Big Data Supporting Drug Discovery Cautionary Tales from the World of Chemistry for Translational Informatics Valery Tkachenko RSC-CSIR/OSDD meeting Pune, India February 3 rd 2014

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

Science map

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

Chemical space

Navigation in chemical space

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

Structure-based Drug Design

Ligand-based Drug Design

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

Machine learning

Applied machine learning

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

~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

ChemSpider

Properties - experimental

Properties - ACDLabs

Properties – EPI Suite

Properties - ChemAxon

Literature references

Patents references

Books

Classification

Chemical vendors and datasources

Multimedia

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

ChemSpider Reactions

ChemSpider Spectra

ChemSpider Databases ChemSpider Compounds ChemSpider Reactions ChemSpider Spectra ChemSpider Crystals ChemSpider Materials ChemSpider Assays ChemSpider Algorithms

Research data inflow

Research data outflow

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

RSC Archive – since 1841

DERA - Digitally Enabling RSC Archive

Semantic mark-up of articles

It is so difficult to navigate… What’s the structure? Are they in our file? What’s similar? What’s the target? Pharmacology data? Known Pathways? Working On Now? Connections to disease? Expressed in right cell type? Competitors? IP?

Data quality issue and CVSP –Robochemistry –Proliferation of errors in public and private databases –Automated quality control system

DrugBank dataset (6516 records) J. Brechner, IUPAC Graphical Representation of stereochem. configurations Section: ST DB06287

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

Research data management

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

Crowdsourcing

AltMetrics

RSC/Rewards and Recognition Congratulations! Your 1st CSSP article has been published. Philosopher Lao Tzu said “A journey of a thousand miles begins with a single step”. In the same way we hope that this will be the first of many submissions that you make to CSSP. The First Step badge is awarded when a user submits (& has published) their 1 st CSSP article.

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Visualization and navigation Building Global Chemistry Network

Visualization

Visualization and navigation

Big Data Chemical Space Drug Discovery pipeline Machine learning Training sets RSC/ChemSpider platforms RSC/Archive Research data management Data quality, crowdsourcing and AltMetrics Building Global Chemistry Network

We are a part of a larger world

ChemSpider APIs

National Chemistry Database

Open PHACTS is an Innovative Medicines Initiative (IMI) project, aiming to reduce the barriers to drug discovery in industry, academia and for small businesses. Semantic web is one of the corner stones

OSDD

Thank you Slides: