CEBS: a comprehensive annotated database of toxicological data

D964–D971 Nucleic Acids Research, 2017, Vol. 45, Database issue doi: 10.1093/nar/gkw1077 Published online 29 November 2016 CEBS: a comprehensive annotated database of toxicological data Isabel A. Lea1,* , Hui Gong1 , Anand Paleja1 , Asif Rashid1 and Jennifer Fostel2,* 1 ASRCFederal Vistronix, 430 Davis Dr, Suite 260, Morrisville, NC 27569, USA and 2 Division of the National Toxicology Program, National Institute of Environmental Health Sciences, PO Box 12233, Research Triangle Park, NC 27709, USA Received August 08, 2016; Revised October 12, 2016; Editorial Decision October 24, 2016; Accepted November 01, 2016 ABSTRACT The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data (to date). The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets. The CEBS database can be accessed online at http://www.niehs.nih.gov/research/resources/ databases/cebs/. INTRODUCTION The National Toxicology Program (NTP) was established by the US Department of Health and Human Services in 1978 in response to concerns about potential human health effects of environmental chemicals. The NTP provides scientific data to regulatory agencies and other health-related research groups. Chemicals studied at the NTP can be endocrine disruptors, occupational exposure mixtures, pesticides, pharmaceuticals, metals, food additives and herbal supplements; anything with the potential to impact health. The NTP conducts comprehensive testing of each substance or test article (exposure agent) in an effort to provide data for a strong scientific basis to make credible decisions that will protect public health. Testing can include evaluations of toxicity and carcinogenicity, prenatal developmental and reproductive toxicology, neurobehavioral effects, immunological effects, genetic toxicity, toxicogenomic responses, as well as chemical disposition and toxicokinetic analysis. Results and conclusions from the NTP testing program are released into the public domain as published reports or journal articles. A great deal of toxicity information has been generated by the NTP since its inception in the 1970s. Until recently these data were made available to the public only as webbased PDF reports on an individual study basis. This made it a challenge to compare and contrast results for multiple test articles or different data endpoints for individual animals. To address this issue, the NTP designated the Chemical Effects in Biological Systems (CEBS) database as the primary repository for its data and has invested significant effort into making the data available for searching, downloading and data mining. CEBS was developed as a public repository for toxicogenomics data by the National Center for Toxicogenomics (NCT) within the National Institute of Environmental Health Science (NIEHS). Our most recent publication in 2008 described development of CEBS to capture microarray (gene expression) and proteomics (protein expression) data (1,2) and illustrated the integration of study design parameters with toxicological assay data. The CEBS SysTox Object Model (3) and the CEBS Data Dictionary (4) were developed to promote this database model. This first version of the database permitted the CEBS user to select groups of subjects drawn from different studies, and analyze the associated microarray data. It also provided a good platform on which to build the current NTP data reposi- * To whom correspondence should be addressed. Tel: +1 919 972 7985; Email: Correspondence may also be addressed to Jennifer Fostel. Email: Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. Nucleic Acids Research, 2017, Vol. 45, Database issue D965 tory. Since this time, CEBS has had three major goals: (i) be a repository for NTP toxicology testing data; (ii) provide a public resource for accessing, searching and reviewing all NTP toxicology data and (3) provide a public data mining resource that could be used to address toxicology related questions. With the advent of new technologies in the field of biological science coupled with advances in database technology, access to on-line data analysis tools and large toxicological datasets is ever expanding. Many open databases and resources for toxicological information and risk assessment exist. Many of these are curated resources built on information garnered from the literature and other online resources, for example: the Comparative Toxicological Database (CTD) (5) and the Swiss Institute of Bioinformatics (SIB) (6). Some databases, including the EPA’s Aggregated Computational Toxicology Resource system (ACToR) (7), PubChem (8) and Chemical Entities of Biological Interest (ChEBI) (9) act as central resources for chemical information compiled from external collections, in tandem with direct submissions or empirically generated data. Still others, Open TG-Gates (10), ArrayExpress (11) and ACuteTox (12) contain solely experimental data but with limited data types and with somewhat restricted access to metadata and study event timelines. CEBS is unique in its role as a repository for NTP testing data and in providing access to individual animal level data in a biologically relevant framework that facilitates interpretation of data by assessment of experimental design. In this update paper we describe recent improvements and additions to CEBS. We have approached this in three ways: (i) update the back-end database design to provide the flexibility to capture as many types of data as possible; (ii) increase the data content in CEBS by capturing electronically available NTP legacy data; (iii) develop and improve search tools available on the CEBS home page to assist users in accessing individual subject (animal or plate) and NTP summary and conc (...truncated)