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Enhancing the Interoperability of the Ecotoxicology (ECOTOX) Knowledgebase via Mapping to Existing Controlled Vocabularies and Ontologies
Citation:
Olker, J., K. Fay, C. LaLone, R. Wang, C. Elonen, M. Skopinski, T. Karschnik, A. Pilli, AND D. Hoff. Enhancing the Interoperability of the Ecotoxicology (ECOTOX) Knowledgebase via Mapping to Existing Controlled Vocabularies and Ontologies. OpenTox 2021 Virtual Conference, Duluth, MN, September 20 - 24, 2021. https://doi.org/10.23645/epacomptox.16915183
Impact/Purpose:
Presentation to the OpenTox 2021 Virtual Conference September 2021. The ECOTOXicology Knowledgebase (ECOTOX) is the world’s largest compilation of curated environmental toxicity data on aquatic life, terrestrial plants, and wildlife. ECOTOX was developed to address the need to rapidly identify relevant toxicity data for risk assessment and management with methods that are also thorough, cost-effective, and transparent methods. ECOTOX currently includes data for over 12,000 chemicals and 13,000 ecological species, with over one million records from over 52,000 references, with quarterly updates to public website (www.epa.gov/ecotox). The goal of the work presented here is to enhance the interoperability of ECOTOX with other EPA tools (e.g., CompTox Chemicals Dashboard, Adverse Outcome Pathway wiki) as well as various external databases and tools relevant for toxicology and chemical risk assessment. The addition of species and chemical identifiers to ECOTOX and mapping ECOTOX-specific terms to ontology classes enhance the interoperability of ECOTOX and lay the groundwork for computational functionality using ECOTOX data for modeling of phenotype effects, species sensitivity and putative adverse outcome pathways.
Description:
The ECOTOXicology Knowledgebase (ECOTOX) has been locating and curating ecologically-relevant toxicity data for over 30 years and is now a nationally and internationally recognized source of single-chemical toxicity test results for aquatic and terrestrial organisms. Through decades of reviewing and curating data from the ecotoxicological literature, ECOTOX has established a standard format and controlled vocabularies for extracting pertinent study and toxicity effects information. ECOTOX data extraction captures author-reported information about species, chemicals, test methods and conditions, and toxicity results using 90 different study entities (e.g., species scientific and common name, chemical name and CASRN, media type, type of control, endpoint, statistical significance), each with acceptable data type and set of terms defined. These controlled vocabularies currently include over 7,000 terms across all entities. This presentation will describe on-going efforts to harmonize the ECOTOX-specific terminologies with existing controlled vocabularies and ontologies in order to support integration and exchange with other data resources. Nearly all 12,326 chemicals with data in ECOTOX were successfully mapped to DSSTox Substance IDs (based on chemical name and CASRN already in ECOTOX). NCBI TaxIDs were added for ~80% of the 13,610 biological species based on scientific name, with updates occuring annually. Initial mapping of ECOTOX terms to ontological classes was then completed using a Java-based lookup tool for the ontology browser BioPortal (https://bioportal.bioontology.org/). This semi-automated mapping identified potential ontological class identifiers for the majority of the ECOTOX terms. However, manual review was required to ensure proper context for the mapped classes and some highly relevant ecotoxicological terms (e.g., ‘LC50’, ‘concurrent control’, gene names) remained unmapped due to absence in existing ontologies and/or term complexity. These results led to current efforts to complete annotation of ECOTOX terms (e.g., mapping gene names to NCBI, simplifying complex terms) and planning for development of an Application Ontology as the foundation to semanticize ECOTOX. In combination, the mappings to OBO ontologies and the incorporation of unique identifiers from public domains will enable linking to a variety of chemical, toxicological, and biological databases, increase the accessibility of data in ECOTOX, support advanced querying capabilities, and, ultimately, expand the ECOTOX functionalities and applications.
URLs/Downloads:
DOI: Enhancing the Interoperability of the Ecotoxicology (ECOTOX) Knowledgebase via Mapping to Existing Controlled Vocabularies and Ontologies
OLKER_ECOTOX_OPENTOX2021_FINAL.PDF (PDF, NA pp, 2003.388 KB, about PDF)