Open innovation contributions from RSC resulting from the Open Phacts project

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The Royal Society of Chemistry was pleased to contribute to the Open PHACTS project, a 3 year project funded by the Innovative Medicines Initiative fund from the European Union. For three years we …

The Royal Society of Chemistry was pleased to contribute to the Open PHACTS project, a 3 year project funded by the Innovative Medicines Initiative fund from the European Union. For three years we developed our existing platforms, created new and innovative widgets and data platforms to handle chemistry data, extended existing chemistry ontologies and embraced the semantic web open standards. As a result RSC served as the centralized chemistry data hub for the project. With the conclusion of the Open PHACTS project we will report on our experiences resulting from our participation in the project and provide an overview of what tools, capabilities and data have been released into the community as a result of our participation and how this may influence future projects. This will include the Open PHACTS open chemistry data dump including the chemistry related data in chemistry and semantic web consumable formats as well as some of the resulting chemistry software released to the community. The Open PHACTS project resulted in significant contributions to the chemistry community as well as the supporting pharmaceutical companies and biomedical community.

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  • Mx/psa, how calculated who did it?
    Mash up. With your data too,
    - top layer join together but need them all
    commerical
  • 10
    Can go get everything
    OPS not a repo of the world, specific sources

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  • 1. Open innovation and chemistry data management contributions from RSC resulting from the Open PHACTS project Antony Williams, Valery Tkachenko, Ken Karapetyan, Alexey Pshenichnov, Colin Batchelor, Jon Steele & David Sharpe ACS San Francisco August 2014
  • 2. 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. Fundamental issue: •There is a LOT of science online! •Chaotic, varying quality and very valuable! •Scientists want to find information quickly and easily •Often they just “can’t get there” (or don’t even know where “there” is) •And you have to manage it all (or not)
  • 4. Pre-competitive Informatics: Pharma are all accessing, processing, storing & re-processing external research data Literature PubChem Genbank Patents Databases Downloads Data Integration Data Analysis Firewalled Databases Repeat @ each company x Lowering industry firewalls: pre-competitive informatics in drug discovery Nature Reviews Drug Discovery (2009) 8, 701-708 doi:10.1038/nrd2944
  • 5. ChEMBLChEMBL DrugBankDrugBank Gene Ontology Gene Ontology WikipathwaysWikipathways UniProtUniProt ChemSpiderChemSpider UMLSUMLS ConceptWikiConceptWiki ChEBIChEBI TrialTroveTrialTrove GVKBioGVKBio GeneGoGeneGo TR IntegrityTR Integrity “Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM” “What is the selectivity profile of known p38 inhibitors?” “Let me compare MW, logP and PSA for known oxidoreductase inhibitors”
  • 6. Business Question Driven Approach
  • 7. • 3-year Innovative Medicines Initiative project • Integrating chemistry and biology data using semantic web technologies • Open source code, open data and open standards • Academics, Pharmas, Publishers… • To put medicines in the pipeline…
  • 8. The Open PHACTS community ecosystem
  • 9. Originally used ChemSpider..
  • 10. Open PHACTS Deliverables • Many details but overall… • Deliver an Open Source chemical registry service, independent of ChemSpider • Development of Open Source CVSP platform • Deliver widgets and APIs to the project • Deliver high quality, standardized Open Data • Deliver structure data in RDF format
  • 11. Standardize • Use the SRS as guidance for standardization • Adjust as necessary to our needs
  • 12. Nitro groups
  • 13. Salt and Ionic Bonds
  • 14. Depositions Gateway User Interface
  • 15. Validate and Standardize
  • 16. CVSP Filtering
  • 17. CVSP Filtering of DrugBank
  • 18. ChEMBL (1.3 million records) • 11,020 records with 4 bonds and zero charge, e.g. CHEMBL501101 or CHEMBL501973 • 271 records with hypervalent oxygen (e.g. , CHEMBL2219679), carbon (e.g. 1005895), boron, chlorine, iodine or phosphine • 6,177 records where direction of bond makes no sense, e.g. CHEMBL12760 and CHEMBL34704
  • 19. OPS1 DrugBank ID DB07241 OPS5OPS4 OPS3 OPS2 OPS6 ops:OPS1 skos:exactMatch <http://www4.wiwiss.fu- berlin.de/drugbank/resource/drugs/DB07241> . ops:OPS2 skos:relatedMatch ops:OPS1 . ops:OPS3 skos:relatedMatch ops:OPS1 . ops:OPS3 skos:closeMatch ops:OPS4 . ops:OPS3 skos:closeMatch ops:OPS5 . ops:OPS4 skos:closeMatch ops:OPS6 . ops:OPS5 skos:closeMatch ops:OPS6 . Chemical Registry Service
  • 20. Open Sourcing Data and Code • All Open PHACTS data is licensed as Open Data and available from Open PHACTS website – ca. 2 Million chemicals • The Chemical Registration Service, including Chemical Validation and Standardization Platform preparing as Open Source now!
  • 21. RSC data in Open PHACTS 1. Molecule synonyms and identifiers 2. Linksets between ChEBI, ChEMBL, DrugBank and OPS identifiers 3. Molecule–molecule relations (“parent–child”) of interest for drug discovery 4. Calculated physicochemical properties for compounds (both molecular and macroscopic)
  • 22. Our RDF schema Two dozen calculated properties >106 molecules •CHEMINF ontology for cheminformatics •QUDT for units and numeric values •ChemSpider IDs for molecules
