Chemistry Validation and Standardization Platform v2.0
In recent years there has been explosive growth in the number of public chemical databases available online, a number of these containing 10s of millions of chemical structures. Examples include PubChem, ChemSpider and ChEMBL and users of these databases have become increasingly aware of the issue of data quality associated with these public resources. Seamless integration and mapping between databases, even for some common chemicals, is challenged by differing approaches to chemical standardization prior to registration into a database. The lack of standards in representing and handling chemical information certainly contributes to aspects of this problem. The Chemistry Validation and Standardization Platform (CVSP), originally developed to support the European Innovative Medicines Initiative project known as OpenPHACTS, was developed with the intention of providing an open platform for processing and standardizing chemical compounds. The system has been used to process millions of chemical compounds for dissemination through public websites and, unlike other validation and standardization systems, the system provides support for both standard and custom rulesets. We will provide an overview of CVSP 2.0, the next generation of the platform extending support to new cheminformatics toolkits and additional capabilities such as collaborative rules authoring.
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Chemistry Validation and Standardization Platform v2.0
- 1. Chemistry Validation and Standardization Platform Version 2.0 Valery Tkachenko1, Boris Sattarov1, Antony Williams2, Chris Grulke2 and Rick Zakharov1 1Science Data Software, Rockville, USA 2National Center for Computational Toxicology, US-EPA ACS Spring 2017 San Francisco, April 1-6th 2017
- 3. Predictive data models & toolsExperimental Design Data Analysis and Modeling Structured Data Repository Data collection, curation, integration, and structuring (ontology) Literature data Electronic Databases : Processing Experimental Data Disease Experimental Validation 3 Effect Decision support Karmann Mills and Anthony Hickey RTI International, RTP, NC 27709 and Alex Tropsha Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC 27599
- 5. We live in a hyperconnected World
- 7. Fourches, Muratov, Tropsha. Nat Chem Biol. 2015,11(8):535. How the problem is being solved now
- 8. [Very incomplete] list of common problems • Violations of chemical and common sense • Violations of valence bond theory • Unsupported format and chemical model features • Information loss during conversion • Tautomers • Stereochemical issues • Mixtures • Other classes of chemicals (materials, formulations, biologicals, structurally diverse, etc) • Equivalence/mapping issues • Identifiers/names issues • Etc, etc, etc…
- 9. …problems (continued) • Multiple [historical, proprietary, shortcoming] formats • ChemDraw, ChemSketch, AccelrysDraw • MOL, SDF • SMILES • Identifiers • Names and Synonyms • Multiple toolkits/models • Open Source (alphabetical) • CDK • RDKit • Indigo • OpenBabel • Etc… • Commercial (alphabetical) • CACTVS • ChemAxon • OpenEye • Etc… • Hystorical software • No [machine-readable] standards • No authorities No coordinated efforts!!!
- 10. Solution • Agreed and machine-readable (digital) standards • Open-source (and therefore fully transparent) solution • Organizational AND community support and involvement • Accessible solution • Data triaging at data repositories level • Real-time validation/standardization (API, library, “docker”, etc)
- 11. Big Data Integration 11 OpenPHACTS
- 13. OpenPHACTS Chemistry Registry System (CRS)
- 14. OpenPHACTS Chemistry Registry System (CRS)
- 16. Shortcomings of the original OpenPHACTS CRS approach • Platform-dependent • Toolkit-dependent (potential licensing issues) • No deployable library • No [convenient] API
- 17. …OpenPHACTS CRS1 - ongoing work • Microsoft platform independent • .NET Core, Python • Linux • NoSQL • Toolkit independent • Indigo • RDKit (in progress) • CDK (planned) • Docker image • RESTful API 1 Was open-sourced and now supported by the OpenPHACTS Foundation
- 18. CVSP on Jupyter - validation
- 19. CVSP on Jupyter - standardization
- 20. CVSP on Jupyter – ontologies, chemotypes, etc
- 21. The Comptox Chemistry Dashboard data • 747,000 chemical substances and ca. 727k chemical structures! • Diverse structures – organics, inorganics, organometallics • Fully open data available for download, reuse and repurposing: https://comptox.epa.gov/dashboard/downloads • Increasingly an integration hub for EPA chemical structure data • Strong team with cheminformatics experience • Manual curators to provide feedback on CVSP results and processing • Data processing to start shortly…
- 22. Example – Standardization of tautomers What form is preferred – Keto or Enol???
- 23. Open Science Data Repository
- 25. Meet the Team Alexandru Korotcov Data Science Rick Zakharov Technology Valery Tkachenko Ideas and plumbing Boris Sattarov Cheminformatics Slides: https://www.slideshare.net/valerytkachenko16Contact us: info@scidatasoft.com
Editor's Notes
- Open PHACTS was developed to support the key questions of drug discovery Business questions have been at the heart of Open PHACTS and have driven the development of the platform Mx/psa, how calculated who did it? Mash up. With your data too, - top layer join together but need them all commercial Data provided by many publishers Originally in many formats: relational, SD files and RDF Worked closely with publishers Data licensing was a major issue Over 5 billion triples – 14 datasets & growing Hosted on beefy hardware; data in memory (aim) Extensive memcaching Pose complex queries to extract data