Andrea de SouzaDirector, Informatics, Data Analysis & FinanceCenter for the Science of TherapeuticsMay 29, 2013BioAssay Re...
Direct ContributorsNIH Molecular Libraries – Glenn McFadden, Ajay PillaiNIH Chemical Genomics Center – Chris Austin (PI), ...
BARD: BioAssay Research DatabaseMission: Enable biomedical researchers and cheminformaticscientists to effectively use MLP...
BARD: BioAssay Research DatabaseMission: Enable biomedical researchers and cheminformaticscientists to effectively use MLP...
Research Data ManagementThe Value of Context
The Value of ContextResearch Data Management
PubChem BioAssay
PubChem BioAssay and BARDstructure the data
PubChem BioAssay and BARDPubChem BARDMissing or fuzzy assay definitions,experiments and project conceptsIntroduce assay de...
EntrezUniprotGene Ontology Gene OntologyDiseaseOntologyBioAssay Ontology BioAssay Ontology BioAssay Ontology BioAssay Onto...
BARD Technology ComponentsDefine & RegisterAssaysData Dictionary – std termsCatalog of Assay ProtocolsHigh Quality Data &R...
BARD Technology ComponentsDefine & RegisterAssaysData Dictionary – std termsCatalog of Assay ProtocolsHigh Quality Data &R...
Web ClientFilter on annotations, such asdetection method typeGoogle-like searching of: 4,000+ assays, 35M+ compounds, 300+...
Web Client - Project Specific Views
Web Client – Probe Development Workflow
Sunburst VisualizationMolecular activity against target classesTarget classifications from PantherDBPANTHER in 2013: model...
JerseyD3.jsWeb Query & Desktop ClientsData Warehouse & REST API Catalog of Assay ProtocolsCommercial LicenseMySQL support ...
Chemaxon Usage in BARDUNM Promiscuity PluginJChem for scaffold decompositionREST API & WarehouseJChem for rendering struct...
Chemaxon Usage in BARDWeb Query ClientJChem for rendering structuresDesktop ClientJChem for rendering structures,molecule ...
• BioActivity Data AssociativePromiscuity Pattern Learning Engine• Associations via scaffolds for chemicalspace navigation...
Predictive Models• Predicts CYP450 isoformsmetabolism sites with 2Dstructures• Patrik Rydberg et. al• Released under LGPL•...
Navigating the Maze
Long-Term Path ForwardMLPTBDNCI-60TBDDatasetsCAP WebQueryDesktopAPIsToolsBADAppleCYP450TBDTBDMethods Data AnalysisWorkflow...
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BioAssay Research Database Presentation at the Chem Axon UGM 2013

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BioAssay Research Database Presentation at the Chem Axon UGM 2013

