![[logo] US EPA](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 represent one of many possible summarizations of the data in the CPDB. The CPDB includes detailed results and analyses of more than 5000 chronic, long-term carcinogenesis bioassays reported in over 1200 papers in the general literature and more than 400 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 and the calculated statistical significance of the tumorigenic dose response in the experiment. Nearly 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, the strongest level of evidence for carcinogenicity based on the opinion of a published author, carcinogenic potency value (TD50), and target organs in each species tested. 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. Summary evaluations of mutagenicity in Salmonella (positive or negative) are also reported. CPDB Summary Table results are provided for rats and 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 CPDB, 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 CPDB 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
reference the following 4 citations: http://potency.berkeley.edu/
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 L. Rohrbach (1999) Supplement to the Carcinogenic Potency Database (CPDB): Results of animal bioassays published in the general literature in 1993 to 1994 and by the National Toxicology Program in 1995 to 1996. Environ. Health Perspect., 107 (Suppl. 4): 527-600. http://ehpnet1.niehs.nih.gov/docs/1999/suppl-4/toc.html
Summary Table of Chemicals in the Carcinogenic Potency Database: Results for Positivity, Potency (TD50), and Target Sites: http://potency.berkeley.edu/chemicalsummary.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 Gold et al., 1997 (see Main
Citations above) as to inclusion criteria, protocol characteristics, and
derived variables. 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 listed 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 newly published data in the CPDB Summary Tables posted on the CPDB Source website . Since no easy mechanism is provided by the CPDB Source to locate newly added chemical records or experimental results, we were forced to undertake a side-by-side comparison of the newly published Summary Table records with the previously published Summary Table from which CPDBAS_v4a was constructed. Numerous manual checks in content and entered values in the CPDBAS_v5b file were undertaken to ensure accuracy of transcription of experimental results. DSSTox Standard Chemical Fields for the 66 new chemical records were either extracted from (if previously existing), or added to (if not previously existing) the most recent DSSTox Master File according to current Chemical Information Quality Review Procedures. 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 original 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. A table indicating total numbers of records in the various activity categories is provided below for CPDBAS_v5 and later. In particular, note that when the ActivityOutcome_CPDBAS_MultiCellCall has an "active" entry, the largest number of incidences occurs for the ActivityOutcome_CPDBAS_MultiCellCall_Details entry "multisite; multisex; multispecies" (193 incidences). Similarly, when the ActivityOutcome_CPDBAS_MultiCellCall has an "inactive" entry, the largest number of incidences occurs for theActivityOutcome_CPDBAS_MultiCellCall_Details entry "multisite; multispecies" (288 incidences). These two categories represent a more conservative, heaviily weighted carcinogenic activity than the ActivityOutcome_CPDBAS_SingleCellCall (806 actives vs. 738 inactives) that is more frequently employed to build structure-activity prediction models. A number of other conditions not shown in the below table are possible, including, e.g., all MultiCellCall actives for which multisex and multispecies conditions apply, irrespective of multisite categorization (37+193 incidences). These various options for considering carcinogenicity activity or inactivity should provide useful avenues for modelers to explore.
| ActivityCategory_ | ActivityCategory_MultiCellCall_Details** | |||||
|---|---|---|---|---|---|---|
Call |
SingleCellCall | MultiCellCall** | multisite*** | multisex | multispecies | Total Incidences* (CPDBAS_v5) |
Active (1) |
active |
* |
. |
. |
. |
223 |
active |
active |
 |
. |
. |
81 |
|
active |
active |
. |
|
. |
113 |
|
active |
active |
. |
. |
|
8 |
|
active |
active |
|
|
. |
123 |
|
active |
active |
|
. |
|
27 |
|
active |
active |
. |
|
|
37 |
|
active |
active |
|
|
|
193 |
|
active |
active |
Total MultiCellCall Incidences (active/active) |
582 |
|||
Inactive (0) |
inactive |
. |
|
. |
. |
169 |
inactive |
inactive |
|
|
. |
266 |
|
inactive |
inactive |
|
. |
|
16 |
|
inactive |
inactive |
. |
|
|
288 |
|
inactive |
inactive |
Total MultiCellCall Incidences (inactive/inactive) |
570 |
|||
* SingleCell and MultiCell Calls total 1544, or 3 short of the CPDBAS_v5 inventory of 1547 total records; for 3 records in CPDBAS_v5, calls were not provided due to "NTP bioassay inadequate".
** A blank cell in the above table indicates a negative condition, i.e. condition not met. For example, in the third row of results, the multisex condition applies but NOT multisite or multispecies, i.e., a single tumor site is observed exclusively in both sexes of the same species.
*** For any Sex/Species (e.g., Male/Rat) experiment in CPDB that reports an "inactive" (negative) call, multisite inactive is implied.
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 field listing below). These include ActivityOutcome_CPDBAS_,,, fields (entries of active, inactive, or inconclusive) for Mutagenicity, SingleCellCall, MultiCellCall, Rat, Mouse, Hamster, and Dog_Primates, and ActivityScore_CPDBAS_... fields [Log(1/TD50mmol) mapped onto 0-100 integer range] for Rat, Mouse, Hamster, and Dog_Primates. 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 reported in v5b but not implemented until v5c, and one correction to a record that incorrectly listed an inactive bioassay result for Mouse (but MultiCellCall was correct).
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 SDF Content Summary - 29 April 2008
CPDBAS SDF Content |
Totals_v3b | Totals_v4a | Totals_v5a | Totals_v5b,c |
|---|---|---|---|---|
# Records
|
1481
|
1481
|
1547
|
1547
|
DSSTox Standard Chemical Fields
|
18 |
18 |
18 |
19 |
DSSTox Standard Toxicity Fields
|
3 |
3 |
3 |
3 |
CPDBAS Source Fields
|
27 |
32 |
32 |
39 |
Total # Fields
|
48 |
53 |
53 |
61 |
Chemical Content |
Counts_v3b | Counts_v4a | Counts_v5a | Counts_v5b,c |
defined organic |
1344
|
1345
|
1404
|
1404
|
inorganic |
58 |
58 |
60 |
60 |
organometallic |
42 |
43 |
44 |
44 |
no structure |
37 |
35 |
39 |
39 |
| STRUCTURE_TestedForm_ DefinedOrganic: |
||||
parent |
1122
|
1123
|
1176
|
1176
|
complex |
151 |
151 |
155 |
155 |
salt |
74 |
74 |
73 |
73 |
salt complex |
3 |
3 |
3 |
3 |
| TestSubstance_Description: | ||||
single chemical compound |
1386
|
1380
|
1431
|
1431
|
defined mixture or formulation |
58 |
* (NA) |
* (NA) |
* (NA) |
undefined mixture |
27 |
* (NA) |
* (NA) |
* (NA) |
macromolecule |
10 |
14 |
16 |
16 |
mixture or formulation |
* (NA)
|
87
|
100
|
100
|
* (NA) = field entry not applicable for DSSTox file version indicated
Note: For SDF content summary information on previous versions of CPDBAS, view CPDBAS_LogFile in Download Table below.
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