NanoPUZZLES ISA-TAB-Nano dataset: Cytotoxicity and physicochemical data for nanomaterials extracted from Murdock et al. 2008 (DOI:10.1093/toxsci/kfm240)

2015-12-18T14:23:50Z (GMT) by Richard Marchese Robinson

This file is a ZIP archive which contains three different copies of an ISA-TAB-Nano dataset developed within the NanoPUZZLES EU project [http://www.nanopuzzles.eu]. The (meta)data in this dataset were primarily extracted from the following reference, with additional references consulted as indicated in the Investigation file:

Cytotoxicity and physicochemical data for nanomaterials extracted from Murdock et al. 2008 (DOI:10.1093/toxsci/kfm240)

*****Before working with this dataset, you are strongly advised to read the following text - especially the "Disclaimers".*****

ISA-TAB-Nano [1,2,3] has been proposed as a nanomaterial data exchange standard. As is explained in the README file contained within this dataset, as well as the "Investigation Description" field of the Investigation file regarding dataset specific deviations, the manner in which certain data and metadata were recorded within these datasets deviates from the expectations of the generic ISA-TAB-Nano specification. Marchese Robinson et al. [3], distributed within this dataset, discusses this in more detail. However, some additional new business rules, going beyond those described in Marchese Robinson et al. [3], may also have been applied to this dataset - as documented in the README file.

This dataset was developed using Excel-based templates developed in the NanoPUZZLES project [4]. (N.B. The latest version of the templates, at the time of writing, was version 4 as opposed to version 3 which was described in Marchese Robinson et al. [3]. This latest version of the templates should be contained within the README file of this dataset.) Since these templates were iteratively updated, not all datasets may be perfectly consistent with the latest version - although efforts were made to minimise inconsistencies.

The three copies of this dataset are as follows:
(a) 10.1093_FS_toxsci_FS_kfm240.zip: the original dataset prepared within Excel
(b) 10.1093_FS_toxsci_FS_kfm240-txt_opt-N.zip: a tab-delimited text version of this dataset prepared using version 2.0 of the cited Python program [5], with the -N flag selected (designed to minimise inconsistencies with the latest version of the NanoPUZZLES templates)
(c) 10.1093_FS_toxsci_FS_kfm240-txt_opt-a_opt-c_opt-N.zip: a tab-delimited text version of this dataset prepared using version 2.0 of the cited Python program [5], with the -N, -a (truncate ontology IDs) and -c (remove Investigation file comments) flags selected, as required for submission to the nanoDMS online database system [3,6]. 


Disclaimers:

(1) this work has not undergone peer review
(2) no endorsement by third parties should be inferred
(3) *You are strongly advised to read the README file and the "Investigation Description" field of the Investigation file before working with this dataset. The latter field may document dataset specific caveats such as possible problems or uncertainties associated with curation from the original reference(s).

Cited references:
[1] Thomas, D.G. et al. BMC Biotechnol. 2013, 13, 2. doi:10.1186/1472-6750-13-2
[2] https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano (accessed 18th of December 2015)
[3] Marchese Robinson, R.L. et al. Beilstein J. Nanotechnol. 2015, 6, 1978–1999. doi:10.3762/bjnano.6.202
[4] http://www.myexperiment.org/files/1356.html (accessed 18th of December 2015)
[5] https://github.com/RichardLMR/xls2txtISA.NANO.archive (accessed 18th of December 2015)
[6] http://biocenitc-deq.urv.cat/nanodms (accessed 18th of December 2015)

Funding:

The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/ 2007-2013) under grant agreement no. 309837 (NanoPUZZLES project).