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The Royal Society of Chemistry is building a Global Chemistry Network which will connect chemical resources and chemists across the globe in a single scientific information network dynamically updated in real time. We have been working on a number of the foundation technologies for a number of years including a structure database containing almost 30 million chemicals, a micropublishing environment, a platform for the validation and standardization of chemical structure representations and a text-mining and semantic markup platform for data enabling our published articles. Our goal is to provide seamless tools for researchers, librarians, publishers, informational technology specialists and government agencies to facilitate scientific research by providing a free flow of information. This talk will review our work to date to provide a chemistry data platform for the community and will highlight some of the challenges we face as we expand the architecture for our Global Chemistry Network platform.
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Building Global Chemistry Network at the Royal Society of Chemistry
Valery Tkachenko
ICSTI Workshop
Data and Non-Data Integration –
A Journey Across Disciplines
Ottawa, October 16th 2013
The World we live in
Internet World20+ years into the Internet RevolutionWeb 2.0 -> Web 3.0
Connected WorldSocial NetworksReal-time Communications
Big Data WorldSemantic contentNew Interfaces
Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network
Chemistry on the Internet
Why disproportion?Scientific complexity
Conservative nature
Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network
Royal Society of Chemistry (RSC)
Largest European organisation for advancing the chemical sciencesFounded 1841Not-for profit “To be the leading voice and trusted partner for science and humanity”Professional body with a worldwide network of 48,000 members International publisher ~400 employeesEducation facilitator, Science leader, E-Science leaders
About the RSC• Headquarters in London• Offices in Cambridge, Beijing, Shanghai, Philadelphia, TokyoBangalore, Sao Paulo
STM publisher
Knowledge
Our User Interfaces(Desktop, Web, Mobile, etc)
Customers
Delivery Magic
3rd party integrations(our web services)
ChemSpider Suite
Data Layer
ChemSpider Assays
ChemSpider Compounds
ChemSpider Reactions
ChemSpider Spectra
ChemSpider Materials
ChemSpider Algorithms
Business Objects Layer
CSAs BOCSC BO CSR BO CSS BO CSM BO CSA BO
APIs Layer
DS APIExport APISearch API Processing API
CSAs APICSC API CSR API CSS API CSM API CSA API
Components Layer
JS Components Google AppsComponents
Python widgets
SharePointComponents
PHP snippets
ASP.NET Components
UIs
ChemSpider website
ChemSpider Reactions
mobile web app
ChemSpider desktop app
Depositions client
Java Beans
• 29 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
ChemSpider
ChemSpider
ChemSpider
ChemSpider
ChemSpider
ChemSpider
ChemSpider
ChemSpider
ChemSpider Reactions
ChemSpider Reactions
ChemSpider Reactions
ChemSpider Reactions
RSC Archive – since 1841
DERA - Digitally Enabling RSC Archive
Semantic Mark-up of Articles
It is so difficult to navigate…
What’s the structure?What’s the structure?
Are they in our file?
Are they in our file?
What’s similar?What’s
similar?
What’s the target?
What’s the target?Pharmacology
data?Pharmacology
data?
Known Pathways?
Known Pathways?
Working On Now?
Working On Now?Connections
to disease?Connections to disease?
Expressed in right cell type?Expressed in
right cell type?
Competitors?Competitors?
IP?IP?
DERA Architecture
Text, PDF, XML
Structures
Reactions
Spectra
Materials
Chemistry Validation andStandardization Platform
(CVSP)
DERA(Text Mining)
Biological Activities
Data quality issue and CVSP
Robochemistry
Proliferation of errors in public and private databases
Automated quality control system
DrugBank dataset (6516 records)
~60 records that can’t be dearomatized unambiguously
DB04283 DB04462
~30 records with bonds that do not make sense
DB04283
DDB04009
DB08128
J. Brechner, IUPACGraphical Representation of stereochem. configurationsSection: ST-1.1.10
DB06287
7 records with 2 stereo bonds at chiral atoms
“Direction of bond makes no sense” – 63%
“Stereo types of non-opposite bonds match” – 2%
ChemSpider Suite
Data Layer
ChemSpider Assays
ChemSpider Compounds
ChemSpider Reactions
ChemSpider Spectra
ChemSpider Materials
ChemSpider Algorithms
Business Objects Layer
CSAs BOCSC BO CSR BO CSS BO CSM BO CSA BO
APIs Layer
DS APIExport APISearch API Processing API
CSAs APICSC API CSR API CSS API CSM API CSA API
Components Layer
JS Components Google AppsComponents
Python widgets
SharePointComponents
PHP snippets
ASP.NET Components
UIs
ChemSpider website
ChemSpider Reactions
mobile web app
ChemSpider desktop app
Depositions client
Java Beans
Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network
AltMetrics
Plum Analytics
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 1st CSSP article.
Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network
Visualization
ChemSpider APIs
Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network
We are a part of a larger world
National Chemistry Database
National Data Repository
University 1
Data Hub
Workstations
University 2
Data Hub
Workstations
Company 3
Data Hub
Workstations
Data Repositoryindexed storage
Data Repository provideddata storage
Chemically intelligent services
Indexes
Data
External clients Publishers
Scientists Funding bodies
http://www.openphacts.org
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
We know about Natural Products
Marinlit
OSDD
Internet Data
The Future
Commercial SoftwarePre-competitive Data
Open ScienceOpen DataPublishersEducators
Open DatabasesChemical Vendors
Small organic moleculesUndefined materialsOrganometallicsNanomaterialsPolymersMineralsParticle boundLinks to Biologicals
