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. 2022 Jan 7;50(D1):D1156-D1163.
doi: 10.1093/nar/gkab981.

CEBS update: curated toxicology database with enhanced tools for data integration

Cari Martini  1 , Ying Frances Liu  1 , Hui Gong  1 , Nicole Sayers  1 , German Segura  1 , Jennifer Fostel  2
Affiliations

CEBS update: curated toxicology database with enhanced tools for data integration

Cari Martini et al. Nucleic Acids Res. .

Abstract

The Chemical Effects in Biological Systems database (CEBS) contains extensive toxicology study results and metadata from the Division of the National Toxicology Program (NTP) and other studies of environmental health interest. This resource grants public access to search and collate data from over 10 250 studies for 12 750 test articles (chemicals, environmental agents). CEBS has made considerable strides over the last 5 years to integrate growing internal data repositories into data warehouses and data marts to better serve the public with high quality curated datasets. This effort includes harmonizing legacy terms and metadata to current standards, mapping test articles to external identifiers, and aligning terms to OBO (Open Biological and Biomedical Ontology) Foundry ontologies. The data are made available through the CEBS Homepage (https://cebs.niehs.nih.gov/cebs/), guided search applications, flat files on FTP (file transfer protocol), and APIs (application programming interface) for user access and to provide a bridge for computational tools. The user interface is intuitive with a single search bar to query keywords related to study metadata, publications, and data availability. Results are consolidated to single pages for each test article with NTP conclusions, publications, individual studies, data collections, and links to related test articles and projects available together.

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Figures

Figure 1.
Figure 1.
Using CEBS (additional details of each use case are provided in Supplemental Materials). The user can 1) review files supporting NTP reports, 2) download pre-defined bulk data for a given data domain or 3) interact with CEBS data using a CEBS Guided Search or an API.
Figure 2.
Figure 2.
CEBSR Data Pipeline. CEBS supports active data streams which are stored in relational databases and maintains several legacy systems. These data are moved using ETL (extract transform load) processes and through curation efforts to the current CEBSR Data Warehouse. Subsets of the data are moved to individual Data Marts for specific data types or to allow users to answer targeted questions with refined metadata. There are APIs available for the data marts and select CEBS guided search applications are powered by the data marts.
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References

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