Jim Gray Award Lecture

The Reaming of Life
Philip E. Bourne
University of California San Diego
pbourne@ucsd.edu
Jim Gray eScience Award Lecture
Oct. 12, 2010

Disclaimer
I am a domain (life) scientist not a computer or information scientist
I am fortunate enough to have a major biological resource (the Protein Data Bank) and a major biological journal (PLoS Computational Biology) as my playground
I am part of the long tail
I am naïve, but I am the majority
Oct. 12, 2010

The Reaming of Life -What on Earth is He Talking About?
A reamer is a tool for turning a roughly punched hole into an accurate and smooth one
The digital data deluge has punched that rough hole
For the life {other?} sciences to optimally advance we need an accurate and smooth conduit through which data can be distilled, analyzed, visualized, distributed and above all else comprehended
Oct. 12, 2010

… and we need to accelerate the process by which this is donehere is why ….
This is just another way of saying what Jim said and is embodied in the Fourth Paradigm
Oct. 12, 2010

The Scientific Process is Too Slow to Respond to a Crisis – Either Global or Personal
Oct. 12, 2010
By the time the paper is published
we could all be dead
http://knol.google.com/k/plos-currents-influenza#
Motivation

In a time of crisis the need for fast access
to accurate data and any knowledge of
that data are paramount
Structure Summary page activity for
H1N1 Influenza related structures
Jan. 2008
Jan. 2009
Jan. 2010
Jul. 2009
Jul. 2008
Jul. 2010
3B7E: Neuraminidase of A/Brevig Mission/1/1918
H1N1 strain in complex with zanamivir
1RUZ: 1918 H1 Hemagglutinin
* http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm
Motivation

If that is not enough…For some people the scientific process may be too slow to save their life
Oct. 12, 2010
Motivation

Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma Foundation
Oct. 12, 2010
http://sagecongress.org/Presentations/Sommer.pdf
Motivation

Chordoma
A rare form of brain cancer
No known drugs
Treatment – surgical resection followed by intense radiation therapy
Oct. 12, 2010
http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG
Motivation

Oct. 12, 2010
Motivation

Oct. 12, 2010
If I have seen further it is only by
standing on the shoulders of giants
Isaac
Isaac Newton
From Josh’s point of view the climb
up just takes too long
> 15 years and > $850M to be
more precise
Adapted: http://sagecongress.org/Presentations/Sommer.pdf
Motivation

Oct. 12, 2010
Motivation

Oct. 12, 2010
http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation
Motivation

Now we are all hopefully motivated let us break this down to what actually needs to be done in my opinion Here are a few big things …
Oct. 12, 2010

A Few Things to Accelerate the Rate of Scientific Discovery
Better communication, data and knowledge access, and new modes of discovery, which means:
We need data and knowledge about that data to interoperate i.e. we need new kinds of fast, versatile publications and data archives
We need to be more open with both
We need to think more about the tools that analyze, visualize and annotate data to maximize knowledge discovery
Reward systems need to change
We need scientist management tools
We need to be less fixated on the big data problems
We need to unleash the full power of the Internet
Oct. 12, 2010
Hard
Easy

We Need Data and Knowledge About That Data to Interoperate
The Knowledge and Data Cycle
0. Full text of PLoS papers stored
in a database
4. The composite view has
links to pertinent blocks
of literature text and back to the PDB
User clicks on content
Metadata and webservices to data provide an interactiveview that can be annotated
Selecting features provides a data/knowledge mashup
Analysis leads to new content I can share
4.
1.
3. A composite view of
journal and database
content results
1. A link brings up figures
from the paper
3.
2.
2. Clicking the paper figure retrieves
data from the PDB which is
analyzed
PLoS Comp. Biol. 2005 1(3) e34

We Need Data and Knowledge About That Data to Interoperate – What is Stopping US?
Governance – publishers vs. database providers
Reward
Metadata standards for provenance, privacy etc.
Exemplars
….
Oct. 12, 2010
Caveat: Each discipline is different – I speak very much from a biomedical
sciences perspective

Certainly the Argument for Interoperability in the Biomedical Sciences is Strong
1078 databases reported in NAR 2008
MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 times
PubMed contains 18,792,257 entries
~100,000 papers indexed per month
In Feb 2009:
67,406,898 interactive searches were done
92,216,786 entries were viewed
Data as of April 14, 2009
We need data and knowledge about that data to interoperate

A Small Example - The World Wide Protein Data Bank
The single worldwide repository for data on the structure of biological macromolecules
Vital for drug discovery and the life sciences
39 years old
Free to all
http://www.wwpdb.org

The World Wide Protein Data Bank – The Best Case Scenario
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.wwpdb.org

Example Interoperability: The Database View
www.rcsb.org/pdb/explore/literature.do?structureId=1TIM
BMC Bioinformatics 2010 11:220

Example Interoperability: The Literature Viewhttp://biolit.ucsd.edu
Nucleic Acids Research 2008 36(S2) W385-389

ICTP Trieste, December 10, 2007

Semantic Tagging & Widgets are a Powerful Tool to Integrate Data and Knowledge of that Data, But as Yet Not Used Much
Oct. 12, 2010
Will Widgets and Semantic Tagging Change Computational Biology?
PLoS Comp. Biol. 6(2) e1000673

Semantic Tagging of Database Content in The Literature or Elsewhere
http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp
PLoS Comp. Biol. 6(2) e1000673
Semantic Tagging

