The Path to Open Science with Illustrations from Computational

Biology

Philip E. BourneUniversity of California San Diego

pbourne@ucsd.eduhttp://www.sdsc.edu/pbRelevant Work from Us:

http://www.sdsc.edu/pb/SummaryScholarComm.pdf

MURPHA Sept 8, 2011

My Perspective …• Background in both IT and science (chemistry,

computational biology)• My lab. distributes for free data equivalent to ¼ the

Library of Congress every month• I am a supporter of open access (provided there is a

business model) and editor in chief of PLoS Computational Biology

• I am Co-founder of SciVee Inc. • I am becoming increasingly interested in scholarly

communication

I Readily Acknowledge Each Discipline is Different

My Objective…

• To Excite You to the Changes that Are Taking Place and Get You Thinking on How You Might Participate

What is Open Science

• Open science is the idea that scientific data and knowledge of all kinds should be openly shared as early as is practical in the discovery process.

• Which implies:– Free and unrestricted access to scientific output –

ideas, data, software, the process itself, the knowledge generated …

Open Science Can Accelerate the Scientific Process…

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

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

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

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

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

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

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

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

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

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

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

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

Other Reasons for Open Science

We Cannot Possibly Read a Fraction of the Papers We Should

Why Open Science Renear & Palmer 2009 Science 325:828-832

Hence We Are Scanning More Reading Less

Renear & Palmer 2009 Science 325:828-832Why Open Science

We Need Tools That Can Automatically Scan the Literature

and Make Sense of It

Automatic Knowledge Discovery for Those with No Time to Read

Immunology Literature

Cardiac DiseaseLiterature

Shared Function

Open Science Does Not Just Mean the Final Publication, But the

Scientific Process Itself

The Scientific Process

Research[Grants]

JournalArticle

ConferencePaper

PosterSession

Reviews

BlogsCommunity Service/Data

Curation

The Truth About the Scientific eLaboratory

• I generate way more negative that positive data, but where is it?

• Content management is a mess– Slides, posters…..– Data, lab notebooks ….– Collaborations, Journal clubs …

• Software is open but where is it?• Farewell is for the data too

Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136

We Need Better Tools to Manage the Scientific Enterprise

Many Great Tools Out There

We Need Scientist Management Tools

Taverna

Our Own Experiment in Capturing the Scientific Process to Make it Open

• Its hard and embarrassing• We have a working prototype using Wings• I can feel the potential productivity gains• Its been a lot of fun and will enable us to

improve our processes regardless of the workflow system itself

Yes The Workflow is Real

Problems with Publishing Workflows

• Workflows are not linear• Workflow : paper is not 1:1• Confidentiality• Peer review• Infrastructure• Community acceptance• Reward system

The Problem at this Time is There is Little Reward for Such

Activities

The Not so Hidden Truth About Science

• Scientists place more emphasis on writing and less on reading

• We are H factor obsessed, but interested in other metrics

• We are driven by (in order): – Grants– Papers– Teaching– Community service

Are There Killer Apps Out There That Could be A Game Changer for Improving Science as Well as

the Reward Process?

Data – Knowledge Integration Perhaps?

Publishing Limitations

• A paper is an artifact of a previous era• It is not the logical end product of eScience,

hence:– Work is omitted– Article vs supplement is a mess– Visualization may be limited– Interaction and enquiry are non-existent– Rich media can help, but are rarely used

Funding Agencies Are Imposing Data Sharing Policies

• From the NSF:

• Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants. Grantees are expected to encourage and facilitate such sharing. See Award & Administration Guide (AAG) Chapter VI.D.4.

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

Here is What I Want

1. User clicks on thumbnail2. Metadata and a

webservices call provide a renderable image that can be annotated

3. Selecting a features provides a database/literature mashup

4. That leads to new papers

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) e34

Interactive PDFs etc..

Article of the Future

The Embracing of Rich Media Perhaps?

Yes YouTube Can Increase the Rate of Discovery

Unleash the full power of the Internet

Pubcast – Video Integrated with the Full Text of the Paper

Postercasts

The Semantic Web Perhaps?

Unimaginable Connections Made Automatically Through RDF Descriptions

http://richard.cyganiak.de/2007/10/lod/lod-datasets_2010-09-22_colored.html

Living Documents

The Journal Has A Copy of Record that Provides a Reward

The App Model

General References

• What Do I Want from the Publisher of the Future http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000787

• Fourth Paradigm: Data Intensive Scientific Discovery http://research.microsoft.com/enus/collaboration/fourthparadigm/

What Are Your Ideas To Accelerate the Rate of Scientific

Discovery?

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

Questions?

pbourne@ucsd.edu