Beyond the Journal ArticleOne Scientist’s Perspective

Philip E. BourneUniversity of California San Diego

pbourne@ucsd.eduhttp://www.sdsc.edu/pbRelevant Work from Us:

http://www.sdsc.edu/pb/SummaryScholarComm.pdfhttp://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 AuthorCorrections 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 NumberPLoS 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

1. All published materials available on-line free to all (author pays model)

2. Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)

3. Copyright remains with the author

PLoS Comp Biol 2008 4(3) e10000377

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?

A. OA publishers think in papers not research objects?

B. No R&D budgets?C. No/unidentifiable competitions?D. Not enough content?E. Content is not consistently available?F. Not a collective vision?G. Too early?H. 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 325:828-832Rule 2 Foster Low Hanging Fruit

Automatic Knowledge Discovery for Those with No Time to Read

Immunology Literature

Cardiac DiseaseLiterature

Shared FunctionRule 2 Foster Low Hanging Fruit

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…

Rule 3 Recognize Data

1. A link brings up figures from the paper

0. Full text of PLoS papers stored in a database

2. Clicking the paper figure retrievesdata from the PDB which is

analyzed

3. A composite view ofjournal and database

content results

Data Becomes Part fo the Article

1. User clicks on thumbnail2. Metadata and a

webservices call provide a renderable image that can be annotated

3. Selecting a features provides a database/literature mashup

4. That leads to new papers

4. The composite view haslinks 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 3 Recognize 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]

JournalArticle

ConferencePaper

PosterSession

Reviews

BlogsCommunity 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?

pbourne@ucsd.edu