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eScience at the Royal Society of
Chemistry: Current Initiatives
Antony Williams
Cornell University, May 14th 2013
We Have …Too Much Data!!!
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
e-Science and Primary Data
•How much data generated in a lab, that COULD go public, is
lost forever?
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
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?
RSC’s ChemSpider
ChemSpider
•>28.5 million unique chemicals from >400
data sources
•Focus on improving data quality, enhancing
functionality, integrating and enabling
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
Spectra
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
Crowdsourced Curation
•Crowd-sourced curation: identify/tag errors,
edit names, synonyms, identify records to
deprecate
Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
“Curate” Identifiers
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
I want to know about “Vincristine”
Vincristine: Identifiers and Properties
Vincristine: Vendors and Sources
Linked by Structure
Vincristine: Patents
Linked by Name
Vincristine: Articles
Linked by Name
Semantic Mark-up of Articles
Linking Names to Structures
The InChI Identifier
InChIStrings Hash to InChIKeys
Vancomycin –Search the Internet
Vancomycin
Search Molecular
SKELETON
Search Full Molecule
Full Skeleton Search: 104 Hits
Full Molecule Search: 4 Hits
ChemSpider Resources for Chemistry
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
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
Flexible ChemSpider API
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?
Micropublishing Syntheses
ChemSpider SyntheticPages
Olympicene
So you Want a Profile???
Interactive Data
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…
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
It is so difficult to navigate…
What’s the
structure?
Are they in
our file?
What’s
similar?
What’s the
target?
Pharmacology
data?
Known
Pathways?
Working On
Now?
Connections to
disease?
Expressed in
right cell type?
Competitors?
IP?
•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….
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
Natural Products Updates
•Names hard, Structures
“Obvious”
•New content based on
monthly updates of the
database
•Click through to the Natural
Products Updates entry
National Chemical Database Service
Chemical Database
Service
•National Chemical Database
Service for UK Academics
•Integrating Commercial
Databases and Services
•Chemicals, analytical data,
prediction algorithms
•Development of data repository
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
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
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?
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…
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?
What if we could capture it all?
Digitally Enhancing the RSC Archive
Start with data in publications
Data Validation and Curation Required
Encouraging Participation with
Rewards and RECOGNITION
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
Structure Review
Future Recognition in AltMetrics?
ChemSpider
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
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…