chemspider compound database as one of the pillars of a semantic web for …
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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?
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: [email protected] Blog: www.chemspider.com/blog SLIDES: http://www.slideshare.net/valerytkachenko16