The Publishers are Starting to Do It
Oct. 12, 2010
From Anita de Waard, Elsevier

This is Literature Post-processingBetter to Get the Authors Involved
Authors are the absolute experts on the content
More effective distribution of labor
Add metadata before the article enters the publishing process

Word 2007 Add-in for authors
Allows authors to add metadata as they write, before they submit the manuscript
Authors are assisted by automated term recognition
OBO ontologies
Database IDs
Metadata are embedded directly into the manuscript document via XML tags, OOXML format
Open
Machine-readable
Open source, Microsoft Public License
http://www.codeplex.com/ucsdbiolit

Challenges
Authors
Carrot IF one or more publishers fast tracked a paper that had semantic markup it might catch on
Publishers
Carrot Competitive advantage

The Promise – A Hypothetical Example
Cardiac Disease
Literature
Immunology Literature
Shared Function

Oct. 12, 2010
Hard
Easy

One Small Example – The Molecular Biology Toolkit (MBT)
jMol, VMD … are de facto standard important tools for rendering biological molecules .. but
They are not versatile ie do not for example:
Respond to the data they are reading
Offer views that match the users interests
Allow the user to annotate the data
Allow those annotations to be shared (published?)
Oct. 12, 2010
Think More About the Tools

MBT Featureshttp://mbt.sdsc.edu
Offer a framework not an end user application
Responds to the data type
Support read write access
Encourages others to write end user applications
Discourages feature creep
Oct. 12, 2010
Immunologists
Immunome Research, 2007 3(1):3
Medicinal
Chemists
BMC Bioinformatics 2005, 6:21.
Think More About the Tools

Oct. 12, 2010
Hard
Easy

Reward Systems Need to ChangeWhat is Needed?
Author disambiguation
Auditing (identification and metrics) of all scholarship - means new tools
Seniors need to promote alternative forms of scholarship
Juniors need to respond
Oct. 12, 2010
Ten Simple Rules for Getting Promoted as a Computational Biologist in Academia
PLoS Comp Biol to appear
Reward Systems Need to Change

Example Tools
Oct. 12, 2010
http://www.researcherid.com/
http://pubnet.gersteinlab.org/
http://www.biomedexperts.com

What Are these Alternative Forms of Scholarship?
Reviews
Curation
Research
[Grants]
Journal
Article
Poster
Session
Conference
Paper
Blogs
Community Service/Data

A Unique Identifier is Going to Happen
It is DOIs for people
Some scientists will resist
The winner is ORCHID?

Ideally the ID will be Tagged to Every Piece of Scholarly Communication
I an Not a Scientist I am a Number
PLoS Comp. Biol. 2008 4(12) e1000247

Oct. 12, 2010
Hard
Easy

The Truth About My Laboratory
I have ?? mail folders!
The intellectual memory of my laboratory is in those folders
This is an unhealthy hub and spoke mentality
We Need Scientist Management Tools

The Truth About My Laboratory
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
http://artbyvida.com/portfolio.php
Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 2008 4(7): e1000136

Many Great Tools Out There
Oct. 12, 2010
Taverna

Where I See the Problems
The long tail is confused
Lack of interoperability between the options
The reward (publishing) is still removed from the available tools
Oct. 12, 2010

Oct. 12, 2010
Hard
Easy

Yes YouTube Can Increase the Rate of Discovery
Unleash the full power of the Internet

The Lab ExperimentPaper+Rich Media
My students enjoyed the experience
The shyest student was actually the most bold in front of the camera
“We will become a generation of “science castors”
They liked the exposure for the most part – rather than the PI it puts them out in front

Organic Growth
3 Years Later
www.scivee.tv
Some of their work viewed 20,000+ times
Global audience of researchers, educators and academic/research institutions
60,000 unique visitors & 2M pageviews/month
16,000 registered users & 600 communities
5,000 uploads of video content (about journal articles, conferences, research news and classes)
Growing 4-5% monthly
Sustainability - evolving a business model supporting journals and conferences

What Emerged: SciveeCasts
Products
ApplicationProductPrimary Customers
Journals PubCastJournals, publishers, societies
Meetings PosterCast Societies, conference orgs.
SlideCast
Comm. PaperCast Societies, journals
Podcast
SlideCast
Education PosterCast Societies, universities
SlideCast
BooksBookCast Publishers, book sellers

Summarizing the Reaming of Life
By “Life” I mean experiences in the Life Sciences
By “Reaming” I mean the the making of something smooth, fast and accurate
The Monty Python parody is on conversation cards for getting a dialog going ..
The rest is just a few examples of the small ways we are trying to address big problems in the hope they will inspire us all to think more deeply about the problem
Oct. 12, 2010

Acknowledgements
BioLit Team
Lynn Fink
Parker Williams
Marco Martinez
RahulChandran
Greg Quinn
MBT
John Moreland
John Beaver
Microsoft Scholarly Communications
Pablo Fernicola
Lee Dirks
SavasParastitidas
Alex Wade
Tony Hey
wwPDB team
Andreas Prilc
DimitrisDimitropoulos
SciVee Team
Apryl Bailey
Leo Chalupa
Lynn Fink
Marc Friedman (CEO)
Ken Liu
Alex Ramos
Willy Suwanto
Ben Yukich
http://www.scivee.tv
http://biolit.ucsd.edu
http//www.pdb.org
http://www.codeplex.com/ucsdbiolit

pbourne@ucsd.edu
Questions?

Jim Gray Award Lecture

by Philip Bourne on Oct 12, 2010

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