Robin J. Johnson

Works (11)

Updated: April 23rd, 2025 23:31

2023 article

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

Davis, A. P., Wiegers, T. C., Wiegers, J., Wyatt, B., Johnson, R. J., Sciaky, D., … Mattingly, C. J. (2023, July 21). Toxicological Sciences, Vol. 195, pp. 155–168.

By: A. Davis n, T. Wiegers n, J. Wiegers n, B. Wyatt n, R. Johnson n, D. Sciaky n, F. Barkalow n, M. Strong n, A. Planchart n , C. Mattingly n 

author keywords: database tool; chemical-disease pathway; molecular mechanisms; environmental health; knowledge gaps; adverse outcome pathway
MeSH headings : Male; Humans; Toxicogenetics; Databases, Factual; Environmental Health; Phenotype; Environmental Exposure
topics (OpenAlex): Health, Environment, Cognitive Aging; Bioinformatics and Genomic Networks; Computational Drug Discovery Methods
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Sources: Web Of Science, NC State University Libraries
Added: April 1, 2024

2022 article

Comparative Toxicogenomics Database (CTD): update 2023

Davis, A. P., Wiegers, T. C., Johnson, R. J., Sciaky, D., Wiegers, J., & Mattingly, C. J. (2022, September 28). Nucleic Acids Research, Vol. 9.

By: A. Davis n, T. Wiegers n, R. Johnson n, D. Sciaky n, J. Wiegers n & C. Mattingly n 

MeSH headings : Humans; Toxicogenetics; Databases, Factual; Phenotype
topics (OpenAlex): Health, Environment, Cognitive Aging; Biomedical Text Mining and Ontologies; Cell Image Analysis Techniques
TL;DR: A 20% increase in overall CTD content is reported and 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 are presented. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 11, 2022

2021 article

CTD anatomy: Analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies

Davis, A. P., Wiegers, T. C., Wiegers, J., Grondin, C. J., Johnson, R. J., Sciaky, D., & Mattingly, C. J. (2021, January 1). Current Research in Toxicology.

By: A. Davis n, T. Wiegers n, J. Wiegers n, C. Grondin n, R. Johnson n, D. Sciaky n, C. Mattingly n 

author keywords: Anatomy; Chemical; Phenotype; Disease; Environmental health; Database
topics (OpenAlex): Health, Environment, Cognitive Aging
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Sources: Web Of Science, NC State University Libraries
Added: January 3, 2022

2021 article

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

Grondin, C. J., Davis, A. P., Wiegers, J. A., Wiegers, T. C., Sciaky, D., Johnson, R. J., & Mattingly, C. J. (2021, January 1). Current Research in Toxicology.

By: C. Grondin n, A. Davis n, J. Wiegers n, T. Wiegers n, D. Sciaky n, R. Johnson n, C. Mattingly n 

author keywords: E-cigarettes; Vaping; Juul; Respiratory disease; Database; Environmental exposure
topics (OpenAlex): Air Quality and Health Impacts; Smoking Behavior and Cessation; Health, Environment, Cognitive Aging
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 3, 2022

2020 article

Comparative Toxicogenomics Database (CTD): update 2021

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., Wiegers, T. C., & Mattingly, C. J. (2020, October 1). Nucleic Acids Research, Vol. 49, pp. D1138–D1143.

By: A. Davis n, C. Grondin n, R. Johnson n, D. Sciaky n, J. Wiegers n, T. Wiegers n, C. Mattingly n 

MeSH headings : 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
topics (OpenAlex): Biomedical Text Mining and Ontologies; Bioinformatics and Genomic Networks; Computational Drug Discovery Methods
TL;DR: This biennial update of the public Comparative Toxicogenomics Database (CTD) reports a 20% increase in CTD curated content and provides 45 million toxicogenomic relationships and introduces new CTD Anatomy pages that allow users to uniquely explore and analyze chemical–phenotype interactions from an anatomical perspective. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: February 8, 2021

2020 article

Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease

Davis, A. P., Wiegers, T. C., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., & Mattingly, C. J. (2020, July 8). Toxicological Sciences, Vol. 177, pp. 392–404.

By: A. Davis*, T. Wiegers*, C. Grondin*, R. Johnson*, D. Sciaky*, J. Wiegers*, C. Mattingly n 

author keywords: environmental health; chemical-induced pathways; air pollution; cardiovascular disease; database
MeSH headings : Air Pollutants / toxicity; Air Pollution; Cardiovascular Diseases / chemically induced; Environmental Exposure; Environmental Health; Humans; Toxicogenetics
topics (OpenAlex): Health, Environment, Cognitive Aging; Air Quality and Health Impacts; Air Quality Monitoring and Forecasting
TL;DR: This paper systematically compute the genes, molecular mechanisms, and biological events for the environmental health association linking air pollution toxicants with two cardiovascular diseases as a test case and identifies 19 genes and 96 phenotypes shared between these two air pollutant-induced outcomes. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: December 14, 2020

2018 article

Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways

Davis, A. P., Wiegers, T. C., Wiegers, J., Johnson, R. J., Sciaky, D., Grondin, C. J., & Mattingly, C. J. (2018, May 23). Toxicological Sciences, Vol. 165, pp. 145–156.

