Using OA Content

Using Open Access Content: Ten Simple Observations SciVee & Beyond the PDF Philip E. Bourne University of California San Diego [email_address] www.sdsc.edu/pb http://www.slideshare.net/pebourne/p-lo-s

My Two Lectures
The promise - Open Access, Open Science with particular reference to PLoS
The fulfillment - What Open Access facilitates and examples of how it benefits science

The fulfillment - What Open Access facilitates and examples of how it benefits science
What you might get from this lecture:
How others are using open science including open access content
Ideas for how you might use the content

Todays Exemplars http://www.mendeley.com/ http://getutopia.com/documents/ http://www.scivee.tv/node/17389

Let me Start with a Few Observations Observation 1. Scientific culture is causing us to try and write more and read more

You Cannot Possibly Read a Fraction of the Papers You Should write more and read more Renear & Palmer 2009 Science 325:828-832

Scanning More Reading Less Renear & Palmer 2009 Science 325:828-832 write more and read more

And So…
There has been a paradigm shift which places more emphasis on writing and less on reading – witness blogs, use of literature aggregators (e.g. PubMed), H-factors, etc.
We need help in assimilating knowledge
write more and read more

Observation 2 In 1993 there were very few electronic journals, by 2003 nearly all were on-line, by 2013 there will be little or no paper Most traditional publishers have only really achieved an electronic print like experience – the power of the medium is for the taking

Observation 3. The Sociology of Scientific Disciplines is Different

Observation 4:
The biomedical sciences is progressive:
Alternative business models have gained ground – Open Access
Databases are becoming more like journals and journals are becoming more like databases
New modes of knowledge and data access are gaining some ground e.g.
Textpresso – ontology-based mining and retrieval system
iHOP Information Hyperlinked over Proteins

Observation 5. I Believe Open Access IF Fully Accepted Could Profoundly Change Scholarly Discourse It remains a big IF Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. 2008 4(3) e1000037

Its Happening in the Closed Access Space
A very clever idea – The App model
Leverage content
Provide an open API
Get the community to do all the work
Drive folks to buy content
Why Don’ t We Have Such Developments in OA?

Growth of PubMed Central Open access could profoundly change scholarly discourse

Open Access (Creative Commons License)
All published materials available on-line free to all (author pays model)
Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)
Copyright remains with the author
Open access could profoundly change scholarly discourse

Open Access (Creative Commons License)
All published materials available on-line free to all (reader pays model)
Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)
Copyright remains with the author
Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. 2008 4(3) e1000037 Open access could profoundly change scholarly discourse

Observation 6 A biological database is not really that different from a biological journal – this can be exploited PLoS Comp. Biol . 2005 1(3) e34

The Data Knowledge Cycle Biocuration Electronic Supplements Databases versus journals

Both Are Under Stress
PubMed contains ~21M entries (May 2011)
~100,000 papers indexed per month
In Feb 2009:
67,406,898 interactive searches were done
92,216,786 entries were viewed
1330 databases reported in NAR 2011
MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 times
PLoS Comp. Biol . 2005 1(3) e34

Some More Comparisons
Journals have a pretty standardized interface
Journals have a business model
The quality is declining as numbers increase (?)
Audience believes they are sustainable
Efforts to make the interfaces different!
Little attempt at a business model compared to the Web 2.0 world
Quality is increasing (?)
Not well sustained
PLoS Comp. Biol. 2008. 4(7): e1000136 Databases versus journals

Some More Comparisons
New publishing models eg open access, self publishing, open review
Web 2.0 influence eg social networks
Use of rich media
The review process is failing
New metrics
Read and write eg Wikis
New services eg restful, widgets
Use of Rich Media
Crowd review emerging
Databases versus journals

Duh
If we need to acquire more knowledge quickly
If more literature and data are becoming open
If both are under stress
Why don ’t we merge journals and databases for a new learning experience

The Test Bed http://www.wwpdb.org/ http://www.plos.org/ http://www.pubmedcentral.nih.gov/ Merge journals and databases

The World Wide Protein Data Bank
The single worldwide repository for data on the structure of biological macromolecules
Vital for drug discovery and the life sciences
38 years old
Free to all
http://www.wwpdb.org Merge journals and databases

The World Wide Protein Data Bank
Paper not published unless data are deposited – strong data to literature correspondence
Highly structured data conforming to an extensive ontology
DOI ’s assigned to every structure
http://www.wwpdb.org Merge journals and databases

The PLoS/PMC Corpus – Under the Hood
Conforms well/partially to the NLM DTD – little markup of content
PMC – some PDFs !
The lack of conformance will come back to haunt us!

Author Submission via the Web Depositor Submission via the Web Syntax Checking Syntax Checking Review by Scientists & Editors Review by Annotators Corrections by Author Corrections by Depositor Publish – Web Accessible Release – Web Accessible Similar Processes Lead to Similar Resources Merge journals and databases

So the processes are not that dissimilar it is the final product that is perceived so differently Even that might be changing slowly? PLoS Comp. Biol. 2008 4(12) e1000247 Merge journals and databases

Merged: The Database View www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Merge journals and databases

Merged: The Literature View Nucleic Acids Research 2008 36(S2) W385-389 http://biolit.ucsd.edu Merge journals and databases

Merge journals and databases

ICTP Trieste, December 10, 2007 Merge journals and databases

The Near Future
User reads a paper
Clicks on a figure. Figure can be manipulated, annotated, interrogated
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 http://biolit.ucsd.edu Enhanced modes of learning

Observation 7: This is Literature Post-processing Better to Get the Authors Involved
Authors are the absolute experts on the content
More effective distribution of labor
Add metadata before the article enters the publishing process
Merge journals and databases – requires semantic enrichment

Word 2007 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 Merge journals and databases – requires semantic enrichment

Challenges
Author use
Familiarity with ontologies, terms
Agreement between co-authors
End-use of semantically enriched manuscript
Combine with NLM XML standard
Article Authoring Add-in
Merge journals and databases – requires semantic enrichment

Challenges: Author Use IF one or more publishers fast tracked a paper that had semantic markup I would argue it would catch on in no time Merge journals and databases – requires semantic enrichment

Observation 8: There Are Some Simple Things We Can Do to Mine the Corpus

Where We Would Like to Be: Data Clustering via the Literature Shared Function Enhanced modes of learning Immunology Literature Cardiac Disease Literature

Observation 9: The Use of Rich Media is Underutilized

Yes YouTube Can Increase the Rate of Discovery

Pubcast – Video Integrated with the Full Text of the Paper

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 Proposal - The TeachU Workflow Mac PC Step 4 slides are uploaded

Lessons
It is a form of expression the current YouTubers embrace and may become as ubiquitous as papers and slide presentations in the next few years
We are reinventing television
Its only going to work if it is easy to publish and the reward is obvious

Observation 10: Scientific Reproducability Requires we Publish Workflows

Yes The Workflow is Real

Reproducibility
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

Workflow Tools Might be the Answer Taverna Wings

Consider an Example: Our Own Experience in Capturing the Scientific Process to Make it Open and Reproducable
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

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

Where Will It All End? http://richard.cyganiak.de/2007/10/lod/lod-datasets_2010-09-22_colored.html

General References
What Do I Want from the Publisher of the Future PLoS Comp Biol 6(5): e1000787
Fourth Paradigm: Data Intensive Scientific Discovery http://research.microsoft.com/enus/ collaboration/fourthparadigm/

References to Exemplars
Semantic Biochemical Journal - 2010: Using Utopia
Article of the Future, Cell, 2009: 
Prospect, Royal Society of Chemistry, 2009: 
Adventures in Semantic Publishing, Oxford U, 2009:
The Structured Digital Abstract, Seringhaus/Gerstein, 2008 
CWA Nanopublications – 2010 
https://sites.google.com/site/beyondthepdf/
https://sites.google.com/site/futureofresearchcommunications/

Acknowledgements
BioLit Team
Lynn Fink
Parker Williams
Marco Martinez
Rahul Chandran
Greg Quinn
Microsoft Scholarly Communications
Pablo Fernicola
Lee Dirks
Savas Parastitidas
Alex Wade
Tony Hey
wwPDB Team
Boki Beran
Wolfgnag Bluhm
Andreas Prlic
Greg Quinn
Peter Rose
Ben Yutick
Chunxaio Zhu
http://biolit.ucsd.edu http://www.codeplex.com/ucsdbiolit

Questions? [email_address]

Using OA Content

by Philip Bourne on Sep 27, 2011

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Using OA Content — Presentation Transcript