Some Thoughts on Scholarly Communication and the Role of

Bio-ontologies

Philip E. Bourne

University of California San Diego

pbourne@ucsd.edu

Disclaimer – I am not an expert in ontologies

Some would argue quite the opposite!

I would claim to have an interest in scholarly communication and

am beginning to see the role that bio-ontologies have to play in what I believe will be a very

different type of scientific discourse

Let me cast that role into a vision that we can state and then

dissect to see what role bio-ontologies have to play

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 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 and data are on-line but not integrated

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 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 and data are on-line but not integrated

Role for Bio-ontologies

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 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 and data are on-line but not integrated

Role for Bio-ontologies

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

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) e1000037

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?

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

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

Database and Journal Integration- The Test Bed

http://www.wwpdb.org/

Journals

Database

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.org

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.edu

http://biolit.ucsd.edu

PSP Washington DC Feb. 2008

ICTP Trieste, December 10, 2007

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

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– MML (Borya Shakhnovich)

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.

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

PSP Washington DC Feb. 2008

YouTube for Scientists www.scivee.tv

Motivation

Pubcast – Video Integrated with the Full Text of the Paper

Pubcast - Making

PSP Washington DC Feb. 2008

Channels – Just Like TV

ICTP Trieste, December 2007

Professional Profile

ICTP Trieste, December 2007

Create & Join Communities and Discussion Groups

ICTP Trieste, December 2007

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

• “Pubumentaries”

Acknowledgements

• SciVee Team– Apryl Bailey– Tim Beck

– Leo Chalupa

– Marc Friedman– Alex Ramos– Willy Suwanto

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

CT Watch 2007, 3(3) 26-31

Questions?

pbourne@ucsd.edu