ICE: Integrated Chemical Environment
Successful computational toxicology projects depend on high-quality data that are freely available and formatted for use in computational workflows. The Integrated Chemical Environment (ICE) addresses the data needs frequently expressed by NICEATM stakeholders. Launched in March 2017, ICE provides curated data from NICEATM, its partners, and other resources, as well as tools to facilitate the safety assessment of chemicals. An article in published in November 2022 in Frontiers in Toxicology (Daniel et al. 2022) provides the most recent detailed overview of ICE.
In March 2023, NICEATM released ICE 4.0, which implemented these features:
- A new Exposure Predictions data set from the EPA Systematic Empirical Evaluation of Models (SEEM3) model. The data set can be exported or visualized as an overlay option in the ICE IVIVE tool results.
- Acceptance of chemical names and synonyms as input, in addition to existing options of CASRNs, DTXSIDs, SMILES, or InChIKeys.
- Updates to the ICE PBPK and IVIVE tools, including:
- Implementation of the latest version of EPA's httk R package, v2.2.2.
- Addition of a human gestational model from httk v2.2.2 to both tools.
- Availability of predicted half-life and area under curve values in the PBPK model output.
- Ability to input chemical concentration as parts per million per unit volume (ppmv) when modeling inhalation exposure.
- New Beta Search results page with improved data navigation and query summary visualizations.
A training event organized by PCRM shortly after the ICE 3.6 update featured NICEATM developers demonstrating how to use ICE tools for data and assay exploration. Videos from the training are available on the PCRM website.
Three posters at the March 2023 meeting of the Society of Toxicology (SOT) described features to be included in ICE version 4.0 and future releases:
- Unnikrishan et al. (Bioinformatics session) provided an overview of ICE version 4.0.
- Hull et al. (Computational Toxicology II session) described how future versions of ICE will integrate variability in metabolic enzyme activity into physiologically based kinetic models.
- Karmaus et al. (Computational Toxicology II session) described how existing controlled vocabularies have been leveraged to annotate high-throughput screening data in ICE version 4.0 to facilitate assay interpretation and data use.
ICE Data and Curation
ICE includes data from animal and non-animal tests that measure toxic effects described in chemical safety regulations. These effects include acute oral toxicity, skin and eye irritation, skin sensitization, and endocrine activity. ICE also contains curated HTS data from the EPA ToxCast program and the Tox21 consortium and physicochemical property data about chemicals including solubility, melting point, and molecular weight.
Inclusion of data from (Mansouri et al. 2018) means that ICE tools can utilize predictions of physicochemical and ADME properties and toxicity endpoints for thousands of chemicals lacking experimental data. ICE REST APIs, implemented in version 3.7 (July 2022), allow users to access ICE data more easily via database searches outside of the ICE graphical user interface environment.
Curation by NICEATM of all data that go into ICE (described in Daniel et al. 2022) is paramount to ensuring that robust data are available to users. NICEATM staff critically curate, review, and harmonize all ICE data. Curation of HTS data for ICE first retrieves Tox21 and ToxCast data from EPA’s invitrodb, which houses all HTS data analyzed using the ToxCast Pipeline (tcpl) package. NICEATM then applies curation steps to minimize low-confidence hit calls, providing a processed version of the HTS data, referred to as cHTS, that is ready for any application. Factors considered in the curation include chemical purity, quality control data, concentration-response curve fits, and testing range. To facilitate targeted access of cHTS data by ICE tools, NICEATM also maps assay endpoints to mechanistic targets, facilitating interpretation of assay readouts based on biological processes, and to modes of action relevant to toxicity endpoints of regulatory concern.
ICE Tools
The ICE Search tool enables users to easily query and integrate data streams and explore the results interactively.
Assays selected in one ICE tool can be used to query other ICE tools. Various ICE tools support uploads of custom data, results visualizations, and results filtering options. Outputs provide publication-quality graphics and downloadable data files.
ICE IVIVE and PBPK tools leverage EPA’s httk package to provide users with an approachable, easy-to-use interface for running analyses. Users can leverage curated datasets in ICE or upload their own data. Furthermore, the IVIVE outputs can be visualized with in vivo or predicted exposure data overlays to provide additional context to results.
The ICE Chemical Quest tool conducts chemical similarity searches based on Saagar fingerprints (Sedykh et al. 2021) to help ICE users identify similar chemicals based on their own input chemicals. This tool allows users to draw novel structures or in put any chemical descriptor as input. The ICE Chemical Characterization tool allows the user to comprehensively evaluate a chemical or chemical list or compare two chemical lists, and review their chemicals' physicochemical properties, chemical product use information, and bioactivity across cHTS data backgrounds.
For more information about ICE, email [email protected] or visit the ICE About page.