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

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

www.SpectralGame.comhttp://www.jcheminf.com/content/1/1/9

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…

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: williamsa@rsc.orgORCID: 0000-0002-2668-4821 Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams