Jump to main content or area navigation.

Contact Us

Computational Toxicology Research Program

EPA Collaborations & Activities

Listed below are on-going or planned collaborations of the DSSTox project within EPA working towards the aims of chemical data standards and annotation, toxicity data standard ontologies and vocabularies, open data access, and structure-searchability.

EPA Activities

blue bullet graphic ACToR ** Update (Feb 2009)

blue bullet graphic Chemoinformatics Community of Practice

blue bullet graphic Computational Toxicology New Start Award

blue bullet graphic Environmental Modeling & Visualization Laboratory Project - Chemical Structure Browser ** Update (Aug 2007)

blue bullet graphic HPV Challenge Program ** Update (Aug 2007)

blue bullet graphic Integrated Risk Information System (IRIS) On-line Database ** Update (Aug 2007)

blue bullet graphic Tox21** Update (Feb 2009)

blue bullet graphic ToxCast ** Update (Feb 2009)

blue bullet graphic ToxRef ** Update (Feb 2009)

blue bullet graphic Pesticides Ingredients Lists Structure-Index Files

 

ACToR
(contact: Richard Judson, email: judson.richard@epa.gov)

The Aggregated Computational Toxicology Resource (ACToR) is a research project and newly available on-line resource (Dec 2008) within EPA's Computational Toxicology Research Program, affiliated with the ToxCast and DSSTox projects. ACToR is a collection of databases collated or developed by the NCCT. More than 200 sources of publicly available data on environmental chemicals have been brought together and made searchable by chemical name and other identifiers, such as chemical structure. Data includes chemical structure, physico-chemical values, in vitro assay data and in vivo toxicology data. Chemicals include, but are not limited to, high and medium production volume industrial chemicals, pesticides (active and inert ingredients), and potential ground and drinking water contaminants. All published DSSTox chemical inventories and chemical structures have been incorporated into ACToR, including chemical structure inventories for ToxCast and ToxRef. ACToR provides the ability to cross reference a much larger number of chemical inventories pertaining to environmental toxicology, and to determine which chemicals have highest representation across databases as well as which chemicals are associated with the most ecomplete toxicity data. These capabilities in ACToR are being used to prioritize chemicals for testing within the ToxCast and Tox21 research programs. ACToR will also serve as the primary informatics resource for ToxCast high throughput testing assay data and ToxRef in vivo data.


Return to the list above. Return to Top

Chemoinformatics Community of Practice
(contacts: Ann Richard, email: richard.ann@epa.gov; Chris Russom, email: russom.chris@epa.gov)

The purpose of this EPA Community of Practice (see Chemoinformatics CoP Charter) is to facilitate, coordinate and integrate efforts to address the challenges of chemical structure annotation (or indexing), retrieval, and mining of chemically-related data and documents, including newer toxicogenomics and metabonomics data, across EPA Program Offices, Labs and Centers. Much of EPA's public and internal chemical data records and databases currently are indexed only by chemical name (imprecise and non-unique) and CAS registry numbers (proprietary) and are not searchable by the more universal and informative metric of chemical structure. Additionally, there is unnecessary duplication of efforts and lack of coordination in the area of chemical structure-annotation and quality review of chemical information (e.g., structures, CAS) across diverse EPA databases. Finally, no Agency-wide chemical structure searching capability currently exists to enable EPA scientists, regulators, and outside parties to efficiently and precisely locate Agency chemical information based on chemical structure. Initial discussions are focusing on communicating common problems, software needs and solutions, chemical data inventories, promoting common solutions for chemical structure annotation and structure-searching, and charting a path forward for expanded Agency-wide adoption of capabilities in these areas.

Return to the list above. Return to Top

Environmental Modeling & Visualization Laboratory (EMVL) Project - Chemical Structure Browser
(contact: Tom Transue, Lockheed Martin - Contractor to the EPA, email: transue.tom@epa.gov)

Project: Computational Chemistry
Project Title: Technical Support for the Evaluation and Implementation of a Web-based Chemical Structure Annotation and Searching Tool
Principal Investigator: Ann Richard
Lab: Computational Toxicology Research Program
Division: Computational Chemistry
Project Description: EMVL staff are assisting in evaluating existing chemical structure annotation and search tools and will assist in implementing a Web-based product that can be used across the Agency. The search tool will allow the user to specify, by use of pull down lists or by freehand drawing, the structure of a compound or molecule for the purpose of searching for similar structures.

