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SDF Download Page
TOXCST: Research Chemical Inventory for EPA's ToxCastTM Program
Structure-Index File
** Version 2c, revised 29 April 2008
correction to single record in v2c.
v2b Included new InChIKey Standard Chemical Field, and a few structure modifications after additional quality review of chemical inventory against Certificates of Analysis (COAs) of purchased chemicals.
Quick & Easy File Downloads: FTP Download Instructions
Description
New Users: For general information, see DSSTox Project Goals and About DSSTox. For additional information on DSSTox SDF (Structure Data Format) files and their use in Chemical Relational Databases, see More on SDF and More on CRDs.
Description: EPA's National Center for Computational Toxicology is conducting research to develop the ability to forecast toxicity based on bioactivity profiling: the ToxCastTM Program for Prioritizing Toxicity Testing of Environmental Chemicals. Ultimately, the goal is to develop methods of prioritizing chemicals for further screening and testing to assist EPA in the management and regulation of environmental contaminants. For more information on the purpose, goals, and parameters of the program, see the Main Citation or ToxCastTMPublications.
Within the ToxCast Program, data is being generated on a selected chemical library of environmentally relevant chemicals using various high- and medium-throughput screening assays (e.g., cell-based, biochemical, and genomics) that evaluate a broad spectrum of bioactivities potentially relevant to toxicity (see ToxCastTMAssays). The essential first step is to conduct an initial testing phase using reference chemicals that have an existing, rich toxicological database (i.e., registered chemical pesticide active ingredients). Thus, ToxCastTM Phase I includes several hundred reference chemicals, representative of differing structural classes and phenotypic outcomes (e.g., tumorigens, reproductive toxicants, neurotoxicants). The objective of Phase I is to develop a set of predictive signatures, derived from ToxCastTM bioactivity profiles, that identify toxicity potential.
The DSSTox TOXCST Structure-Index File offers the full complement of DSSTox Standard Chemical Fields for the ToxCastTMPhase I testing - chemical inventory. A field entitled ToxCast_TestingStatus will be used to update the status of these Phase I chemicals as they move into testing and beyond, and to indicate testing status of new chemicals added in subsequent Phases of the ToxCastTM research program. The DSSTox TOXCST chemical structure inventory will also be directly associated with any published bioassay information generated for this set and made available in public resources, such as PubChem. The DSSTox TOXCST file enables structure-searching (structure/substructure/similarity) capability from the DSSTox Structure-Browser across all DSSTox structure-data files. Linkage of this structure-browser to PubChem, and deposition of the DSSTox TOXCST SDF into PubChem will enable broad structure and analog-searching capabilities across the very large bioassay data inventory maintained within that large public resource. Future enhancements to the DSSTox TOXCST file or related files will include publication of summary toxicity reference data and/or bioassay information as these data become publicly available.
Source Contacts: For questions concerning the EPA ToxCastTM Program, contact David Dix, email: dix.david@epa.gov or Keith Houck, email: houck.keith@epa.gov.
Source Website: EPA National Center for Computational Toxicology ToxCastTM Program
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Main Citation: Publications reporting use of the DSSTox TOXCST data files are asked to list the full DSSTox file name, including date stamp, and to cite as primary reference the following:
Dix, D.J., Houck, K.A., Martin, M.T., Richard, A.M., Setzer, W., Kavlock, R.J. (2007) The ToxCast program for prioritizing toxicity testing of environmental chemicals. Tox. Sci., 95:5-12.
See also: http://nheerlpub.rtord.epa.gov/ncct/toxcast/publications.html
DSSTox Standard Chemical Fields (19) * STRUCTURE_InChIKey field added in v2b
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TOXCST SDF Content Summary - 29 April 2008
TOXCST SDF Content |
Totals_v2b* | Totals_v2c* |
|---|---|---|
# Records
|
320
|
320
|
DSSTox Standard Chemical Fields
|
19 |
19 |
TOXCST Source Fields
|
2 |
2 |
Total # Fields
|
21 |
21 |
Chemical Content |
Counts_v2b | Counts_v2c |
defined organic |
313
|
313
|
inorganic |
1 |
1 |
organometallic |
6 |
6 |
no structure |
0 |
0 |
| STRUCTURE_TestedForm_ DefinedOrganic: |
||
parent |
299
|
300
|
complex |
8 |
8 |
salt |
6 |
5 |
salt complex |
0 |
0 |
| TestSubstance_Description: | ||
single chemical compound |
308
|
308
|
macromolecule |
0 |
0 |
unspecified or multiple forms |
0
|
0
|
mixture or formulation |
12
|
12
|
* v2 contains 309 unique substances (distinct DSSTox_SIDs and CIDs), 5 sets of duplicate compounds, and 3 sets of triplicate compounds.
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Version 2 Update: The original v1a published list of Phase I candidate ToxCastTM chemicals was submitted to EPA ToxCastTM program contractors for chemical procurement and sample preparation for HTS. The v2a file represents the final inventory with changes due to procurement issues (compound unavailability, duplication, or substitution). Details of changes from v1a to v2a are provided in the TOXCST_LogFile offered for download in the table below. The contents of the TOXCST_v2a file represents the actual list of purchased chemicals undergoing sample preparation and plating for generating ToxCast program assay results.
Version 2b Revision: Additional chemical QA was performed after obtaining full Certificates of Analysis (COAs) for purchased chemicals. Relatively minor modifications (stereochemistry, salt/complex form) were made to 8 structure records, with version changes documented in the corresponding record in the Note_TOXCST field. The field, EPA_PC_Code of EPA Pesticide Chemical Codes has been removed from v2b file due to need for further internal QA and some inconsistencies in usage. Additionally, STRUCTURE_InChIKey was added as a new DSSTox Standard Chemical Field.
Version 2c Revision: Correction was made to DSSTox_FileID = 20_TOXCST_v2b record: several fields other than STRUCTURE incorrectly referred to Na salt form and were changed to correspond to parent form.
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File Download Notes: The following files are offered in the DownLoad table below:
Log File (PDF) provides SDF data file version history and summary information (field, chemical counts, etc.), and a description of procedures and quality assurance checks used in SDF file creation;
| You will need Adobe Acrobat Reader, available as a free download, to view the Adobe PDF files on this page. See EPA's PDF page to learn more about PDF, and for a link to the free Acrobat Reader. |
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These files constitute the main DSSTox products. Documentation Files use standard templates, and DSSTox Structure Data Files and DSSTox File Names adhere to strict formatting standards and conventions. For additional information, see More on DSSTox Standard Chemical Fields, Known Problems & Fixes, Chemical Information Quality Review Procedures, and How to Use DSSTox Files.
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Acknowledgements: The DSSTox SDF file of the TOXCST chemical list was constructed from larger lists of candidate chemicals from the DSSTox inventory of files, EPA pesticide lists, and other candidate chemical lists for which existing toxicological data is expected to be available. Many persons aided in the compilation of such lists, including EPA Office of Pesticide Programs (OPP) personnel. Chemical structure annotation, QA review, and problem resolution were carried out by Maritja Wolf (Lockheed Martin, Contractor for EPA).
DSSTox Citation: Houck, K., D. Dix, R. Judson, M. Martin, M. Wolf, R. Kavlock, and A.M. Richard (2008) DSSTox EPA ToxCast High Throughput Screening Testing Chemicals Structure-Index File: SDF File and Documentation, Updated version: TOXCST_v2c_320_29Apr2008, www.epa.gov/ncct/dsstox/sdf_toxcst.html
Disclaimer: Every effort is made to ensure that DSSTox SDF files and associated documentation are error-free, but neither the DSSTox Source collaborators nor the EPA DSSTox project team make guarantees of accuracy, nor are any of these persons to be held liable for any subsequent use of these public data. The contents of this webpage and supporting documents have been subjected to review by the EPA National Center for Computational Toxicology and approved for publication. Approval does not signify that the contents reflect the views of the Agency, nor does mention of trade names or commercial products constitute endorsement or recommendation for use.
EPA/600/C-06/012
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