Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database

Abstract

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org) is a free resource that provides manually curated information on chemical, gene, phenotype, and disease relationships to advance understanding of the effect of environmental exposures on human health. Four core content areas are independently curated: chemical-gene interactions, chemical-disease and gene-disease associations, chemical-phenotype interactions, and environmental exposure data (e.g., effects of chemical stressors on humans). Since releasing exposure data in 2015, we have vastly increased our coverage of chemicals and disease/phenotype outcomes; greatly expanded access to exposure content; added search capability by stressors, cohorts, population demographics, and measured outcomes; and created user-specified displays of content. These enhancements aim to facilitate human studies by allowing comparisons among experimental parameters and across studies involving specified chemicals, populations, or outcomes. Integration of data among CTD's four content areas and external data sets, such as Gene Ontology annotations and pathway information, links exposure data with over 1.8 million chemical-gene, chemical-disease and gene-disease interactions. Our analysis tools reveal direct and inferred relationships among the data and provide opportunities to generate predictive connections between environmental exposures and population-level health outcomes. https://doi.org/10.1289/EHP2873.

Figure 1.

Querying Exposure Studies in Comparative Toxicogenomics Database (CTD). Exposure studies can be queried in CTD from an Exposure Studies search page that allows specification of one or more of 12 query terms from different exposure categories (A). Here, the database is queried for studies conducted in China and/or the United States in which particulate matter is an exposure stressor by entering “particulate matter” in the chemical search field and co-selecting “China” and “United States” in the Country field. The bold black arrow connects the query form to the results page (B). Results are returned in summary format, with each curated exposure paper represented by one row of 11 data fields, including the primary reference, associated study title, author’s summary, study factors, stressor, receptor, country, medium, exposure marker, outcome, and a link to detailed measurements. Dashed rectangles correspond to Chemical Stressor and Country fields that were queried in part A. Query parameters are highlighted in yellow on results pages, along with any hierarchically related terms. A chemical may appear in both the Stressor and Exposure Marker fields if the chemical stressor was experimentally measured as a result of the exposure event, but the Exposure Marker may also be an unrelated entity whose concentration may have been affected by the exposure event, such as a metabolite or a gene. References, chemical, gene, disease, and phenotype-related GO-BP terms hyperlink to their individual CTD pages. Results can be downloaded via CSV, Excel, XML, or TSV formats. Image: ©2012–2017 MDI Biological Laboratory & North Carolina State University.

Figure 2.

Accessing detailed exposure information in Comparative Toxicogenomics Database (CTD). Detailed exposure data in CTD can be accessed from an Exposure Details query page (A), which allows users to specify search terms in one or more of five categories (Exposure Stressor, Exposure Receptor, Exposure Event, Exposure Outcome, and Exposure Reference) that can be expanded or collapsed by clicking on the toggle boxes to the left of the headings. Additional search fields for each section are shown to the left of the toggle boxes, totaling 21 query fields. Here, a search for positive correlations between particulate matter and disease or phenotype outcomes can be done by entering “particulate matter” in the chemical (marker) field and “positive correlation” in the Exposure Outcome section. The bold black arrow connects the query form to the returned results (B). Users can specify up to 33 unique data fields to display on the results page, or display 14 default fields. The queried term(s) is highlighted in yellow, along with any hierarchically related terms (here, dashed rectangles correspond to the queried fields of Exposure Event Chemical Marker and Exposure Outcome Relationship). References, chemical, gene, disease, and phenotype-related GO-BP terms hyperlink to their individual CTD pages. Results can be downloaded via CSV, Excel, XML, or TSV formats. Image: ©2012–2017 MDI Biological Laboratory & North Carolina State University.