The eNanoMapper database for nanomaterial safety information.
- Jeliazkova N Ideaconsult Ltd., Sofia, Bulgaria.
- Chomenidis C National Technical University of Athens, School of Chemical Engineering, Athens, Greece.
- Doganis P National Technical University of Athens, School of Chemical Engineering, Athens, Greece.
- Fadeel B Karolinska Institutet, Stockholm, Sweden.
- Grafström R Karolinska Institutet, Stockholm, Sweden.
- Hardy B Douglas Connect GmbH, Zeiningen, Switzerland.
- Hastings J European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.
- Hegi M Douglas Connect GmbH, Zeiningen, Switzerland.
- Jeliazkov V Ideaconsult Ltd., Sofia, Bulgaria.
- Kochev N Ideaconsult Ltd., Sofia, Bulgaria ; Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria.
- Kohonen P Karolinska Institutet, Stockholm, Sweden.
- Munteanu CR Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands ; Computer Science Faculty, University of A Coruna, A Coruña, Spain.
- Sarimveis H National Technical University of Athens, School of Chemical Engineering, Athens, Greece.
- Smeets B Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands.
- Sopasakis P National Technical University of Athens, School of Chemical Engineering, Athens, Greece ; IMT Institute for Advanced Studies Lucca, Lucca, Italy.
- Tsiliki G National Technical University of Athens, School of Chemical Engineering, Athens, Greece.
- Vorgrimmler D in silico toxicology Gmbh (IST), Basel, Switzerland.
- Willighagen E Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands.
- 2015-10-02
Published in:
- Beilstein journal of nanotechnology. - 2015
EU NanoSafety Cluster
NanoQSAR
database
nanoinformatics
nanomaterials
nanomaterials ontology
safety testing
English
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).
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).
- Language
-
- English
- Open access status
- gold
- Identifiers
-
- DOI 10.3762/bjnano.6.165
- PMID 26425413
- Persistent URL
- https://sonar.ch/global/documents/279012
Statistics
Document views: 56
File downloads:
- Full-text: 0