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Article ; Online: Comparative Toxicogenomics Database (CTD): update 2023.

Davis, Allan Peter / Wiegers, Thomas C / Johnson, Robin J / Sciaky, Daniela / Wiegers, Jolene / Mattingly, Carolyn J

2022 Volume 51, Issue D1, Page(s) D1257–D1262

Abstract: The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions by manually curating and interrelating chemical, gene, phenotype, anatomy, disease, ... ...

Abstract	The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions by manually curating and interrelating chemical, gene, phenotype, anatomy, disease, taxa, and exposure content from the published literature. This curated information is integrated to generate inferences, providing potential molecular mediators to develop testable hypotheses and fill in knowledge gaps for environmental health. This dual nature, acting as both a knowledgebase and a discoverybase, makes CTD a unique resource for the scientific community. Here, we report a 20% increase in overall CTD content for 17 100 chemicals, 54 300 genes, 6100 phenotypes, 7270 diseases and 202 000 exposure statements. We also present CTD Tetramers, a novel tool that computationally generates four-unit information blocks connecting a chemical, gene, phenotype, and disease to construct potential molecular mechanistic pathways. Finally, we integrate terms for human biological media used in the CTD Exposure module to corresponding CTD Anatomy pages, allowing users to survey the chemical profiles for any tissue-of-interest and see how these environmental biomarkers are related to phenotypes for any anatomical site. These, and other webpage visual enhancements, continue to promote CTD as a practical, user-friendly, and innovative resource for finding information and generating testable hypotheses about environmental health.
MeSH term(s)	Humans ; Toxicogenetics ; Databases, Factual ; Phenotype
Language	English
Publishing date	2022-09-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac833
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Article ; Online: Developmental cadmium exposure disrupts zebrafish vestibular calcium channels interfering with otolith formation and inner ear function.

Green, Adrian J / Wall, Alex R / Weeks, Ryan D / Mattingly, Carolyn J / Marsden, Kurt C / Planchart, Antonio

Neurotoxicology

2023 Volume 96, Page(s) 129–139

Abstract: Dizziness or balance problems are estimated to affect approximately 3.3 million children aged three to 17 years. These disorders develop from a breakdown in the balance control system and can be caused by anything that affects the inner ear or the brain, ...

Abstract	Dizziness or balance problems are estimated to affect approximately 3.3 million children aged three to 17 years. These disorders develop from a breakdown in the balance control system and can be caused by anything that affects the inner ear or the brain, including exposure to environmental toxicants. One potential environmental toxicant linked to balance disorders is cadmium, an extremely toxic metal that occurs naturally in the earth's crust and is released as a byproduct of industrial processes. Cadmium is associated with balance and vestibular dysfunction in adults exposed occupationally, but little is known about the developmental effects of low-concentration cadmium exposure. Our findings indicate that zebrafish exposed to 10-60 parts per billion (ppb) cadmium from four hours post-fertilization (hpf) to seven days post-fertilization (dpf) exhibit abnormal behaviors, including pronounced increases in auditory sensitivity and circling behavior, both of which are linked to reductions in otolith growth and are rescued by the addition of calcium to the media. Pharmacological intervention shows that agonist-induced activation of the P2X calcium ion channel in the presence of cadmium restores otolith size. In conclusion, cadmium-induced ototoxicity is linked to vestibular-based behavioral abnormalities and auditory sensitivity following developmental exposure, and calcium ion channel function is associated with these defects.
MeSH term(s)	Animals ; Zebrafish ; Cadmium/toxicity ; Otolithic Membrane ; Vestibule, Labyrinth ; Vestibular Diseases
Chemical Substances	Cadmium (00BH33GNGH)
Language	English
Publishing date	2023-04-14
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	800820-6
ISSN	1872-9711 ; 0161-813X
ISSN (online)	1872-9711
ISSN	0161-813X
DOI	10.1016/j.neuro.2023.04.006
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Article: Public data sources to support systems toxicology applications.

