What Open Access Potentially Means to a Scientist

Philip E. BourneUniversity of California San Diego

pbourne@ucsd.eduwww.sdsc.edu/pb

NBIC April 19, 2011

My Bias Towards Open Access (OA)

• Co-founder and EIC of an open OA journal• Co-director of the RCSB PDB which has always

been open – see parallels between databases and the literature

• Always been a supporter of open source software• Have a small company trying to leverage OA

content• Believe OA must have a successful business model

What OA Means to a Scientist

• $$ to publish• A broader readership – more citations?• Retention of copyright• Misconceptions by fellow scientists

• Potentially a change in the way scholarship is disseminated and comprehended

Open Access – The Driver(Creative Commons License)

1. All published materials available on-line free to all (author pays model)

2. Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)

3. Copyright remains with the author

Open Access

Open Access – The Driver(Creative Commons License)

1. All published materials available on-line free to all (reader pays model)

2. Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)

3. Copyright remains with the author

Open Access: Taking Full Advantage of the ContentPLoS Comp. Biol. 2008 4(3) e1000037Open Access

Why is OA Important?

It enables scientists to take matters into their own hands –

We have done so for a long time with biological databases, why not with the biological literature?

Why is OA Important?

• In the time I have been talking ~20 papers have been indexed by PubMed

We Cannot Possibly Read a Fraction of the Papers We Should

Renear & Palmer 2009 Science 325:828-832

We Are Scanning More Reading Less

Renear & Palmer 2009 Science 325:828-832

We Need Tools Beyond the Aggregation Provided by PubMed, ISI etc. to Digest the Literature ..

The Development of Such Tools Require Open Access to the Literature

But Wait There is More….

More Drivers of Change

• Scientific publication has not changed since the invention of the printing press – the Internet changed the mode of delivery is all. Hence even in an eScience environment:– The publication is divorced from the experiments

that produced it– Data and the publication are not integrated– A printed format may be the worst way to

comprehend the science

Data and Knowledge are Disparate Which Makes no Sense in the Digital Age

• PubMed contains 18,792,257 entries

• ~100,000 papers indexed per month

• In Feb 2009:– 67,406,898 interactive

searches were done– 92,216,786 entries were

viewed

• 1078 databases reported in NAR 2008

• MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 times

Data as of April 14, 2009

We need data and knowledge about that data to interoperatePLoS Comp. Biol. 2005 1(3) e34

Journals are Becoming More Like Databases and Databases are Becoming More like Journals

BiocurationElectronic Supplements

Unstructured data are submitted as supplements

A great deal of moneyis spent extracting from the

literature to structure in databasesDatabases vs Journals

Lets Do A Mashup!

PLoS Comp. Biol. 2008. 4(7): e1000136Databases vs Journals

UKSG 2011

We Are Making Progress But it is Incremental

www.rcsb.org/pdb/explore/literature.do?structureId=1TIM

The Database View

The Literature View – Web 3.0?

Databases vs Journals http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp

PLoS Comp Biol 2010 6(2) e1000673

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

The New Reader Workflow

1. User clicks on thumbnail

2. 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

Databases vs Journals

Take This Notion to its Logical ConclusionData Clustering via the Literature &

Databases

Immunology Literature

Cardiac DiseaseLiterature

Shared FunctionDatabases vs Journals

Lets Do Another Mashup!

PLoS Comp. Biol. 2008. 4(7): e1000136

More Drivers of Change

Drivers of Change

So What Will Happen? – Integrated Multimedia

Present - www.scivee.tv

UKSG 2011 23

Why Do I Want This?Integrated Rich Media Can Improve Comprehension

• Already happening but post publication not Prepublication

• Lab discussions, presentations of the work etc. are part of the new discourse

So Lets Take This to Its Logical Conclusion …

The Research Article of the Future …

.. will be the select parts of of a container that holds thecomplete academic work flow

PLoS Comp Biol 2010 6(5): e1000787

26

• Open source cohesive tools• New standards• Business rights and IP• Attribution/evaluation/

archiving• A “publisher” to take the

plunge

Beyond the PDF

What Will It Take to Get There?

https://sites.google.com/site/beyondthepdf/

What Will It Take to Get There?

You as advocates of OA and of change

Questions?

pbourne@ucsd.edu