Allan Peter Davis

The Environmental Health Language Collaborative (EHLC) Adverse Outcome Pathway (AOP) Standards Workshop Report

Mortensen, H., Hench, V., Nymark, P., Lynn, S., Hogberg, H., Feshuk, M., … Schmitt, C. (2026, February 26). F1000Research.

Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database

Wiegers, T. C., Davis, A. P., Wiegers, J., Sciaky, D., Barkalow, F., Wyatt, B., … Mattingly, C. J. (2025, January 1). Database, Vol. 2025.

Linking chemical data from the Comparative Toxicogenomics Database with adverse outcome pathways from the AOP-Wiki: a mechanistic data-oriented approach to help inform environmental health

Davis, A. P., Wiegers, T. C., Sciaky, D., Barkalow, F., Wyatt, B., Wiegers, J., … Mattingly, C. J. (2025, November 17). F1000Research.

Comparative Toxicogenomics Database’s 20th anniversary: update 2025

Davis, A. P., Wiegers, T. C., Sciaky, D., Barkalow, F., Strong, M., Wyatt, B., … Mattingly, C. J. (2024, October 10). Nucleic Acids Research, Vol. 10.

Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms

Wyatt, B., Davis, A. P., Wiegers, T. C., Wiegers, J., Abrar, S., Sciaky, D., … Mattingly, C. J. (2024, July 22). Frontiers in Toxicology, Vol. 6.

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.

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.

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.

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.

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

Pinkhasova, D. V., Jameson, L. E., Conrow, K. D., Simeone, M. P., Davis, A. P., Wiegers, T. C., … Leung, M. C. K. (2021, January 1). Current Research in Toxicology.

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.

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.

Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database

Grondin, C. J., Davis, A. P., Wiegers, T. C., Wiegers, J. A., & Mattingly, C. J. (2018, January 16). Environmental Health Perspectives, Vol. 126.

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.

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.

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

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

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

Wei, C.-H., Peng, Y., Leaman, R., Davis, A. P., Mattingly, C. J., Li, J., … Lu, Z. (2016, January 1). Database.

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.

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.

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.

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

Davis, A. P., Grondin, C. J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., … Mattingly, C. J. (2014, October 17). Nucleic Acids Research, Vol. 43, pp. D914–920.

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

Wiegers, T. C., Davis, A. P., & Mattingly, C. J. (2014, June 10). Database.

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

Davis, A. P., Wiegers, T. C., Roberts, P. M., King, B. L., Lay, J. M., Lennon-Hopkins, K., … Mattingly, C. J. (2013, November 28). Database.

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

Davis, A. P., Wiegers, T. C., Johnson, R. J., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., … Mattingly, C. J. (2013, April 17). PLoS ONE, Vol. 8.

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

King, B. L., Davis, A. P., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2012, November 7). PLoS ONE, Vol. 7.

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

Database-The Journal of Biological Databases and Curation.

The Comparative Toxicogenomics Database: update 2013

Nucleic Acids Research, 41(D1), D1104–D1114.