EPA/NCCT: Distributed Structure-Searchable Toxicity (DSSTox): SDF Download Page/IMMTOX Page 1 of 4 U.S. Environmental Protection Agency Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network Home About DSSTox Work in Progress Frequent Questions Structure Data Files Central Field Definition Table Apps, Tools & More DSSTox Community Site Map Glossary of Terms Help Recent Additions | Contact Us | Print Version Search: E3 EPA Home > Research & Development > Computational Toxicology Research > DSSTox > StructureDataFiles > SDF Download Page: NTPHTS SDF Download Page: ¦ NTPHTS: National Toxicology Program High Throughput Screening Project Structure-Index File ** New DSSTox Structure-Index File 10Apr2006 Quick & Easy File Downloads: FTP Download Instructions * Description * Source Website * Source Contacts * PubChem Bioassav Data * SDF Fields * SDF Content Summary SDF Version History * SDF Download Table |Download| * DSSTox Citation <* Disclaimer Description: The National Toxicology Program (NTP) has initiated a High Throughput Screening (HTS) Project exit Disclaimer to explore new approaches to evaluating chemicals across a spectrum of high-throughput biological assays. Assays are being selected based on their potential be informative of animal bioassay results and relevant to human health risk assessments. As an initial phase of this project, the NTP has provided a set of 1408 chemicals from NTP inventories for HTS in bioassays relevant to toxicology, to the NIH Chemical Genomics Center (NCGO, part of the NIH Molecular Libraries & Imaging Roadmap (MLR) Initiative ExiTDisciaimerl. Assays will be described and assay results reported in PubChem for this NTPHTS chemical data set in the same manner as for compounds from the Molecular Libraries Small Molecule Repository Exit Disciaimeri. For a recent interview on this NTP HTS project, see: Newsletter of the Society for Biomolecular Sciences - Chris Portier: HTS Takes US National Toxicology Program to Next Level ev IT Disci ai Tier I. The DSSTox project is collaborating with the NTP HTS project to provide structure-annotation and chemoinformatics support for this effort. Drawing largely from the contents of the existing NTPBSI Structure-Index Locator File, with many of the 1408 NTP HTS chemicals having been used in historical NTP toxicity studies, the DSSTox NTPHTS Structure-Index File provides the full complement of DSSTox Standard Chemical Fields for the NTP HTS chemical set. Additionally, the DSSTox NTPHTS file includes the PubChemSID (Substance Identifier) code for each chemical record listed (assigned upon depositing the NTPHTS SDF into PubChem). These PubChem SID codes correspond directly to the relevant PubChem SID record that will contain the corresponding NTP HTS assay results deposted by the NCGC. Maintenance of this DSSTox NTPHTS file will be coordinated with expansion of the NTP HTS program. Inclusion of the DSSTox NTPHTS structure-index content in the DSSTox Master Structure-Index File additionally allows linkages to be made to other DSSTox Structure-Data Files, including the NTPBSI Structure-Index Locator File which links to the chemical-specific content of the NTP Bioassav On-line Database. Deposition of the DSSTox NTPHTS SDF into PubChem http://www.epa.gov/ncct/dsstox/sdf ntphts.html 9/18/2006 ------- EPA/NCCT: Distributed Structure-Searchable Toxicity (DSSTox): SDF Download Page/IMMTOX Page 2 of 4 enables broad structure and analog-searching capabilities both across the entire DSSTox data inventory, and across the very large bioassay data inventory maintained within PubChem. See Coordinating Public Efforts and Work in Progress for additional information on DSSTox NTP collaborations. Source Website: NIEHS's National Toxicology Program, NTP High Throughput Screening Project EXIT Disclai merl Source Contact: Ray Tice, email: tice@niehs.nih.gov; Cynthia Smith, email: smithl 9@niehs.nih.gov PubChem Bioassay Data: HTS bioassay data is to be deposited in PubChem emit Disclaimer! for the NTPHTS substance list under the depositor keywords: "EPA DSSTox" [sourcename] "ntphts" and will be additionally searchable by substance keywords "ntphts" or "ntphts_ncgc". HTS bioassays used to screen this NTPHTS set will be further described in PubChem and will be used to screen larger sets of chemicals. These larger chemical sets will be retrievable within PubChem using the appropriate Bioassay search criteria. For example, HTS data for NTPHTS has been generated by the NCGC EXIT Disclaimei for: Cell viability assay (AID 421): http://pubchem.ncbi. nlm.nih.gov/assav/assay.cgi?aid=421 As data and bioassay