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NTPBSI: National Toxicology Program Bioassay On-line Database
Structure-Index Locator File

** Version 4c, updated 04 August 2009
Update corresponds to chemical and Study Area content of NTP On-line Database Source Website as of 28 July 2009, with 15 new chemical records from v4b (26 January 2009), a few changes to Study Area listings, one structure modification, and one chemical name change. For additional details, see Log file in Download Table below.

Quick & Easy File Downloads: FTP Download Instructions

blue bullet graphic Description
blue bullet graphic Source Website & Contact
blue bullet graphic SDF Fields
blue bullet graphic NTP Study Area Counts
blue bullet graphic Version 4 Update

blue bullet graphic SDF Download Table

blue bullet graphic Acknowledgements, DSSTox Citation & Disclaimer

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: The National Toxicology Program makes available data from more than 500 two-year, two species, toxicology and carcinogenesis studies collected by the NTP and its predecessor, the National Cancer Institute's Carcinogenesis Testing Program. The NTP database also contains results collected on approximately 300 toxicity studies from shorter duration tests and from more than 2000 genetic toxicity studies, some of which include both in vitro and in vivo tests. In addition, test data from the immunotoxicity, genetic toxicity, and developmental toxicity studies are continually being added to this database. Data from these various studies are indexed on the NTP On-line Database exit EPAby Chemical Name and CASRN and organized into 4 Study Areas. These data are publicly viewable and accessible from the NTP Website exit EPA, hosted at the National Institute of Environmental Health Sciences (NIEHS) [choose the "Study Data Search" option].

The DSSTox NTPBSI Structure-Index Locator File offers the full complement of DSSTox Standard Chemical Fields for that portion of the NTP Bioassay On-line Database inventory exit EPA related to explicit chemical exposures. NTPBSI also contains indicator fields for each of the 4 toxicity study areas (e.g., StudyArea_GeneTox) represented in the NTP On-line database (a value of "1" indicates study data availability for the chemical record, whereas a value of "0" indicates no study data). Additionally, NTPBSI contains URLs for each of the indexed NTP compounds (ChemicalPage_URL) linking a user directly to the NTP On-line Database Study index page for each compound. Updates of this DSSTox NTPBSI file are performed regularly in collaboration with the NTP Source Contact.

The DSSTox NTPBSI file enables structure-searching (structure/substructure/similarity) capability for the NTP Bioassay On-line Database from the DSSTox Structure-Browser and linkage back to the corresponding NTP On-line Database Study page for the retrieved compound. In addition, deposition of the DSSTox NTPBSI SDF into PubChem under the "EPA DSSTox" [sourcename] 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.

Toxicity data content DSSTox files, with overlapping structure-index content to NTPBSI, are being constructed in the areas of genetox (NTPGTZ) and immunotox (IMMTOX). Collaborations with the NTP High-Throughput Screening exit EPA program are also currently underway involving publication of a structure-index file (NTPHTS) for a chemical data set (content largely overlapping with NTPBSI) submitted for bioassay screening at the NIH Molecular Libraries Roadmap - Chemical Genomics Center (NCGC) exit EPA. See Coordinating Public Efforts and Work in Progress for additional information on DSSTox NTP collaborations.

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Source Website: NIEHS's National Toxicology Program, NTP On-line Database Main Search Page: http://ntp-apps.niehs.nih.gov/ntp_tox/index.cfm exit EPA

Note: The NTP On-line Database is updated regularly. In contrast, the NTPBSI is a static file, but content will be updated to a new dated version at least quarterly in coordination with NTP Source Contact collaborators. Also, the NTPBSI file does not index the entire content of the NTP On-line Database, but only that content related to an explicit chemical exposure. NTP studies for non-chemical stressors such as electromagnetic field studies, or transgenic studies, etc., are not indexed in the DSSTox NTPBSI file but can be located on the NTP Bioassay On-line Database.

 

Source Contact: National Institute of Environmental Health Sciences, National Toxicology Program: Beth Bowden, email: bowden1@niehs.nih.gov

NTPBSI SDF Fields (28 total)

DSSTox Standard Chemical Fields (20)

Source_ChemicalName new field added Jan2009

NTP_StudyArea_ImmunoTox
NTP_StudyArea_GeneTox
NTP_StudyArea_CancerChronicTox
NTP_StudyArea_DevelopTox

NTP_StudyArea field entries = 1 or 0, indicating presence or absence of link to an electronic data page in NTP on-line database for each of 4 NTP study areas.

