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Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content

Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase... Introduction: The AOP-Wiki is the main platform for the development and storage of adverse outcome pathways (AOPs). These AOPs describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content, and to link it with chemical and biological resources. Together, this allows more detailed exploration, which can be automated.Materials and Methods: We converted the complete AOP-Wiki content into resource description framework (RDF) triples. We used >20 ontologies for the semantic annotation of property–object relations, including the Chemical Information Ontology, Dublin Core, and the AOP Ontology.Results: The resulting RDF contains >122,000 triples describing 158 unique properties of >15,000 unique subjects. Furthermore, >3500 link-outs were added to 12 chemical databases, and >7500 link-outs to 4 gene and protein databases. The AOP-Wiki RDF has been made available at https://aopwiki.rdf.bigcat-bioinformatics.orgDiscussion: SPARQL queries can be used to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries.Conclusion: Overall, the AOP-Wiki RDF allows new ways to explore the rapidly growing AOP knowledge and makes the integration of this database in automated workflows possible, making the AOP-Wiki more FAIR. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Applied In Vitro Toxicology Mary Ann Liebert

Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content

Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content

Applied In Vitro Toxicology , Volume 8 (1): 12 – Mar 1, 2022

Abstract

Introduction: The AOP-Wiki is the main platform for the development and storage of adverse outcome pathways (AOPs). These AOPs describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content, and to link it with chemical and biological resources. Together, this allows more detailed exploration, which can be automated.Materials and Methods: We converted the complete AOP-Wiki content into resource description framework (RDF) triples. We used >20 ontologies for the semantic annotation of property–object relations, including the Chemical Information Ontology, Dublin Core, and the AOP Ontology.Results: The resulting RDF contains >122,000 triples describing 158 unique properties of >15,000 unique subjects. Furthermore, >3500 link-outs were added to 12 chemical databases, and >7500 link-outs to 4 gene and protein databases. The AOP-Wiki RDF has been made available at https://aopwiki.rdf.bigcat-bioinformatics.orgDiscussion: SPARQL queries can be used to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries.Conclusion: Overall, the AOP-Wiki RDF allows new ways to explore the rapidly growing AOP knowledge and makes the integration of this database in automated workflows possible, making the AOP-Wiki more FAIR.

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Publisher
Mary Ann Liebert
Copyright
© Marvin Martens et al., 2022; Published by Mary Ann Liebert, Inc.
ISSN
2332-1512
eISSN
2332-1539
DOI
10.1089/aivt.2021.0010
Publisher site
See Article on Publisher Site

Abstract

Introduction: The AOP-Wiki is the main platform for the development and storage of adverse outcome pathways (AOPs). These AOPs describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content, and to link it with chemical and biological resources. Together, this allows more detailed exploration, which can be automated.Materials and Methods: We converted the complete AOP-Wiki content into resource description framework (RDF) triples. We used >20 ontologies for the semantic annotation of property–object relations, including the Chemical Information Ontology, Dublin Core, and the AOP Ontology.Results: The resulting RDF contains >122,000 triples describing 158 unique properties of >15,000 unique subjects. Furthermore, >3500 link-outs were added to 12 chemical databases, and >7500 link-outs to 4 gene and protein databases. The AOP-Wiki RDF has been made available at https://aopwiki.rdf.bigcat-bioinformatics.orgDiscussion: SPARQL queries can be used to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries.Conclusion: Overall, the AOP-Wiki RDF allows new ways to explore the rapidly growing AOP knowledge and makes the integration of this database in automated workflows possible, making the AOP-Wiki more FAIR.

Journal

Applied In Vitro ToxicologyMary Ann Liebert

Published: Mar 1, 2022

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