Foundation
Nov. 4, 2010http://sagecongress.org/Presentations/Sommer.pdf
Motivation
Physician Scientist Careeer Development
Chordoma
• A rare form of brain cancer
• No known drugs• Treatment – surgical
resection followed by intense radiation therapy
Nov. 4, 2010Motivation
http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG
Physician Scientist Careeer DevelopmentNov. 4, 2010
http://sagecongress.org/Presentations/Sommer.pdf
Motivation
Physician Scientist Careeer DevelopmentNov. 4, 2010
http://sagecongress.org/Presentations/Sommer.pdf
Motivation
Physician Scientist Careeer DevelopmentNov. 4, 2010
http://sagecongress.org/Presentations/Sommer.pdf
Motivation
Physician Scientist Careeer DevelopmentNov. 4, 2010
Adapted: http://sagecongress.org/Presentations/Sommer.pdf
Motivation
Isaac
If I have seen further it is only by standing on the shoulders of giants
Isaac Newton
From Josh’s point of view the climb up just takes too long
> 15 years and > $850M to be more precise
Physician Scientist Careeer DevelopmentNov. 4, 2010
http://sagecongress.org/Presentations/Sommer.pdf
Motivation
Physician Scientist Careeer DevelopmentNov. 4, 2010Motivation
http://sagecongress.org/Presentations/Sommer.pdf
Physician Scientist Careeer DevelopmentNov. 4, 2010
http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation
Motivation
Physician Scientist Careeer Development
Now we are all hopefully motivated let us break this down to what actually needs to be done in my opinion
Here are a few big things …
Nov. 4, 2010
Physician Scientist Careeer Development
A Few Things to Accelerate the Rate of Scientific Discovery
• A commitment to greater openness • Improved characterization (i.e. metadata
including provenance) and persistence of data• A change in the reward system• Seamless integration between the data and the
knowledge derived from that data• Better management of the digital scientific
workflow• Unleash the full power of the Internet Nov. 4, 2010
1. A link brings up figures from the paper
0. Full text of PLoS papers stored in a database
2. Clicking the paper figure retrievesdata from the PDB which is
analyzed
3. A composite view ofjournal and database
content results
We Need Data and Knowledge About That
Data to Interoperate
1. User clicks on content2. Metadata and
webservices to data provide an interactive view that can be annotated
3. Selecting features provides a data/knowledge mashup
4. Analysis leads to new content I can share
4. The composite view haslinks 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) e34Nov. 4, 2010
Physician Scientist Careeer Development
Seamless Integration Between the Data and the Knowledge Derived from that Data
– What is Stopping US?
• Technology - NO
• STM publishers - Yes
• Funding agencies - Yes
• You - ???
Nov. 4, 2010
Physician Scientist Careeer Development
The Publishers are Starting to Do It
Nov. 4, 2010 From Anita de Waard, Elsevier
Physician Scientist Careeer Development
A Few Things to Accelerate the Rate of Scientific Discovery
• A commitment to greater openness • Improved characterization (i.e. metadata
including provenance) and persistence of data• A change in the reward system• Seamless integration between the data and the
knowledge derived from that data• Better management of the digital scientific
workflow• Unleash the full power of the Internet Nov. 4, 2010
Physician Scientist Careeer Development
Reward Systems Need to ChangeWhat is Needed?
• Author disambiguation• Auditing (identification and metrics) of all
scholarship - means new tools• Seniors need to promote alternative forms of
scholarship• Juniors need to respond to it
Nov. 4, 2010Reward Systems Need to Change
Ten Simple Rules for Getting Promoted as a Computational Biologist in Academia PLoS Comp Biol to appear Nov. 2010
Physician Scientist Careeer Development
Example Tools
Nov. 4, 2010
http://pubnet.gersteinlab.org/
http://www.researcherid.com/
http://www.biomedexperts.com
Physician Scientist Careeer Development
What Are these Alternative Forms of Scholarship?
Research[Grants]
JournalArticle
ConferencePaper
PosterSession
Reviews
BlogsCommunity Service/Data
Curation
Reward Systems Need to ChangeNov. 4, 2010
Physician Scientist Careeer DevelopmentReward Systems Need to Change
Nov. 4, 2010
Physician Scientist Careeer Development
A Unique Identifier is Going to Happen
• It is DOIs for people• Some scientists will
resist• The winner is ORCHID?
Reward Systems Need to ChangeNov. 4, 2010
I an Not a Scientist I am a NumberPLoS Comp. Biol. 2008 4(12) e1000247
Physician Scientist Careeer Development
Ideally the ID will be Tagged to Every Piece of Scholarly Communication
I an Not a Scientist I am a NumberPLoS Comp. Biol. 2008 4(12) e1000247
Reward Systems Need to ChangeNov. 4, 2010
Physician Scientist Careeer Development
A Few Things to Accelerate the Rate of Scientific Discovery
• A commitment to greater openness • Improved characterization (i.e. metadata
including provenance) and persistence of data• A change in the reward system• Seamless integration between the data and the
knowledge derived from that data• Better management of the digital scientific
workflow• Unleash the full power of the Internet Nov. 4, 2010
Yes YouTube Can Increase the Rate of Discovery
Unleash the full power of the InternetNov. 4, 2010
Physician Scientist Careeer Development
The Lab ExperimentPaper+Rich Media
• My students enjoyed the experience• The shyest student was actually the most bold
in front of the camera• “We will become a generation of “science
castors”• They liked the exposure for the most part –
rather than the PI it puts them out in front
Unleash the full power of the InternetNov. 4, 2010
Physician Scientist Careeer Development
Products
ApplicationProduct Primary Customers
Journals PubCast Journals, publishers, societies
Meetings PosterCast Societies, conference orgs.SlideCast
Comm. PaperCast Societies, journalsPodcastSlideCast
Education PosterCast Societies, universitiesSlideCast
Books BookCast Publishers, book sellers
What Emerged: SciveeCasts
Unleash the full power of the InternetNov. 4, 2010
Physician Scientist Careeer Development
The Promise – A Hypothetical Example
Immunology Literature
Cardiac DiseaseLiterature
Shared Function
Nov. 4, 2010
Acknowledgements• BioLit Team
– Lynn Fink– Parker Williams– Marco Martinez– Rahul Chandran– Greg Quinn
• MBT– John Moreland– John Beaver
• Microsoft Scholarly Communications– Pablo Fernicola– Lee Dirks– Savas Parastitidas– Alex Wade– Tony Hey
• wwPDB team– Andreas Prilc– Dimitris Dimitropoulos
• SciVee Team– Apryl Bailey– Leo Chalupa– Lynn Fink– Marc Friedman (CEO)– Ken Liu– Alex Ramos– Willy Suwanto– Ben Yukich
http://www.scivee.tv
http://biolit.ucsd.eduhttp//www.pdb.orghttp://www.codeplex.com/ucsdbiolit
Nov. 4, 2010
Physician Scientist Careeer Development
Questions?
pbourne@ucsd.edu
Nov. 4, 2010
http://www.slideshare.net/pebourne/jim-gray-award-lecture
top related