overview nano wg the national cancer institute (nci) cabig® nanotechnology working group (nano wg)...
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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)