One Scientist’s Wish List for Scientific Publishers

One Scientist’s Wish List for Scientific Publishers Philip E. Bourne University of California San Diego [email_address] www.sdsc.edu/pb http://www.slideshare.net/pebourne Conference of ACS Editors Jan 6, 2012, La Jolla CA

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

What Drives Me…. The Story of Meredith

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..

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

It’ s a Start…
We have scratched the surface, but have yet to explore the core
But look what we could do…

My Dream
User reads a paper (one view of the info)
Clicks on a figure which can be analyzed
Clicking the figure gives a composite database + journal view
This takes you to yet more papers or databases
1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle

The Dream Can Only be Realized in the Context of the Complete Research Enterprise Literature Data Methods

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

Let Me Try and Illustrate What is Possible Through Our Own Little Contributions

Much of What We Try and Do Leverages Open Access Content 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 Data Methods

Literature: Semantically Enriched Version of PubMed Central Literature Data Methods http://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….
Literature Data Methods

Data & Literature: Integration www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Literature Data Methods 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 Data Methods BMC Bioinformatics 2010 11:103.

Literature: Knowledge Discovery Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature

Lets Turn Our Attention to Data ….

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

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 Data Methods http://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

.. And Finally Methods

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 Data Methods Nature 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 Data Methods

Methods: Workflow Tools Might be the Answer? Taverna Wings Literature Data Methods

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

Methods: Yes The Workflow is Real Literature Data Methods

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

And Now for Something Completely Different http://www.scivee.tv

Experiments in Rich Media Mashups http://www.scivee.tv

Pubcast – Video Integrated with the Full Text of the Paper http://www.scivee.tv

Rich Media as Scholarship Products Application Product Primary Customers Journals PubCast Journals, publishers, societies Meetings PosterCast Societies, conference orgs. SlideCast Comm. PaperCast Societies, journals Podcast SlideCast Education PosterCast Societies, universities SlideCast Books BookCast Publishers, book sellers http://www.scivee.tv

Android iPhone Windows Phone 7 Step 1 presenter starts PowerPoint Step 2 presenter starts recording on smart phone Step 3 presenter stops recording and initiates upload Slides Website Step 5 slides and podcast are automatically synchronized Sync File Podcast Step 6 listener plays back synchronized presentation Podium Capture Mac PC Step 4 slides are uploaded http://www.scivee.tv

Nothing is Going to Change Unless The Reward System Changes The Right Thing To Do Reward P.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

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 Workflow Scientist 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 ?

Questions? [email_address]

One Scientist’s Wish List for Scientific Publishers

by Philip Bourne on Jan 06, 2012

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