Providing support for JC Bradleys vision of open science using RSC cheminformatics platforms
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Providing support for JC Bradleys vision of open science using RSC cheminformatics platforms

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Jean-Claude Bradley had an incredible passion for providing open science tools and data to the community. He had boundless energy, no shortage of ideas and ran so many projects in parallel that it......

Jean-Claude Bradley had an incredible passion for providing open science tools and data to the community. He had boundless energy, no shortage of ideas and ran so many projects in parallel that it was often difficult to keep up. But at RSC we tried. We provided access to our data, our application programming interfaces and lots of our out-of-hours time to help turn his vision into reality. As a result we helped in the delivery of the SpectralGame to help people learn about NMR and we supported the integration of our services into GoogleDocs underpinning the management and curation of physicochemical property data. We tweaked a number of our services based on JC’s input and as a result we have ended up with a suite of capabilities that serve many of our existing efforts to integrate to electronic lab notebooks and support the ongoing shift towards Open Chemistry. JC was very much ahead of his time….and we were glad to have supported his work. This presentation will give a snapshot of some of the work we did to support his vision.

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  • 1. Providing Support for JC Bradley’s Vision of Open Science using RSC Cheminformatics Platforms Antony Williams Jean-Claude Bradley Memorial Symposium July 14th 2014
  • 2. 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??
  • 3. • ~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
  • 4. ChemSpider
  • 5. APIs
  • 6. APIs
  • 7. ChemSpider Spectra
  • 8. www.SpectralGame.com http://www.jcheminf.com/content/1/1/9
  • 9. 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…
  • 10. Javascript viewer NMR, MS, IR
  • 11. 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???
  • 12. Supporting Open Data
  • 13. Data Validation/Standardization is critical – about to apply to MP
  • 14. Thanks to Igor Tetko, OCHEM
  • 15. 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
  • 16. Text-mining Data – Daniel Lowe
  • 17. 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
  • 18. 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
  • 19. 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
  • 20. 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…
  • 21. Open Source Drug Discovery
  • 22. 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
  • 23. • 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…
  • 24. 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)
  • 25. Thank you Email: williamsa@rsc.org ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams