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Open Access Highly Accessed Correspondence

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format

Dennis G Thomas1, Sharon Gaheen2, Stacey L Harper3, Martin Fritts2, Fred Klaessig4, Elizabeth Hahn-Dantona5, David Paik6, Sue Pan2, Grace A Stafford7, Elaine T Freund8, Juli D Klemm9 and Nathan A Baker10*

Author Affiliations

1 Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA

2 SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA

3 Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA

4 Pennsylvania Bio Nano Systems, LLC, Doylestown, PA, USA

5 Lockheed Martin, Rockville, MD 20852, USA

6 Department of Radiology, Stanford University, Stanford, CA 94305, USA

7 The Jackson Laboratory, Bar Harbor, Maine 04609, USA

8 3rd Millennium, Inc, North Smithfield, RI 02896, USA

9 Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20852, USA

10 Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, Richland, WA 99352, USA

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BMC Biotechnology 2013, 13:2  doi:10.1186/1472-6750-13-2

Published: 14 January 2013

Abstract

Background and motivation

The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.

Results

We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.

Conclusion

The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.