Thomas Conrad Wiegers

Works (27)

Updated: April 6th, 2024 05:04

2023 journal article

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

TOXICOLOGICAL SCIENCES, 195(2), 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
Sources: Web Of Science, ORCID
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
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)
Sources: Web Of Science, ORCID
Added: October 11, 2022

2021 journal article

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

CURRENT RESEARCH IN TOXICOLOGY, 2, 128–139.

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
Sources: Web Of Science, ORCID
Added: January 3, 2022

2021 journal article

Comparative Toxicogenomics Database (CTD): update 2021

NUCLEIC ACIDS RESEARCH, 49(D1), 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
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)
Sources: Web Of Science, ORCID
Added: February 8, 2021

2021 journal article

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

CURRENT RESEARCH IN TOXICOLOGY, 2, 272–281.

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
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: January 3, 2022

2021 journal article

Regulatory status of pesticide residues in cannabis: Implications to medical use in neurological diseases

CURRENT RESEARCH IN TOXICOLOGY, 2, 140–148.

By: D. Pinkhasova*, L. Jameson*, K. Conrow*, M. Simeone*, A. Davis n, T. Wiegers n, C. Mattingly n, M. Leung*

author keywords: Cannabis; Pesticide; Database; Regulation; Seizure; Contaminant
TL;DR: Network analysis reveals potential interactions of insecticides, cannabinoids, and seizure at a functional level in cannabis. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: January 3, 2022

2020 journal article

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

TOXICOLOGICAL SCIENCES, 177(2), 392–404.

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
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)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: December 14, 2020

2019 journal article

The Comparative Toxicogenomics Database: update 2019

NUCLEIC ACIDS RESEARCH, 47(D1), 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
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)
UN Sustainable Development Goal Categories
9. Industry, Innovation and Infrastructure (OpenAlex)
Sources: Web Of Science, ORCID
Added: April 9, 2019

2018 journal article

Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database

ENVIRONMENTAL HEALTH PERSPECTIVES, 126(1).

By: C. Grondin n, A. Davis n, T. Wiegers n, J. Wiegers n & C. Mattingly n

MeSH headings : Databases, Factual; Environmental Exposure / adverse effects; Gene Ontology; Humans; Phenotype; Toxicogenetics
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2018 journal article

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

TOXICOLOGICAL SCIENCES, 165(1), 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
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)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: October 16, 2018

2017 journal article

The Comparative Toxicogenomics Database: update 2017

NUCLEIC ACIDS RESEARCH, 45(D1), D972–D978.

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
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)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database

Environmental Health Perspectives, 124(10), 1592–1599.

By: C. Grondin n, A. Davis n, T. Wiegers n, B. King*, J. Wiegers n, D. Reif n, J. Hoppin n, C. Mattingly n

Contributors: C. Grondin n, A. Davis n, T. Wiegers n, B. King*, J. Wiegers n, D. Reif n, J. Hoppin n, C. Mattingly n

TL;DR: Curation and integration of exposure data within the CTD provides researchers with new opportunities to correlate exposures with human health outcomes, to identify underlying potential molecular mechanisms, and to improve understanding about the exposome. (via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2016 journal article

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

MeSH headings : Biomedical Research; Data Mining / methods; Databases, Factual; Disease; Humans; Statistics as Topic; Time Factors
TL;DR: This task was found to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of automatic disease recognition and CDR extraction. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

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

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

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
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)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

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

PLOS ONE, 11(5).

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
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)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

By: D. Pelletier*, T. Wiegers n, A. Enayetallah*, C. Kibbey*, M. Gosink*, P. Koza-Taylor*, C. Mattingly n, M. Lawton*

MeSH headings : Animals; Computational Biology / methods; Computer Simulation; Database Management Systems; Databases, Factual; Humans; Mice; Toxicogenetics / methods; User-Computer Interface
TL;DR: ToxEvaluator was developed jointly by Pfizer and the Comparative Toxicogenomics Database as an in silico platform to facilitate interpretation of toxicity findings in light of prior knowledge and rapidly identified direct and indirect linkages between cerivastatin and myopathy. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015

NUCLEIC ACIDS RESEARCH, 43(D1), D914–D920.

By: A. Davis n, C. Grondin n, K. Lennon-Hopkins n, C. Saraceni-Richards n, D. Sciaky n, B. King*, T. Wiegers n, C. Mattingly n

MeSH headings : Databases, Chemical / history; Disease / etiology; Disease / genetics; Genomics / history; History, 21st Century; Internet; Phenotype; Toxicogenetics / history
TL;DR: The prototype database originally described in its first report has transformed into a sophisticated resource used actively today to help scientists develop and test hypotheses about the etiologies of environmentally influenced diseases. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

BioC interoperability track overview

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

By: D. Comeau*, R. Batista-Navarro*, H. Dai*, R. Dogan*, A. Yepes*, R. Khare*, Z. Lu*, H. Marques* ...

