![[logo] US EPA](https://webarchive.library.unt.edu/eot2008/20081019224614im_/http://www.epa.gov/epafiles/images/logo_epaseal.gif){kind=logo}
SDF Download Page
CPDBAS: Carcinogenic Potency Database Summary Tables - All Species
Database File
ogenic Potency Database Summary Tables - All Species
** Version 5c, revised 29 April 2008:
One Mouse bioassay correction (Inactive result removed) and 2 structure corrections.
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: The CPDB Summary Tables list summarized results for experiments on 1547 substances in the Carcinogenic Potency Database (CPDB). These Summary Tables report the strongest evidence of carcinogenicity for each chemical, in each sex/species and represent one of many possible summarizations of the data in the CPDB. The CPDB includes detailed results and analyses of 6540 chronic, long-term carcinogenesis bioassays reported in 1513 papers in the general literature and 452 Technical Reports of the National Cancer Institute/National Toxicology Program. Details on each experiment can be obtained from the CPDB Source website. For all experiments in the CPDB, detailed information is provided on each experiment, including the species, sex, strain, route of administration, duration of exposure and of experiment, dose levels, target sites, shape of the dose response, estimates of carcinogenic potency and the confidence limits surrounding it, statistical significance of the carcinogenic dose response, tumor incidences, and bibliographic citation to the published paper or to the NCI/NTP Technical Report. All experiments in the complete database meet a specific set of inclusion criteria that were designed to permit the estimation of carcinogenic potency; therefore, reasonable consistency of experimental protocols is assured. Bioassays are included in the database only if the test agent was administered alone rather than in combination with other substances; if the bioassay included a control group; if the route of administration was either diet, water, gavage, inhalation, intravenous injection or intraperitoneal injection; and if the length of experiment was at least half the standard lifespan for the species with dosing for at least one fourth lifespan. Evidence of carcinogenicity in an experiment was not determined for the CPDB; rather, the CPDB reports the evaluation of the published author of each experiment and the statistical significance of the tumorigenic dose response calculated by the CPDB. Fewer than thirty percent of the chemicals have been tested by the NCI/NTP.
The CPDB Summary Tables provide an overview of bioassay results on a given chemical with information on: the sex-species groups tested, and the strongest level of evidence for carcinogenicity based on the opinion of a published author; the carcinogenic potency value (TD50), and target organs in each species tested. If there are both positive and negative experiments in a sex-species, the negative results are ignored in the Summary Table. When there is more than one positive experiment in a species, the TD50 value in the CPDB Summary Table is the harmonic mean of the most potent TD50 value from each positive experiment in the species. The target organs listed for each sex-species group may be from more than one positive experiment. Summary evaluations of mutagenicity in Salmonella (positive or negative) are also reported. CPDB Summary Table results are provided for rats, mice, hamsters, dogs, and nonhuman primates.
DSSTox SDF files were originally provided separately for each of these for 4 data tables. In CPDBAS_v2a and later versions, all data tables have been consolidated into a single SDF for easier implementation and use in a relational database application. In CPDBAS_v3b and later, URLs are provided to chemical-specific data page summaries posted on the CPDB Source Website. In CPDBAS_v5b and later, summary activity fields are provided for each rodent species, with primates grouped into a single summary field, consistent with representation of DSSTox CPDB Assays in PubChem.
Return to Top
Source Website: The complete, updated CPDB of 6540 experiments, from which
the Summary Tables and CPDBAS are derived, is available in several formats at http://potency.berkeley.edu/
.
Source Contact: Please contact Lois
Swirsky Gold for questions pertaining to the content of the CPDB Summary
Tables; email: cpdb@potency.berkeley.edu.
Please Contact Us
for questions or comments pertaining to the DSSTox CPDBAS SDF files.
