DSSTox Log File:

EPA Fathead Minnow Acute Toxicity Database (EPAFHM)

*(last updated 15 June 2007)*

**Description:** Information in this file documents the creation,
review, and update process for the DSSTox EPAFHM SDF file and provides
summary information on database content. The first section summarizes
the process used for creating the initial DSSTox SDF files, and the
quality assurance checks and procedures employed. A table providing
field and data counts offers summary overview of EPAFHM file contents
and chemical composition. The Log Table documents modifications and
revisions to the database content or format in version updates. To
obtain the most current version of this Log File and a record of any new
modifications, a user should consult the DSSTox EPAFHM database page:
[http://www.epa.gov/ncct/dsstox/sdf_epafhm.html](http://www.epa.gov/nheerl/dsstox/sdf_epafhm.html)

**QA and Development Notes for v1a:**

EPAFHM SDF files underwent an extensive series of quality review checks
prior to publication of initial launch versions. The original EPA MED
Fathead Minnow database was obtained from the Source in dbf format,
imported into Excel, and was used for cross-referencing and checking of
all modified and added fields. We thank Chris Russom for invaluable
assistance in various stages of development and quality review,
clarifying numerous issues pertaining to the experimental data and their
representation in the original database, and approving all changes to
field names and contents. Chemical structures were initially obtained by
conversion of SMILES codes provided in the original database using
CambridgeSoft ChemOffice 2002 ChemDraw (ver 7.0 for Windows) for MS
Excel. The ChemFinder website (<http://chemfinder.cambridgesoft.com/>)
was used extensively for checking CAS-to-structures and for retrieving
CAS numbers for parent forms of salts and complexes. CambridgeSoft
ChemFinder (ver 7.0 for Windows) was also used for automatic generation
of SMILES codes from structures and both ChemFinder and ACD ChemFolder
(ver 6.0 for Windows) were employed for "Structure-to-Name" or
"Name-to-Structure" features. Original SMILES codes provided by the
Source were converted to ChemFinder-generated SMILES and verified within
the ChemFinder application.

**Notes for v2a:**

For version 2a, a variety of fields have been added. IUPAC systematic
chemical names, **ChemName_IUPAC**, were computed by Marc Nicklaus (NCI)
using the ACD Labs IUPAC Name-Generation software (ACD/NameBatch,
version 8.05). **INChI** codes were automatically generated from the
final DSSTox SDF using a pre-release version of the publicly available
program, wINChI11b.exe, accessible from the NIST INChI developers
(<http://chemdata.nist.gov/IChI/INChIv11b.zip>). We thank Chris Hardy
(Lhasa Limited, UK) for alerting us to the 14 invalid CAS provided in
the original EPAFHM Source database and DSSTox EPAFHM_v1a files, and
providing us with the correct CAS for these structures. These CAS were
originally unavailable to the Main Citation Source authors, so invalid
CAS placeholders were used.

**Notes for v3a,b:**

Revised DSSTox Standard Chemical Fields are included (see
[http://www.epa.gov/ncct/dsstox/MoreonStandardChemFields.html](http://www.epa.gov/nheerl/dsstox/MoreonStandardChemFields.html))
along with updated InChI codes (version 1.0), recomputed IUPAC chemical
names (ACDLabs ACD/Name, version 9.0), and many regenerated 2D
structures with stereochemistry of steroidal compounds rendered in more
standardized form. Many EPAFHM Source Toxicity Fields were also provided
more descriptive names and Chemical Names were converted to lower case
from all CAPS. Additionally, an extensive quality review of all DSSTox
chemical records was performed, resulting in numerous corrections and
modifications to chemical structures and added information (CASRN,
representative structures for mixtures, etc) throughout DSSTox data
files. For more information on current review procedures, see
[http://www.epa.gov/ncct/dsstox/ChemicalInfQAProcedures.html](http://www.epa.gov/nheerl/dsstox/StructureReviewProcedures.html)

**Notes for v4a:**

EPAFHM_v4 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
<http://www.epa.gov/ncct/dsstox/MoreonStandardChemFields.html>). 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**).

