Overview

Nano WG

The National Cancer Institute (NCI) caBIG® Nanotechnology Working Group (Nano WG)Jessica M. Adamick 1, Nathan A. Baker 2, Alan R. Chappell 3, Joseph A. Fisher 4-5, Gilberto Fragoso 6, Elaine T. Freund 7, Martin Fritts 8, Elizabeth Hahn-Dantona 9, Stacey L. Harper 10, Mark D. Hoover 11, Fred Klaessig 12, Juli D. Klemm 13, David S. Paik 14, Dennis G. Thomas 15

1. University of Massachusetts, 2. Pacific Northwest National Laboratory, 3. Pacific Northwest National Laboratory, 4. Oregon State University, 5. Air Force Medical Service Corps, 6. National Institutes of Health, 7. 3rd Millennium, Inc., 8. SAIC-Frederick, Inc., 9. Lockheed Martin, Corp., 10. Oregon State University, 11. National Institute for Occupational Safety and Health, 12. Pennsylvania Bio Nano Systems, LLC., 13. National Cancer Institute, 14. Stanford University, 15. Pacific Northwest National Laboratory.

The National Cancer Institute (NCI) Cancer Biomedical

Informatics Grid (caBIG®) project provides a collaborative

information network for scientists and institutions. The

infrastructure is open and broad, supports interoperability and

access to data and information from basic through clinical

research. The Nanotechnology Working Group (Nano WG) was

established as part of caBIG in 2008 to support the specific

informatics needs of its nanotechnology researchers. It is

comprised of over 20 active participants with a broad range of

expertise and background who communicate regularly with the

goal of demonstrating the use of interoperable and open data

information systems for the nano related sciences. The Nano

WG has documented its objectives and timetable. This list is

publicly maintained and periodically reviewed. Weekly web

teleconferences promote direct communication and discussion.

Content is shared freely through open web standards. A large

community of collaborative participants interacts with the Nano

WG and provides valuable input, feedback, and exchange.

The Nano WG activities focus on critical needs to support

computational approaches such as modeling and prediction,

including: (1) reliable curated data and a common understanding

of nanomaterial characterization (2) advancing the

interoperability of databases for aggregation of data and to

support modeling and simulation (3) semantic search and

retrieval of nanomaterial, protocol, and outcome data-sets and

information to support prediction. Outcomes of the ontology and

discovery tools include support for semantic search, nano bio-

compatibility and design, and pharmacokinetic modeling. Major

projects include the ongoing development of and support for

both the NanoParticle Ontology (NPO) and the nano-TAB data

exchange format. NPO represents the description, preparation,

and characterization of nanomaterials in nanotechnology

research. It is developed within the Basic Formal Ontology

framework and is implemented in OWL (Ontology Web

Language) and is accessed through the NCI. The nano-TAB

exchange format is a specification developed to facilitate the

import/export of data on nanomaterials and their use to and from

nanotechnology informatics resources. The nano-TAB is a

human and machine readable specification utilizing delimited

files (where most data is initially captured), to leverage and

extend concepts from the caBIG Life Sciences Domain Analysis

Model (LS DAM), and to use the NanoParticle Ontology and

other ontologies as sources for its terms. It leverages and

extends the ISA-TAB standard because of its flexibility in

supporting several different types of assays of interest including:

in silico, in vitro, and in vivo assays as well as nanomaterial

characterization attributes.

NanoParticle Ontology

HIGH-LEVEL OBJECTIVES

The Nano WG currently supports the design and development of new and existing nanomaterial bio-informatics information systems by supporting and developing the standards and schemas for its related data interoperability.

Enabling: – Develop data exchange standards– Develop ontologies– Build a community of interest

Support: – Predictive models of nanomaterial activity– Rational design of nanomaterials– Data sharing

PARTICIPATION & COLLABORATIONS

There are over 20 active participants in the group. They represent a broad range of expertise and come from academic, industrial, government agency and other institutions.

Rational: • The field of nanotechnology faces challenges in the development of standards to support meaningful data submission and information exchange.

Significance: • Establishes standard methods for representing the diversity and complexity of nanomaterials and their formulation and characterization.

NANOPARTICLE ONTOLOGY (NPO)

The NPO provides a subset of the terms and relationships for the description and characterization of nanomaterials in the annotation of nanotechnology research data. It enables use of standards, data-sharing and semantic integration of data.

• Designed within the Basic Formal Ontology framework

• Includes domain specific characterization terms for Biological, Chemical, Physical and Medical properties; touch points to other ontologies including GO and ChEBI

• Incorporated into NCI meta thesaurus

• Terms used in caNanoLab

• nano-TAB specification recommends use of NPO

• Views for easy access to nano-TAB terms

• Maps to biological entities, events, and effects

nano-TAB leverages and extends ISA-TAB files:

An investigator must specify four files in developing a nano-TAB implementation:

Upon completion, nano-TAB files are validated and submitted into nanotechnology resources like the NCI cancer Nanotechnology Laboratory (caNanoLab) portal [https://cananolab.nci.nih.gov/] and the Oregon State University Nanomaterial Biological Interactions (NBI) knowledgebase [http://nbi.oregonstate.edu/].

https://wiki.nci.nih.gov/display/ICR/Nanotechnology+Working+Group https://wiki.nci.nih.gov/display/ICR/NanoParticle+Ontology

Academia: UMASS, OSU, GATECH, STANFORD, UNC, UCLA

Industry: PA BIO NANO, IAI, NNN

Government: PNNL, EPA, CDC, DoD, USACE, NCI-F/NCL, NIEHS, NIBIB

Standards: ISO, ASTM, NIST

Collaborating Projects: BioPortal, caNanoLab, Good Nano Guide, PubNano, Nanoinformatics Roadmap, Nanomaterial Biological Interactions (NBI), NCBO knowledgebase, Nanomaterial Registry, Nanoparticle Information Library (NIL)

https://wiki.nci.nih.gov/display/ICR/nano-TAB

Nano-TAB

1. Investigation File: Describes the study, design, factors, assays, protocols, contacts, and publications. 2. Material File: Defines the composition and formulations of the agents being tested. 3. Study File: Provides the mappings between biospecimens and materials and events associated with the study. 4. Assay File: References results including raw and derived data, images, and other files.

nano-TAB is a specification to facilitate the import/export of data on nanomaterials, small molecules, biological specimens, and their characterizations to/from nanotechnology informatic resources.

Zebrafish ExperimentNPO references:

NPO 1410: In Vivo AssayNPO 589: Quantum DotNPO 1477: Imaging

Exchange

Nanotechnology

Data Discovery

Status: – Validated against a wide variety of use cases– In ASTM ballot, Nano WG has done outreach and briefs – Harmonized to caBIG Life Sciences Domain Analysis Model

Next Steps: – User guide and manuscript in development– Register nano-TAB in the meta data repository (caDSR)