Cancer Nanotechnology Knowledgebase for Nanoparticle Analysis and Design caOBR-caB2B integration Nathan Baker, David Paik, and Persistent Systems

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

What is the biological problem? D. Tomalia

Classification and Structural Representation of Nanoparticles Is Immature Alexa Fluor 680-labeled transferrin- cationic (NBD-labeled DOPE- DOTAP) liposome-encapsulated gadopentetate dimeglumine complex [TfNIR-LipNBD-CA complex] 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] e.g.

Nanoparticle Characterization Data Is Diverse

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

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

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

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

caB2B uses caOBR to Search BioPortal Resource Index

caB2B-caOBR overview caB2B caNanoLab RAT caOBR service caB2B-caOBR Integration Advantages of caB2B-caOBR Integration Demo

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

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.

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-basedcaGRID analyses

caB2B-caOBR Integration

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

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.

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.