Its Not Just About Papers Anymore

Philip E. Bourne

University of California San Diego

pbourne@ucsd.edu

www.sdsc.edu/pb

http://www.slideshare.net/pebourne

My Perspective

• I am a domain scientist (computational molecular biology)

• I co-founded and am EIC of one Public Library of Science (PLoS) open access journals

• I co-founded a company, SciVee Inc., that is attempting to leverage the perceived changes in scholarly communication

• I support a small academic scholarly communication group

What is Wrong Today?

• Formal science communication:– Occurs too slowly – Reaches too few people– Costs too much– Ignores the data– Is very hard to reproduce

• Is stuck in the era of the printing press – we need to move Beyond the PDF and use the power of the medium

https://sites.google.com/site/beyondthepdf/http://www.force11.org

Literature

DataMethods

The Research Enterprise

My Current Reality

http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/

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

My Dream

1. User reads a paper (one view of the info)

2. Clicks on a figure which can be analyzed

3. Clicking the figure gives a composite database + journal view

4. This takes you to yet more papers or databases

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

Our Own Little Contributions

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Semantically Enriched Version of PubMed Centralhttp://biolit.ucsd.edu

Word Add-in for Authors

• Allows authors to add metadata as they write, before they submit the manuscript

• Authors are assisted by automated term recognition– OBO ontologies– Database IDs

• Metadata are embedded directly into the manuscript document via XML tags, OOXML format– Open– Machine-readable

• Open source, Microsoft Public License

http://www.codeplex.com/ucsdbiolit

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Knowledge Discovery

Immunology Literature

Cardiac DiseaseLiterature

Shared Function

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

Data & Literature IntegrationLiterature

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PLoS Data Pages

• Currently being worked out

• Shared metadata description?

• Data in Dryad or equivalent

• History could repeat itself – JMS revisited

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Myth: Reproducibility

• My views of reproducibility:– We all express the importance, but the only time

it is tested is when something is truly novel or error is suspected

– Reproducability covers a spectrum of meaning – by whom and with how much effort

– The longer the time lag the less likely something is reproducible

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PLoS Comp Biol Software

• Requires source be deposited in an open source public repository

• Encourages a copy of record be deposited with the article

• Requires that the reviewer be able to test the software if they wish (implies data, documentation, test parameters and output be provided for checking

Motivation: S.Veretnik, J.L.Fink, and P.E. Bourne 2008 Computational Biology Resources Lack Persistence and Usability.

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

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Workflow Tools Might be the Answer

Taverna

Wings

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Our Own Experience

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

improve our processes regardless of the workflow system itself

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Yes The Workflow is RealLiterature

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Problems with Publishing Workflows

• Workflows are not linear• Workflow : paper is not 1:1• Confidentiality• Peer review• Infrastructure• Community acceptance• Reward system• No publisher seems willing to touch them

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And Now for Something Completely Different

http://www.scivee.tv

Experiments in Rich MediaMashups

http://www.scivee.tv

Pubcast – Video Integrated with the Full Text of the Paper

http://www.scivee.tv

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

Rich Media as Scholarship

http://www.scivee.tv

AndroidiPhone

Windows Phone 7

Step 1presenter starts

PowerPoint

Step 2presenter starts

recording onsmart phone

Step 3presenter stops recording and

initiates upload

Slides

Website

Step 5slides and podcastare automatically

synchronizedSync FilePodcast

Step 6listener

plays back synchronized presentation

Podium CaptureMacPC

Step 4slides areuploaded

http://www.scivee.tv

Nothing is Going to Change Unless The Reward System Changes

The Right Thing To Do Reward

Interim Solution: Use the Traditional Reward System

The Wikipedia Experiment – Topic Pages

• Identify areas of Wikipedia that relate to the journal that are missing of stubs

• Develop a Wikipedia page in the sandbox

• Have a Topic Page Editor Review the page

• Publish the copy of record with associated rewards

• Release the living version into Wikipedia

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In Summary:

I Do Not Want to Do Any of This – I Want You to Do It

P.E. Bourne 2010 What Do I Want from the Publisher of the Future? PLoS Comp Biol 6(5): e1000787

What Does That Mean? The “Publisher” becomes Part of the

Scientific WorkflowScientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Maybe The Line is Somewhere Else?

uzar.wordpress.com

Maybe The Line is Somewhere Else?

Scientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Institution?

Lab Notebook

?

Scientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Institution?

Lab Notebook

Maybe The Line is Somewhere Else??

Questions?

pbourne@ucsd.edu