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The eNanoMapper database for nanomaterial safety information

Jeliazkova, Nina and Chomenides, Haralambos and Doganis, Philip and Fadeel, Bengt and Grafström, Roland and Hardy, Barry and Hastings, Janna and Hegi, Markus and Jeliazkov, Vedrin and Kochev, Nikolay and Kohonen, Pekka and Munteanu, Cristian and Sarimveis, Haralambos and Smeets, Bart and Sopasakis, Pantelis and Tsiliki, Georgia and Vorgrimmler, David and Willighagen, Egon The eNanoMapper database for nanomaterial safety information. Beilstein Journal of Nanotechnology, 6. pp. 1609-1634. ISSN 2190-4286 (2015)

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Abstract

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).

Item Type: Article
Identification Number: 10.3762/bjnano.6.165
Uncontrolled Keywords: Database; EU NanoSafety Cluster; Nanoinformatics; Nanomaterials; Nanomaterials ontology; NanoQSAR; Safety testing
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QA Mathematics > QA76 Computer software
Q Science > QD Chemistry
Q Science > QH Natural history > QH301 Biology
R Medicine > R Medicine (General)
R Medicine > RZ Other systems of medicine
Research Area: Computer Science and Applications
Depositing User: Pantelis Sopasakis
Date Deposited: 24 Nov 2015 13:00
Last Modified: 24 Nov 2015 13:00
URI: http://eprints.imtlucca.it/id/eprint/2931

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