Main Citations: Publications reporting use of DSSTox SDF files for the CPDB Summary Tables are asked to list the full DSSTox file name(s), including date stamp, and to cite as primary references the following citations:
Gold, L.S., T.H. Slone, B.N. Ames, N.B. Manley, G.B. Garfinkel, and L. Rohrbach (1997) Chapter 1: Carcinogenic Potency Database. In: Gold, L.S., and E. Zeiger, Eds. Handbook of Carcinogenic Potency and Genotoxicity Databases. Boca Raton, FL: CRC Press, pp. 1-605. http://potency.berkeley.edu/text/methods.html
Gold, L.S., N.B. Manley, T.H. Slone, and J.M. Ward (2001) Compendium of chemical carcinogens by target organ: Results of chronic bioassays in rats, mice, hamsters, dogs and monkeys. Toxicol. Pathol. 29: 639-652. http://potency.berkeley.edu/text/ToxicolPathol.pdf
Gold, L. S., Manley, N. B., Slone, T. H., Rohrbach, L., and Garfinkel, G.B. Supplement to the Carcinogenic Potency Database (CPDB): Results of Animal Bioassays Published in the General Literature through 1997 and by the National Toxicology Program in 1997 and 1998. Toxicol. Sci. 85: 747-800 (2005). http://potency.berkeley.edu/pdfs/ToxSciPlot.pdf
Carcinogenicty Potency Data Base (2008) http://potency.berkeley.edu/
Summary Table of Chemicals in the Carcinogenic Potency
Database: Results for Positivity, Potency (TD50), and Target
Sites: http://potency.berkeley.edu/chemicalsummary.html
See also, a full listing of Data Plots (from which the CPDB Summary Table was derived) and CPDB publications at:
http://potency.berkeley.edu/listofpubs.topic.html#plots
http://potency.berkeley.edu/listofpubs.topic.html
Guidance for Use: These CPDB Summary Tables
can be used as an overview of the literature of animal cancer tests, as
an index of results in the CPDB, and to investigate associations between
carcinogenic potency and other factors such as mutagenicity, teratogenicity,
chemical structure, and human exposure. The complete CPDB, which is summarized
in these tables, has been fully described in several data plots and publications (see Main
Citations above), and details of the inclusion criteria, protocol characteristics, and
derived variables are available at: http://potency.berkeley.edu/methods.html . A user of the DSSTox CPDBAS SDF file is encouraged
to consult the extensive documentation and content of the CPDB website
[http://potency.berkeley.edu/
]
for further information, details, and references pertaining to each entry
of the CPDB Summary Tables. In addition, the CPDBAS Field Definition File
below contains definitions of each field in the DSSTox CPDBAS SDF file,
and information pertaining to any discrepancies between these fields (and
their contents) and the data in the original CPDB Summary Tables.
The CPDBAS Field Definition File contains essential documentation and
should be downloaded with, and accompany any use of the DSSTox CPDBAS
SDF file. The CPDBAS LogFile provides SDF file summary information (field,
chemical counts, etc.), a description of procedures and quality assurance
checks used in SDF file creation, and a listing of unavailable CASRN or
Structure information in the SDF file. The Log File also contains a full version history, documenting modifications
incorporated into version/revision updates of the DSSTox CPDBAS (and earlier)
SDF files.
CPDBAS_v3b and later versions contain the full inventory of chemical-specific data page URLs from the CPDB Source Website Chemical Index that can be used in combination with structure-searching capabilities to link to the specific chemical data page summary on the CPDB website. These links can be accessed from within the newly launched DSSTox Structure-Browser (August 2007). The CPDB Source Website Chemical Index data pages also have directly incorporated some DSSTox Standard Chemical Field content (SMILES, InChI's).
To report errors in any CPDBAS documentation or data file, click on File Error Report here or below. For additional information on DSSTox SDF files and their use in Chemical Relational Databases, see More on SDF and More on CRDs.
Note: CPDBAS_v3a was previously posted to PubChem as a single "activity" Assay ID (AID) file, with activity defined by the ActivityOutcome_CPDBAS_SingleCellCall. CPDBAS_v5c has been deposited under several separate CPDBAS_AID listings, each representating one of the several indicators of summarized mutagenic and carcinogenic activity contained within CPDBAS_v5c, i.e. ActivityOutcome_CPDBAS_[Mutagenicity, Rat, Mouse, Hamster, etc], ActivityScore_CPDBAS_[Mutagenicity, Rat, Mouse, Hamster, etc].
Return to Top
Version 5 Update: CPDBAS_v5a represents a major update of the CPDBAS data file, with 66 new chemical records added and over 400 new or modified experimental results affecting nearly 100 existing data records. These changes correspond to the most recently published data in the CPDB Summary Tables posted on the CPDB Source website . In addition to 66 added records and hundreds of new or modified experimental results, additional quality review and a user error-report led to correction of 3 previously included chemical structures and a small number of previous experimental results with errors in transcription. For more information and version history, consult the CPDBAS Log File in the Download Table below.