MeSH headings : Biomedical Research; Computational Biology; Data Mining; Database Management Systems; Databases, Factual; Internet; Natural Language Processing; Software
TL;DR: The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format, which included additional implementations of BioC, many new corpora in the format, biomedical NLP tools consuming and producing the format and online services using the format. (via Semantic Scholar)
UN Sustainable Development Goal Categories
4. Quality Education (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 article

BioCreative-IV virtual issue

Arighi, C. N., Wu, C. H., Cohen, K. B., Hirschman, L., Krallinger, M., Valencia, A., … Wiegers, T. C. (2014, May 22). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

MeSH headings : Computational Biology; Congresses as Topic; Data Mining; Databases as Topic; Gene Ontology; Natural Language Processing
TL;DR: This DATABASE virtual issue captures the major results from the Fourth bioCreative Challenge Evaluation Workshop, and is the sixth special issue devoted to BioCreative. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

By: T. Wiegers n, A. Davis n & C. Mattingly n

MeSH headings : Data Mining / methods; Databases, Chemical; Databases, Genetic; Disease / genetics; Genes; Internet; Time Factors; Toxicogenetics
TL;DR: A description of the challenge and summary of results are presented, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

By: A. Davis n, T. Wiegers n, P. Roberts n, B. King n, J. Lay n, K. Lennon-Hopkins n, D. Sciaky n, R. Johnson n ...

MeSH headings : Cooperative Behavior; Data Mining; Databases, Factual; Disease; Drug Industry; Humans; Pharmaceutical Preparations / metabolism; Phenotype; Publications; Toxicogenetics
TL;DR: A collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88 629 articles relating over 1 200 pharmaceutical drugs to their potential involvement in cardiovascular, neurological, renal and hepatic toxicity. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

BioC: a minimalist approach to interoperability for biomedical text processing

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

By: D. Comeau*, R. Dogan*, P. Ciccarese*, K. Cohen*, M. Krallinger*, F. Leitner*, Z. Lu*, Y. Peng* ...

MeSH headings : Biomedical Research; Data Mining; Humans; Natural Language Processing; Software
TL;DR: A simple extensible mark-up language format to share text documents and annotations, which allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities is proposed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
4. Quality Education (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2013 journal article

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

PLOS ONE, 8(4).

By: A. Davis n, T. Wiegers n, R. Johnson*, J. Lay*, K. Lennon-Hopkins*, C. Saraceni-Richards*, D. Sciaky*, C. Murphy n, C. Mattingly n

MeSH headings : Algorithms; Data Mining / methods; Databases, Factual; Disease / genetics; Documentation; Humans; Metals, Heavy / toxicity; Molecular Sequence Annotation; Publications; Reproducibility of Results; Toxicogenetics
TL;DR: It is demonstrated how fully incorporating text mining-based DRS scoring into the curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 article

BioCreative-2012 Virtual Issue

Wu, C. H., Arighi, C. N., Cohen, K. B., Hirschman, L., Krallinger, M., Lu, Z. Y., … al. (2012, December 5). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

By: C. Wu*, C. Arighi*, K. Cohen*, L. Hirschman*, M. Krallinger*, Z. Lu*, C. Mattingly*, A. Valencia* ...

MeSH headings : Congresses as Topic; Cooperative Behavior; Data Mining; Databases, Genetic; Periodicals as Topic; Workflow
TL;DR: This DATABASE virtual issue captures the major results from the BioCreative-2012 Workshop on Interactive Text Mining in the Biocuration Workflow and is the fifth special issue devoted to Biocreative. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Collaborative biocuration--text-mining development task for document prioritization for curation

Database, 2012(0), bas037–bas037.

By: T. Wiegers n, A. Davis n & C. Mattingly n

MeSH headings : Cooperative Behavior; Data Mining / methods; Databases, Genetic; Disease; Documentation / methods; Genes; Humans; Internet; Toxicogenetics; User-Computer Interface
TL;DR: A detailed description of the Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation is presented and a summary of the results are presented. (via Semantic Scholar)
Sources: Web Of Science, Crossref, ORCID
Added: August 6, 2018

2012 journal article

Ranking Transitive Chemical-Disease Inferences Using Local Network Topology in the Comparative Toxicogenomics Database

PLOS ONE, 7(11).

By: B. King*, A. Davis n, M. Rosenstein*, T. Wiegers n & C. Mattingly n

MeSH headings : Cluster Analysis; Databases, Factual; Drug-Related Side Effects and Adverse Reactions / genetics; Gene Regulatory Networks; Humans; Protein Interaction Mapping; Toxicogenetics / methods
TL;DR: A statistic to score and rank inferences based on the topology of the local network consisting of the chemical, disease and each of the genes used to make an inference is implemented, which uniquely takes into account the number of common neighbors and the connectivity of each entity involved. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database

Database-The Journal of Biological Databases and Curation.

By: A. Davis, R. Johnson, K. Lennon-Hopkins, D. Sciaky, M. Rosenstein, T. Wiegers, C. Mattingly

Source: NC State University Libraries
Added: August 6, 2018

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