CSS.3.2.2.1 NaKnowBase

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.

Data and Resources

Field Value
accessLevel public
bureauCode {020:00}
catalog_conformsTo https://project-open-data.cio.gov/v1.1/schema
describedBy https://pasteur.epa.gov/uploads/10.23719/1523156/documents/NKB%20Data%20Dictionary%20-%20version%201.0.xlsx
describedByType application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
identifier https://doi.org/10.23719/1523156
license https://pasteur.epa.gov/license/sciencehub-license.html
modified 2021-09-23
programCode {020:000}
publisher U.S. EPA Office of Research and Development (ORD)
publisher_hierarchy U.S. Government > U.S. Environmental Protection Agency > U.S. EPA Office of Research and Development (ORD)
resource-type Dataset
source_datajson_identifier true
source_hash f32a047cceafae2a27bff2fd04d59c18e15d8166
source_schema_version 1.1
Groups
  • AmeriGEOSS
  • National Provider
  • North America
Tags
  • amerigeo
  • amerigeoss
  • chemistry-dashboard
  • ckan
  • data-integration
  • geo
  • geoss
  • nanomaterials
  • national
  • new-approach-methodologies
  • north-america
  • relational-database
  • united-states
isopen False
license_id other-license-specified
license_title other-license-specified
maintainer Holly Mortensen
maintainer_email mortensen.holly@epa.gov
metadata_created 2025-11-22T22:36:53.984022
metadata_modified 2025-11-22T22:36:53.984026
notes 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.
num_resources 3
num_tags 13
title CSS.3.2.2.1 NaKnowBase