**Log of SDF Modifications and Version/revision updates:**

+-----+-----------------+-------------------------+------------------+
| **  | **DSSTox SDF    | **Modifications from    | **Additional     |
| Dat | File Names**    | previous version**      | Notes**          |
| e** |                 |                         |                  |
+-----+-----------------+-------------------------+------------------+
| # 1 | EPAFHM_         | Initial launch          | EPAFHM is        |
| 5Oc | v1a_617_15Oct03 | publication; no         | considered a     |
| t03 |                 | previous published      | "static"         |
|     | EPAFHM_DOP_     | versions.               | historical       |
|     | v1a_610_15Oct03 |                         | database meaning |
|     |                 |                         | that further     |
|     |                 |                         | expansion of the |
|     |                 |                         | database to      |
|     |                 |                         | include          |
|     |                 |                         | additional test  |
|     |                 |                         | data is          |
|     |                 |                         | unlikely. Future |
|     |                 |                         | updates will     |
|     |                 |                         | correct reported |
|     |                 |                         | errors provided  |
|     |                 |                         | by users or      |
|     |                 |                         | incorporate      |
|     |                 |                         | DSSTox format    |
|     |                 |                         | changes.         |
+-----+-----------------+-------------------------+------------------+
| 1Ma | EPAFHM          | New Fields: **INChI**,  | Major format     |
| r05 | _v2a_617_1Mar05 | *                       | modification to  |
|     |                 | *ChemName**\_**IUPAC**, | include INChI,   |
|     |                 | **StudyType**,          | IUPAC names, and |
|     |                 | **Species**,            | ToxML fields.    |
|     |                 | **Endpoint**            |                  |
|     |                 |                         | Separate         |
|     |                 | Corrected **CAS** for   | "desalted"       |
|     |                 | first 14 records        | defined organic  |
|     |                 | (**DSSTox_ID**=1-14).   | parent (DOP)     |
|     |                 |                         | file not         |
|     |                 | Corrected Structure for | provided. Users  |
|     |                 | **DSSTox_ID**=97        | can easily       |
|     |                 | (changed from penta to  | generate DOP     |
|     |                 | trichlorophenol).       | file by          |
|     |                 |                         | extracting       |
|     |                 | Addition of             | "defined         |
|     |                 | **SMILES_Parent** to    | organic" records |
|     |                 | Main file.              | and converting   |
|     |                 |                         | *                |
|     |                 | Moved 3                 | *SMILES_Parent** |
|     |                 | **S                     | to structures.   |
|     |                 | ubstanceType**="mixture |                  |
|     |                 | or unknown" records to  |                  |
|     |                 | end of file so that     |                  |
|     |                 | first 614 chemicals     |                  |
|     |                 | listed are those with   |                  |
|     |                 | structures.             |                  |
+-----+-----------------+-------------------------+------------------+
| 10A | EPAFHM_v3       | Updated with new DSSTox | Numerous         |
| pr2 | b_617_10Apr2006 | Standard Chemical       | structure        |
| 006 |                 | Fields and entries      | modifications    |
|     |                 | (*revised Aug 2005*).   | and changes in   |
|     |                 |                         | stereochemical   |
|     |                 | Updated InChI codes     | rendering        |
|     |                 | (version 1.0).          | throughout       |
|     |                 |                         | DSSTox data      |
|     |                 | Updated IUPAC chemical  | files following  |
|     |                 | names (ACDLabs Name to  | major quality    |
|     |                 | Structure, version      | review.          |
|     |                 | 9.0).                   |                  |
|     |                 |                         | EPAFHM_v3        |
|     |                 | Expanded "ddmmmyear"    | a_617_22Oct2005: |
|     |                 | format for dates in     |                  |
|     |                 | DSSTox file names       | Note: earlier    |
|     |                 | (e.g., 23Jan2006).      | version of this  |
|     |                 |                         | file was         |
|     |                 | Renamed Source-related  | provided to      |
|     |                 | fields to be more       | PubChem, with    |
|     |                 | descriptive:            | identical format |
|     |                 |                         | to v3b but       |
|     |                 | > **ChemClass FHM** to  | latter has       |
