UKSG Meeting April 4, 2011

Digital Research Analog Publishing – One Scientist’s View
Philip E. Bourne
University of California San Diego
pbourne@ucsd.edu
http://www.sdsc.edu/pb
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My Bias..
Computational biologist (only one of many domains)
Open access advocate
Maintainer of an important biological data resource (PDB)
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My Wish…
As a scientist I want an interaction with a “publisher” that does not begin when the scientific process ends, but begins at the beginning of the scientific process itself
What I want from a Publisher of the Future
PLoS Comp Biol 2010 6(5): e1000787
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What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow
Scientist
Laboratory
Idea
Experiment
Data
Conclusions
Publisher
uzar.wordpress.com
Maybe The Line is Somewhere Else?
Publish
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Laboratory
Scientist
?
Idea
Experiment
Institution?
Data
Lab Notebook
Conclusions
Publisher
Publish
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?
Laboratory
Scientist
Idea
Experiment
Institution?
Data
Lab Notebook
Conclusions
Publisher
Publish
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Why Do I Want This?
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I Want Interoperability with the Data and Applications that Understand That Data
What is needed?
Standard set of apps for data exploration
Standard calling interfaces
Who manages the data?
Publisher
Author
Database
3rd party
User annotates
view
Metadata stored with the article
Fetches the data and provides a
Staring point for interactive enquiry
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We Are Making Progress But it is Incremental
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Already Being Done by Databases and on Mobile
Tight Integration with MyPDB
Access to saved queries
Add/delete queries
Flag interesting entries
Add personal structure annotations
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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
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Mashup with Content from Other Articles / Data
Sure its happening already, but…
It remains too difficult
It must be at the point of capture not post anything
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Proposal - The TeachU Workflow
Step 1
presenter starts
PowerPoint
Mac
PC
Step 4
slides are
uploaded
Slides
Website
Step 3
presenter stops
recording and
initiates upload
Step 5
slides and podcast
are automatically
synchronized
Step 2
presenter starts
recording on
smart phone
Step 6
listener
plays back
synchronized
presentation
Sync File
Podcast
Android
iPhone
Windows Phone 7

Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery
www.rcsb.org/pdb/explore/literature.do?structureId=1TIM
BMC Bioinformatics 2010 11:220
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Cardiac Disease
Literature
Immunology Literature
Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery
Shared Function
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Why Do I Want This?
?
Laboratory
Scientist
Idea
Experiment
Institution?
Data
Lab Notebook
Conclusions
Publisher
Publish
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Why I Want This?The Truth About the Scientific eLaboratory
I have ?? mail folders!
The intellectual memory of my laboratory is in those folders
This is an unhealthy hub and spoke mentality
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Why I Want This?The Truth About the Scientific eLaboratory
I generate way more negative that positive data, but where is it?
Content management is a mess
Slides, posters…..
Data, lab notebooks ….
Collaborations, Journal clubs …
Software is open but where is it?
Farewell is for the data too
Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136
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Why I Want ThisThe Truth About the Published Record
Preservation of the digital record?
Reproducibility?
The need for the library to reinvent itself/ institutional repositories to invent themselves?
Digital chaos in the long tail?
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What Will It Take to Get There?
As a scientist I want an interaction with a “publisher” that does not begin when the scientific process ends, but begins at the beginning of the scientific process itself
What I want from a Publisher of the Future
PLoS Comp Biol 2010 6(5): e1000787
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Open source cohesive tools
New standards
Business rights and IP
Attribution/evaluation/archiving
A “publisher” to take the plunge
Beyond the PDF
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What Will It Take to Get There?
https://sites.google.com/site/beyondthepdf/

Sounds Insurmountable?
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But Wait..There Are Many Great Tools Out There
Taverna
We Need Scientist Management Tools
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But Wait..There Are Many Great Ideas Out There
Nano publications
Semantic tagging of PDFs and beyond
Citation ontologies
Scholarly HTML
Authoring tools
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A Test BedSpinal Muscular Atrophy (SMA)
Coalesce a set of disparate tools
Engage the publishers
Make some progress on a treatable disease
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Acknowledgements
Beyond the PDF Workshop
Funded by DDCF, Microsoft, NCI, Science Commons
The SciVee Team including:
Marc Friedmann, J. Lynn Fink, Alex Gramos, Willy Suwanto
The PDB Team including:
Andreas Prlic, DimitrisDimitanopolos
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pbourne@ucsd.edu
Discussion
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UKSG Meeting April 4, 2011

by Philip Bourne

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