The NCIP Nanotechnology Working Group Nano WG Fall 2013 Kick-Off

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 2

The Nano WG – Historical Perspective Three white papers were authored, all available at 28NanoWG% NanoWG% –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. 3

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, Accepted as an ASTM Guide, E Published in BMC Biotechnology earlier this year, Commentary in Nature Nanotechnology, ISA-TAB-Nano codefest building-and-coding-to-advance-nanotechnology-data-exchange- bethesda-maryland-may / building-and-coding-to-advance-nanotechnology-data-exchange- bethesda-maryland-may / –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,

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 POhttp://purl.bioontology.org/ontology/N PO 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

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 11 Shaw et al., Perturbational profiling of nanomaterial biologic activity. PNAS, 105(21): 7387–7392