Future of Data Sharing

Physician Scientist Careeer Development

The Future of Data Sharing Platforms in Academic Medicine

A Basic Science Perspective

Philip E. BourneUniversity of California

San Diego

[email protected]

Nov. 4, 2010

http://www.slideshare.net/pebourne/jim-gray-award-lecture

mailto:[email protected]



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


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


If that is not enough…

For some people the scientific process may be too slow to save their life



Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma Foundation

Nov. 4, 2010http://sagecongress.org/Presentations/Sommer.pdf

Motivation


Chordoma

• A rare form of brain cancer

• No known drugs• Treatment – surgical

resection followed by intense radiation therapy


http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG

Physician Scientist Careeer DevelopmentNov. 4, 2010

http://sagecongress.org/Presentations/Sommer.pdf

Motivation



Motivation



Motivation


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



Motivation

Physician Scientist Careeer DevelopmentNov. 4, 2010Motivation



http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation

Motivation


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


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


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


The Publishers are Starting to Do It

Nov. 4, 2010 From Anita de Waard, Elsevier








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


Example Tools

Nov. 4, 2010

http://pubnet.gersteinlab.org/

http://www.researcherid.com/

http://www.biomedexperts.com


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


A Unique Identifier is Going to Happen

• It is DOIs for people• Some scientists will

resist• The winner is ORCHID?


I an Not a Scientist I am a NumberPLoS Comp. Biol. 2008 4(12) e1000247

http://www.youtube.com/watch?v=29JewlGsYxs&feature=related


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








Yes YouTube Can Increase the Rate of Discovery

Unleash the full power of the InternetNov. 4, 2010


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



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



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

http://www.codeplex.com/ucsdbiolit




Questions?

[email protected]

Nov. 4, 2010

http://www.slideshare.net/pebourne/jim-gray-award-lecture


Documents

Future of Data Sharing