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An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology
Richard L Marchese Robinson1, Mark T D Cronin1, Andrea-Nicole Richarz1
1School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom.
Beilstein Journal of Nanotechnology
|December 15, 2015
Summary
Standardized electronic reporting of nanotoxicology data, using ISA-TAB-Nano format, aids nanotoxicity modeling. This study introduces resources to overcome challenges in creating these datasets from literature.
Area of Science:
- Nanotoxicology
- Nanoinformatics
- Data Science
Background:
- Standardized electronic reporting of nanotoxicology data is crucial for trend analysis and developing data-driven nanotoxicity models.
- ISA-TAB-Nano is a proposed standard format, but challenges exist in defining and reporting necessary metadata.
- Existing literature lacks comprehensive, standardized datasets for nanotoxicology research.
Purpose of the Study:
- To address challenges in creating ISA-TAB-Nano datasets from nanotoxicology literature.
- To present resources developed within the NanoPUZZLES EU project to facilitate manual dataset creation.
- To improve the usability and integration of nanotoxicology data in nanoinformatics.
Main Methods:
- Development of data collection templates for ISA-TAB-Nano.
- Definition of business rules to extend the generic ISA-TAB-Nano specification.
- Creation of Python code for parsing and integrating ISA-TAB-Nano datasets.
- Illustration of resource utility with a "Toy Dataset".
Main Results:
- A set of resources, including templates, business rules, and Python code, has been developed to facilitate ISA-TAB-Nano dataset creation.
- The resources streamline the process of extracting and standardizing nanotoxicology data from scientific literature.
- A "Toy Dataset" demonstrates the practical application and integration capabilities of the developed resources.
Conclusions:
- The developed resources effectively address challenges in manual ISA-TAB-Nano dataset creation from nanotoxicology literature.
- These resources facilitate the generation of standardized, high-quality datasets for nanoinformatics and nanotoxicity modeling.
- Further development is planned to enhance the utility and scope of these resources for the scientific community.