  • 23. Synonyms and identifiers Newly added to the CHEMINF ontology: •Validated ChemSpider synonyms •Unvalidated ChemSpider synonyms •Validated database identifiers •Unvalidated database identifiers •InChI, InChIKey, SMILES •Preferred ChemSpider name
  • 24. Physicochemical properties • log P • log D (at pH 5.5 and 7.4) • bioconcentration factor KOC (at pH 5.5, at pH 7.4) • index of refraction • polar surface area • molar refractivity • molar volume • Polarizability • surface tension • density at STP • flash point at 1 atm • boiling point at 1 atm • enthalpy of vaporization at STP • vapour pressure at STP
  • 25. RDF exports from CRS
  • 26. benzene’s connection table OPS benzene calculation result QUDT dimensionless quantity “2.17”^^xsd:float IAO is about OBI has specified output OBI has specified input QUDT has value QUDT has standard uncertainty QUDT has unit CHEMINF calculated log P rdf:type CHEMINF connection table rdf:type “0.234”^^xsd:float calculation process CHEMINF execution of ACD/Labs PhysChem software library version 12.01 rdf:type It is actually more complicated..
  • 27. What’s built on top of this?
  • 28. Important for other projects • Multiple outputs from the project available for reuse to underpin other projects: • Chemical registry service • Chemical validation and standardization • APIs and visualization widgets
  • 29. New Repository Architecture doi: 10.1007/s10822-014-9784-5
  • 30. New Repository Architecture Compounds Reactions Spectra Materials Documents Compounds API Reactions API Spectra API Materials API Documents API Compounds Widgets Reactions Widgets Spectra Widgets Materials Widgets Documents Widgets Data tier Data access tier User interface components tier Analytical Laboratory application User interface tier (examples) Electronic Laboratory Notebook Paid 3rd party integrations (various platforms – SharePoint, Google, etc) Chemical Inventory application
  • 31. Input data pipeline Deposition Gateway Staging databases Compounds Reactions Spectra Materials Articles / CSSP Compounds Module Spectra Module Reactions Module Materials Module Textmining Module ͙ Module Web UI for unified depositions DropBox, Google Drive, SkyDrive, etc LabTroveand other templated data Documents API, FTP, etc Raw data Validated data Staging databases Alldatabases are sliced by data sources/data collections and havesimple security model where each data slice/sourceis private, public or embargoed
  • 32. Compounds
  • 33. Reactions
  • 34. Analytical data
  • 35. For Deposition of Data • Quality of data at source • ensuring chemicals are correct - VALIDATION • reactions map and balance as appropriate – VALIDATION and STANDARDIZATION • file format handling for analytical data types – binary file formats are proprietary - STANDARDIZATION • valid interpretation of data – VALIDATION and ANNOTATION
  • 36. Input data pipeline Deposition Gateway Staging databases Compounds Reactions Spectra Materials Articles / CSSP Compounds Module Spectra Module Reactions Module Materials Module Textmining Module ͙ Module Web UI for unified depositions DropBox, Google Drive, SkyDrive, etc LabTroveand other templated data Documents API, FTP, etc Raw data Validated data Staging databases Alldatabases are sliced by data sources/data collections and havesimple security model where each data slice/sourceis private, public or embargoed
  • 37. Deposition of Data
  • 38. User Interface Approach Compounds Reactions Spectra Materials Documents Compounds API Reactions API Spectra API Materials API Documents API Compounds Widgets Reactions Widgets Spectra Widgets Materials Widgets Documents Widgets Data tier Data access tier User interface components tier Analytical Laboratory application User interface tier (examples) Electronic Laboratory Notebook Paid 3rd party integrations (various platforms – SharePoint, Google, etc) Chemical Inventory application
  • 39. User Interface Approach Compounds Reactions Spectra Materials Documents Compounds API Reactions API Spectra API Materials API Documents API Compounds Widgets Reactions Widgets Spectra Widgets Materials Widgets Documents Widgets Data tier Data access tier User interface components tier Analytical Laboratory application User interface tier (examples) Electronic Laboratory Notebook Paid 3rd party integrations (various platforms – SharePoint, Google, etc) Chemical Inventory application
  • 40. Work in Progress
  • 41. User Interface Approach Compounds Reactions Spectra Materials Documents Compounds API Reactions API Spectra API Materials API Documents API Compounds Widgets Reactions Widgets Spectra Widgets Materials Widgets Documents Widgets Data tier Data access tier User interface components tier Analytical Laboratory application User interface tier (examples) Electronic Laboratory Notebook Paid 3rd party integrations (various platforms – SharePoint, Google, etc) Chemical Inventory application
  • 42. A Compounds Repository Interface
  • 43. The PharmaSea Website
  • 44. The Open PHACTS community ecosystem
  • 45. Open PHACTS Project Partners Pfizer Limited – Coordinator Universität Wien – Managing entity Technical University of Denmark University of Hamburg, Center for Bioinformatics BioSolveIT GmBH Consorci Mar Parc de Salut de Barcelona Leiden University Medical Centre Royal Society of Chemistry Vrije Universiteit Amsterdam Spanish National Cancer Research Centre University of Manchester Maastricht University Aqnowledge University of Santiago de Compostela Rheinische Friedrich-Wilhelms-Universität Bonn AstraZeneca GlaxoSmithKline Esteve Novartis Merck Serono H. Lundbeck A/S Eli Lilly Netherlands Bioinformatics Centre Swiss Institute of Bioinformatics ConnectedDiscovery EMBL-European Bioinformatics Institute Janssen OpenLink
  • 46. Thank you Email: williamsa@rsc.org ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams