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

Thomas, Dennis G.; Gaheen, Sharon; Harper, Stacey L.; Fritts, Martin; Klaessig, Fred; Hahn-Dantona, Elizabeth; Paik, David; Pan, Sue; Stafford, Grace A.; Freund, Elaine T.; Klemm, Juli D.; Baker, Nathan A.

doi:10.1186/1472-6750-13-2

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

Journal Article · Mon Jan 14 00:00:00 EST 2013 · BMC Biotechnology (Online)

DOI:https://doi.org/10.1186/1472-6750-13-2· OSTI ID:1626537

Thomas, Dennis G. ^[1]; Gaheen, Sharon ^[2]; Harper, Stacey L. ^[3]; Fritts, Martin ^[4]; Klaessig, Fred ^[5]; Hahn-Dantona, Elizabeth ^[6]; Paik, David ^[7]; Pan, Sue ^[4]; Stafford, Grace A. ^[8]; Freund, Elaine T. ^[9]; Klemm, Juli D. ^[10]; Baker, Nathan A. ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Knowledge Discovery and Informatics
SAIC-Frederick, Inc, Rockville, MD (United States). Frederick National Lab. for Cancer Research. Information Systems Program
Oregon State Univ., Corvallis, OR (United States). School of Chemical, Biological and Environmental Engineering. Dept. of Environmental and Molecular Toxicology
SAIC-Frederick, Inc, Rockville, MD (United States). Frederick National Lab. for Cancer Research. Information Systems Program
Pennsylvania Bio Nano Systems, LLC, Doylestown, PA (United States)
Lockheed Martin, Rockville, MD (United States)
Stanford Univ., CA (United States). Dept. of Radiology
The Jackson Lab., Bar Harbor, ME (United States)
3rd Millennium, Inc, North Smithfield, RI (United States)
National Cancer Institute, Bethesda, MD (United States). Center for Biomedical Informatics and Information Technology

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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; USDOE Laboratory Directed Research and Development (LDRD) Program; US Air Force Office of Scientific Research (AFOSR); National Institutes of Health (NIH)

Grant/Contract Number:: AC05-76RL01830; FA8650-05-1-5041; P30 ES03850; U54 HG004028; U01 NS073457; R01 GM069702; ES016896-01; U54 CA119367; U54 CA151459

OSTI ID:: 1626537

Journal Information:: BMC Biotechnology (Online), Vol. 13, Issue 1; ISSN 1472-6750

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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