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

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Valery Tkachenko

Technology Education

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)

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?

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 UI

Filters

APIs
Data

BPF
(distributed computing)

User Interface
 Web

 Mobile

 GUI components

UI

Filters

APIs
Data

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

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OMPOL – visualisation of large chemical spaces

Valery Tkachenko

The need for a high quality reaction database underpins synthetic reaction planning, as highlighted by the roadmap of the Dial-a-Molecule grand challenge [1] (the aims of which are to be able to predict the outcome of a reaction a priori and therefore generate products on demand, and also to optimise a reaction). A number of reaction databases are available [2] - most of these focus on storing basic reaction schemas and details and link to publications for more details. However their main limitation is that because their major source is the abstraction of published literature, insufficient structured reaction detail is recorded: for someone else to reproduce the reaction to fully record all reaction products (not just the target product) previous attempts to reach the optimised reaction route so that this "work-up" can be correlated to allow better prediction of reaction outcomes. As a result, the reactions domain of the chemical data repository that the Royal Society of Chemistry is developing will capture: reactions and processes directly from Electronic Lab Notebooks reactions which gave low yields or unintended products processes, parameters and equipment in S88 process recipe [3] style for maximum reproducibility multistep reactions reactants, products etc. not just as small organic molecules raw characterisation data linked to products We will demonstrate a first version, populated with reactions text-mined from RSC articles and examples of notebook reactions and processes as recorded by an academic research group at Cornell University. [1] Dial a Molecule Grand Challenge, http://generic.wordpress.soton.ac.uk/dial-a-molecule/ (accessed Oct 8, 2015) [2] Organic Chemistry Resources Worldwide, http://www.organicworldwide.net/content/reaction-databases (accessed Oct 8, 2015) [3] ISA, "Batch Control Part 1: Model and Terminology," The International Society for Measurement and Control, ISA Press, ISA - S88.01-1995

Not just another reaction database

Valery Tkachenko

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