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EPAFHM: EPA Fathead Minnow Acute Toxicity
Database File

ogenic Potency Database Summary Tables - All Species

** Version 4b, updated 15 February 2008:
Includes 2 new summary activity fields (ActivityOutcome, ActivityScore) to coordinate with PubChem EPAFHM Assay deposits.
Includes new InChIKey Standard Chemical Field.

Quick & Easy File Downloads: FTP Download Instructions

blue bullet graphic Description
blue bullet graphic Source Website & Contact
blue bullet graphic Main Citation
blue bullet graphic Guidance for Use
blue bullet graphic Version 4 Update
blue bullet graphic SDF Fields
blue bullet graphic SDF Content Summary

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 EPA Fathead Minnow Acute Toxicity database was generated by the U.S. EPA Mid-Continental Ecology Division (MED) for the purpose of developing an expert system to predict acute toxicity from chemical structure based on mode of action considerations. Hence, an important and unusual characteristic of this toxicity database is that the 617 tested industrial organic chemicals were expressly chosen to serve as a useful training set for development of predictive quantitative structure-activity relationships (QSARs). A second valuable aspect of this database, from a QSAR modeling perspective, is the inclusion of general mode-of-action (MOA) classifications of acute toxicity response for individual chemicals derived from study results. These MOA assignments are biologically based classifications, allowing definition of chemical similarity based upon biological activity instead of organic chemistry functional class as most commonly employed in QSAR study. MOA classifications should strengthen the scientific basis for construction of individual QSARs. However, it is cautioned that the broad MOA categorizations should not be construed to represent a single molecular mechanism; for example, CNS seizure agents and respiratory inhibitors are known to act through a variety of receptors. The DSSTox EPAFHM database includes information pertaining to organic chemical class assignments (ChemClass_FHM), acute toxicity in fathead minnow (LC50_mg), dose-response assessments (LC50_Ratio, ExcessToxicityIndex), behavioral assessments (FishBehaviorTest), joint toxicity MOA evaluations of mixtures (MOA_MixtureTest), and additional MOA evaluation of fish acute toxicity syndrome (FishAcuteToxSyndrome) in rainbow trout. All of these indicators, to the extent available, were considered in the determination of MOA and, additionally, were used to determine a level of confidence in the MOA assignment for each chemical (MOA_Confidence).

The EPA Fathead Minnow database and results have been used by EPA MED to build components of the ASTER prediction system, which incorporates MOA-based QSARs for the prediction of aquatic toxicity of environmental and industrial chemicals. Briefly, MOA classifications for individual chemicals, derived from experiments and provided in the EPA Fathead Minnow database, were used to derive substructural rules for assigning a new chemical to an MOA category based solely on chemical structure. Once a new chemical is assigned to an MOA category on this basis, the logP-based QSAR for that MOA category is applied. ASTER is currently accessible only to EPA and government users [for information on use see http://www.epa.gov/med/prods_pubs.htm]; however the EPAFHM Main Citation listed below (Russom et al., 1997) provides details of the expert system construction, including QSARs and a table describing the substructural fragments associated with MOA categories.

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Source Website: http://www.epa.gov/med/Prods_Pubs/fathead_minnow.htm

Source Contact: Scientific questions pertaining to this database should be directed to Chris Russom, Mid-continent Ecology Division, National Health & Environmental Effects Research Laboratory, US EPA, Duluth, MN; email: russom.chris@epa.gov

 

Main Citation: Publications reporting use of DSSTox data files for the EPA Fathead Minnow database are asked to list the full DSSTox file name(s), including date stamp, and to cite as primary reference the following:

Russom, C.L., S.P. Bradbury, S.J. Broderius, D.E. Hammermeister, and R.A. Drummond (1997) Predicting modes of action from chemical structure: Acute toxicity in the fathead minnow (Pimephales promelas). Environmental Toxicology and Chemistry, 16(5): 948-967.

pdf document icon Download PDF (PDF, 20 pp, 360 KB)
Posted with the permission of Environmental Toxicology and Chemistry (ET&C) and the Society of Environmental Toxciology and Chemistry (SETAC). Copyright SETAC, Pensacola, Florida, USA (http://www.setac.org/ exit EPA). Standard personal-use copy restrictions apply.

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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Guidance for Use: The EPA Fathead Minnow database provided here could be used to reexamine existing QSARs, to explore new SAR or QSAR associations within MOA or chemical classes, or to explore associations of the fathead minnow results with other types of toxicity endpoints and systems. A user of these DSSTox EPAFHM SDF files is encouraged to consult the Main Citation provided here as a pdf (Russom et al., 1997). In addition, the EPAFHM Field Definition file offered below contains extended definitions of each field provided in the DSSTox EPAFHM SDF files, abstracted from Russom et al., 1997 and reviewed by the main author of that study. A number of modifications in fields (and their allowable contents) were made to the original EPA Fathead Minnow database to improve consistency in notations, eliminate the need for table addendums, provide geometric mean LC50 values when replicate experiments were performed, and facilitate use of the DSSTox SDF file in relational searching applications. The EPAFHM Field Definition File provides essential documentation and should be downloaded with, and accompany any use of the DSSTox EPAFHM SDF file. The EPAFHM Log File provides database summary information (field, chemical counts, etc.) and a description of procedures and quality assurance checks used in SDF file creation. In addition, the Log File documents modifications incorporated into version/revision updates of the DSSTox EPAFHM SDF file.

