Dataset Open Access

All NanoPUZZLES ISA-TAB-Nano datasets

Marchese Robinson, Richard L.; Cassano, Antonio

This file is a ZIP archive which contains ALL publicly released ISA-TAB-Nano datasets developed within the NanoPUZZLES EU project [http://www.nanopuzzles.eu]. The (meta)data in these datasets were extracted from literature references.

These datasets are also available via FigShare (see below). ****Any necessary updates, e.g. to correct errors not spotted during the review of the datasets within the NanoPUZZLES project prior to their being released, will be uploaded to FigShare and the changes documented in the FigShare dataset descriptions. This Zenodo entry corresponds to the original publicly released versions of these datasets.****

*****Before working with these datasets, 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 each 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 each 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 each dataset - as documented in the README file.

Each 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 each 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 each dataset contained within each individual [DATASET ID]_all_copies.zip  are as follows:
(a) [DATASET ID].zip: the original dataset prepared within Excel
(b) [DATASET ID]-txt_opt-N.zip: a tab-delimited text version of each 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) [DATASET ID]-txt_opt-a_opt-c_opt-N.zip: a tab-delimited text version of each 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]. 

The original datasets prepared in Excel were prepared via manual curation. In some cases, it was necessary to extract data from graphs. In some cases, the GSYS software program was employed to facilitate estimation of the values of numerical data points reported in graphs [7,8].


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 anyone of these datasets. The latter field may document dataset specific caveats such as possible problems or uncertainties associated with curation from the original reference(s). *Other such comments may be found in Study, Material or Assay file "Comment" fields.

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)

[7] http://www.jcprg.org/gsys/2.4/ (last accessed 11th of April 2016)

[8] R. Suzuki, "Introduction, Design and Implementation of Digitization Software GSYS", IAEA Report INDC(NDS)-0629, p. 19, IAEA, Vienna, Austria (2013)

FigShare versions:

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Cytotoxicity_and_some_physicochemical_data_reported_by_Wang_et_al_2014_DOI_10_3109_17435390_2013_796534_/2056140

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Zebrafish_mortality_and_basic_nanomaterial_composition_data_extracted_from_Kovriznych_et_al_2013_doi_10_2478_intox_2013_0012_/2056137

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Physicochemical_and_in_vitro_cytotoxicity_data_LDH_membrane_damage_extracted_from_Sayes_and_Ivanov_2010_DOI_10_1111_j_1539_6924_2010_01438_x_/2056134

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Cytotoxicity_and_physicochemical_data_for_nanomaterials_extracted_from_Murdock_et_al_2008_DOI_10_1093_toxsci_kfm240_/2056131

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Data_reported_in_Shaw_et_al_2008_DOI_10_1073_pnas_0802878105_/2056128

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Data_extracted_from_Puzyn_et_al_2011_DOI_10_1038_NNANO_2011_10_/2056125

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Toxicity_and_physicochemical_data_extracted_from_Zhang_et_al_2012_DOI_10_1021_nn3010087_/2056122

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Curation_of_carbon_nanotubes_experimental_data_reported_by_Zhou_et_al_2008_DOI_10_1021_nl0730155_supplemented_with_carbon_nanotubes_structure_files_3D_SDF_created_according_to_the_approach_described_by_Shao_et_al_/2056110

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_C60_fullerene_nanoparticle_Ames_test_and_in_vivo_micronucleus_data_extracted_from_Shinohara_et_al_2009_DOI_10_1016_j_toxlet_2009_09_012_/2056104

https://figshare.com/articles/NanoPUZZLES_ISA_TAB_Nano_dataset_Data_extracted_from_NanoCare_project_final_scientific_report/2056095


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).

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