chemspider as an integration hub for interlinked chemistry data

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: williamsa@rsc.org Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams