The eNanoMapper database for nanomaterial safety information

Abstract

Summary Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state transfer” (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR).

Grouping of nanomaterials to read-across hazard endpoints: a review

“…Efforts are ongoing to develop databases where toxicity data and PC properties are collected in one place, in order to improve data availability and enable investigations supporting grouping for readacross and development of in silico methods (Chen et al 2017). eNanoMapper (Jeliazkova et al 2015) is supporting read-across applications and in silico modeling, and the running project GRACIOUS is defining a grouping framework that takes more explicitly into account similarity.…”

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences

“…Toxicological studies have shown that TiO 2 nanoparticles (NPs) induce oxidative stress in cells resulting in immune response, inflammation, genotoxicity, and cell damage [ 21 ]. The researcher looked for a dataset in the search engine of four databases eNanoMapper [ 22 ], caNanoLab [ 23 ], ChEMBL [ 24 ], and NanoCommons [ 25 ] for data related to TiO 2 induced cytotoxicity, immunotoxicity, genotoxicity, or oxidative stress.…”

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

“…The API is REST-like. eNanoMapper separates the API design from the server implementation; AMBIT is one of the reference implementations of OpenTox services (Jeliazkova and Jeliazkova, 2011) and more recently eNanoMapper database (Jeliazkova et al, 2015), and on the server-side uses Apache’s Tomcat. The API implements user authentication and authorization.…”

“…The eNanoMapper server currently does not use other web services, besides being able to retrieve chemical structures from public databases (e.g. PubChem). The full details of the eNanoMapper API, including a description of the computational services implementation (which uses and integrates a variety of technologies and also reads and writes from/to data services) are published (Jeliazkova et al, 2015)(Chomenidis et al, 2017). …”