New Modes of Scholarly Communication and Learning Philip E. Bourne University of California San Diego [email protected] 1WSU December 2, 2008.

New Modes of Scholarly Communication and Learning

Philip E. Bourne

University of California San Diego

[email protected]

1WSU December 2, 2008

Disclaimer

I am not an expert, but through my involvement with Open Access

(OA) I have seen the possibilities for improved scholarly

communication and learning

It is this vision I would like to share with you today

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Let me cast that vision into a scenario that we can dissect and

study


The Vision…

Prior to leaving home a UCSD graduate student syncs her IPOL with the latest papers delivered overnight by the journal via RSS feed. On the bus she reviews the stream, selecting a paper close to her interest in HIV-1 proteases. The data shows apparent anomalies with her own work. Being on-line she notices that a colleague has also discovered the same paper and they IM annotating the results. By the time the bus stops she has recomputed the results, proven the anomaly and made a rebuttal in the form of a “pubcast” to the Editor and sent it to the journal.


Science Fiction – Yes or No?

I would argue that the only part of this vision that is science fiction is

finding a bus in San Diego


Science Fiction?• Five years ago Yes… Today No…• Five years ago the idea of downloading data on a bus

would have been absurd – not today• Five years ago an IPOL would be absurd - not today

(consider the smart phone)• Journals and databases are providing RSS feeds today• IM is prevalent but not for scientific discourse• Video and podcasting are prevalent but not for scientific

discourse• Full text journal articles and data are on-line but not

integrated


What is Missing to Make the Vision a Reality?

1. Seamless integration between the data and the publication upon which that data are based

2. Seamless integration of the authoring and publishing process

3. Notion of traditional publications being associated with podcasts and video

4. Professional networking akin to social networking


What are the Catalysts for Change?

• New publishing paradigms, most importantly open access publishing

• The emerging generation of digital scientists

• The increased ease of working with digital media, notably sound and video


SSPPS 205 9

NIH Public Access Policy“The research supported by the National Institutes of Health (NIH) is essential to improving human health. Public access to this research is vital – today and for generations to come.”From a letter from NIH Director Zerhouni to grantees, February 3rd, 2005

SSPPS 205 10

More and more authors care about improving access to their papers…

“Faced with the option of submitting to an open-access or closed-access journal, we now wonder whether it is ethical for us to opt for closed access on the grounds of impact factor or preferred specialist audience.”

-- Costello and Osrin in The Lancet

SSPPS 205 11

Where are we Today?

• NIH and other government funders have mandated open access

• Full text increasingly on-line and potentially usable

• Traditional publishers have used the internet as a distribution medium, but the power of the medium has yet to be realized

• Data increasingly on-line but not integrated with the publication derived from it

The Growth of Open Access Literature


Open Access(Creative Commons License)

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


Open Access(Creative Commons License)

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 The catalyst

PLoS Comp Biol 2008 4(3) e100003714WSU December 2, 2008

Community Reaction?

Most scientists have no idea that this implies that anyone can take their material and enhance it e.g., via

mashup and effectively republish it


Okay so much for the 1% inspiration, where is the 99%

perspiration?







PLoS Comp. Biol. 2005 1(3), e34


Database and Journal Integration- The Test Bed

http://www.wwpdb.org/

Journals

Database18WSU December 2, 2008

http://www.pdb.org/pdb

http://www.wwpdb.org/index.html

The 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.doi.org

http://www.pdb.org19WSU December 2, 2008

Seamless Integration between Data and the Literature – What

Does That Imply?

• Improving semantic consistency in the literature – best done at the point of authoring

• Post processing to establish semantic content

• New forms of visualization and interaction at the presentation layer


Seamless Integration between Data and the Literature – What

Does That Imply?

• Improving semantic consistency in the literature – best done at the point of authoring

• Post processing to establish semantic content

• New forms of visualization and interaction at the presentation layer


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

BioLit: Tools for New Modes of Scientific Dissemination

• Biolit integrates biological literature and biological databases and includes:– A database of journal

text– Authoring tools to

facilitate database storage of journal text

– Tools to make static tables and figures interactive

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

http://biolit.ucsd.edu22

http://biolit.ucsd.edu

PSP Washington DC Feb. 2008 23




ICTP Trieste, December 10, 2007 27WSU December 2, 2008

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Author Paper

Word File in Docx formatPublisher

BioLit Plugin Project


Sidebar: Imagine a Future Where…

• The relationship between author and publisher is quite different

• The publisher is a warehouse for the workflow of scientific endeavor not just a repository for the end product

• Evidence:– www.researchgate.net– MetaLab (Borya Shakhnovich)


http://www.researchgate.net/

BioLit Plugin Project

• Leverages Office Open XML used in Microsoft Office 2007

• Custom schema attached to document and used to automatically XML tag ontology terms and database identifiers within a research paper

• Ontology tagging assists publication of scientific research by aiding efficient and accurate automated categorization and promotion of information dissemination

• Conversion of manuscript to NLM DTD for direct submission to publisher

Automated Ontology & ID Tagging within Microsoft Word Documents


BioLit Plugin ProjectRather than Post-processing the Document the

Author Controls the Semantic Tagging


Plugin Architecture


Context-Sensitive Data Access

• Display of information of database entries when the user clicks on the ID in the document

• Display of ontology terms related to terms in the document text, using local database search


Ontologies are Stored in a Local Database


User Configurable Selection

• Fully user configuration ontology and database identifier selection

• All searches occur within the user’s desktop computer

• Desired ontologies are downloaded and installed automatically, and update periodically

• BioLit installer XML file provides the application with the information needed to download and install ontologies.







PSP Washington DC Feb. 2008 38WSU December 2, 2008

YouTube for Scientists www.scivee.tv


Motivation


Pubcast – Video Integrated with the Full Text of the Paper

41

http://www.scivee.tv/pubcast/17306029

Pubcast - Making


Channels – Just Like TV

ICTP Trieste, December 2007 43

http://www.scivee.tv/channels

Professional Profile


Create & Join Communities and Discussion Groups


The Role of Ontologies

• Tag clouds generated automatically from MESH headings

• Semantic enrichment can be included with a pubcast


SciVee – Viral Projects

• Sweetwater School District

• “Postercasts”

• Science video competitions

• “CVcasts”


Acknowledgements

• SciVee Team– Apryl Bailey– Tim Beck

– Leo Chalupa

– Marc Friedman– Alex Ramos– Willy Suwanto

• BioLit Team• J. Lynn Fink• Sergey Kushch• Marco Martinez• Greg Quinn• Parker Williams

CT Watch 2007, 3(3) 26-31


Questions?

[email protected]


New Modes of Scholarly Communication and Learning Philip E. Bourne University of California San Diego [email protected] 1WSU December 2, 2008.

Documents

access journal

lancet slide

closed access

open access oa

nih public access policy

science fiction

scientific discourse

text journal articles