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2015 ; 6
(ä): 1609-34
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The eNanoMapper database for nanomaterial safety information
#MMPMID26425413
Jeliazkova N
; Chomenidis C
; Doganis P
; Fadeel B
; Grafström R
; Hardy B
; Hastings J
; Hegi M
; Jeliazkov V
; Kochev N
; Kohonen P
; Munteanu CR
; Sarimveis H
; Smeets B
; Sopasakis P
; Tsiliki G
; Vorgrimmler D
; Willighagen E
Beilstein J Nanotechnol
2015[]; 6
(ä): 1609-34
PMID26425413
show ga
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).
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