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

BMC Biotechnology (Impact Factor: 2.03). 01/2013; 13(1):2. DOI: 10.1186/1472-6750-13-2
Source: PubMed


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.

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.

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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Available from: Nathan Andrew Baker, Oct 13, 2015
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    • "(For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.) Table 6 ISA-TAB-NANO file types (Thomas et al., 2013). "
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    • "A standardised data exchange format to share data and a unified ontology for data collection is needed to ensure a certain quality standard in terms of completeness, avoid duplication, allow a comparison between data from different sources and make it possible to integrate different datasets into one database. ISA-TAB-nano (Thomas et al., 2013) has been identified as a suitable standard format, defining a set of linked spreadsheet files (Investigation, Study, Assay and Material), with a pre-defined file structure and syntax for (meta)data. Furthermore, the quality and suitability of the data for developing predictive toxicology models are being assessed. "
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