Transcript 2010-05 NCBO webinar caB2B

Cancer Nanotechnology
Knowledgebase for
Nanoparticle Analysis and
Design
caOBR-caB2B integration
Nathan Baker, David Paik, and Persistent Systems
Nanoinformatics Community
NCBO
BioPortal
CCNE
NPO
caBIG
caNanoLab
MICAD
ISO
ASTM
NCBI
What is the biological problem?
D. Tomalia
Classification and Structural Representation of
Nanoparticles Is Immature
e.g.
Alexa Fluor 680-labeled transferrincationic (NBD-labeled DOPEDOTAP) liposome-encapsulated
gadopentetate dimeglumine complex
[TfNIR-LipNBD-CA complex]
e.g.
[(Biotin-Ala-Ser-Lys-Lys-Pro-Lys-Arg-AsnIle-Lys-Ala)4-dendrimer]-streptavidin-[biotingadolinium 1,4,7-tris(carboxymethyl)-10-(2’hydroxypropyl)-1,4,7,10tetraazacyclododecane-loaded apoferritin]
[C3d-SA-GdAF]
Nanoparticle Characterization Data
Is Diverse
Nano Databases Are Diverse
Research Map
EthicsNews
Simulations
Literature
Curated
Patents
Chapters
Manufacturing
MassData
Spec
FACS
Imaging
Data Data
EHS LiteratureSafety
Scientific
Processes
Materials
Biological
Literature
Literature
EHS Data
Suppliers
Interactions
Characterizatio
n Data
Structures
Research Strategy
Ontology Development
 Add Nanoparticle Resources
 Enable caGRID Queries
 Enable Data Sharing

NanoParticle Ontology (NPO) on BioPortal
Thomas, 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
Integrating Nanoparticle Resources
into BioPortal Resource Index
MICAD Annotations
Also caNanoLab,
InterNano, etc.
Tag cloud generated from
one MICAD chapter
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, caNanoLabStanford 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-based caGRID analyses

caB2B-caOBR Integration
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
Find annotations over grid
and Outside caGrid
Annotations
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

◦ Mark Musen
◦ All NCBO staff


◦ Stanley Shaw

GaTech
◦ May Wang
caBIG
◦
◦
◦
◦
Oregon State University
MGH
NIH
◦ Sharon Gaheen
◦ Marty Fritts
◦ Raul Cachau
◦ Stacey Harper

NCBO

Elaine Freund
Juli Klemm
Liz Hahn-Dantona
Patti Kwong
ASTM
◦ Tim Brooke

Persistent Systems Ltd.