Translating nanoEHS data using EPA NaKnowBase and the Resource Description Framework
Citation:
Mortensen, H., B. Beach, W. Slaughter, J. Senn, A. Williams, AND W. Boyes. Translating nanoEHS data using EPA NaKnowBase and the Resource Description Framework. F1000 Research. Faculty of 1000, London, Uk, 13(169):141056, (2024). https://doi.org/10.12688/f1000research.141056.1
Impact/Purpose:
This work focuses on methods to improve interoperability of nanoEHS data. This work promotes FAIR data standards for nanoEHS data for the US Federal Government. Through the use of the NAMs presented here, we are able to translate nanoEHS data produced by US Federal Agency partners. The methods presented here facilitate traversing the separate and diverse nanoEHS data to address human health and environmental concerns. EPA OntoSearcher tool has been created and continues to developed to improve interoperability with nanoEHS data integration efforts in the EU and US. This manuscript will describe the tool itself, with focus on EPA NKB interoperability and mapping to the RDF framework. This manuscript also describes previous efforts at nomenclature consistency and interoperability with both ISA-TAB Nano and the CSS Chemistry Dashboard.
Description:
Background: The U.S. Federal Government has supported the generation of extensive amounts of nanomaterials and related nano Environmental Health and Safety (nanoEHS) data, there is a need to make these data available to stakeholders. With recent efforts, a need for improved interoperability, translation, and sustainability of Federal nanoEHS data in the United States has been realized. The NaKnowBase (NKB) is a relational database containing experimental results generated by the EPA Office of Research and Development (ORD) regarding the actions of engineered nanomaterials on environmental and biological systems. Through the interaction of the National Nanotechnology Initiative’s Nanotechnology Environmental Health Implications (NEHI) Working Group, and the Database and Informatics Interest Group (DIIG), a U.S. Federal nanoEHS Consortium has been formed. Methods: The primary goal of this consortium is to establish a “common language” for nanoEHS data that aligns with FAIR data standards. A second goal is to overcome nomenclature issues inherent to nanomaterials data, ultimately allowing data sharing and interoperability across the diverse U.S. Federal nanoEHS data compendium, but also in keeping a level of consistency that will allow interoperability with U.S. and European partners. The most recent version of the EPA NaKnowBase (NKB) has been implemented for semantic integration. Computational code has been developed to use each NKB record as input, modify and filter table data, and subsequently output each modified record to a Research Description Framework (RDF). To improve the accuracy and efficiency of this process the EPA has created the OntoSearcher tool. This tool partially automates the ontology mapping process, thereby reducing onerous manual curation. Conclusions: Here we describe the efforts of the US EPA in promoting FAIR data standards for Federal nanoEHS data through semantic integration, as well as in the development of NAMs (computational tools) to facilitate these improvements for nanoEHS data at the Federal partner level.
URLs/Downloads:
DOI: Translating nanoEHS data using EPA NaKnowBase and the Resource Description Framework