Providing Support for JC Bradley’s Vision of Open Science using RSC
Cheminformatics Platforms
Antony Williams
Jean-Claude Bradley Memorial Symposium
July 14th 2014
How Visions Aligned…• We serve the community with data, services
and platforms to support science
• So much of what JC (and Andy!) needed already existed on ChemSpider
• Many members of our team helped for the sake of science…working outside work hours…data curation
• Some of us bought into the vision of Open Notebook Science…ahead of the curve
• So how did we help??
• ~30 million chemicals and growing
• Data sourced from >500 different sources
• Crowdsourced curation and annotation
• Ongoing deposition of data from our journals and our collaborators
• A structure centric hub for web-searching
• JC tapped into ChemSpider a lot for data validation and integration to his ONS wikis
ChemSpider
APIs
APIs
ChemSpider Spectra
Where can SpectralGame Go?
• We are interested in supporting extensions and enhancements to SpectralGame
• More data required….our spectral data repository can host it
• Hosting assigned spectral data and using in SpectralGame makes sense!
• And what about educating/testing students as they do real time assignments?
• A project for when there is time and interest…
Javascript viewer NMR, MS, IR
Collaborations in Openness
• JC believed in HIGH-QUALITY data
• He invested himself, and his students, in validating, checking and re-measuring data
• He demanded openness of data, free of restrictions and constraints
• Do his efforts make a difference???
Supporting Open Data
Data Validation/Standardization is critical – about to apply to MP
Thanks to Igor Tetko, OCHEM
Collaborations in Openness
• JC believed in HIGH-QUALITY data
• He invested himself, and his students, in validating, checking and re-measuring data
• He demanded openness of data, free of restrictions and constraints
• Do his efforts make a difference???
• How can the resulting models be used?
• Free prediction engines, warning/flagging data in ELNs, at deposition into databases
Text-mining Data – Daniel Lowe
Open Notebook Science Wikis
• The vast majority of scientists don’t want or don’t have the skills to manage ONS systems
• If they had the right platform for ONS they might just use it…
• But we hear: privacy before sharing, more functionality required, not what I need etc.
• We provided data storage and access first (and JC used it) and are now collaborating on ELNs
Building the RSC Data Repository
• Registration of chemical compounds• Deposition of chemical syntheses• Addition of analytical data • Integration to electronic notebooks• Rewards and recognition for data sharing• Document processing• Hosting of data as private, embargoed or
public
What we will deliver for all data
• Simple interfaces for uploading of data
• Embeddable widgets and programming interfaces to utilize in in-house systems, ELNs
• Automated harvesting approaches
• Data validation approaches where possible
JC and Drug Discovery
• JC cared passionately about neglected disease research
• Many of our conversations were around better data-sharing for the various groups
• We are trying to help…
Open Source Drug Discovery
OSDD Collaboration
• We will provide access and support to the ChemSpider API to integrate to their OSDD cheminformatics platform
• We will extend our data model to support their Open Data – compounds, pharmacology data
• Synthetic reactions will be published to ChemSpider SyntheticPages and Reactions
• Analytical Data to be hosted in Data Repository
• 3-year Innovative Medicines Initiative project
• Integrating chemistry and biology data using semantic web technologies
• Open source code, open data and open standards
• Academics, Pharmas, Publishers…• To put medicines in the pipeline…
Open Sourcing Data and Code
• All Open PHACTS data is licensed as Open Data and available from Open PHACTS website – ca. 2 Million chemicals
• The Chemical Registration Service, including Chemical Validation and Standardization Platform will be released as Open Source code to the community (from Open PHACTS github site)
Thank you
Email: [email protected]: 0000-0002-2668-4821 Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams
