File Entry: NanoPUZZLES ISA-TAB-Nano Templates

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

Version 2 (of 4)

Version created on: 2015-03-31 09:56:13 | Revision comment Expand

Last edited on: 2015-09-04 12:53:33

Title	NanoPUZZLES ISA-TAB-Nano Templates
File name	NanoPUZZLES.Templates.BJNANO.March.2015.lo.zip
File size	238206
SHA1	47ec057f3d4b9489c69b5c2ce612845d02935096
Content type	ZIP archive

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 Journal of Nanotechnology (Article In Press)

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].

Furthermore, in the current version of the templates, the “Factor Value [vehicle]” field, in the Study file template for in vitro (cell-based) studies (“s_InvID_InVitro.CB.xls”), is documented to capture the “exposure media” i.e. the terms “vehicle” and “exposure media” are used interchangeably. However, elsewhere in the literature, this may not be the case. The “exposure media” (or “exposure medium”) refers to the entire medium via which a tested chemical (e.g. nanomaterial) is exposed to the cells in an in vitro (cell-based) study and, in contrast to the current version of the templates, the “vehicle” may be used to refer to a component of the “exposure medium” in which the chemical is originally dissolved (or nanomaterial suspended) prior to mixing with other components (e.g. the original “culture medium” or “growth media” in which the cells are grown prior to nanomaterial exposure) to obtain the final “exposure medium”, which may be carried out prior to or at the point of exposure to the cells.

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

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Version History

In chronological order:

NanoPUZZLES ISA-TAB-Nano Templates

Created on Friday 27 March 2015 14:29:30 (UTC)
NanoPUZZLES ISA-TAB-Nano Templates

Created on Tuesday 31 March 2015 09:56:13 (UTC)

Last edited on Friday 04 September 2015 12:53:33 (UTC)

Revision comment:

The cytotoxicity Assay file templates were updated to refer to LOEL rather than LOAEL.
NanoPUZZLES ISA-TAB-Nano Templates

Created on Thursday 10 September 2015 13:37:25 (UTC)

Last edited on Thursday 10 September 2015 13:44:48 (UTC)

Revision comment:

*Various changes were made to the contents of the in vitro (cell-based) Study file template ("s_InvID_InVitro.CB.xls") and the Investigation file template ("i_InvID.xls") such that the term "exposure medium" is now used instead of "vehicle" to describe the "exposure medium" (or "exposure media") used when studying the biological effects of nanomaterials in in vitro (cell-based) studies.
*Corresponding changes to the (Excel 2010 "Review" tab inserted) comments were made.
*A minor change was made to the "Factor Value[cells Exposure Duration]" comment.
*The factor "exposure medium serum" is linked to a "Study Factor Type" taken from an ontology.
NanoPUZZLES ISA-TAB-Nano Templates

Created on Friday 18 December 2015 15:59:53 (UTC)

Last edited on Friday 18 December 2015 16:02:30 (UTC)

Revision comment:

1. The major difference to version 3 is that support for in vivo Studies and corresponding mortality assay (meta)data has been added.
2. The physicochemical Study file "blood serum ..." fields have been updated to more general "serum ..." fields.
3. Support for isoelectric point determinations was added.
4. Other, miscellaneous changes, were made.

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