Davis, Allan Peter / Wiegers, Jolene / Wiegers, Thomas C / Mattingly, Carolyn J

Current opinion in toxicology

2019 Volume 16, Page(s) 17–24

Abstract: Public databases provide a wealth of freely available information about chemicals, genes, proteins, biological networks, phenotypes, diseases, and exposure science that can be integrated to construct pathways for systems toxicology applications. Relating ...

Abstract	Public databases provide a wealth of freely available information about chemicals, genes, proteins, biological networks, phenotypes, diseases, and exposure science that can be integrated to construct pathways for systems toxicology applications. Relating this disparate information from public repositories, however, can be challenging since databases use a variety of ways to represent, describe, and make available their content. The use of standard vocabularies to annotate key data concepts, however, allows the information to be more easily exchanged and combined for discovery of new findings. We explore some of the many public data sources currently available to support systems toxicology, and demonstrate the value of standardizing data to help construct chemical-induced outcome pathways.
Language	English
Publishing date	2019-03-11
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-2934
ISSN	2468-2934
DOI	10.1016/j.cotox.2019.03.002
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CTD tetramers: a new online tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health.

Davis, Allan Peter / Wiegers, Thomas C / Wiegers, Jolene / Wyatt, Brent / Johnson, Robin J / Sciaky, Daniela / Barkalow, Fern / Strong, Melissa / Planchart, Antonio / Mattingly, Carolyn J

Toxicological sciences : an official journal of the Society of Toxicology

2023 Volume 195, Issue 2, Page(s) 155–168

Abstract: The molecular mechanisms connecting environmental exposures to adverse endpoints are often unknown, reflecting knowledge gaps. At the Comparative Toxicogenomics Database (CTD), we developed a bioinformatics approach that integrates manually curated, ... ...

Abstract	The molecular mechanisms connecting environmental exposures to adverse endpoints are often unknown, reflecting knowledge gaps. At the Comparative Toxicogenomics Database (CTD), we developed a bioinformatics approach that integrates manually curated, literature-based interactions from CTD to generate a "CGPD-tetramer": a 4-unit block of information organized as a step-wise molecular mechanism linking an initiating Chemical, an interacting Gene, a Phenotype, and a Disease outcome. Here, we describe a novel, user-friendly tool called CTD Tetramers that generates these evidence-based CGPD-tetramers for any curated chemical, gene, phenotype, or disease of interest. Tetramers offer potential solutions for the unknown underlying mechanisms and intermediary phenotypes connecting a chemical exposure to a disease. Additionally, multiple tetramers can be assembled to construct detailed modes-of-action for chemical-induced disease pathways. As well, tetramers can help inform environmental influences on adverse outcome pathways (AOPs). We demonstrate the tool's utility with relevant use cases for a variety of environmental chemicals (eg, perfluoroalkyl substances, bisphenol A), phenotypes (eg, apoptosis, spermatogenesis, inflammatory response), and diseases (eg, asthma, obesity, male infertility). Finally, we map AOP adverse outcome terms to corresponding CTD terms, allowing users to query for tetramers that can help augment AOP pathways with additional stressors, genes, and phenotypes, as well as formulate potential AOP disease networks (eg, liver cirrhosis and prostate cancer). This novel tool, as part of the complete suite of tools offered at CTD, provides users with computational datasets and their supporting evidence to potentially fill exposure knowledge gaps and develop testable hypotheses about environmental health.
MeSH term(s)	Male ; Humans ; Toxicogenetics ; Databases, Factual ; Environmental Health ; Phenotype ; Environmental Exposure
Language	English
Publishing date	2023-07-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1420885-4
ISSN	1096-0929 ; 1096-6080
ISSN (online)	1096-0929
ISSN	1096-6080
DOI	10.1093/toxsci/kfad069
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Article ; Online: CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies.

Davis, Allan Peter / Wiegers, Thomas C / Wiegers, Jolene / Grondin, Cynthia J / Johnson, Robin J / Sciaky, Daniela / Mattingly, Carolyn J

Current research in toxicology

2021 Volume 2, Page(s) 128–139

Abstract: The Comparative Toxicogenomics Database (CTD) is a freely available public resource that curates and interrelates chemical, gene/protein, phenotype, disease, organism, and exposure data. CTD can be used to address toxicological mechanisms for ... ...

Abstract	The Comparative Toxicogenomics Database (CTD) is a freely available public resource that curates and interrelates chemical, gene/protein, phenotype, disease, organism, and exposure data. CTD can be used to address toxicological mechanisms for environmental chemicals and facilitate the generation of testable hypotheses about how exposures affect human health. At CTD, manually curated interactions for chemical-induced phenotypes are enhanced with anatomy terms (tissues, fluids, and cell types) to describe the physiological system of the reported event. These same anatomy terms are used to annotate the human media (e.g., urine, hair, nail, blood, etc.) in which an environmental chemical was assayed for exposure. Currently, CTD uses more than 880 unique anatomy terms to contextualize over 255,000 chemical-phenotype interactions and 167,000 exposure statements. These annotations allow chemical-phenotype interactions and exposure data to be explored from a novel, anatomical perspective. Here, we describe CTD's anatomy curation process (including the construction of a controlled, interoperable vocabulary) and new anatomy webpages (that coalesce and organize the curated chemical-phenotype and exposure data sets). We also provide examples that demonstrate how this feature can be used to identify system- and cell-specific chemical-induced toxicities, help inform exposure data, prioritize phenotypes for environmental diseases, survey tissue and pregnancy exposomes, and facilitate data connections with external resources. Anatomy annotations advance understanding of environmental health by providing new ways to explore and survey chemical-induced events and exposure studies in the CTD framework.
Language	English
Publishing date	2021-03-05
Publishing country	Netherlands
Document type	Journal Article
ISSN	2666-027X
ISSN (online)	2666-027X
DOI	10.1016/j.crtox.2021.03.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Chemical databases for environmental health and clinical research.

Mattingly, Carolyn J

Toxicology letters

2009 Volume 186, Issue 1, Page(s) 62–65

Abstract: The increasing number of publicly available biological databases reflects the evolving need for managing and evaluating abundant and complex data in biological, clinical and computational research. Currently there are over 1000 biologically relevant ... ...

Abstract	The increasing number of publicly available biological databases reflects the evolving need for managing and evaluating abundant and complex data in biological, clinical and computational research. Currently there are over 1000 biologically relevant databases in the public domain with varied content and diverse approaches to capturing and presenting data. This review summarizes the comparatively small niche of sophisticated databases and other resources that aim to enhance understanding of chemicals and their biological actions. The databases reviewed include 1 that emphasizes environmental chemicals and 9 that emphasize drugs and small molecules. These databases and their associated resources are incrementally strengthening the expanding field of toxicogenomics-based research by providing centralized sources of manually and computationally curated datasets and highly sophisticated tools for the meta-analysis of continually increasing environmental chemical, drug and small-molecule datasets.
MeSH term(s)	Animals ; Databases, Factual ; Drug-Related Side Effects and Adverse Reactions ; Environmental Exposure ; Environmental Health ; Environmental Medicine ; Environmental Pollutants/toxicity ; Humans ; Toxicogenetics
Chemical Substances	Environmental Pollutants
Language	English
Publishing date	2009-04-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	433788-8
ISSN	1879-3169 ; 0378-4274
ISSN (online)	1879-3169
ISSN	0378-4274
DOI	10.1016/j.toxlet.2008.10.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Predicting molecular mechanisms, pathways, and health outcomes induced by Juul e-cigarette aerosol chemicals using the Comparative Toxicogenomics Database.

