File Entry: NanoPUZZLES ISA-TAB-Nano Templates

Created: 2015-03-27 14:29:30      Last updated: 2015-12-18 15:59:53
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Last edited on: 2015-12-18 16:02:30


Information Description

The files hosted here are Excel-based templates for the creation of ISA-TAB-Nano datasets [https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano] which were developed within the context of the NanoPUZZLES EU project [http://www.nanopuzzles.eu/]. (Up to date information on ISA-TAB-Nano can be found here: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano ISA-TAB-Nano is a derivative of ISA-TAB, for which further information may be found here: http://www.isa-tools.org/format/specification/)

The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement number 309837 (NanoPUZZLES project).


Further information regarding these resources is provided in the following article: Richard L. Marchese Robinson, Mark T. D. Cronin, Andrea-Nicole Richarz, Robert Rallo, "An ISA-TAB-Nano based data collection framework to support data driven modelling of nanotoxicology", Beilstein J. Nanotechnol. 2015, 6, 1978–1999. doi:10.3762/bjnano.6.202

*However, this article refers to version 3 of these templates. The current version of these templates has been extended (see update notes).*


IMPORTANT CAVEATS:

As is explained in Marchese Robinson et al. (see above), and in the Supporting Information, whilst the basic structure of these templates conforms to the general ISA-TAB-Nano specification (as of version 1.2 [https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano+1.2+Release+Notes]), the manner in which certain (meta)data are intended to be captured via these templates may deviate from the manner in which these (meta)data would otherwise be expected to be captured via ISA-TAB-Nano: [1] the introduction of the Material file template "Characteristics [Product impurities found {MEDDRA: http://purl.bioontology.org/ontology/MDR/10069178 }]" field (associated with the corresponding "Characteristics [Impurities proportions]" field) to record "impurities" may not be required, as these might be treated as per any other chemical component i.e. recorded using separate rows of the Material file, each row being associated with a unique "Material Name" value [https://wiki.nci.nih.gov/display/ICR/Material]; [2] the use of "Factor Value [...]" columns to capture certain metadata may deviate from expected practice as some of these metadata might otherwise be captured via "Parameter Value [...]" or "Sample Name" associated "Characteristics [...]" columns (i.e. "Characteristics [...]" columns located immediately after - to the right hand side of - a "Sample Name" column) e.g. the "s_InvID_InVitro.CB.xls" Study file template "Factor Value [final cell density]" field might be replaced with a "Characteristics [final cell density]" field located to the right hand side of the "Sample Name" column [see http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf for further guidance].

As is also explained in Marchese Robinson et al. (see above), ISA-TAB-Nano files are typically expected in tab-delimited text format so datasets created using these resources would need to be converted e.g. via using the following software: https://github.com/RichardLMR/xls2txtISA.NANO.archive

[The following formatting characters should be ignored! Scroll down to download (a specific version of) the templates and/or see comments!]

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