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Enhancing the Utility of the ECOTOX knowledgebase (ECOTOX KB) via ontology-based semantics mapping
Citation:
Fay, K., C. Elonen, D. Hoff, M. Skopinski, A. Pilli, R. Wang, AND C. LaLone. Enhancing the Utility of the ECOTOX knowledgebase (ECOTOX KB) via ontology-based semantics mapping. SETAC Europe, Rome, ITALY, May 14 - 18, 2018.
Impact/Purpose:
The US Environmental Protection Agency’s Ecological Toxicology (ECOTOX) knowledgebase contains more than 30 years of reported single chemical toxicity effects data on aquatic and terrestrial organisms. Approximately 900,000 test results covering more than 11,000 chemicals and 12,000 species are available in ECOTOX. While the database is currently used by many sectors for a variety of purposes, a future goal is to allow for computational modeling of the data to identify novel adverse outcome pathways and networks, and assist in predicting species sensitivity. To accomplish these goals, the initial steps entailed:1) validating the chemicals within ECOTOX 2) mapping species to NCBI taxids and 3) mapping all relevant ECOTOX codes to corresponding ontological terms so chemical effects can be turned into computable phenotypic ontology classes. To semi-automate the code mapping, a Java-based lookup tool was developed using the ontology browser BioPortal (https://bioportal.bioontology.org/) REST API to conduct batch code mapping. This tool was designed to make use of BioPortal’s annotator and recommender functions so that all ontological class identifiers relevant to a particular ECOTOX term would be returned and specific ontologies recommended. Using this approach, the majority of the 2000+ ECOTOX codes were mapped to ontological class identifiers; some terms required multiple identifiers to properly describe them. Further, manual curation was necessary for a proportion of terms. The results of the automated code mapping approach were evaluated against a set of manually annotated phenotypes as induced by exposures to ten well studied chemicals (atrazine, bisphenol A, cadmium chloride, chlorpyrifos, copper sulfate, cypermethrin, dioxin, EE2, malathion, or Tris(1,3-dichloroisopropyl) phosphate) in six vertebrate species (carp, zebrafish, fathead minnow, mouse, rat, trout).
Description:
The US Environmental Protection Agency’s Ecological Toxicology (ECOTOX) knowledgebase contains more than 30 years of reported single chemical toxicity effects data on aquatic and terrestrial organisms. Approximately 900,000 test results covering more than 11,000 chemicals and 12,000 species are available in ECOTOX. While the database is currently used by many sectors for a variety of purposes, a future goal is to allow for computational modeling of the data to identify novel adverse outcome pathways and networks, and assist in predicting species sensitivity. To accomplish these goals, the initial steps entailed:1) validating the chemicals within ECOTOX 2) mapping species to NCBI taxids and 3) mapping all relevant ECOTOX codes to corresponding ontological terms so chemical effects can be turned into computable phenotypic ontology classes. To semi-automate the code mapping, a Java-based lookup tool was developed using the ontology browser BioPortal (https://bioportal.bioontology.org/) REST API to conduct batch code mapping. This tool was designed to make use of BioPortal’s annotator and recommender functions so that all ontological class identifiers relevant to a particular ECOTOX term would be returned and specific ontologies recommended. Using this approach, the majority of the 2000+ ECOTOX codes were mapped to ontological class identifiers; some terms required multiple identifiers to properly describe them. Further, manual curation was necessary for a proportion of terms. The results of the automated code mapping approach were evaluated against a set of manually annotated phenotypes as induced by exposures to ten well studied chemicals (atrazine, bisphenol A, cadmium chloride, chlorpyrifos, copper sulfate, cypermethrin, dioxin, EE2, malathion, or Tris(1,3-dichloroisopropyl) phosphate) in six vertebrate species (carp, zebrafish, fathead minnow, mouse, rat, trout).