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Cancer Nanotechnology Knowledgebase for Nanoparticle Analysis and Design caOBR-caB2B integration

Cancer Nanotechnology Knowledgebase for Nanoparticle Analysis and Design caOBR-caB2B integration. Nathan Baker, David Paik, and Persistent Systems. Nanoinformatics Community. CCNE. NCBO. caBIG. caNanoLab. BioPortal. NPO. MICAD. ISO. ASTM. NCBI. What is the biological problem?.

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Cancer Nanotechnology Knowledgebase for Nanoparticle Analysis and Design caOBR-caB2B integration

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  1. Cancer Nanotechnology Knowledgebase for Nanoparticle Analysis and DesigncaOBR-caB2B integration Nathan Baker, David Paik, and Persistent Systems

  2. Nanoinformatics Community CCNE NCBO caBIG caNanoLab BioPortal NPO MICAD ISO ASTM NCBI

  3. What is the biological problem? D. Tomalia

  4. Classification and Structural Representation of Nanoparticles Is Immature e.g. e.g. [(Biotin-Ala-Ser-Lys-Lys-Pro-Lys-Arg-Asn-Ile-Lys-Ala)4-dendrimer]-streptavidin-[biotin-gadolinium 1,4,7-tris(carboxymethyl)-10-(2’-hydroxypropyl)-1,4,7,10-tetraazacyclododecane-loaded apoferritin] [C3d-SA-GdAF] Alexa Fluor 680-labeled transferrin-cationic (NBD-labeled DOPE-DOTAP) liposome-encapsulated gadopentetate dimeglumine complex [TfNIR-LipNBD-CA complex]

  5. Nanoparticle Characterization Data Is Diverse

  6. Nano Databases Are Diverse Ethics Literature FACS Data Manufacturing Processes News Curated Chapters Patents EHS Data Biological Interactions EHS Literature Research Map Mass Spec Data Materials Suppliers Safety Literature Imaging Data Simulations Structures Scientific Literature Characterization Data

  7. Research Strategy • Ontology Development • Add Nanoparticle Resources • Enable caGRID Queries • Enable Data Sharing

  8. NanoParticle Ontology (NPO) on BioPortalThomas, Pappu, Baker • 14 releases on BioPortal since March 2008 • 1500+ classes • Basic Formal Ontology (BFO) upper ontology • Developed by at Wash U • npo.wustl.edu • 1st review by caBIG VCDE • 70%+ structure/content criteria

  9. Integrating Nanoparticle Resources into BioPortal Resource Index MICAD Annotations Also caNanoLab,InterNano, etc. Tag cloud generated fromone MICAD chapter

  10. caB2B uses caOBR to Search BioPortal Resource Index

  11. caB2B-caOBR overview • caB2B • caNanoLab RAT • caOBR service • caB2B-caOBR Integration • Advantages of caB2B-caOBR Integration • Demo

  12. caB2B • cancer Bench-to-Beside - caB2B - is an open-source, secure query tool that permits translational research scientists to search and combine data virtually from any caGrid data service. • The caB2B Web Application provides query templates that allow easy search and retrieval of data across caGrid by domains, like biospecimen (caTissue Core), microarray (caArray), imaging data (National Biomedical Imaging Archive, NBIA), and nanoparticle data (caNano Lab). • caB2B allows executing queries across multiple instances of an application available at different hosting research centers. For Example we can retrieve Nanoparticle data from caNanoLab-WUSTL , caNanoLab-GTEM, caNanoLab-Stanford etc in a single query

  13. caNanoLab RAT • RAT(Resource access tool) is a program that enables to harvest data from the original resource(Eg. caNanoLab), to transform this data in a format compliant with the OBS database and then to insert them in this database. • Make caNanoLab available to NCBO Resource Index for indexing • Make caNanoLab nanomaterial data available to NCBO Resource Index and Annotator for: • Browsing via BioPortal • Semantic searching using NPO and related terminologies • Increasing user interaction with caNanoLab which would be no more limited to caGrid users.

  14. caOBR • caOBR is a caGrid analytical service which provides caGrid compliance API to access NCBO ontology web services and NCBO Resource Index annotations from grid. • Expose NCBO Resource Index indices to caGRID applications • Identification of concepts and fetching annotations from public resources(NCBI,GEO etc ) • Offer additional caBIG interfaces for NCBO Resource Index and Annotator-based caGRID analyses

  15. caB2B-caOBR Integration

  16. caB2B-caOBR Integration Workflow Keyword Search ”Dendrimer” Saved Search –”Gold Dendrimer” caB2B Search data Over caGrid Results Search concepts through caOBR service across all ontologies Find Concepts caB2B –caOBR Integration Find annotations over grid and Outside caGrid Annotations

  17. Advantages of caB2B-caOBR Integration • caB2B-caOBR integration bridges the gap between resources that are available inside and outside caGrid • Any caGrid enabled data service could be queried through caB2B and caOBR can fetch annotations for any resource which is registered to NCBO Resource Index database. • caOBR –caB2B integration overcomes with the limitation of caGrid being connected to limited valuable resources.

  18. Acknowledgements • Washington Univ. at St. Louis • Nathan Baker • Dennis Thomas • Rohit Pappu • Stanford • Sam Gambhir • David Paik • Daniel Rubin • Samira Guccione • Kranthi Kode • Oregon State University • Stacey Harper • MGH • Stanley Shaw • GaTech • May Wang • NCBO • Mark Musen • All NCBO staff • NIH • Sharon Gaheen • Marty Fritts • Raul Cachau • caBIG • Elaine Freund • Juli Klemm • Liz Hahn-Dantona • Patti Kwong • ASTM • Tim Brooke • Persistent Systems Ltd.

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