Project also assisted in the conversion of the DSSTox Master File to a relational database format that can be easily managed and integrated with an on-line structure browser.

** Update (Aug 2007): DSSTox Structure-Browser has been launched and is available from the DSSTox website or external websites. >More

Return to the list above. Return to Top

High Production Volume Challenge Program
(contact: Todd Holderman, email: holderman.todd@epa.gov)

EPA's High Production Volume Challenge Program is supervising the collection and public dissemination of toxicity data on several thousand chemicals. These data are being incorporated into the HPV Information System (HPV-IS), a relational, searchable data warehouse publicly available on the EPA HPV-IS website. A DSSTox Structure-Index File, HPVCSI, was created that consolidates all HPV Chemical Lists associated with multiple public notices of the HPV voluntary chemical adoption program.

** Update (Aug 2007): In v2a, HPVCSI has been augmented with Test Status information extracted from the EPA HPV website, as well as >900 URLs to chemical data pages in the HPV Information System (HPVIS). This latest file will be used to augment existing information and create a structure-searching capability on the EPA HPVIS website through use of the DSSTox Structure-Browser. HPVCSI also enables comparison to other chemical lists being compiled for other purposes, such as the NIH MLR High Through-put Screening collaborations.

Return to the list above. Return to Top

Integrated Risk Information System (IRIS) On-line Database
(contact: IRIS Information Hotline, email: hotline.iris@epa.gov )

EPA's Integrated Risk Information System (IRIS) is an electronic database containing information on human health effects that may result from exposure to various chemicals in the environment. The information in IRIS summarizes data used to formulate risk assessments and is intended for those without extensive training in toxicology, but with some knowledge of health sciences. The current EPA IRIS website is chemically indexed by chemical name and CAS listings linking to the corresponding chemical data pages for over 540 chemicals.

** Update (Aug 2007): The DSSTox IRISTR Data File contains the full complement of DSSTox Standard Chemical Fields in addition to content extracted from the on-line searchable IRIS database and the URLs of the corresponding IRIS chemical "Quick View" summary data pages. Hence, incorporated into a larger structure-searchable database, such as PubChem, this file can directly point a user to the specific data page containing relevant information on the chemical in IRIS. In addition to its current searchability in the DSSTox Structure-Browser, future collaboration with the EPA IRIS program will enable structure-searching by a user from the IRIS website, as well as through externally hosted databases and "locator" services, such as PubChem and eMolecules.

Return to the list above. Return to Top

Computational Toxicology New Start Award
(contact: Robert Kavlock, email: kavlock.robert@epa.gov)

Following an EPA Office of Research & Development solicitation for research proposals to support the "Research Framework for a Computational Toxicology Research Program", the Computational Toxicology Implementation and Steering Committee (CTISC) selected seven EPA projects for funding. These projects represent broad, multi-disciplinary efforts that collectively support the three objectives of the Framework, and present a balance of efforts directed at human and wildlife effects. Project awards followed an external scientific peer review and an internal relevancy review and were formally announced on January 11, 2005. Titles, Lead Investigators, and Project Abstracts are provided on the New Start Awards page.

Project Title: Chemoinformatics Enhancement of the NIEHS/National Center for Toxicogenomics (NCT) Chemical Effects in Biological Systems (CEBS) Knowledge-Base
Lead Investigator: Ann Richard
Project Description: The current proposal involves coordination and collaboration between the DSSTox project and the CEBS and NTP public database projects, helping to create the foundation and infrastructure to enable expanded SAR structure-analog search capabilities encompassing both historical toxicity databases and newer toxicogenomics data. The primary objectives of this research are twofold: firstly, to incorporate the ability to survey data from a chemical structural analog perspective across toxicity endpoints, levels of biological organization, and patterns of gene expression represented within CEBS; and, secondly, to expand the data foundation for deriving useful SAR associations for classes of similar environmental chemicals by establishing linkages of the CEBS and NTP projects with the expanding DSSTox database network.