Grondin, Cynthia J / Davis, Allan Peter / Wiegers, Jolene A / Wiegers, Thomas C / Sciaky, Daniela / Johnson, Robin J / Mattingly, Carolyn J

Current research in toxicology

2021 Volume 2, Page(s) 272–281

Abstract: There is a critical need to understand the health risks associated with vaping e-cigarettes, which has reached epidemic levels among teens. Juul is currently the most popular type of e-cigarette on the market. Using the Comparative Toxicogenomics ... ...

Abstract	There is a critical need to understand the health risks associated with vaping e-cigarettes, which has reached epidemic levels among teens. Juul is currently the most popular type of e-cigarette on the market. Using the Comparative Toxicogenomics Database (CTD; http://ctdbase.org), a public resource that integrates chemical, gene, phenotype and disease data, we aimed to analyze the potential molecular mechanisms of eight chemicals detected in the aerosols generated by heating Juul e-cigarette pods: nicotine, acetaldehyde, formaldehyde, free radicals, crotonaldehyde, acetone, pyruvaldehyde, and particulate matter. Curated content in CTD, including chemical-gene, chemical-phenotype, and chemical-disease interactions, as well as associated phenotypes and pathway enrichment, were analyzed to help identify potential molecular mechanisms and diseases associated with vaping. Nicotine shows the most direct disease associations of these chemicals, followed by particulate matter and formaldehyde. Together, these chemicals show a direct marker or mechanistic relationship with 400 unique diseases in CTD, particularly in the categories of cardiovascular diseases, nervous system diseases, respiratory tract diseases, cancers, and mental disorders. We chose three respiratory tract diseases to investigate further, and found that in addition to cellular processes of apoptosis and cell proliferation, prioritized phenotypes underlying Juul-associated respiratory tract disease outcomes include response to oxidative stress, inflammatory response, and several cell signaling pathways (p38MAPK, NIK/NFkappaB, calcium-mediated).
Language	English
Publishing date	2021-08-05
Publishing country	Netherlands
Document type	Journal Article
ISSN	2666-027X
ISSN (online)	2666-027X
DOI	10.1016/j.crtox.2021.08.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways.

Kosnik, Marissa B / Planchart, Antonio / Marvel, Skylar W / Reif, David M / Mattingly, Carolyn J

Computational toxicology (Amsterdam, Netherlands)

2019 Volume 12

Abstract: Addressing the complex relationship between public health and environmental exposure requires multiple types and sources of data. An important source of chemical data derives from high-throughput screening (HTS) efforts, such as the Tox21/ToxCast program, ...

Abstract	Addressing the complex relationship between public health and environmental exposure requires multiple types and sources of data. An important source of chemical data derives from high-throughput screening (HTS) efforts, such as the Tox21/ToxCast program, which aim to identify chemical hazard using primarily
Language	English
Publishing date	2019-06-27
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-1113
ISSN	2468-1113
DOI	10.1016/j.comtox.2019.100094
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Heavy Metal Exposure and Metabolic Syndrome: Evidence from Human and Model System Studies.

Planchart, Antonio / Green, Adrian / Hoyo, Cathrine / Mattingly, Carolyn J

Current environmental health reports

2018 Volume 5, Issue 1, Page(s) 110–124

Abstract: Purpose of review: Metabolic syndrome (MS) describes the co-occurrence of conditions that increase one's risk for heart disease and other disorders such as diabetes and stroke. The worldwide increase in the prevalence of MS cannot be fully explained by ... ...