NTP_CAS_Code
Note_NTPBSI

ChemicalPage_URL
field name changed in v3a

e.g. (Diethylamino)ethanol exit EPA

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NTPBSI Study Area Counts - 04 August 2009

NTP Toxicity Study Area Names
NTPBSI
NTP_Study Area_
Totals_v2
Totals_v3
Totals_v4a
Totals_v4b
Totals_v4c
Bioassay
_CancerChronicTox
693
694
698
699
703
Immunology
_ImmunoTox
41
45
45
45
45
Developmental
_DevelopTox
69
70
70
70
70
Genetox
_GeneTox
2181
2186
2194
2194
2210
Total # Studies
2984
2995
3007
3008
3028

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Version 4a Update: NTPBSI_v4b includes updated chemical records and Study Area indices from v3a, corresponding to changes to the NTP On-line Database Source Website content as of 21 August 2008.   Additions of 12 chemical records with a total of 12 corresponding studies were made to NTP Study Areas "GeneTox" (8 studies) and "StandardTox and Carcinogenesis" (4 studies) – the latter formerly titled "Cancer and Chronic Tox" on the NTP website.  There were no deletions or additions to ImmunoTox and Developmental Study Areas.  One new addition to the GeneTox Study Area on the NTP website, "alpha-Lipoic acid", is listed under a retired CAS [62-46-4] and is a duplicate of another NTP website entry – alpha-Lipoic acid, CAS [1077-28-7]; the record corresponding to the retired CAS was not included in NTPBSI_v4b.

Version 4b Update: NTPBSI_v4b includes updated Study Area indices from v4a (21 August 2008), corresponding to changes to the NTP On-line Database Source Website content as of 13 January 2009.   2 chemicals added and 1 chemical deleted from CancerChronicTox, documented in the Note_NTPBSI field. No structures were changed. Approx. 50 ChemicalPage_URL entries were updated. STRUCTURE_InChI and STRUCTURE_InChIKey field entries have been updated to conform to newly released InChI 1.02 Standards exit EPA.

Version 4c Update: NTPBSI_v4c includes updated Study Area indices from v4b (26 January 2009), corresponding to changes to the NTP On-line Database Source Website content as of 28 July 2009.   15 chemicals were added, all in GeneTox Study Area. In addition, 4 new CancerChronicTox studies and 1 new GeneTox study were added for previously listed chemicals. One structure was modified and one TestSubstance_ChemicalName and Source_ChemicalName were modified. All changes are documented in the Note_NTPBSI field.

For more information and version history, consult the NTPBSI_LogFile in the Download Table below.

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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;
Field Definition File (PDF or MS Word doc file) provides field definitions and essential documentation, and should be downloaded with and accompany any use of the DSSTox SDF file;
Structure Data File (SDF) is the main DSSTox product, providing the complete inventory of chemical structures, DSSTox Standard Chemical Fields, and all Source-specific data fields [Note: the structure field is blank for all records containing mixtures or undefined substances];
Data Table MS Excel (MS Office 2003) file contains the full SDF data contents in spreadsheet table form, minus the chemical structure field [file created with CambridgeSoft ChemFinder plug-in to MS Excel 2003];
Structures Table (PDF) file contains a tiled format graphical view of all chemical structures contained in the SDF file, annotated with TestSubstance_CASRN and truncated TestSubstance_ChemicalName field entries for the tested form of the chemical [file created with ACD ChemFolder, ver. 11, ACD Labs].

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 JZip. Exit EPA Disclaimer

File Types   Description File Size Format

Documentation Files: NTPBSI
Log File  
42KB
pdf document icon
Field Definition File  
28KB
pdf document icon
   
75KB
ms word document icon
Data Files: NTPBSI
SDF Structure Data File  
*.zip
2.1MB
Included in Zip file.
• Data Table
(no structures)
  Included in Zip file.
• Structures Table   pdf document icon
file error report graphic link to submit error report form    

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.

Quick & Easy File Downloads: FTP Download

Acknowledgements: The original DSSTox SDF file of the NTP Bioassay On-line Database was created by Jamie Burch (EPA/NC Central Univ Student COOP), with assistance provided by the William (Skip) Eastin and Beth Bowden of the NTP in compiling lists of Study Area indicators. Subsequent QA review and structure modifications were carried out by Maritja Wolf (Lockheed Martin, Contractor for EPA), with content update assisted by Ann Richard (EPA). Joe Roycroft (NTP) and Beth Bowden (NTP) provided helpful comments and suggestions in review of v2a. Additionally, we are extremely grateful to Beth Bowden and NTP support staff for helping us to reconcile website content for v3a, for incorporating suggested changes to the NTP website to assist users in better accessing content inventory, and for working with us to provide NTP website content updates at least quarterly. Subsequent NTP version updates were provided by Anand Paleja and John Hodorowicz (NTP).

DSSTox Citation: Burch, J., W.C. Eastin, B. Bowden, M.A. Wolf, and A.M. Richard (2009) DSSTox National Toxicology Program Bioassay On-line Database Structure-Index Locator File: SDF File and Documentation, Updated version: NTPBSI_v4c_2330_04Aug2009, www.epa.gov/ncct/dsstox/sdf_ntpbsi.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. See additional disclaimers.

EPA/600/C-06/011

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