One Scientist’s Wish List for Scientific Publishers

Philip E. Bourne

University of California San Diego

pbourne@ucsd.edu

www.sdsc.edu/pb

http://www.slideshare.net/pebourne

Conference of ACS Editors

Jan 6, 2012, La Jolla CA1

My {Biased} Perspective

• I am a domain scientist (computational molecular biology)

• I co-direct the RCSB Protein Data Bank• I co-founded and am EIC of one Public Library of

Science (PLoS) open access journals – There must be a business model

• 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

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What Drives Me….

The Story of Meredith

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Meredith was Successful Because….

• She is an exceptional individual

• Much of the data and knowledge she needed she had to beg for; she used the UCSD library

• She easily got access to computer time

I want others less smart like myself to be successful too..

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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

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It’s a Start…

• We have scratched the surface, but have yet to explore the core

• But look what we could do…

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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

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Literature

DataMethods

The Dream Can Only be Realized in the Context of the Complete

Research Enterprise

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My Current Reality

http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/9

Let Me Try and Illustrate What is Possible Through Our Own

Little Contributions

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Much of What We Try and Do Leverages Open Access

Content

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2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. 4(3) e1000037

Literature: OA Biosciences

• Meredith certainly benefited from the OA literature, but not enough …

• … we have a long way to go in several respects

PubMed Central Contents Nov 8, 2011

PubMed Contents Nov 8, 2011

Literature

DataMethods

Literature

DataMethods

Literature: Semantically Enriched Version of PubMed Central

13http://biolit.ucsd.edu; NAR 2008 36(S2) W385-389

Literature: So What has Happened with This?

• The value seems to be in restful services that enable databases to recognize where in the literature their data are referenced

• We use this in the PDB in the following way….

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Literature

DataMethods

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

Data & Literature: IntegrationLiterature

DataMethods

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BMC Bioinformatics 2010 11:220

Literature: 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

Literature

DataMethods

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BMC Bioinformatics 2010 11:103.

Literature: Knowledge Discovery

Immunology Literature

Cardiac DiseaseLiterature

Shared Function

Literature

DataMethods

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Lets Turn Our Attention to Data ….

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Data: Thoughts from the Biosciences

• Growth – DNA sequence data are doubling every 5 months

• NLM/NCBI is amazing• Other great resources – but a slow realization

they are appearing stove piped• Data are undervalued (more on this)• We need a data registry for deep search and

comparison

Literature

DataMethods

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Data: Data Journals – Lots of Talk

• Nature Publishing Group• F1000• PLoS at Large• eLife• Global Biodiversity Information Facility

• Some fields do it naturally – Astronomy, Earth Sciences …

Literature

DataMethods

20http://www.astro.caltech.edu/~pls/astronomy/archives.html

Data: PLoS Data Pages

• To be introduced later this year

• Shared metadata description?

• Data in Dryad or equivalent

• History could repeat itself – JMS revisited

Literature

DataMethods

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.. And Finally Methods

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Methods: Is Reproducibility a Myth?

• 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

Literature

DataMethods

23Nature Reviews Drug Discovery 10, 643-644 (September 2011)

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

Literature

DataMethods

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Methods: Workflow Tools Might be the Answer?

Taverna

Wings

Literature

DataMethods

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Methods: Workflows - 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

Literature

DataMethods

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Methods: Yes The Workflow is Real

Literature

DataMethods

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Methods: 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

Literature

DataMethods

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And Now for Something Completely Different

http://www.scivee.tv

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Experiments in Rich MediaMashups

http://www.scivee.tv30

Pubcast – Video Integrated with the Full Text of the Paper

http://www.scivee.tv31

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.tv32

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

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Nothing is Going to Change Unless The Reward System Changes

The Right Thing To Do Reward

34P.E. Bourne 2011 Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comp. Biol. 7(1) e1002001.

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

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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

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Maybe The Line is Somewhere Else?

Scientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Institution?

Lab Notebook

?

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Scientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Institution?

Lab Notebook

Maybe The Line is Somewhere Else??

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Questions?

pbourne@ucsd.edu

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