A Few Overarching Thoughts on Digital Publishing and How You

Can Participate

Philip E. Bourne

University of California San Diego

pbourne@ucsd.edu

Opinionated Moi?

• The Internet demanded new business models to support scholarly communication

• Open access was one such sustainable model: – Began with the community – Was driven by new organizations (PLOS, BMC,

F1000, eLife, Dryad, Mendeley etc.)– Was NOT driven by academic institutions– Was driven by policies and funders

Got Us Thinking About…

• A paper as only one form of knowledge discovery

• The use of interaction and rich media from which to learn and actually do science

• Reproducibility• Reward structures• Better management of the research lifecycle

P.E. Bourne 2005 In the Future will a Biological Database Really be Different from a Biological Journal? PLOS Comp. Biol. 1(3) e34

The Research Lifecycle

IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION

AuthoringTools

Lab Notebooks

DataCapture

SoftwareRepositories

Analysis Tools

Visualization

ScholarlyCommunication

Commercial &Public Tools

Git-likeResources

By Discipline

Data JournalsDiscipline-

Based MetadataStandards

Community Portals

Institutional Repositories

New Reward Systems

Commercial Repositories

Training

The Research Lifecycle

IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION

AuthoringTools

Lab Notebooks

DataCapture

SoftwareRepositories

Analysis Tools

Visualization

ScholarlyCommunication

Commercial &Public Tools

Git-likeResources

By Discipline

Data JournalsDiscipline-

Based MetadataStandards

Community Portals

Institutional Repositories

New Reward Systems

Commercial Repositories

Training

Most Laboratories

• We are the long tail• Goodbye to the student is

goodbye to the data• Very few of us have

complied (or will comply with the data management plans we write into grants)

• Too much software is unusable

S.Veretnik, J.L.Fink, and P.E. Bourne 2008 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. . 4(7): e1000136

Today’s Research Lifecycle is Digitally Fragmented at Best

• Proof:– I cant immediately reproduce the research in

my own laboratory• It took an estimated 280 hours for an average user

to approximately reproduce the paper

– Workflows are maturing and becoming helpful– Data and software versions and accessibility

prevent exact reproducability

Daniel Garijo et al. 2013 Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome PLOS ONE under review.

• In the US alone..– March 2012 OSTP

commits $200M to Big Data

– OSTP demands sharing plans by August 2013

– GBMF/Sloan provide institutional awards for data science

– NCBI considers data catalog and MyBibliography

And the Disruption Continues

Where Will It End?

First We Should Ask What It Is We Wish to Accomplish

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 – The Paper As Experiment

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.

PLoS Comp. Biol. 2005 1(3) e34

Here is What I Want – Knowledge Push

• Each evening the labs “Evernote” notebooks are scanned for commonalities from the days activities. These are seeds in a deep search of the webs research lifecycles that has become available since last searched. Results are ranked and presented for consideration over coffee the next morning

http://www.discoveryinformaticsinitiative.org/diw2012

Will End With …

• Infrastructure:– Science, Nature, Cell and megajournals all

“open access” – An array of coupled institutional repositories – A central repository – PubMed Central – Open software in full support of the research

lifecycle – The research lifecycle in the cloud

Will End With …

• Sociologically:– An end to build it and they will come– Alternative metrics accepted by the

community– Alternative reward systems that recognize the

realities of today’s scholarship, namely:• Open data availability• Software availability• Collaborative research

We Have a Way to Go

• Good News– We have NCBI/EBI– Publishers are starting

to embrace data– Workflows in support

of the research lifecycle are catching on

• Bad News– Data are organized by

type not by questions asked (silos)

– Tenure committees are still in the dark ages

What Can You Do?Think Globally Act Locally

• Support emergent community portals• Be involved in the support and development

of metadata standards• Contribute to workflow development etc. to

drive an open research lifecycle• Educate your mentors on the importance of

open science and scholarly communication • Write software thinking of an App model

What Do We Need to Do to Get There? An App+ Store?

• The App model– Think of it operating on a content base rather

than a mobile device– Simple and consistent user interface– Needs to pass some quality control– Has a reward

• The App+ Model– Apps interoperate through a generic workflow

interface

In Summary

• We have at hand the means to accelerate the rate of discovery

• To do so we need to place more value on the data, the individuals that produce it and the institutions that maintain it

• We are all stakeholders in this endeavor

• Here is one way to get involved….

Get Involved: FORCE11

• Tools and Resource catalog

• Article database in Mendeley

• Discussion Forum via Google

• Blogs courtesy of blog sites and RSS feeds

• Web site via Drupal• Announcements via

Twitter

http://force11.org

pbourne@ucsd.edu

• Force11 Manifesto• Fourth Paradigm: Data Intensive Scientific

Discovery http://research.microsoft.com/enus/collaboration/fourthparadigm/