OpenTox Virtual Conference 2021 Session 14
National Toxicology Program Histopathology and Clinical Pathology Dictionary
Authors: Jamie Moose1, Ying Liu1, David Burrows1, Cari Martini1, Cynthia J. Willson2, Michelle Cora3, Amy E. Brix4, Ronald A. Herbert3, Susan A. Elmore3, Mark F. Cesta3, Jennifer Fostel3
- ASRC Federal, 430 Davis Dr., Morrisville, NC 27560
- Integrated Laboratory Systems, LLC, Research Triangle Park, NC 27709
- NIEHS, Division of the National Toxicology Program (DNTP), Research Triangle Park, NC 27560 4EPL, Inc., Research Triangle Park, NC 27560
The Division of the National Toxicology Program (DNTP) has been collecting and reporting clinical pathology and histopathology data for technical reports and other publications since 1976. During the past 45 years, pathology terminologies have evolved, which limited data accessibility. To make DNTP data more Findable, Accessible, Interoperable, and Reusable (FAIR), the vast number of pathology terms have been standardized and linked to ontologies contained in various Open Biological and Biomedical Ontologies (OBO) Foundry collections. Ontologies are important tools for organizing knowledge by categorizing, harmonizing names, and defining properties and relationships. The DNTP Pathology Dictionary is built and multiple histopathologies and clinical pathology datasets with standard terms and ontologies are published on the Chemical Effects in Biological Systems (CEBS) website. Over 4500 legacy pathology terms in 2500 studies are reviewed. Each term for a histopathological finding (organ, locations, morphology, modifiers) was standardized to build a DNTP Legacy Histopathology Mapping to DNTP Standard Term document covering both legacy and current histopathology terms. Standardized histopathology terms and clinical pathology assays were linked to ontologies to build a DNTP Histopathology Standard Terms, and a DNTP Clinical Pathology Standard Terms, respectively. Standardized terms and ontologies are integrated into multiple histopathologies or clinical pathology datasets. Standardized terms published by DNTP are publicly available in DNTP Pathology Dictionary (https://doi.org/10.22427/NTP-DATA-002-00092-0001-0000-4) in CEBS. Standardized terms are integrated into multiple datasets, including NTP Individual Animal Pathology Lesions dataset (https://doi.org/10.22427/NTP-DATA-022-00002-0028-000-6); CEBSR: Statistically Analyzed NTP Pathology Lesions (with Incidence, Benchmark Dose (BMD), No Effect Level (NEL), and Lowest Effect Level (LEL) dataset (http://doi.org/10.22427/NTP-DATA-022-00002-0024-000-2); CEBSR: NTP Clinical Pathology Data dataset (http://doi.org/10.22427/NTP-DATA-022-00002-0023-000-1), and more. These datasets are published through the CEBS NTP Data Collections Application.
DNTP pathology terms are standardized and linked to ontologies for the first time. The harmonized terminologies are integrated with data from 2500 histopathology and clinical pathology studies. The DNTP Pathology Dictionary and studies with standardized terms are published on the CEBS home page. These resources are available to the public for search and download. DNTP standardized terminology and ontology harmonize legacy terms, meet FAIR data standards and facilitate data integration. The updates to the DNTP Pathology Dictionary in CEBS allow for easier searching and data discovery for DNTP data leading to more reusable data that can be integrated into external datasets. Pathology datasets published at CEBS NTP Data Collections allow the public to query across the data from legacy and modern DNTP pathology studies.