The significant number of new chemical records added to v5a presents a unique opportunity to structure-activity modelers to use these new data for validation of existing carcinogenicity models; however, the significant number of modified and new experimental results in v5a should necessitate model rederivation prior to validation. From the SDF Content Summary Table below, it can be inferred that of the 66 new records, 59 are defined organics, 53 correspond to the parent structure (i.e., neither salt nor complex), and 51 are a "single chemical compound" as opposed to a macromolecule or mixture. To assist users in locating modified or newly added records from one DSSTox CPDBAS file version to the next, we have incorporated controlled text entries (separated by semicolons) into the Note_CPDBAS field where applicable, e.g. for this v5a update:
Also of interest to structure-activity modelers should be the various summary activity representations provided in CPDBAS_v5 and later. These various options for considering carcinogenicity activity or inactivity should provide useful avenues for modelers to explore.
Version 5b Revision: CPDBAS_v5b includes no new carcinogenicity experimental data, but includes several new and modified summary activity fields for use in PubChem and structure-activity relationship studies (see CPDBAS SDF Field listing below). These include:
"active"... at least one positive experiment reported in CPDB, with TD50 and tumor site listed
"inactive" ... at least one experiment reported with "no positive results", and no other positive experiment reported in CPDB
"inconclusive" ... NCI/NTP bioassays were the only available experiments in the species, and results for both sexes in the species were evaluated by NCI/NTP as inadequate
blank ... no experiments reported in CPDB
Log(1/TD50mmol), mapped onto 1-100 integer range ... for "active" chemicals (see above)
"0" ... for "inactive" chemicals (see above)
blank ... no experiments reported in CPDBNote: Some fields, such as ActivityOutcome_CPDBAS_SingleCellCall will have entries for all 1547 compounds, whereas others, such as ActivityOutcome_CPDBAS_Hamster will have non-blank entries only for the relatively small number of compounds in the CPDB with experiments reported in Hamsters (i.e., 87 total).
Since two species listed in the Source CPDB Summary Tables (Bush Baby and Tree Shrew) have data for only a single chemical record each, and the chemical record in each case is also listed in the CPDB Rat Mouse Summary Table, data for these species are provided in the new TD50_Dog_Primates_Note field of the corresponding chemical record. In addition, the new STRUCTURE_InChIKey field (25 character abbreviated InChI for use in structure-indexing applications) has been added as a DSSTox Standard Chemical Field to all DSSTox files.
Version 5c Revision: CPDBAS_v5c includes 2 structure modifications, and one correction to a record that incorrectly listed an inactive bioassay result for Mouse (but MultiCellCall was correct). See CPDBAS_LogFile for details.
For more information and version history, consult the CPDBAS_LogFile in the Download Table below.
Return to Top
DSSTox Standard Chemical Fields (19) * STRUCTURE_InChIKey field added in v5b
DSSTox Standard Toxicity Fields (3)
ActivityOutcome_CPDBAS_Mutagenicity *modified in v5b (formerly Mutagenicity_SAL_CPDB)
TD50_Rat_mg
TD50_Rat_mmol
ActivityScore_CPDBAS_Rat *new to v5b
TD50_Rat_Note
TargetSites_Rat_Male
TargetSites_Rat_Female
TargetSites_Rat_BothSexes
ActivityOutcome_CPDBAS_Rat*new to v5b
TD50_Mouse_mg
TD50_Mouse_mmol
ActivityScore_CPDBAS_Mouse*new to v5b
TD50_Mouse_Note
TargetSites_Mouse_Male
TargetSites_Mouse_Female
TargetSites_Mouse_BothSexes
ActivityOutcome_CPDBAS_Mouse*new to v5b
TD50_Hamster_mg
TD50_Hamster_mmol
ActivityScore_CPDBAS_Hamster*new to v5b
TD50_Hamster_Note
TargetSites_Hamster_Male
TargetSites_Hamster_Female
TargetSites_Hamster_BothSexes
ActivityOutcome_CPDBAS_Hamster*new to v5b
TD50_Dog_mg
TargetSites_Dog
TD50_Rhesus_mg
TargetSites_Rhesus
TD50_Cynomolgus_mg
TargetSites_Cynomolgus
TD50_Dog_Primates_Note*modified in v5b
ActivityOutcome_CPDBAS_Dog_Primates *new to v5b
ActivityOutcome_CPDBAS_SingleCellCall*modified in v5b
ActivityOutcome_CPDBAS_MultiCellCall *modified in v5b
ActivityOutcome_CPDBAS_MultiCellCall_Details *modified in v5b
Note_CPDBAS ......contains controlled text entries for version content updates
NTP_TechnicalReport
ChemicalPage_URL .....(formerly Website_URL in v4a), contains link to the record-specific CPDB Chemical Index data page, e.g. see ACETALDEHYDE
* Note: For detailed information on SDF content, see CPDBAS Field Definition File in Download Table below.