To report errors in any EPAFHM 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.

Version 4 Update: EPAFHM_v4a has no new chemical records but has several minor QA corrections, field entry revisions, field changes, etc. Changes to DSSTox Standard Chemical Fields include new ID fields: DSSTox_RID, DSSTox_Generic_SID and DSSTox_FileID (replacing DSSTox_SID and DSSTox_ID_FileName - see More on Standard Chemical Fields). Also, entries in TestSubstance_Description field have been simplified. LC50_Ratio field has been converted to a pure numeric field, with field notes moved to LC50_Note field. Expanded text entries are provided for several Source-Specific fields (MLOGP, LC50_Note, MOA, MOA_MixtureTest, FishAcuteToxSyndrome, FishBehaviorTest). For more information and version history, consult the EPAFHM_LogFile in the Download Table below.

Version 4b Update: EPAFHM_v4b includes minor structure changes/modifications and two new summary activity fields for use in PubChem and structure-activity relationship studies: ActivityOutcome_EPAFHM (entries of active, inactive, or inconclusive) and ActivityScore_EPAFHM (INTEGER[0-100]). In addition, the MOA_Confidence field has expanded text entries, and 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.

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

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EPAFHM SDF Fields (38 total)*

DSSTox Standard Chemical Fields(19) * STRUCTURE_InChIKey field added in v4b

DSSTox Standard Toxicity Fields (3)

ChemClass_FHM
CLOGP
MLOGP
LC50_mg
LC50_mmol
ActivityOutcome_EPAFHM *new to v4b
ActivityScore_EPAFHM *new to v4b
LC50_Ratio
LC50_Note
MOA
MOA_Confidence
MOA_MixtureTest
ExcessToxicityIndex
FishAcuteToxSyndrome
FishBehaviorTest
Note_EPAFHM

* Note: For detailed information on SDF content, see EPAFHM_FieldDefinitionFile in Download Table below.

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EPAFHM SDF Content Summary - 15 February 2008

EPAFHM SDF Content
Totals_v3b Totals_v4a Totals_v4b
# Records
617
617
617
DSSTox Standard Chemical Fields
18
18
19
DSSTox Standard Toxicity Fields
3
3
3
EPAFHM Source Fields
13
14
16
Total # Fields
34
35
38
Chemical Content
Counts_v3b Counts_v4a Counts_v4b
     
defined organic
613
613
613
inorganic
1
1
1
organometallic
3
3
3
no structure
0
0
0
STRUCTURE_TestedForm_
DefinedOrganic
:
     
parent
591
591
591
complex
11
11
11
salt
13
13
13
salt complex
2
2
2
TestSubstance_Description:
single chemical compound
610
609
609
defined mixture or formulation
7
* (NA)
* (NA)
undefined mixture
0
* (NA)
* (NA)
macromolecule
0
0
0
mixture or formulation
* (NA)
8
8

* (NA) = field entry not applicable for DSSTox file version indicated

Note: For SDF content summary information on previous versions of EPAFHM, view EPAFHM_LogFile in 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. 10.01, 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

Log File  
37KB
pdf document icon
Field Definition File  
54KB
pdf document icon
   
133KB
ms word document icon
Data Files: EPAFHM
SDF Structure Data File  
*.zip
1.2MB
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. 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

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Acknowledgements: The original DSSTox SDF file for the EPA Fathead Minnow database 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), and Ann Richard (EPA). A special debt of gratitude is owed to Chris Russom for collaboration and involvement throughout this initial DSSTox project phase, for careful review of all documentation pertaining to the EPAFHM on this website, and for numerous clarifications and suggestions for improvements to this documentation. Thanks to Patricia Schmieder and Stephen Nesnow for review of all documentation and helpful suggestions, and Patricia de Cerqueira Lima for alerting us to differences in the way that LC50 values were reported for cases with replicate experiments in the original EPA Fathead Minnow database vs the Main Citation. For version 2a, we thank Chris Hardy (LHASA Limited, UK) for alerting us to invalid CAS for several records (placeholders added by the Source) and providing the correct CAS for these listings. All subsequent QA review and structure modifications to EPAFHM_v2 and later versions were carried out by Maritja Wolf (Lockheed Martin, Contractor for EPA).

DSSTox Citation: Russom C.L., C.R. Williams, T.W. Stewart, A.E. Swank, and A.M. Richard (2008) DSSTox EPA Fathead Minnow Acute Toxicity Database (EPAFHM): SDF Files and Documentation, Updated version: EPAFHM_v4b_617_15Feb2008, www.epa.gov/ncct/dsstox/sdf_epafhm.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.

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