By: A. Davis*, T. Wiegers*, J. Wiegers*, R. Johnson*, D. Sciaky*, C. Grondin, C. Mattingly n 

author keywords: phenotype; database; curation; chemical; disease; adverse outcome pathway
MeSH headings : Adverse Outcome Pathways; Animals; Databases, Factual; Drug-Related Side Effects and Adverse Reactions / genetics; Gene Ontology; Gene-Environment Interaction; Humans; Phenotype; Toxicogenetics / methods
topics (OpenAlex): Computational Drug Discovery Methods; Bioinformatics and Genomic Networks; Metabolomics and Mass Spectrometry Studies
TL;DR: This work introduces a new chemical-phenotype module that describes how chemicals can affect molecular, cellular, and physiological phenotypes, and presents 3 diverse case studies discerning the effect of vehicle emissions on altered leukocyte migration, the role of cadmium in influencing phenotypes preceding Alzheimer disease, and the connection of arsenic-induced glucose metabolic phenotypes with diabetes. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 16, 2018

2018 article

The Comparative Toxicogenomics Database: update 2019

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., McMorran, R., Wiegers, J., … Mattingly, C. J. (2018, September 17). Nucleic Acids Research, Vol. 47, pp. D948–D954.

By: A. Davis n, C. Grondin n, R. Johnson n, D. Sciaky n, R. McMorran*, J. Wiegers n, T. Wiegers n, C. Mattingly n 

MeSH headings : Databases, Pharmaceutical; Disease / genetics; Environmental Exposure; Humans; Phenotype; Toxicogenetics; Vocabulary, Controlled
topics (OpenAlex): Biomedical Text Mining and Ontologies; Bioinformatics and Genomic Networks; Gene expression and cancer classification
TL;DR: This biennial update presents a new chemical–phenotype module that codes chemical-induced effects on phenotypes, curated using controlled vocabularies for chemicals, phenotype, taxa, and anatomical descriptors, and describes new querying and display features for the enhanced chemical–exposure science module, providing greater scope of content and utility. (via Semantic Scholar)
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9. Industry, Innovation and Infrastructure (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 9, 2019

2016 article

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

Li, J., Sun, Y. P., Johnson, R. J., Sciaky, D., Wei, C. H., Leaman, R., … al. (2016, January 1). Database.

By: J. Li *, Y. Sun *, R. Johnson n, D. Sciaky n, C. Wei *, R. Leaman *, A. Davis n, C. Mattingly n  ...

MeSH headings : Computational Biology / methods; Data Mining / methods; Databases, Factual; Disease; Humans; Toxicogenetics / methods
topics (OpenAlex): Biomedical Text Mining and Ontologies; Topic Modeling; Advanced Text Analysis Techniques
TL;DR: The BC5CDR corpus was successfully used for the BioCreative V challenge tasks and should serve as a valuable resource for the text-mining research community. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2016 article

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database

Davis, A. P., Wiegers, T. C., King, B. L., Wiegers, J., Grondin, C. J., Sciaky, D., … Mattingly, C. J. (2016, May 12). PLoS ONE, Vol. 11.

By: A. Davis n, T. Wiegers n, B. King *, J. Wiegers n, C. Grondin n, D. Sciaky n, R. Johnson n, C. Mattingly n 

MeSH headings : Computational Biology; Databases, Genetic; Disease / genetics; Drug Repositioning; Gene Ontology; Humans; Toxicogenetics
topics (OpenAlex): Bioinformatics and Genomic Networks; Computational Drug Discovery Methods; Biomedical Text Mining and Ontologies
TL;DR: This inference set should aid researchers, bioinformaticists, and pharmaceutical drug makers in finding commonalities in disease mechanisms, which in turn could help identify new therapeutics, new indications for existing pharmaceuticals, potential disease comorbidities, and alerts for side effects. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2016 article

The Comparative Toxicogenomics Database: update 2017

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., King, B. L., McMorran, R., … Mattingly, C. J. (2016, September 19). Nucleic Acids Research, Vol. 45, pp. D972–978.

By: A. Davis n, C. Grondin n, R. Johnson n, D. Sciaky n, B. King *, R. McMorran*, J. Wiegers n, T. Wiegers n, C. Mattingly n 

MeSH headings : Computational Biology / methods; Databases, Chemical; Databases, Genetic; Gene Ontology; Humans; Search Engine; Signal Transduction; Toxicogenetics / methods; User-Computer Interface; Web Browser
topics (OpenAlex): Computational Drug Discovery Methods; Bioinformatics and Genomic Networks; Gene expression and cancer classification
TL;DR: This update describes the new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduces a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies). (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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