uksg meeting april 4, 2011
DESCRIPTION
A talk of what one scientist wants of publishers delivered to UK and European publishers at the UKSG meeting.TRANSCRIPT
UKSG 2011 1
Digital Research Analog Publishing – One Scientist’s View
Philip E. BourneUniversity of California San Diego
[email protected]://www.sdsc.edu/pb
UKSG 2011 2
My Bias..
• Computational biologist (only one of many domains)
• Open access advocate
• Maintainer of an important biological data resource (PDB)
UKSG 2011
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 FuturePLoS Comp Biol 2010 6(5): e1000787
UKSG 2011 4
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
UKSG 2011 5
Maybe The Line is Somewhere Else?
Scientist
Idea
Experiment
Data
Conclusions
Publish
Laboratory
Publisher
Institution?
Lab Notebook
?
UKSG 2011 6
Scientist
Idea
Experiment
Data
Conclusions
Publish
Laboratory
Publisher
Institution?
Lab Notebook
Maybe The Line is Somewhere Else?
?
UKSG 2011 7
Why Do I Want This?
UKSG 2011
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
Metadata stored with the articleFetches the data and provides a Staring point for interactive enquiry
User annotates view
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We Are Making Progress But it is Incremental
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Already Being Done by Databases and on Mobile
• Access to saved queries • Add/delete queries • Flag interesting entries• Add personal structure annotations
Tight Integration with MyPDB
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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
UKSG 2011
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
AndroidiPhone
Windows Phone 7
Step 1presenter starts
PowerPoint
Step 2presenter starts
recording onsmart phone
Step 3presenter stops
recording andinitiates upload
Slides
Website
Step 5slides and podcastare automatically
synchronizedSync FilePodcast
Step 6listener
plays back synchronized presentation
Proposal - The TeachU WorkflowMacPC
Step 4slides areuploaded
UKSG 2011 14www.rcsb.org/pdb/explore/literature.do?structureId=1TIM
Why Do I Want This?Semantic Linking of Data Can Lead to New
Knowledge Discovery
BMC Bioinformatics 2010 11:220
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Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery
Immunology Literature
Cardiac DiseaseLiterature
Shared Function
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Scientist
Idea
Experiment
Data
Conclusions
Publish
Laboratory
Publisher
Institution?
Lab Notebook
Why Do I Want This??
UKSG 2011 17
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?
UKSG 2011
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 FuturePLoS Comp Biol 2010 6(5): e1000787
UKSG 2011 21
• Open source cohesive tools• New standards• Business rights and IP• Attribution/evaluation/
archiving• A “publisher” to take the
plunge
Beyond the PDF
What Will It Take to Get There?
https://sites.google.com/site/beyondthepdf/
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Sounds Insurmountable?
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But Wait..There Are Many Great Tools Out There
We Need Scientist Management Tools
Taverna
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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, Dimitris Dimitanopolos
