1.
ChemSpider – disseminating data
and enabling an abundance of
chemistry platforms
Antony Williams, Valery Tkachenko, Ken Karapetyan, Alexey
Pshenichnov, Dmitry Ivanov, Colin Batchelor, Jon Steele
and David Sharpe
ACS New Orleans April 2013

2.
ChemSpider
• >28.5 million unique chemicals from >400
data sources
• Focus on improving data quality, enhancing
functionality, integrating and enabling

3.
Some usage statistics
• ca. 200 visitors at any one time, ~30,000 visits per day
• Mar 4-Apr 3, 2013
– Visits = 731,656
– Unique Visitors = 527,008
• Independent servers to support other projects

4.
Access ChemSpider
• APIs
– Programmatic access used by Mobile Apps, Funded
Consortia projects, many Academic groups
• Widgets
– UI components for embedding in other websites
• Data
– Data access, downloads, reuse, licensing

5.
Supporting the Semantic Web
rdf.chemspider.com/CSID

6.
ChemSpider Resources for Chemistry

7.
ChemSpider Audiences
Simplified interface
…..to this
From this…..

8.
Substance Pages

9.
It is so difficult to navigate…
IP?
IP?
What’s the
What’s the
structure?
structure?
Are they in
Are they in
our file?
our file?
What’s
What’s
similar?
similar?
What’s the
What’s the
Pharmacology
Pharmacology target?
target?
data?
data?
Known
Known
Pathways?
Pathways?
Competitors?
Competitors?
Working On
Working On
Connections to
Connections to Now?
Now?
disease?
disease?
Expressed in
Expressed in
right cell type?
right cell type?

10.
• 3-year knowledge management IMI project
• Integrating chemistry and biology data and delivering
using semantic web technologies
• Open source code, open data and open standards
• Academics, Pharma companies, Publishers….

11.
ChemSpider Contributions
• The host of the chemistry services
– Supplier of “standardized” chemical data files
– Chemistry searching (structure, substructure etc)
– Provider of data in RDF format
– Curator and data quality checking
• Now building the Open PHACTS chemical
registration system

12.
ChemSpider Contributions
• Supplier of chemistry UI components
• “Quality Police” for data checking
• Chemical Validation and Standardization Platform
• Nanopublications from RSC publications

13.
• FP7 Initiative. PharmaSea: increasing value and flow in
the marine biodiscovery pipeline

14.
PharmaSea
• Dereplication via ChemSpider
• Segregation of natural products datasets
• Analytical data algorithms & integration
– Mass spec searching – predicted fragmentation
– NMR feature searching – NMR prediction
– Computer-assisted structure elucidation

15.
Integrate to instruments and software
• Integration to analytical instrumentation vendors
already in place
– Agilent, Bruker, Thermo, Waters
• Also, Cheminformatics vendors link to ChemSpider
– Accelrys, ACD/Labs, ChemAxon, iChemLabs, and…

16.
Natural Products Updates
• Names hard, Structures
“Obvious”
• New content based on
monthly updates of the
database
• Click through to the Natural
Products Updates entry

17.
National Chemical Database Service

18.
Chemical Database
Service
• National Chemical Database Service
for UK Academics
• Integrating Commercial Databases
and Services
• Chemicals, analytical data,
prediction algorithms
• Development of data repository

19.
Retrosynthetic Analysis

20.
Publications - a summary of work
• Scientific publications are a summary of work
– Is all work reported?
– How much science is lost to pruning?
– What of value sits in notebooks and is lost?
• How much data is lost?
– How many compounds never reported?
– How many syntheses fail or succeed?
– How many characterization measurements?

21.
Community Repository for Data
• Funding agencies encourage sharing of data
• Increasing availability of “Open Data”
• Institutional repositories no specific domain
support
• Develop a community repository for chemistry
data – private, public, embargoed
• Provides data to develop models/algorithms

22.
Community Repository for Data
• Automated depositions of data
• DOI’ed data objects for citation purposes
• A database of reference data, but validated by
the community
• National services feeding the repository –
crystallography, mass spectrometry
• Integrate to blogging tools for chemistry
• Integrate to Electronic Lab Notebooks as feeds

23.
Model Building with Community Data
• Community data as a basis of model building
– Consume data from available databases, community
data, new publications and build predictive
algorithms for the community
– How many algorithms are reported and lost? How
much repeat work is done in the domain of
algorithmic development?

24.
Recognition on
Data
IC50 Measurements for 62 substituted benzoxazoles
ChemSpider Data Repository: DOI: 10.1356/CSID784.4

25.
Integrate to electronic lab notebooks

26.
E-Lab Notebooks
• Previous work with IDBS and
University of Cambridge
• Working on LabTrove integration
win U. Southampton
• Integration between ELNs and:
• ChemSpider
• ChemSpider Reactions
• CDS Repository
• Publish data from ELNs issue DOIs
• Data aggregated into fully indexed
ESI format for publication

27.
Support for Chemical Reactions
• Integrating mined reaction data from patents
(Daniel Lowe)
• Will also incorporate and integrate: Methods
of Organic Synthesis, Catalysts and Catalyzed
Reactions and…

28.
Micro-publishing Chemical Reactions

29.
ChemSpider SyntheticPages

30.
Retrosynthetic Analysis

31.
Inside our Publication Archive
• How much data is in the archive, in the
publications and in the supplementary info?
– How many compounds for ChemSpider?
– How many syntheses for ChemSpider reactions?
– How many characterization measurements?
• Property Data
• Spectral Data
• Graphs and charts to be used for modeling?

32.
What if we could capture it all?
Digitally Enhancing the RSC Archive

33.
Start with data in publications

34.
Recent Work

35.
Comparison of Spectra

36.
Data Validation and Curation Required

37.
CVSP: Validation and Standardization

38.
Data Validation and Curation Required
Encouraging Participation with
Rewards and RECOGNITION

39.
Manual Curation
• Integrated commenting, curating and validation
platform across ALL eScience and publishing
platforms
• All integrated to a central RSC profile and
feeding the AltMetrics tools

40.
Structure Review

41.
Where we are now…

42.
Rewards and Recognition
The First Step badge is
awarded when a user
submits (& has published)
their 1st CSSP article.
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.

43.
Future Recognition in AltMetrics?
ChemSpider

44.
Why is ChemSpider “different”
• Interfaces for integration
• Sharing of data – and increasingly open
• Open for community participation
– Deposition
– Annotation
– Curation
• We are clear…the world is changing

45.
The Future
Internet Data
Small organic molecules Commercial Software
Undefined materials Pre-competitive Data
Organometallics Open Science
Nanomaterials Open Data
Polymers Publishers
Minerals Educators
Particle bound Open Databases
Links to Biologicals Chemical Vendors

46.
Acknowledgments
• The RSC eScience and infrastructure teams
• Our data providers, depositors, collaborators
and curators
• Daniel Lowe for Reaction Data
• William Brouwer, Penn State
• Software providers – OpenEye, ChemDoodle,
ACD/Labs, GGA Software, Open Source (Jmol,
JSpecView, OpenBabel)

47.
Thank you
Email: williamsa@rsc.org
Twitter: ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams