Cancer Cancer Nanotechnology Nanotechnology Knowledgebase for Knowledgebase for Nanoparticle Analysis Nanoparticle Analysis and Designand Design

caOBR-caB2B caOBR-caB2B integrationintegration

Nathan Baker, David Paik, and Persistent Systems

Nanoinformatics Nanoinformatics CommunityCommunity

CCNECCNENCBONCBO caBIGcaBIG

caNanoLab

caNanoLabNPONPOBioPorta

lBioPorta

l

ASTMASTMISOISO

MICADMICAD

NCBINCBI

What is the biological What is the biological problem?problem?

D. Tomalia

Classification and Structural Classification and Structural Representation of Nanoparticles Is Representation of Nanoparticles Is ImmatureImmature

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 DiverseNano Databases Are Diverse

SimulationsSimulations

Research Map

Research Map

EHS Literature

EHS Literature

StructuresStructures

Manufacturing

Processes

Manufacturing

Processes

Ethics Literature

Ethics Literature

NewsNews

EHS DataEHS Data

Safety Literature

Safety LiteratureBiological

InteractionsBiological

InteractionsMaterials SuppliersMaterials Suppliers

PatentsPatents

Scientific LiteratureScientific Literature

Curated ChaptersCurated Chapters

Characterization Data

Characterization Data

FACS DataFACS DataImaging Data

Imaging DataMass Spec

DataMass Spec

Data

Research StrategyResearch StrategyOntology DevelopmentAdd Nanoparticle ResourcesEnable caGRID QueriesEnable Data Sharing

14 releases on BioPortal since March 2008

1500+ classesBasic Formal Ontology

(BFO) upper ontologyDeveloped by at Wash U

◦ npo.wustl.edu1st review by caBIG VCDE

◦ 70%+ structure/content criteria

NNanoanoPParticle article OOntology (NPO) on ntology (NPO) on BioPortalBioPortalThomas, Pappu, BakerThomas, Pappu, Baker

MICAD Annotations

Also caNanoLab,InterNano, etc.

Tag cloud generated fromone MICAD chapter

Integrating Nanoparticle Resources into BioPortal Resource Index

caB2B uses caOBR to Search caB2B uses caOBR to Search BioPortal Resource IndexBioPortal Resource Index

caB2B-caOBR overviewcaB2B-caOBR overviewcaB2B caNanoLab RATcaOBR servicecaB2B-caOBR IntegrationAdvantages of caB2B-caOBR

IntegrationDemo

caB2BcaB2B 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 RATcaNanoLab 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.

caOBRcaOBR 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

caB2B-caOBR IntegrationcaB2B-caOBR Integration

caB2B-caOBR Integration caB2B-caOBR Integration WorkflowWorkflow

caB2B

Find ConceptsFind Concepts

Results

Find annotations over grid and Outside caGrid

AnnotationsAnnotations

Search data Over caGrid

Search concepts through caOBR service across all ontologies

Saved Search –”Gold Dendrimer”

Keyword Search ”Dendrimer”

caB2B –caOBR

Integration

caB2B –caOBR

Integration

Advantages of caB2B-caOBR Advantages of caB2B-caOBR IntegrationIntegration

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.

AcknowledgementsAcknowledgements 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.