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

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  • 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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  • Thomas, D. G., Freund, E. T., Klemm, J. D., Baker, N. A., Gaheen, S., Harper, S. L., . . . Stafford, G. A. (2013). ISA-TAB-nano: A specification for sharing nanomaterial research data in spreadsheet-based format. BMC Biotechnology, 13(1), 2-2. doi: 10.1186/1472-6750-13-2
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  • 13
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  • 1
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  • N.A.B. and D.G.T. acknowledge support from the NIH NCI caBIGW Working Group, Pacific Northwest National Laboratory HHS sector LDRD funds, as well as NIH grants U54 HG004028 (National Center for Biomedical Ontology), U01 NS073457, and R01 GM069702. S.L.H. would like to acknowledge support from NIEHS Environmental Health Sciences Center P30 ES03850, National Institute of Environmental Health Sciences ES016896-01, and the Air Force Research Laboratory FA8650-05-1-5041 under an agreement with the Oregon Nanoscience and Microtechnologies Institute/Safer Nanomaterials and Nanomanufacturing Initiative. D.P. acknowledges support for funding from Stanford CCNE-TR/CCNE-T (NIH U54 CA119367) and National Center for Biomedical Ontology (NIH U54 CA151459).
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  • description.provenance : Made available in DSpace on 2013-04-01T17:57:10Z (GMT). No. of bitstreams: 3 license_rdf: 22765 bytes, checksum: 56265f5776a16a05899187d30899c530 (MD5) license_text: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) HarperStaceyLEnvironmentalMolecularToxicologyISATABNanoSpecificationSharing.pdf: 1847059 bytes, checksum: 94d701ccc4d2197bec487898006e604a (MD5) Previous issue date: 2013-01-14
  • description.provenance : Approved for entry into archive by Deborah Campbell(deborah.campbell@oregonstate.edu) on 2013-04-01T17:57:10Z (GMT) No. of bitstreams: 3 license_rdf: 22765 bytes, checksum: 56265f5776a16a05899187d30899c530 (MD5) license_text: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) HarperStaceyLEnvironmentalMolecularToxicologyISATABNanoSpecificationSharing.pdf: 1847059 bytes, checksum: 94d701ccc4d2197bec487898006e604a (MD5)
  • description.provenance : Submitted by Deborah Campbell (deborah.campbell@oregonstate.edu) on 2013-04-01T17:34:25Z No. of bitstreams: 3 license_rdf: 22765 bytes, checksum: 56265f5776a16a05899187d30899c530 (MD5) license_text: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) HarperStaceyLEnvironmentalMolecularToxicologyISATABNanoSpecificationSharing.pdf: 1847059 bytes, checksum: 94d701ccc4d2197bec487898006e604a (MD5)

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