Data Collection from the Nanotoxicology Literature Using ISA-TAB-Nano

These are the slides of an oral presentation delivered at the CompNanoTox 2015 conference:


(1) this presentation has not undergone peer review

(2) this presentation may report preliminary results which may have been revised in subsequent publications

(3) no endorsement by third parties should be inferred

Presentation abstract:

In light of concerns regarding the potential toxicity of nanomaterials, the use of computational approaches to predict their toxicity is gaining interest. These approaches depend upon experimental datasets linking the chemical composition and other physicochemical characteristics of nanomaterials to their toxicity. Computational analysis of these datasets is facilitated by making them available using an electronic, structured and standardised format. The ISA-TAB-Nano specification has been proposed as the basis for a common data exchange format [1,2]. However, in order to create datasets according to this specification, various challenges need to be addressed. This presentation will discuss some of these challenges and will describe a set of resources developed within the NanoPUZZLES EU project which facilitate the manual creation of ISA-TAB-Nano datasets from the nanotoxicology literature: templates, new business rules and software [3]. Nanomaterial toxicity datasets, which were developed using these resources within the NanoPUZZLES project and which will be publicly released at the end of the project, will also be presented. This work will be placed within the wider context of ongoing work to further the use of ISA-TAB-Nano within the nanoinformatics community.

The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/ 2007-2013) under grant agreements no. 309837 (NanoPUZZLES project) and no. 309314 (MODERN project).

N.B. The image on slide 8 was taken from Marchese Robinson et al. []

1. Thomas, D. G.; Gaheen, S.; Harper, S. L.; Fritts, M.; Klaessig, F.; Hahn-Dantona, E.; Paik, D.; Pan, S.; Stafford, G. A.; Freund, E. T.; Klemm, J. D.; Baker, N. A. BMC Biotechnol., 13, 2013, 2.

2. (accessed Sept 22, 2015)

3. Marchese Robinson, R.L.; Cronin, M.T.D.; Richarz, A.-N.; Rallo, R. Beilstein J. Nanotechnol. 2015, 6, 1978–1999. doi:10.3762/bjnano.6.202