chemspider compound database as one of the pillars of a semantic web for …

ChemSpider compound database as one of the pillars of a semantic web

for chemistry of the pillars of a

Valery Tkachenko, Antony J Williams,Ken Karapetyan, Colin Batchelor, Jon Steele, Aileen Day

and David Sharpe

ACS Philly August 2012

Outline

The world we live in Pillars of the world ChemSpider as a semantic web system Example of federated semantic web system

The World we live in Internet World

~20 years of WWW and inflationary expansion Web 2.0

Connected World Social Networks Mobile Communications Internet TV

Big Data World Semantic content New Interfaces

Pillars of the World Data is King

New data model approach: SQL NoSQL

Inflow of data

Structured data

Search and Navigation

Search by all domain specific information

Navigate inside and link out

Cloud

Data and code are distributed and self-sustained

Federated systems take precedence over standalone solutions

Interfaces

Sophisticated HCI (human computer interface)

Pervasive M2M (machine to machine)

Chemistry on the Internet

What’s wrong?!?! Is science (and chemistry in particular) so miserable in the

world we live in? Or too obscure and complex to be easily presented? Or scientists are rather conservative beasts?

Scientific data complexity

Chemical data complexity

ChemCloud

ChemSpider Database of small organic molecules

Properties

Names and synonyms

Spectra

Contribute in an easy way

New data depositions

Existing data curations

Search engine for chemistry

Search a chemical by a, b, c

Cluster and navigate relationships

Extensive infrastructure

Computer farm

Components

Standard interfaces

SOAP

REST

JSON

ChemSpider

Data

Filt

ers APIs

UI

BPF(distributed computing)

Deposition System

ChemSpider

Data

Filt

ers APIs

UI

BPF(distributed computing)

Validation and Standardization

ChemSpider

Data

Filt

ers APIs

UI

BPF(distributed computing)

User Interface

Web

Mobile

GUI components

JS Components

Google Search

Data

Filt

ers APIs

UI

BPF(distributed computing)

APIs SOAP

Traditional web services

REST/JSON Used in JS applications

RDF Exchange format for semantic web

SPARQL Query language

OpenPHACTS

Open PHACTS is an Innovative Medicines Initiative (IMI) – 3 years project

To reduce the barriers to drug discovery in industry, academia and for small businesses

To build an open platform, integrating chemistry and biology data from public domain resources

Open Standards, Open Data and Open Source

Acknowledgements RSC Cheminformatics group

Open PHACTS consortium

Software: GGA Software, ACD/Labs, Scilligence, OpenEye, Accelrys, ChemDoodle, ChemAxon, Dotmatics, OpenBabel, Jmol, JSpecView,

Thank you

Email: tkachenkov@rsc.org Blog: www.chemspider.com/blog SLIDES: http://www.slideshare.net/valerytkachenko16