Return to the list above. Return to Top

ToxCast Project
(contact: David Dix, email: dix.david@epa.gov)

EPA's Computational Toxicology Research Program has initiated a chemical categorization and prioritization research project entitled "ToxCastTM". The ToxCast project is designed to create the ability to predict, or forecast toxicity. Initially, this is entailing a demonstration "proof-of-principle" project based upon a set of chemicals with a rich toxicological database (e.g., mostly registered pesticidal active ingredients). This set of more 320 chemicals (309 unique substances) represent a number of differing structural classes and phenotypic outcomes (e.g., tumorigens, developmental and reproductive toxicants, neurotoxicants, immunotoxicants). The ToxCast project will evaluate chemical properties and effects across a broad spectrum of information domains: physical-chemical properties, predicted biological activities based on existing structure-activity models, biochemical properties based on HTS assays, cell based phenotypic assays, and genomic analysis of cells or organisms. The goal of the ToxCast project is to mine the resulting data for associations between and among the various domains and the known toxicological properties of the base set of chemicals, to provide a structured strategy to categorize chemicals, identify potential toxicities and pathways, and to prioritize chemicals for subsequent testing based on that information. For additional information, see the charter for EPA's Categorization and Prioritization Community of Practice. ToxCast project is closely aligned with the following NCCT research projects in addition to DSSTox: ACToR, ToxRef, and Tox21. DSSTox is primarily responsible for the chemical information quality review and structure annotation, whereas the ACToR system provides the larger informatics and analysis infrastructure for the NCCT ToxCast research project.

** Update (Feb 2009): The DSSTox Structure-Index file TOXCST containing the candidate chemicals in Phase I has been updated to v2a. Consult the TOXCST SDF Download Page for further details.

Return to the list above. Return to Top

ToxRef
(contact: David Dix, email: judson.richard@epa.gov)

The Aggregated Computational Toxicology Resource (ACToR) is a research project and newly available on-line resource (Dec 2008) within EPA's Computational Toxicology Research Program, affiliated with the ToxCast and DSSTox projects. ACToR is a collection of databases collated or developed by the NCCT. More than 200 sources of publicly available data on environmental chemicals have been brought together and made searchable by chemical name and other identifiers, such as chemical structure. Data includes chemical structure, physico-chemical values, in vitro assay data and in vivo toxicology data. Chemicals include, but are not limited to, high and medium production volume industrial chemicals, pesticides (active and inert ingredients), and potential ground and drinking water contaminants. All published DSSTox chemical inventories and chemical structures have been incorporated into ACToR, including chemical structure inventories for ToxCast and ToxRef. ACToR provides the ability to cross reference a much larger number of chemical inventories pertaining to environmental toxicology, and to determine which chemicals have highest representation across databases as well as which chemicals are associated with the most ecomplete toxicity data. These capabilities in ACToR are being used to prioritize chemicals for testing within the ToxCast and Tox21 research programs. ACToR will also serve as the primary informatics resource for ToxCast high throughput testing assay data and ToxRef in vivo data.


Return to the list above. Return to Top

Pesticides Ingredients Lists Structure-Index Files
(contact: Keith Houck, email: houck.keith@epa.gov)

EPA's Office of Pesticide Programs (OPP) is charged with overseeing toxicity data collection and registration review of pesticides, including hundreds of pesticidal actives -- new, in commerce, and no longer in production (biopesticides, antimicrobials, conventional), and thousands of pesticidal "other ingredients", previously referred to as "Inerts".

Preliminary DSSTox Structure-Index Files, incorporated into the DSSTox Master File and soon to be published on this website, have been created for several lists associated with pesticide programs, including Pesticidal Active Ingredients (EPAPAI), Pesticidal Other Ingredients (EPAPOI), Pesticide Eco-toxicity data (ECODEM) included in the DEMETRA project, a European Commission supported project to improve QSARs for regulatory use. These lists are being used for multiple purposes, to augment existing projects, to integrate and compare current chemical lists, to construct candidate chemicals for the EPA ToxCast Project and the NIH MLR collaborations, and to aid in the development of an electronic structure-searchable EPA pesticide toxicity database.

Return to the list above. Return to Top

Jump to main content.