Phil Bourne - One man's perspective on Open Science

Open ScienceOne Person’s View and What We

Are Doing About It

Philip E. BourneUniversity of California San Diego

[email protected]

1PSB Open Science Workshop 2009

mailto:[email protected]


So Why am I Here?

1. Jonathon Eisen could not make it

2. Open science seems to offer many opportunities which are yet to be realized

3. We have some developments which illustrate the promise which I would like to share with you

PSB Open Science Workshop 2009

2

Agenda

• The research contract is changing

• That change can be embodied in a vision

• Components of that vision are already under development


3

Agenda





4

Today’s Research Contract

Research[Grants]

JournalArticle

ConferencePaper

PosterSession

Feds

Societies

Publishers

Reviews

BlogsCommunity Service/Data 5

Tomorrows Research Contract

• The research product will be different

• The relationship between scientist and publisher will be different

• The publisher will be a warehouse for the workflow of scientific endeavor not just a repository for the end product


Tomorrows Research Contract: Evidence

• Publishers hubs:– Elsevier portals– PLoS collections

• Data hubs• Open Access/open review e.g. Biology Direct• NIH Roadmap requires data be accessible• New Resources:

– www.researchgate.net– MetaLab (Borya Shakhnovich)

7

http://www.researchgate.net/

Agenda





8

The Vision…

Prior to leaving home a UCSD graduate student syncs her IPOL with the latest papers delivered overnight by the journal via RSS feed. On the bus she reviews the stream, selecting a paper close to her interest in HIV-1 proteases. The data shows apparent anomalies with her own work. Being on-line she notices that a colleague has also discovered the same paper and they IM annotating the results. By the time the bus stops she has recomputed the results, proven the anomaly and made a rebuttal in the form of a “pubcast” to the Editor and sent it to the journal.


What is Missing to Make the Vision a Reality?

1. Seamless integration between the data and the publication upon which that data are based

2. Seamless integration of the authoring and publishing process

3. Notion of traditional publications being associated with podcasts and video

4. Professional networking akin to social networking


What are the Catalysts for Change?

• New publishing paradigms, most importantly open access publishing

• The emerging generation of digital scientists

• The increased ease of working with digital media, notably sound and video


12

Where are we Today?

• NIH and other government and private funders have mandated open access

• Full text increasingly on-line and potentially usable

• Traditional publishers have used the internet as a distribution medium, but the power of the medium, notably rich media, has yet to be realized

• Data increasingly on-line but not integrated with the publication derived from it


Catalyst for Change: Open Access(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

13PSB Open Science Workshop

2009

Catalyst for Change: Open Access(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 The catalyst

PLoS Comp Biol 2008 4(3) e100003714PSB Open Science Workshop

2009

Community Reaction?

Most scientists have no idea that this implies that anyone can take their material and enhance it e.g., via

mashup and effectively republish it


Agenda

• The research contract will change in years to come




16

Database and Journal Integration- The Test Bed

http://www.pdb.org/

Journals

Database

17

http://www.pubmedcentral.nih.gov


http://www.pdb.org/pdb

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

BioLit: Tools for New Modes of Scientific Dissemination

• Biolit integrates biological literature and biological databases and includes:– A database of journal

text– Authoring tools to

facilitate database storage of journal text

– Tools to make static tables and figures interactive

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

http://biolit.ucsd.edu18

http://biolit.ucsd.eduNucleic Acids Research 2008 36(S2) W385-389

PSP Washington DC Feb. 2008 19

http://biolit.ucsd.edu/


21


ICTP Trieste, December 10, 2007 23

Data Clustering via the Literature


24

Immunology Literature

Cardiac DiseaseLiterature

Author Paper

Word File in Docx formatPublisher

Semantic Richness Should be at the Point of Authoring - BioLit Plugin Project

25

Plugin Architecture

26

Notion of traditional publications being associated with podcasts and video

www.scivee.tv

27

Pubcast – Video Integrated with the Full Text of the Paper

28

http://www.scivee.tv/pubcast/17306029

Professional Profile

ICTP Trieste, December 2007 29

SciVee – Viral Projects

• Sweetwater School District

• “Postercasts”

• Science video competitions

• “CVcasts”

30

Postercasts


Summary

• The contract by which research is undertaken is changing, hence

• Numerous opportunities exist to further the dissemination and comprehension of science

• A couple of examples (Biolit & SciVee) of what is possible have been shown


32

Acknowledgements

• SciVee Team– Apryl Bailey– Tim Beck

– Leo Chalupa

– Marc Friedman– Alex Ramos– Willy Suwanto

• BioLit Team• J. Lynn Fink• Sergey Kushch• Marco Martinez• Greg Quinn• Parker Williams

CT Watch 2007, 3(3) 26-31


Questions?

[email protected]



Technology

Phil Bourne - One man's perspective on Open Science