ChemSpider as an Integration Hub for Interlinked
Chemistry Data
Antony WilliamsSETAC
November 18th 2013
How Much Data Online?
• How much data regarding environmental toxicology and chemistry is online?
• How can it all be mapped together?
A Grand Challenge….
• Let’s map together all historical chemistry data and build systems to integrate new data
• Let’s integrate chemistry, toxicology and biology data and add in disease data too
• Lets model the data and see if we can extract new relationships – quantitative and qualitative
• Let’s make it all available on the web
What about this….
• We’re going to map the world
• We’re going to take photos of as many places as we can and link them together
• We’ll let people annotate and curate the map
• Then let’s make it available free on the web
• We’ll make it available for decision making
• Put it on Mobile Devices, Give it Away
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
How to Map Data Together
• Download the structure representations and map together at the structure level
• Integrate and mesh chemical names, chemical properties, analytical data
• Carry URL links and retain external links to original data sets (assume no link decay)
• It sounds easy….
ChemSpider
• Build a HUB connecting as many data sources as possible
• NOT to harvest all data from each data source
• Today we have >29 million unique chemicals from >500 data sources
• Focus on improving data quality
• Allow users to enhance, curate and annotate
RSC’s ChemSpider
Identifiers are very useful! But what when they are “closed”
CAS Numbers Validation?
Various Registration Numbers
Mappings and Inconsistencies
PubChemDrugbankChemSpider
Imatinib
Mesylate
The InChI Identifier
InChIStrings Hash to InChIKeys
Vancomycin – Search the Internet
Vancomycin
Search Molecular SKELETON
Search Full Molecule
Full Skeleton Search: 529 Hits
Full Molecule Search: 294 Hits
Historical Data for reference
• As evidence that InChI is proliferating and data is improving:
• Three years ago there were only 104 hits on the complete InChI online
• Only 4 were correct
What you might not know about Chemistry Databases on the Internet
NCGC Pharma Collection
NCGC Pharma Collection
NCGC Pharma Collection
PHYSPROP Database
• The freely downloadable database under the EPI Suite prediction software
• Very Basic filters suggest data quality issues
The Stereochemistry challenge.12500 chemicals with “missed” stereo
NIST Webbook
PubChem
Patents
Patents
But Chemspider is curated right?
Originally 15 compounds “called” Yohimbine54 Skeletons for Yohimbine
Crowdsourced Curation
• Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
“Curate” Identifiers
Chemical name dictionaries for:
• Text-mining (publications, patents)• Used to index PubMed and link Google Patents
• Linking to other databases – think Biology!• When structures are not available names link
• Searching the web• Names link to structures link to InChIs
I want to know about “Vincristine”
Vincristine: Identifiers to link
Vincristine: Vendors and SourcesLinked by Structure
Vincristine: PatentsLinked by Name
Vincristine: ArticlesLinked by Name
What needs to happen?
• Standards• Standardization of structures
• More sharing of data – downloadable data collections for mapping, meshing and integration
• InChI adoption
• Collaboration• Stop reinventing the wheel• Share data, share efforts and speed the
process
Adopting Modified FDA Rules
Nitro groups
Salt and Ionic Bonds
Ammonium salts
What if we could capture it all?Digitally Enhancing the RSC Archive
Start with data in publications
Text Mining
The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-thiadiazol-5-yl)urea prepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer, thermometer and reflux condenser.
The reaction mixture was heated at reflux with stirring , for a period of about one-half hour.
After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
ChemSpider Reactions
Turn “Figures” Into Data
FIGURE
EXTRACTED DATA
Conclusions
• There are some amazing online resources for environmental toxicology and chemistry already!
• ChemSpider has an important role in quality data and linking resources
• Crowdsourced deposition, validation and curation works
• Standards are an important part of data linking
• MORE collaboration and data sharing can benefit us all
Thank you
Email: [email protected] Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams
