The NCIP Nanotechnology Working Group

Nano WG Fall 2013 Kick-Off

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The Nano WG – Historical Perspective

• Initiated in 2008 as a working group of the caBIG program, with the objectives of: – Assessing and defining needs of the cancer

nanotechnology research community– Defining standards for cancer nanotechnology research

community in a variety of areas– Defining and prioritize informatics applications in

nanotechnology that fulfill priority needs

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The Nano WG – Historical Perspective

• Three white papers were authored, all available at https://wiki.nci.nih.gov/display/ICR/Nanotechnology+Working+Group+%28NanoWG%29+2008+-+2009 – Nanotechnology Informatics: A comprehensive review of nanotechnology

covering the history of nanotechnology, and the application of nanotechnology in the biomedical field. Identifies the existing resources and current broad informatics need/issues in this field.

– Ontologies: Describes the development of an ontology specifically to meet the needs of the Nano Working Group, the NanoParticle Ontology. It also describes other ontology, terminology and related standards efforts in the community.

– Minimum Standards: Articulates that MIS are required for both the set of experiments using nanoparticles to determine biological activity and the set of experiments characterizing the chemical composition and physical properties of the particle. The paper also articulates the need for community building and why MIS must emerge from a broader community effort.

Today: NCIP Nanoinformatics Working Group High-Level Objectives:

• Enable nanomedicine informatics applications…– Develop data exchange standards– Develop ontologies – Build a community of interest

• …to support ultimate goals of informatics in nanomedicine– Predictive models for nanomaterial activity– Rational design of nanomaterials

Who are we?• Government

• National Institutes of Health• NCI, NHLBI, NIBIB, NIEHS

• Center for Disease Control• Food and Drug Administration• Environmental Protection

Agency• National Institutes of Standards

and Technology

• Academia• Pacific Northwest National Lab• Oregon State• Stanford• UCLA• UNC• Duke • UMass

• Standards organizations• ASTM E56

• ISO TC229

• ISA Commons

• Alliances and organizations• NCI Alliance for Nanotechnology in

Cancer

• International Alliance for NanoEHS Harmonization

• Oregon Nanoscience and Microtechnologies Institute

• National Nanotechnology Initiative

• National Nanomanufacturing Network

• EU NanoSafety Cluster• Industry

• Pennsylvania NanoSystems• NanoSafe, Inc.

Nanoinformatics WG Activities

• ISA-TAB-Nano development– Nanotechnology data sharing standards

• Nanoparticle Ontology (NPO) support and expansion– Standard vocabulary and ontology for nanomedicine

• Structure-activity relationships for nanomaterial-biological interactions– Descriptive analytics

ISA-TAB-Nano

• A standard tab-delimited format for describing data related

to

– Investigations

– Studies

– Assays

– Materials

• Extends the Investigation/Study/Assay (ISA-TAB) format

– Developed by the European Bioinformatics Institute (EBI) for

representing a variety of assays and technology types

– Standard tab-delimited file format

• ISA-TAB-Nano supports ontology-based curation

– Nanomaterials and concepts from the NanoParticle Ontology

(NPO) as well as other ontologies

ISA-TAB-Nano Resources

• Specification, templates, and examples available on the Nano WG wiki, https://wiki.nci.nih.gov/x/MwGGAg

• Accepted as an ASTM Guide, E2909-13 http://www.astm.org/Standards/E2909.htm

• Published in BMC Biotechnology earlier this year, http://www.biomedcentral.com/1472-6750/13/2

• Commentary in Nature Nanotechnology, http://www.nature.com/nnano/journal/v8/n2/full/nnano.2013.12.html

• ISA-TAB-Nano codefest • http://ncip.nci.nih.gov/blog/isa-tab-nano-code-fest-community-buildin

g-and-coding-to-advance-nanotechnology-data-exchange-bethesda-maryland-may-9-10-2013/ – Created a web service for ISA-TAB validation– Identified and implemented changes to ISA-TAB-Nano spec to facilitate

use of ISA Tools

• In use by Nano Registry, caNanoLab curation, PNNL, CEINT, <others>

NanoParticle Ontology (NPO)• Capture knowledge underlying

nanomaterial– Preparation– Chemical composition– Physiochemical

characterization– Biological function/behavior

• Initial focus on cancer diagnosis and therapy

• Current growth to include a broader range of nanotechnology concepts

• Available through the NCImt and Bioportal

• http://ncim.nci.nih.gov/ncimbrowser/ • http://purl.bioontology.org/ontology/N

PO• http://www.nano-ontology.org• Slide courtesy of Nathan Baker, PNNL

Thomas, D.G., Pappu, R.V., Baker, N.A. NanoParticle Ontology for cancer nanotechnology research. Journal of Biomedical Informatics Volume 44, Issue 1, February 2011, Pages 59-74

Example View into the NPO

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Descriptive Analytics for Nanomaterial-Biological Interactions

Goals• Collect and standardize

experimental properties of nanoparticles

• Develop novel approaches to computing descriptors of nanoparticles

• Develop predictive models of nanoparticles’ biological activity Shaw et al., 2008. Perturbational profiling of

nanomaterial biologic activity. PNAS, 105(21): 7387–7392