CDI-Type I: Chemistry Crowdsourcing using Open Notebook
Science
PI: Jean-Claude Bradley, Drexel University
Abstract
The current system of dissemination of scientific data and knowledge is far less efficient than it needs to
be to facilitate improved collaborative science, especially considering current publication vehicles and
infrastructure. There is a growing movement promoting more Open Science with the belief that a more
transparent scientific process can perform far more effectively. The logical extension of this concept is full
transparency - exposing a researcher's complete record of progress to the public in near real time. Not
only will such a process enable ongoing data sharing it also provides an opportunity to develop
collaborative communities of scientists and, at the conclusion of data acquisition, can enable communal
extraction of conclusions when necessary. We have named this approach Open Notebook Science and
have demonstrated its implementation and feasibility with the UsefulChem project, started in the summer
of 2005, with the aim of synthesizing novel anti-malarial compounds. Our system currently uses free
hosted services using general blog and wiki functions to facilitate replication across any scientific
domains. These services are not chemically intelligent and are limited to text and graphic based data
sharing only. For Open Notebook Chemistry the ability to intelligently manipulate, manage and search
chemical structures and associated data is necessary and we have demonstrated proof of concept
capabilities by integrating with the ChemSpider service, a free access online database managing
chemical structures and focused on developing a structure centric community for chemists. This work will
require the development of a chemically intelligent software platform to extend the capabilities of both the
blog and the wiki environment for managing Open Notebook Science. The exposure of raw experimental
procedures and data in a semantically rich format will enable the participation of both human and
autonomous agents in the process of scientific discovery. This phenomenon of spontaneous group
intelligence, referred to as "Crowdsourcing", has proven valuable in several contexts. Already, productive
collaborations have been forged within the UsefulChem project with groups from Indiana University,
Nanyang Technological University, the National Cancer Institute and UC San Francisco.
Intellectual Merit
The trends of Open Science, crowdsourcing, automation and cheminformatics are creating new
opportunities for increasing the efficiency of discovery. The integration of these phenomena promises to
enable new forms of scientific collaboration. This project brings together people who are uniquely
qualified to create an infrastructure to realize that potential.
Broader Impact
By its very nature, crowdsourcing is designed to connect people together in constructive and unexpected
ways. A key component of this project is to leverage the knowledge gained from an experiment in
crowdsourcing in a particular field and make it easier for it to be applied in other scientific collaborations.
The open nature of the project ensures that this knowledge will be disseminated nearly in real-time and
others interested in replicating such systems will have immediate access to advice and resources from
the participants. Already this replication effect has taken place, with other laboratories exposing their
work to Open Notebook Science conditions, stimulated by reports of the UsefulChem project.
Nature Precedings : doi:10.1038/npre.2008.1505.1 : Posted 9 Jan 2008

List of Participants
Jean-Claude Bradley, Drexel University, PI:
Jean-Claude Bradley is an Associate Professor of Chemistry and E-Learning Coordinator for the College
of Arts and Sciences at Drexel University. He leads the UsefulChem project, an initiative started in the
summer of 2005 to make the scientific process as transparent as possible by publishing all research work
in real time to a collection of public blogs, wikis and other web pages. Jean-Claude coined the term Open
Notebook Science to distinguish this approach from other more restricted forms of Open Science. The
main chemistry objective of the UsefulChem project is currently the synthesis and testing of novel anti-
malarial agents. The cheminformatics component aims to interface as much of the research work as
possible with autonomous agents to automate the scientific process in novel ways. Jean-Claude teaches
undergraduate organic chemistry courses with most content freely available on public blogs, wikis, games
and audio and video podcasts. Openness in research meshes well with openness in teaching. Real data
from the laboratory can be used in assignments to practice concepts learned in class. Jean-Claude has a
Ph.D. in organic chemistry and has published articles and obtained patents in the areas of synthetic and
mechanistic chemistry, gene therapy, nanotechnology and scientific knowledge management.
Kevin Owens, Drexel University, co-PI
Kevin Owens is an Associate Professor of Chemistry at Drexel University. His research group focuses on
the use of mass spectrometry for both biological and synthetic polymer analysis, specifically mechanistic
studies of the Matrix-Assisted Laser Desorption/Ionization (MALDI) process, application of MALDI to
synthetic polymer analysis, development of sample preparation methodologies for quantitative analysis by
MALDI Time-of-Flight Mass Spectrometry (TOFMS), TOFMS instrument development, and the application
of chemometric techniques (particularly correlation analysis) to aid in the automated interpretation of
mass spectral data. His latest work in the area of mass spectral interpretation involves the combination of
genetic algorithm techniques with correlation analysis to create mass spectral filters for the automated
identification of chemical substructures. His group maintains a number of wikis describing several of their
current research efforts. Kevin has a Ph.D. in analytical chemistry, and teaches the two-quarter
undergraduate instrumental analysis sequence, the graduate/undergraduate chemical information
retrieval course, as well as the graduate level mass spectrometry and statistics & experimental design
courses.
Antony Williams, ChemSpider, Senior Personnel
Antony Williams is a Senior Fellow at the National Institute of Statistical Sciences, is the President of
ChemZoo Inc., and is the host of ChemSpider, a Structure Centric Community for Chemists. Antony has
worked in academia, in industry (Eastman-Kodak) and in the commercial cheminformatics sector in the
role of Chief Science Officer. He has authored and co-authored over 100 scientific publications and
multiple invited book chapters. He has two issued patents and has one pending. His formal training is as
an NMR Spectroscopist with a focus on small molecule structure elucidation and analytical data
processing algorithms. the last decade of his career has been focused on the development of integrated
sample, structure and analytical data management systems at the desktop and at the enterprise level
utilizing web-based technologies. In the past year he has established a free access website, ChemSpider,
to provide access to chemistry-related information for almost 20 million chemical entities and their
associated data. He is interested in all aspects of cheminformatics, with special interest in chemical
structure handling, nomenclature and computer-assisted structure elucidation. He conducts research in
the area of data processing techniques for spectroscopy and development of the semantic web.
Nature Precedings : doi:10.1038/npre.2008.1505.1 : Posted 9 Jan 2008