1.
eScience at the Royal Society of
Chemistry: Current Initiatives
Antony Williams
Cornell University, May 14th
2013

2.
We Have …Too Much Data!!!

3.
The World of Online Chemistry
• Property databases
• Compound aggregators
• Screening assay results
• Scientific publications
• Encyclopedic articles (Wikipedia)
• Metabolic pathway databases
• ADME/Tox data – eTOX for example
• Blogs/Wikis and Open Notebook Science

4.
e-Science and Primary Data
• How much data generated in a lab, that COULD go public, is
lost forever?

5.
e-Science and Primary Data
• How much data generated in a lab, that COULD go public, is
lost forever?
• Public Domain reference databases of value?
– Syntheses
– Properties
– Spectra
– CIFs
– Images

6.
e-Science and Primary Data
• How much data generated in a lab, that COULD go public, is
lost forever?
• Public Domain reference databases of value?
– Syntheses
– Properties
– Spectra
– CIFs
– Images
• Much of chemistry is chemical structure-based – where and
how could we host these data?

7.
RSC’s ChemSpider

8.
ChemSpider
• >28.5 million unique chemicals from >400
data sources
• Focus on improving data quality, enhancing
functionality, integrating and enabling

9.
Crowdsourced “Annotations”
• Users can add
– Descriptions/Syntheses/Commentaries
– Links to PubMed articles
– Links to articles via DOIs
– Add spectral data
– Add Crystallographic Information Files
– Add photos
– Add MP3 files
– Add Videos

10.
Spectra

11.
Chemistry Data online are messy
• We have inherited errors
• All public compound databases have errors
• “Incorrect” structures – assertions, timelines etc
• “Incorrect” names associated with structures
• Properties
• Links
• Publications
• ENORMOUS CHALLENGE

12.
Crowdsourced Curation
• Crowd-sourced curation: identify/tag errors,
edit names, synonyms, identify records to
deprecate

13.
Search “Vitamin H”

14.
“Curate” Identifiers

15.
“Curate” Identifiers

16.
“Curate” Identifiers

17.
Validated Name-Structure Dictionaries
• Chemical name dictionaries are used for:
• Text-mining (publications, patents)
– Used to index PubMed and link to Google Patents
• Linking to other databases – think Biology!
– When structures are not available drug names link
• Searching the web
– Names link to structures link to InChIs

18.
I want to know about “Vincristine”

19.
Vincristine: Identifiers and
Properties

20.
Vincristine: Vendors and Sources
Linked by Structure

21.
Vincristine: Patents
Linked by Name

22.
Vincristine: Articles
Linked by Name

23.
Semantic Mark-up of Articles

24.
Linking Names to Structures

25.
The InChI Identifier

26.
InChIStrings Hash to InChIKeys

27.
Vancomycin – Search the Internet

28.
Vancomycin
Search Molecular
SKELETON
Search Full Molecule

29.
Full Skeleton Search: 104 Hits

30.
Full Molecule Search: 4 Hits

31.
ChemSpider Resources for Chemistry

32.
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

33.
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

34.
Flexible ChemSpider API
http://www.chemspider.com/google/

35.
Flexible ChemSpider API

36.
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?

37.
Micropublishing Syntheses

38.
ChemSpider SyntheticPages

39.
Olympicene

40.
So you Want a Profile???

41.
Interactive Data

42.
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…

43.
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

44.
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?

45.
• 3-year Innovative Medicines Initiative project
• Integrating chemistry and biology data using semantic
web technologies
• Open source code, open data and open standards
• Academics, Pharma companies, Publishers….

46.
ChemSpider Contributions
• The host of the chemistry services
– Supplier of “standardized” chemical data files
– Chemistry searching (structure, substructure etc)
– Curator and data quality checking
• Now building the Open PHACTS chemical
registration system

47.
Natural Products Updates
• Names hard, Structures
“Obvious”
• New content based on
monthly updates of the
database
• Click through to the Natural
Products Updates entry

48.
National Chemical Database Service

49.
Chemical Database
Service
• National Chemical Database Service
for UK Academics
• Integrating Commercial Databases
and Services
• Chemicals, analytical data,
prediction algorithms
• Development of data repository

50.
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

51.
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

52.
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?

53.
Support for Chemical Reactions
• Integrating mined reaction data from patents
• Will also incorporate and integrate RSC
Databases: Methods of Organic Synthesis,
Catalysts and Catalyzed Reactions and…

54.
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?

55.
What if we could capture it all?
Digitally Enhancing the RSC Archive

56.
Start with data in publications

57.
Data Validation and Curation Required
Encouraging Participation with
Rewards and RECOGNITION

58.
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

59.
Structure Review

60.
Future Recognition in AltMetrics?
ChemSpider

61.
Internet Data
The Future
Commercial Software
Pre-competitive Data
Open Science
Open Data
Publishers
Educators
Open Databases
Chemical Vendors
Small organic molecules
Undefined materials
Organometallics
Nanomaterials
Polymers
Minerals
Particle bound
Links to Biologicals

62.
The Future of Chemistry on the Web?
• Public compound databases federate & build a
linked environment of validated data!
• Data validation needs are not ignored
• Publishers layer on information to make
publications discoverable
• Open Data proliferate
• The “Semantic Web” will continue to develop…

63.
Thank you
Email: williamsa@rsc.org
Twitter: @ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams