CSS.3.2.2.1 NaKnowBase

Description

Product CSS.3.2.2 includes three inter-related components, the delivery of which completes this product. This product represents updates to the NaKnowBase database, which has been cleared under STICS Public accessibility for NaKnowBase ORD-043098. The first component is a tool to automate formatting of ENM data into the standard and universally accepted ISO-TAB Nano format. We have written this code to both WRITE (export) NKB data in ISO-TAB Nano format, as well as READ (input) external data already in the ISO-TAB Nano format for potential inclusion into NKB. The code and corresponding documentation for this tool are made available to the public via the EPA Office of Research and Development at: https://gaftp.epa.gov/EPADataCommons/ORD/NaKnowBase/. The second component is an application, entitled “OntoSearcher”, that automates ontological term mapping for a given ENM dataset. We have developed this code to read in external partner ENM data, and map those data to ontological terms with reported diagnostics on speed and accuracy. This is the first step in the development of a common language for ENMs, aims to minimize necessary human curation time and is critical to EPA efforts to integrate across Federal ENM datasets in a FAIR (Findable, Accessible, Interoperable, Accessible) way. The code and corresponding documentation for this application are made available to the public via the EPA Office of Research and Development at: https://gaftp.epa.gov/EPADataCommons/ORD/NaKnowBase/. The third component is the integration of NaKnowBase ENM data with the EPA Chemistry Dashboard. Currently, we have 373 chemical structure mapped on the Dashboard at https://comptox.epa.gov/dashboard/chemical_lists/NAKNOWBASE. This collaborative, intra-Agency effort between CCTE and CPHEA continues as we update NKB ENMs, establish web-services to update NKB-Dashboard integration with the NKB application, build on our EPA standard nomenclature for ENMs (Beach et al.(2021)), and continue our semantic mapping efforts with Federal and International collaborators.

Resources

Name Format Description Link
57 CSS_3.2.2.1_NKB_IsoTabNano.zip https://pasteur.epa.gov/uploads/10.23719/1523156/CSS_3.2.2.1_NKB_IsoTabNano.zip
57 OntoSearcher_Training_Materials.zip https://pasteur.epa.gov/uploads/10.23719/1523156/OntoSearcher_Training_Materials.zip
0 https://gaftp.epa.gov/EPADataCommons/ORD/NaKnowBase/

Tags

  • chemistry-dashboard
  • data-integration
  • new-approach-methodologies
  • relational-database
  • nanomaterials

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