information relevant to NTPHTS become available from NCGC and PubChem, more guidance on retrieving these HTS data will be provided here (also see Searching DSSTox Files in PubChem). NTPHTS SDF Fields (19 total) DSSTox Standard Chemical Fields (18; includes optional ChemicalReplicateCount field) PubChem SID NTPHTS SDF Content Summary -10 April 2006 NTPHTS SDF Content Totals_v1a # Records 1408 DSSTox Standard Chemical Fields 18 NTPHTS Source Fields 1 Total # Fields 19 Chemical Content Counts_v1a STRUCTURE ChemicalTvpe: http://www.epa.gov/ncct/dsstox/sdf ntphts.html 9/18/2006 ------- EPA/NCCT: Distributed Structure-Searchable Toxicity (DSSTox): SDF Download Page/IMMTOX Page 3 of 4 defined organic 1348 inorganic 27 organometallic 19 no structure 14 STRUCTURE TestedForm DefinedOrganic: parent 1279 complex 51 salt 19 salt complex 1 TestSubstance Description:* single chemical compound 1343 defined mixture or formulation 47 undefined mixture 5 macromolecule 3 unspecified or multiple forms 0 * Note: NTPHTS_v1a contains 55 chemical records with duplicate structures (duplicate DSSTox CID); 1 pair of these consists of a monomer and polymer with same STRUCTURE represented, whereas 54 of these pairs are ostensibly the same Test Substances (same TestSubstanceCASRN and TestSubstanceDescription). but were obtained from different lots or chemical manufacturers (different Lot and Vial numbers are maintained in internal NTP tracking identification). Because these chemical substances are provided as distinct chemical samples for HTS evaluation, they must be differentiated as separate chemical records in the DSSTox SDF, as well as by distinct DSSTox SID and PubChem SID assignments. The HTS data for these duplicates will be presented as separate PubChem SID listings, but will be grouped for easy viewing and comparison by common chemical structures and PubChem CID values. For more information on accessing NTP HTS data within PubChem, see Searching DSSTox Files in PubChem. LI Return to Top SDF Version History: An initial list of NTP HTS chemical names and CASRN was provided to us by NTP Sources Brad Collins and Cynthia Smith. Based initially on CASRN matching, DSSTox Standard Chemical Fields were populated largely from the existing DSSTox Master File content (see also Chemical Information Quality Review Procedures'), with approximately 200 substances not contained in NTPBSI. Some corrections were applied to the original NTP HTS Source information (and communicated back to the NTP Source) and information on new substances not already occurring in the DSSTox Master File were entered into the Master File and NTPHTS after thorough Chemical Information Quality Review Procedures. File Download and View Notes: Provided below, in addition to the main SDF file (see More on SDF). are: a downloadable MS Excel (MS Office 2003) file containing the full SDF data contents in table form, minus the chemical structure field [file created with CambridgeSoft ChemFinder plug- in to MS Excel 2003]; and a PDF tiling view of all chemical structures contained in the SDF, annotated with TestSubstance CASRN and truncated TestSubstance ChemicalName field entries for the tested form of the chemical [file created with ACD ChemFolder, ver. 8.0, ACD Labs], The files contained in the following download table constitute the main DSSTox products. 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. http://www.epa.gov/ncct/dsstox/sdf ntphts.html 9/18/2006 ------- EPA/NCCT: Distributed Structure-Searchable Toxicity (DSSTox): SDF Download Page/IMMTOX Page 4 of 4 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. Zip files may be decompressed using a utility such as WinZip. exit Disclaimer! File File Types Description gjze Format H Data Files: NTPHTS Structure NTPHTS via 1408 10Acr2006.sdf Data File • Oritfl Trihlp * ZID ran . 7 . NTPHTS via 1408 10Apr2006 nostructures.xls . HI (no structures) H 1.4MB ill • qtmrtnrP^TahlP NTPHTS_v1 a_1408_10Apr2006_structures.pdf pP btructures l able (pDF 29pp 3 2MB) File Error Re|>ort Quick & Easy File Downloads: FTP Download DSSTox Citation: Smith, C., B. Collins, R. Tice, M.A. Wolf, and A.M. Richard (2006) DSSTox National Toxicology Program High Throughput Screening Structure-Index File: SDF File and Documentation, Launch version NTPHTS_v1a_1408_10Apr2006, www.epa.gov/nheerl/dsstox/ 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. U Return to Top EPA Home | Privacy and Security Notice | Contact Us Last updated on Monday, July 17th, 2006 URL: http://www.epa.gov/ncct/dsstox/sdf_ntphts.html http://www.epa.gov/ncct/dsstox/sdf ntphts.html 9/18/2006 ------- |