Return to Top
CPDBAS Data Content Summary - 20 August 2008
CPDBAS_v5c contains 1547 total chemical substance records, but not all substances have been tested in all species categories. The table below provides a summary of the total numbers of substances tested for each of the species categories and the corresponding counts within the ActivityOutcome and ActivityScore fields derived from the CPDB Summary Tables. For definitions of these fields and field entries, refer to the field listing in the previous section or consult the CPDBAS_FieldDefFile available in the Download Table below.
Category Field Name |
ActivityOutcome_CPDBAS_Species (v5c) | ActivityScore_CPDBAS_Species* | |||
|---|---|---|---|---|---|
| Active | Inactive | Inconclusive | Total # Entries | Total # Entries* | |
| Mutagenicity (Salmonella) | 403 | 457 | 0 | 860 | NA |
| Rat | 587 | 646 | 7 | 1240 | 1240 |
| Mouse | 445 | 558 | 5 | 1008 | 1008 |
| Hamster | 44 | 42 | 1 | 87 | 87 |
| Dog_Primates | 15 | 17 | 0 | 32 | NA |
| SingleCellCall | 806 | 738 | 3 | 1547 | NA |
| MultiCellCall | 582 | 570 | 0 | 1152 | NA |
** ActivityScore_CPDBAS_Species fields are only included for CPDB species categories where quantitative TD50 values are available. However, this field is not included for the field ActivityOutcome_Dog_Primates (which groups results for species Dog, Rhesus, and Cynomolgus) due to the combined species nature of this field and the small number of chemicals with available data for each of the included species.
Return to Top
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. |
Zip files may be decompressed using a utility such as WinZip. |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
These files constitute the main DSSTox products. DSSTox 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
Return to Top
Acknowledgements: The original DSSTox SDF
file of the Carcinogenic Potency Database Summary Tables was created
by ClarLynda Williams (EPA/NC Central Univ Student COOP; EPA) with the
assistance of Jamie Burch (EPA/NC Central Univ Student COOP), Todd Stewart
(EPA/UNC Student COOP), Adam Swank (EPA), James Beidler (EPA Summer Student
Hire), and Ann Richard (EPA). In addition, a special debt of gratitude
is owed to Lois Swirsky Gold and Thomas H. Slone (Univ Calif Berkeley,
Carcinogenic Potency Project) for their collaboration and involvement
throughout the initial DSSTox project phase and subsequently. In particular,
we thank them for invaluable assistance in the quality review of the CPDBAS
SDF files, for careful review of all documentation pertaining to the CPDB
on this website, for assistance in locating structural information, and
for numerous clarifications and suggestions for improvements to the launch-version
databases and documentation. Thanks to Larry Claxton and Chandrika
Moudgal for careful reviews of the v1a documentation files. All subsequent QA review and structure modifications to CPDBAS_v2 and later versions were carried out by Maritja Wolf (Lockheed Martin, Contractor for EPA).
We thank Emilio Benfenati (Mario Negri, Institute of Pharmacological Research) for reporting 3 structure errors, single-instance chemicals from our earliest DSSTox data entry days. Thanks also to David Hollandsworth (CSC, Contractor to the US EPA) for performing a link-check on the full list of CPDBAS URLs.
DSSTox Citation: Gold, L.S., T.H. Slone,
C.R. Williams, J.M. Burch, T.W. Stewart, A.E. Swank, J. Beidler, and A.M.
Richard (2008) DSSTox Carcinogenic Potency Database Summary Tables - All Species: SDF File
and Documentation, Updated version: CPDBAS_v5c_1547_29Apr2008, www.epa.gov/ncct/dsstox/sdf_cpdbas.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 National Health and Environmental Effects Research Laboratory 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.
Return to Top