  1. 1. Andrea de SouzaDirector, Informatics, Data Analysis & FinanceCenter for the Science of TherapeuticsMay 29, 2013BioAssay Research Database
  2. 2. Direct ContributorsNIH Molecular Libraries – Glenn McFadden, Ajay PillaiNIH Chemical Genomics Center – Chris Austin (PI), John Braisted, MarcFerrer, Rajarshi Guha, Ajit Jadhav, Dac-Trung Nguyen, Tyler Peryea, NoelSouthall, Henrike VeithBroad Institute – Benjamin Alexander, Jacob Asiedu, Kay Aubrey, JoshuaBittker, Steve Brudz, Simon Chatwin, Paul Clemons, Vlado Dancik, SivaDandapani, Andrea de Souza, Dan Durkin, David Lahr, Jeri Levine, JudyMcGloughlin, Phil Montgomery, Jose Perez, Stuart Schreiber (PI), GilWalzer, Xiaorong XiangUniversity of New Mexico – Cristian Bologa, Steve Mathias, Tudor Oprea,Larry Sklar (PI), Oleg Ursu, Anna Waller, Jeremy YangUniversity of Miami – Saminda Abeyruwan, Hande Küküc, VanceLemmon, Ahsan Mir, Magdalena Przydzial, Kunie Sakurai, StephanSchürer, Uma Vempati, Ubbo VisserVanderbilt University – Eric Dawson, Bill Graham, Craig Lindsley (PI),Shaun StaufferSanford-Burnham Medical Research Institute – “T.C.” Chung, JenaDiwan, Michael Hedrick, Gavin Magnuson, Siobhan Malany, Ian Pass,Anthony Pinkerton, Derek Stonich, John Reed (PI)Scripps Research Institute – Yasel Cruz, Mark Southern,Hugh Rosen (PI)
  3. 3. BARD: BioAssay Research DatabaseMission: Enable biomedical researchers and cheminformaticscientists to effectively use MLP data to generate newhypotheses• Unique collaboration amongst 7 NIH & academic centers• Develop and adopt an Assay Definition Standard (ADS)• Provide tools for assay registration, querying &visualizationo Deploy predictive modelso Foster new methods to interpret chemical biology datao Enable private data sharing• Developed as an open-source, industrial-strengthplatform to support public translational research
  4. 4. BARD: BioAssay Research DatabaseMission: Enable biomedical researchers and cheminformaticscientists to effectively use MLP data to generate newhypothesesTeam Science• Provide tools for assay registration and data querying &visualizationo Deploy predictive modelso Foster new methods to interpret chemical biology datao Enable private data sharing• Developed as an open-source, industrial-strength platform toResearch Data ManagementTechnologyPredictive ModelsThe BARD platform will support public translational research
  5. 5. Research Data ManagementThe Value of Context
  6. 6. The Value of ContextResearch Data Management
  7. 7. PubChem BioAssay
  8. 8. PubChem BioAssay and BARDstructure the data
  9. 9. PubChem BioAssay and BARDPubChem BARDMissing or fuzzy assay definitions,experiments and project conceptsIntroduce assay definitions,experiments and projects‘Column header’ centric withconcentration details embeddedResult types and concentrations asexperimental variablesExtensive use of unstructured text Transition to structured use ofcommon languagePubChemMLP-BioAssaystructurethe data
  10. 10. EntrezUniprotGene Ontology Gene OntologyDiseaseOntologyBioAssay Ontology BioAssay Ontology BioAssay Ontology BioAssay OntologyUnitOntologyUniprot UniprotUnitOntologyBARD Dictionary & Term HierarchyChemicalOntologyBARD Assay Definition Hierarchy• Annotate all assays to a minimum standard• Integrate and extend ontologies• Enable assay registration• Represent assays, results, experiments using ADS• Exchange information in ADS via ADFStructuring the Data
  11. 11. BARD Technology ComponentsDefine & RegisterAssaysData Dictionary – std termsCatalog of Assay ProtocolsHigh Quality Data &Result DepositionCalculations & ResultsProject-experiment associationQuery & InterpretInformationIntuitive Guided QueriesCross Assay & SAR centric viewsAdvance applicationsEnableHypothesisGenerationNovice Expert
  12. 12. BARD Technology ComponentsDefine & RegisterAssaysData Dictionary – std termsCatalog of Assay ProtocolsHigh Quality Data &Result DepositionCalculations & ResultsProject-experiment associationQuery & InterpretInformationIntuitive Guided QueriesCross Assay & SAR centric viewsAdvance applicationsEnableHypothesisGenerationNovice Expert
  13. 13. Web ClientFilter on annotations, such asdetection method typeGoogle-like searching of: 4,000+ assays, 35M+ compounds, 300+ projectsSave items ofinterest for furtheranalysisAmazon-like Query Cart
  14. 14. Web Client - Project Specific Views
  15. 15. Web Client – Probe Development Workflow
  16. 16. Sunburst VisualizationMolecular activity against target classesTarget classifications from PantherDBPANTHER in 2013: modeling the evolution of gene function,and other gene attributes, in the context of phylogenetic trees.Huaiyu Mi, Anushya Muruganujan and Paul D. ThomasNucl. Acids Res. (2012) doi: 10.1093/nar/gks1118
  17. 17. JerseyD3.jsWeb Query & Desktop ClientsData Warehouse & REST API Catalog of Assay ProtocolsCommercial LicenseMySQL support forCAP coming soonAs open source as possibleJGoodies
  18. 18. Chemaxon Usage in BARDUNM Promiscuity PluginJChem for scaffold decompositionREST API & WarehouseJChem for rendering structures andmolecule fingerprint generationhttp://bard.nih.gov/api/latest/compounds/6915727/image?s=200http://bard.nih.gov/api/latest/compounds/?filter=n1cccc2ccccc12%5Bstructure%5D&type=sim&cutoff=0.9&expand=truehttp://bard.nih.gov/api/latest/plugins/badapple/prom/cid/6915727?expand=true
  19. 19. Chemaxon Usage in BARDWeb Query ClientJChem for rendering structuresDesktop ClientJChem for rendering structures,molecule import & exportMarvin for drawing query structures
  20. 20. • BioActivity Data AssociativePromiscuity Pattern Learning Engine• Associations via scaffolds for chemicalspace navigationExample URI* description<base>/badapple/prom/cid/752424For compound with specified ID,return scaffold IDs and scores.<base>/badapple/prom/cid/752424?expand=trueAdditional statistics, scaffold smiles,and inDrug flag.<base>/badapple/prom/scafid/233For scaffold with specified ID, returnstatistics and smiles.Predictive Models
  21. 21. Predictive Models• Predicts CYP450 isoformsmetabolism sites with 2Dstructures• Patrik Rydberg et. al• Released under LGPL• BARD plugin– Summary HTML view– Data view
  22. 22. Navigating the Maze
  23. 23. Long-Term Path ForwardMLPTBDNCI-60TBDDatasetsCAP WebQueryDesktopAPIsToolsBADAppleCYP450TBDTBDMethods Data AnalysisWorkflow 1Workflow 2Workflow 3as a PlatformSustained Community EngagementADS

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