Ten Simple Rules for Open Access Publishers

Beyond the Journal Article One Scientist’s Perspective Philip E. Bourne University of California San Diego [email_address] http://www.sdsc.edu/pb Relevant Work from Us: http ://www.sdsc.edu/pb/SummaryScholarComm. pdf http://www.slideshare.net/pebourne/?? COASP Sept 21, 2011 Or.. Ten Simple Rules for OA Publishers

How I Got to Be Standing Here
Researcher in computational biology
Co-developed the Protein Data Bank (PDB)
Felt my field was not well served by the current literature
Saw an opportunity to work through a society
Thought OA was a good idea, but was not passionate about it
Co-founded and remain the EIC of PLoS Computational Biology

How I Got to Be Standing Here http://www.wwpdb.org/ Journals Database 2005: Is a Biological Database Different from a Biological Journal? PLoS Comp. Biol. 2005 1(3) e34

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

So the processes are not that dissimilar it was the final product that was {is} perceived so differently I am not a Scientist I am a Number PLoS Comp. Biol. 2008 4(12) e1000247

Yet What is Better.. A Paper only Ever Cited by the Folks who Wrote it or a Dataset That is Downloaded and Used 100’s of Times? We will come back to this…

But This is What I Really Came to Appreciate was a Wealth of Possibility
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
PLoS Comp Biol 2008 4(3) e1000037

From Someone Who Generates Scholarship And Cares, Have The Possibilities Been Realized Some Six Years Hence? Not Really But I Like to Think the Process Has Started

So I am Here To Tell You Not What is Right with OA – You Know That Already. I Am Here To Tell You in My Humble Opinion What Needs to Be Done To Realize the Promise. Not Necessarily by Publishers, but Catalyzed by Publishers

I realized last night that the catalyst could be for reasons of profit or service to science or something in between

There is Competition Out There
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?

There is Competition Out There Why Don’ t We Have Such Developments in OA?

Why Don’ t We Have Such Developments in OA?
OA publishers think in papers not research objects?
No R&D budgets?
No/unidentifiable competitions?
Not enough content?
Content is not consistently available?
Not a collective vision?
Too early?
All of the above

Content is not consistently available
David Lipman
“ Phil, What you are doing is illegal!”
PMC content available under different licensing conditions
Content conforms to the NLM DTD to different degrees
The latter may come back to haunt us

The Good News is There Are People Out There Who Care
“ Beyond the PDF” crowd
FORCE11
Individual investigators
Librarians forging a new role for themselves
Funding agencies, foundations
Scientists themselves
Commercial companies e.g. Microsoft

Scientists Themselves – New OA Journal
My knee jerk reaction – is this the best a bunch of great minds can come up with!
My more thoughtful reaction – every little bit helps – it will broaden awareness of the value of OA like nothing else

Ten Simple Rules for What OA Publishers Can Do to Move the Ball Forward

Rule 1 – Continue to Do What You Do But Better – More Openness!
Provide fully open content according to CC BY The future of OA might be tied to new business models associated with using the corpus
Lower costs with more efficient journal management systems – OA publishers are beholden to legacy bloated expensive systems – a recognized and committed joint open source development effort is important

Rule 2. Foster Low Hanging Fruit

We Cannot Possibly Read a Fraction of the Papers We Should Rule 2 – Foster Low Hanging Fruit Renear & Palmer 2009 Science 325:828-832

We Are Scanning More Reading Less – Our Level of Detail is Dropping Renear & Palmer 2009 Science 325:828-832 Rule 2 Foster Low Hanging Fruit

Automatic Knowledge Discovery for Those with No Time to Read Shared Function Rule 2 Foster Low Hanging Fruit Immunology Literature Cardiac Disease Literature

This Requires That Publishers Exercise the NLM DTD as Far as Possible

Rule 3 Recognize Data
Not sure that passing the buck to Dryad and others is the best solution?
Need more than a DOI
Maybe the only short term solution?

Data – The State of Play (A Scientist’s Perspective)
Some disciplines have embraced data journals
Some journals have ignored data
Institutional repositories are “roach motels”
The long tail problem is dying to be addressed
Scientists would love a data citation that looks like a paper citation
There are some wonderful opportunities…

Data Becomes Part fo the Article
User clicks on thumbnail
Metadata and a webservices call provide a renderable image that can be annotated
Selecting a features provides a database/literature mashup
That leads to new papers
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 PLoS Comp. Biol. 2005 1(3) e34

There Is a Real Opportunity for “Data Papers”
Structured metadata about the dataset
Hence the opportunity to discover the data
Hence the opportunity to establish metrics on the use of the data
And this is a big one… the opportunity to develop apps (centralized and standardized software) that operate on the data

Rule 4 – Recognize Rich Media as Scholarship
Currently video and podcasts are adjuncts to published work – they could be it (e.g., Jove) or better integrated.

Yes YouTube Can Increase the Rate of Discovery Rule 4 Recognize Rich Media as Scholarship

Pubcast – Video Integrated with the Full Text of the Paper

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
Its only going to work if it is easy to publish and the reward is obvious
Rule 4 Recognize Rich Media as Scholarship

Rule 5 Play Upon a Scientists Guilt re The Reward Sytem The Right Thing To Do Reward

Rule 5 Play Upon a Scientists Guilt re The Reward System
Article level metrics are great but:
Lets have more of them and more transparency
Lets standardize and so..
Lets use them more effectively
Example – you looked at this article therefore you might be interested in this one – within a journal and across journals!
Its like PubMed but based on usage patterns

Rule 6 - Play Upon the Scientists Guilt re 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 Rule 6 Foster Reproducability 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
Rule 6 Foster Reproducibility

Yes The Workflow is Real Rule 6 Foster Reproducibility

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
Rule 6 Foster Reproducibility

Rule 7 - Where Possible Promote the Use of Social Media and Citizen Science
Think of ways beyond blogging, tweeting, social bookmarking etc.
Example – The Wikipedia experiment

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
Rule 7 Foster Social Media and Citizen Science

Rule 8 – Think of a Cycle Not an End Product Research [Grants] Journal Article Conference Paper Poster Session Reviews Blogs Community Service/Data Curation

Rule 9 – Think of Killer Apps That Could be an OA Game Changer P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol . 4(3) e1000037

Here is an Idea to Get You Started
Right now reward is defined almost solely by the H-index
Open access to data, rich media, presentations, etc, etc could begin to change that .. If one could measure the value of other types of open access content
Google scholar, MS Academic Search does it to some degree, but it is not accurate
Help make alternative metrics more available and accurate – need ORCID, need good metadata
Rule 9 – Come up with Killer Apps

Here is Another One.. http://richard.cyganiak.de/2007/10/lod/lod-datasets_2010-09-22_colored.html Rule 9 – Come up with Killer Apps

Rule 10 – Lobby Better
Do more to solicit scientists to support legislation like the Hargreaves data mining proposal
NSF and NIH have new data sharing policies – how can these be mapped to OA activities?

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/

Push-back, Questions? [email_address]

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Ten Simple Rules for Open Access Publishers

by Philip Bourne

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