Chemistry Crowdsourcing and Open Notebook Science

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AbstractThis is a pre-proposal written for the NSF program CDI (Cyber-Enabled Discovery and Innovation) in Jan 2008.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.