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Digital Research Analog Publishing – One Scientist’s View. Philip E. Bourne University of California San Diego [email protected] http://www.sdsc.edu/pb. My Bias. Computational biologist (only one of many domains) Open access advocate Maintainer of an important biological data resource (PDB). - PowerPoint PPT Presentation
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Digital Research Analog Publishing – One Scientist’s View
Philip E. BourneUniversity of California San Diego
[email protected]://www.sdsc.edu/pb
1UKSG 2011
My Bias..
• Computational biologist (only one of many domains)
• Open access advocate
• Maintainer of an important biological data resource (PDB)
UKSG 2011 2
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
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?4UKSG 2011
uzar.wordpress.com
Maybe The Line is Somewhere Else?
Scientist
Idea
Experiment
Data
Conclusions
Publish
Laboratory
Publisher
Institution?
Lab Notebook
5UKSG 2011
?
Scientist
Idea
Experiment
Data
Conclusions
Publish
Laboratory
Publisher
Institution?
Lab Notebook
Maybe The Line is Somewhere Else?
UKSG 2011 6
?
Why Do I Want This?
UKSG 2011 7
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 partyMetadata stored with the article
Fetches the data and provides a Staring point for interactive enquiry
User annotates view
UKSG 2011
We Are Making Progress But it is Incremental
UKSG 2011
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
11UKSG 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
UKSG 2011
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
www.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 14UKSG 2011
Why Do I Want This?Semantic Linking of Data Can Lead to New
Knowledge Discovery
Immunology Literature
Cardiac DiseaseLiterature
Shared Function
15UKSG 2011
Scientist
Idea
Experiment
Data
Conclusions
Publish
Laboratory
Publisher
Institution?
Lab Notebook
Why Do I Want This?
UKSG 2011 16
?
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
17UKSG 2011
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
18UKSG 2011
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?
19UKSG 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
• Open source cohesive tools
• New standards• Business rights and IP• Attribution/evaluation/
archiving• A “publisher” to take the
plunge
Beyond the PDF
21UKSG 2011
What Will It Take to Get There?
https://sites.google.com/site/beyondthepdf/
Sounds Insurmountable?
UKSG 2011 22
But Wait..There Are Many Great Tools Out There
We Need Scientist Management Tools
Taverna
23UKSG 2011
But Wait..There Are Many Great Ideas Out There• Nano publications• Semantic tagging of PDFs and beyond• Citation ontologies• Scholarly HTML• Authoring tools
UKSG 2011 24
A Test BedSpinal Muscular Atrophy (SMA)
• Coalesce a set of disparate tools
• Engage the publishers
• Make some progress on a treatable disease
25UKSG 2011
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
26UKSG 2011
