eScience at the Royal Society of Chemistry and our current initiatives
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eScience at the Royal Society of Chemistry: Current Initiatives Antony Williams Cornell University, May 14 th 2013
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Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this eScience cheminformatics platform and the nature of the solutions that it helps to enable including structure validation, text mining and semantic markup, the National Chemical Database Service for the United Kingdom and the development of a chemistry data repository. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.
Transcript of eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry: Current Initiatives
Antony WilliamsCornell 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 SourcesLinked by Structure
Vincristine: PatentsLinked by Name
Vincristine: ArticlesLinked 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?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?
• 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 SoftwarePre-competitive Data
Open ScienceOpen DataPublishersEducators
Open DatabasesChemical Vendors
Small organic moleculesUndefined materialsOrganometallicsNanomaterialsPolymersMineralsParticle boundLinks 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…
Thank you
Email: [email protected] Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams
