Elsevier02012011

What Do I Want from the Publisher of the Future?

Philip E. BourneUniversity of California San Diego

[email protected]://www.sdsc.edu/pb

PLoS Comp Biol 2010 6(5): e1000787.

What is My Twisted Perspective?

• Background in both IT and science (chemistry, computational biology)

• My lab. distributes for free data equivalent to ¼ the Library of Congress every month

• I am a supporter of open access (provided there is a business model) and editor in chief of PLoS Computational Biology

• I am Co-founder of SciVee Inc. (conflict?)• I am becoming increasingly interested in scholarly

communication

I Readily Acknowledge Each Discipline is Different

My Comments Are Heavily Influenced by a Recent Workshop –

Beyond the PDF

The most vibrant workshop I have attended in over 30 years of workshopshttps://sites.google.com/site/

beyondthepdf/

Driver of Change

• With much of the STM research workflow now being digital it makes no sense to retrofit the finding of that workflow into something essentially analog

The non-STM Game is Afoot

• iTunes model• Blockbuster video• Newspapers (pay wall vs. mining)• iPads/tablets• YouTube• Social networking• ….

The STM Game is Afoot

• Open access• Interactive PDFs• Article of the Future• ORCHID• Datacite, Dryad• Mendelay• Hubs, Currents…• Open publishing platforms• …..

Signs of Change Are All Around

• Open access – new business models• Interactive PDFs – baby steps• Article of the Future – already past• ORCHID – disambiguation of all content• Datacite, Dryad – data treated as publications• Hubs – new forms of integration• Open publishing platforms - competition

What Are the Rate Determining Steps?

• Killer App – Your typical scientist has yet to see a major advantage

• Reward – We have yet to figure out a reward scheme in a changing world

The Article of the Future is Not the Killer App – Yet?

• Semantic tagging to ontological terms is okay, but really only valuable when I gain new knowledge, not the meaning of a term I could look up any way.

• PaperFlick – maybe• Tabs – hey it’s a web site after all• Comments – well we know how well that works so

far• Tables in XLS format – yes!• Bibliometrics – its not open

A Way to Reward a Different Model of Scholarly Achievement Would be the Tipping Point

Change Reward

You don’t get tenure for starting a PLoS hub!

Reward Scheme – One of Scholarship’s Dirty Secrets – We Claim to be Quantitative, Yet we Measure Ourselves Otherwise

• Journal Impact factors are not paper impact factors

• Other forms of scholarly discourse (blogs, database depositions, software etc) don’t rate

• …

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comp. Biol. 7(1) e1002001.

Why Will We Move Beyond the PDF Eventually?

Scholarship Will Demand It

Publishing Limitations

• A paper is an artifact of a previous era• It is not the logical end product of eScience, hence:– Work is omitted– Data and the knowledge of that data are disjoint– Article vs supplement is a mess– Visualization may be limited– Interaction and enquiry are non-existent– Rich media can help, but are rarely used– There is no true aggregation

Drivers of Change

We Cannot Possibly Read a Fraction of the Papers We Should

Drivers of Change Renear & Palmer 2009 Science 325:828-832

Hence We Are Scanning More Reading Less

Renear & Palmer 2009 Science 325:828-832Drivers of Change

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

Drivers of Change

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

Drivers of Change

Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136

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

Here is What I Want as a Scholar

1. User clicks on content2. Metadata and

webservices to data provide an interactive view that can be annotated

3. Selecting features provides a data/knowledge mashup

4. Analysis leads to new content I can share

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

Here is What I Want as a Scholar:Automatic Knowledge Discovery

Immunology Literature

Cardiac DiseaseLiterature

Shared FunctionDrivers of Change

As a Consequence the Traditional PDF is an Inferior Way to Convey the Science

Moreover, the Traditional PDF is not the Natural End

Product of the Research Enterprise

A paper when complete is thrown over a high wall to a publisher and essentially forgotten – Perhaps it is time to climb the wall?

uzar.wordpress.com Drivers of Change

So What Do I Think We Should Do To Solve My Problems and Your Problems?

What Should We Do?

Consider Today’s Academic Workflow

Research[Grants]

JournalArticle

ConferencePaper

PosterSession

Feds

Societies

Publishers

Reviews

BlogsCommunity Service/Data

Curation

What Should We Do?

Consider Tomorrow’s Academic Workflow

Research[Grants]

JournalArticle

ConferencePaper

PosterSession

Feds

Societies

Publishers

Reviews

BlogsCommunity Service/Data

CurationIdeas, Data, Hypotheses

What Should We Do?

What Should We Do?

“We have an interaction with the publisher that does not begin when the scientific process ends,

but begins at the beginning of the scientific process itself “

PLoS Comp Biol 2010 6(5): e1000787

Maybe The Line is Somewhere Else?

Scientist

Idea

Experiment

Data

Conclusions

PublishWhat Should We Do?

Laboratory

Publisher

Maybe The Line is Somewhere Else?

Scientist

Idea

Experiment

Data

Conclusions

PublishWhat Should We Do?

Laboratory

Publisher

Institution

Lab Notebook

This Amounts to Publishing WorkflowsBut That Has its Problems

• Workflows are not linear• Workflow : paper is not 1:1• Confidentiality• Peer review• Infrastructure• Community acceptance• Reward system

What Should We Do?

What is Needed to Publish Workflows?

• New organizations (university as publisher?)• Suitable support frameworks for research

objects• Provenance and appropriate reward systems

for living entities• Shared governance – author, institution, publisher

What Should We Do?

Define a Goal

• Make a positive contribution that would not otherwise happen in such a timely way

https://sites.google.com/site/beyondthepdf/

What is Being Done?

• Research objects of the future (ROFs) – Entities that capture all aspects of scholarship: hypotheses, data, methods, results, presentations etc.) that are semantically enriched, interoperable and easily transmitted and comprehended

• Define a set of requirements to meet the needs of the SMA project.

• Agree on standards and architecture to support the requirements.

• Interface with existing efforts under the W3C umbrella.• Illustrate that the effort has advanced our understanding of

SMA beyond what would otherwise be possible.

https://sites.google.com/site/beyondthepdf/

What is Being Done?

• Writing – Establishing a scholarly discourse that embraces the idea of ROFs.

• New writing tools should create ROF containers that contain all relevant files. These containers should be shared using appropriate network protocols.

• Evaluate existing tools for use in this regard.• Settle on tools or agree to modify tools to address the SMA

goal.• Work to demonstrate the value of the tools in supporting data

integration (with appropriate metadata).• Have graduate students in several research groups evaluate the

tools.https://sites.google.com/site/beyondthepdf/

What is Being Done?

• Attribution, Evaluation, Archiving• Develop a use case for use by funding

agencies to evaluate the effectiveness of funding. A tool to measure citation and attention based metrics across a broad spectrum of sources was proposed. Prototype an impact dashboard to be used by the SMA Foundation.

https://sites.google.com/site/beyondthepdf/

In Summary – Crowd Source the Printing Press of the 21st Century

https://sites.google.com/site/beyondthepdf/

Discussion

[email protected]