eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment
Janna Hastings,Nina Jeliazkova,Gareth Owen,Georgia Tsiliki,Cristian R. Munteanu,Cristian R. Munteanu,Christoph Steinbeck,Egon Willighagen +7 more
TLDR
The eNanoMapper project as discussed by the authors is a pan-European computational infrastructure for toxicological data management for ENM, based on semantic web standards and ontologies, which is used for the development of the eNANOMAP ontology based on the existing ontologies of relevance for the nanosafety domain.Abstract:
Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting proliferation of novel nanomaterials is a challenging race to understand and predict their possibly detrimental effects on human health and the environment. The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. Here, we describe the development of the eNanoMapper ontology based on adopting and extending existing ontologies of relevance for the nanosafety domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated whole. The library is available (open source) at http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive survey of the domain content and identify gap areas. ENM safety is at the boundary between engineering and the life sciences, and at the boundary between molecular granularity and bulk granularity. This creates challenges for the definition of key entities in the domain, which we also discuss.read more
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Journal ArticleDOI
Advanced tools for the safety assessment of nanomaterials.
Bengt Fadeel,Lucian Farcal,Barry Hardy,Socorro Vázquez-Campos,Danail Hristozov,Antonio Marcomini,Iseult Lynch,Eugenia Valsami-Jones,Harri Alenius,Harri Alenius,Kai Savolainen +10 more
TL;DR: Some of the key advances in the hazard and risk assessment of ENMs are highlighted, which may pave the way to safe nanomaterial-driven innovations.
Journal ArticleDOI
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
Pier Luigi Buttigieg,Evangelos Pafilis,Suzanna E. Lewis,Mark Schildhauer,Ramona Walls,Christopher J. Mungall +5 more
TL;DR: ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, ‘omics, and socioeconomic development and is anticipate that ENVO’s growth will accelerate in 2017.
Journal ArticleDOI
ROBOT: A Tool for Automating Ontology Workflows.
Rebecca C. Jackson,James P. Balhoff,Eric Douglass,Nomi L. Harris,Christopher J. Mungall,James A. Overton +5 more
TL;DR: ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions, and packages common high-level ontologyDevelopment functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows.
Journal ArticleDOI
The eNanoMapper database for nanomaterial safety information
Nina Jeliazkova,Charalampos Chomenidis,Philip Doganis,Bengt Fadeel,Roland C. Grafström,Barry Hardy,Janna Hastings,Markus Hegi,Vedrin Jeliazkov,Nikolay Kochev,Pekka Kohonen,Cristian R. Munteanu,Haralambos Sarimveis,Bart Smeets,Pantelis Sopasakis,Georgia Tsiliki,David Vorgrimmler,Egon Willighagen +17 more
TL;DR: It is demonstrated 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).
Journal ArticleDOI
Towards reproducible computational drug discovery
Nalini Schaduangrat,Samuel Lampa,Saw Simeon,Matthew Paul Gleeson,Ola Spjuth,Chanin Nantasenamat +5 more
TL;DR: This article provides an in-depth coverage on the reproducibility of computational drug discovery and explores the current state-of-the-art on reproducible research.
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