Abstract	Purpose of review: Metabolic syndrome (MS) describes the co-occurrence of conditions that increase one's risk for heart disease and other disorders such as diabetes and stroke. The worldwide increase in the prevalence of MS cannot be fully explained by lifestyle factors such as sedentary behavior and caloric intake alone. Environmental exposures, such as heavy metals, have been implicated, but results are conflicting and possible mechanisms remain unclear. To assess recent progress in determining a possible role between heavy metal exposure and MS, we reviewed epidemiological and model system data for cadmium (Cd), lead (Pb), and mercury (Hg) from the last decade. Recent findings: Data from 36 epidemiological studies involving 17 unique countries/regions and 13 studies leveraging model systems are included in this review. Epidemiological and model system studies support a possible association between heavy metal exposure and MS or comorbid conditions; however, results remain conflicting. Epidemiological studies were predominantly cross-sectional and collectively, they highlight a global interest in this question and reveal evidence of differential susceptibility by sex and age to heavy metal exposures. In vivo studies in rats and mice and in vitro cell-based assays provide insights into potential mechanisms of action relevant to MS including altered regulation of lipid and glucose homeostasis, adipogenesis, and oxidative stress. Heavy metal exposure may contribute to MS or comorbid conditions; however, available data are conflicting. Causal inference remains challenging as epidemiological data are largely cross-sectional; and variation in study design, including samples used for heavy metal measurements, age of subjects at which MS outcomes are measured; the scope and treatment of confounding factors; and the population demographics vary widely. Prospective studies, standardization or increased consistency across study designs and reporting, and consideration of molecular mechanisms informed by model system studies are needed to better assess potential causal links between heavy metal exposure and MS.
MeSH term(s)	Animals ; Cadmium/adverse effects ; Disease Models, Animal ; Humans ; Lead/adverse effects ; Mercury/adverse effects ; Metabolic Syndrome/chemically induced ; Metals, Heavy/adverse effects
Chemical Substances	Metals, Heavy ; Cadmium (00BH33GNGH) ; Lead (2P299V784P) ; Mercury (FXS1BY2PGL)
Language	English
Publishing date	2018-02-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2196-5412
ISSN (online)	2196-5412
DOI	10.1007/s40572-018-0182-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Comparative Toxicogenomics Database (CTD): update 2021.

Davis, Allan Peter / Grondin, Cynthia J / Johnson, Robin J / Sciaky, Daniela / Wiegers, Jolene / Wiegers, Thomas C / Mattingly, Carolyn J

Nucleic acids research

2020 Volume 49, Issue D1, Page(s) D1138–D1143

Abstract: The public Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is an innovative digital ecosystem that relates toxicological information for chemicals, genes, phenotypes, diseases, and exposures to advance understanding about human health. ... ...

Abstract	The public Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is an innovative digital ecosystem that relates toxicological information for chemicals, genes, phenotypes, diseases, and exposures to advance understanding about human health. Literature-based, manually curated interactions are integrated to create a knowledgebase that harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions. In this biennial update, we report a 20% increase in CTD curated content and now provide 45 million toxicogenomic relationships for over 16 300 chemicals, 51 300 genes, 5500 phenotypes, 7200 diseases and 163 000 exposure events, from 600 comparative species. Furthermore, we increase the functionality of chemical-phenotype content with new data-tabs on CTD Disease pages (to help fill in knowledge gaps for environmental health) and new phenotype search parameters (for Batch Query and Venn analysis tools). As well, we introduce new CTD Anatomy pages that allow users to uniquely explore and analyze chemical-phenotype interactions from an anatomical perspective. Finally, we have enhanced CTD Chemical pages with new literature-based chemical synonyms (to improve querying) and added 1600 amino acid-based compounds (to increase chemical landscape). Together, these updates continue to augment CTD as a powerful resource for generating testable hypotheses about the etiologies and molecular mechanisms underlying environmentally influenced diseases.
MeSH term(s)	Databases, Chemical ; Databases, Factual ; Databases, Genetic ; Gene-Environment Interaction ; Genome, Human/drug effects ; Genomics/methods ; Genotype ; Humans ; Internet ; Knowledge Bases ; Organ Specificity ; Phenotype ; Prescription Drugs/chemistry ; Prescription Drugs/pharmacology ; Software ; Toxicogenetics/methods ; Xenobiotics/chemistry ; Xenobiotics/toxicity
Chemical Substances	Prescription Drugs ; Xenobiotics
Language	English
Publishing date	2020-10-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa891
Database	MEDical Literature Analysis and Retrieval System OnLINE

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