|     |                 | > **ChemClass_FHM**     | undergone        |
|     |                 | >                       | additional QA    |
|     |                 | > **LC50** to           | review and has   |
|     |                 | > **LC50_mg**           | small number of  |
|     |                 | >                       | correction       |
|     |                 | > **LC50NOTE** to       | s/modifications. |
|     |                 | > **LC50_Note**         |                  |
|     |                 | >                       |                  |
|     |                 | > **LC50RATIO** to      |                  |
|     |                 | > **LC50_Ratio**        |                  |
|     |                 | >                       |                  |
|     |                 | > **MOACONF** to        |                  |
|     |                 | > **MOA_Confidence**    |                  |
|     |                 | >                       |                  |
|     |                 | > **MIXMOA** to         |                  |
|     |                 | > **MOA_MixtureTest**   |                  |
|     |                 | >                       |                  |
|     |                 | > **TOXINDEX** to       |                  |
|     |                 | >                       |                  |
|     |                 | **ExcessToxicityIndex** |                  |
|     |                 | >                       |                  |
|     |                 | > **FATS** to           |                  |
|     |                 | > *                     |                  |
|     |                 | *FishAcuteToxSyndrome** |                  |
|     |                 | >                       |                  |
|     |                 | > **BEHAVIOR** to       |                  |
|     |                 | > **FishBehaviorTest**  |                  |
|     |                 |                         |                  |
|     |                 | Added new field         |                  |
|     |                 | **LC50_mmol**.          |                  |
|     |                 |                         |                  |
|     |                 | Corrected LC50 entries  |                  |
|     |                 | for ID 242              |                  |
|     |                 | Diethanolamine from EPA |                  |
|     |                 | Source.                 |                  |
+-----+-----------------+-------------------------+------------------+
| 15J | EPAFHM_v4       | Revised Standard        |                  |
| un2 | a_617_15Jun2007 | Fields:                 |                  |
| 007 |                 |                         |                  |
|     |                 | > **DSSTox_SID** has    |                  |
|     |                 | > been replaced by two  |                  |
|     |                 | > new ID fields         |                  |
|     |                 | > **DSSTox_RID** and    |                  |
|     |                 | >                       |                  |
|     |                 | **DSSTox_Generic_SID**. |                  |
|     |                 | >                       |                  |
|     |                 | >                       |                  |
|     |                 |  **DSSTox_ID_FileName** |                  |
|     |                 | > has been replaced by  |                  |
|     |                 | > new ID field:         |                  |
|     |                 | > **DSSTox_FileID**.    |                  |
|     |                 | >                       |                  |
|     |                 | > Entries in            |                  |
|     |                 | > **Test                |                  |
|     |                 | Substance_Description** |                  |
|     |                 | > field have been       |                  |
|     |                 | > simplified.           |                  |
|     |                 | >                       |                  |
|     |                 | > Entries in            |                  |
|     |                 | > **ChemicalNote** that |                  |
|     |                 | > pertained             |                  |
|     |                 | > specifically to       |                  |
|     |                 | > EPAFHM have been      |                  |
|     |                 | > moved to              |                  |
|     |                 | > Source-Specific       |                  |
|     |                 | > field:                |                  |
|     |                 | > **Note_EPAFHM**       |                  |
|     |                 |                         |                  |
|     |                 | **LC50_Ratio** field    |                  |
|     |                 | has been converted to a |                  |
|     |                 | pure numeric field,     |                  |
|     |                 | with field notes moved  |                  |
|     |                 | to **LC50_Note** field. |                  |
|     |                 |                         |                  |
|     |                 | Entries in several      |                  |
|     |                 | Source-Specific fields  |                  |
|     |                 | have been unabbreviated |                  |
|     |                 | or expanded:            |                  |
|     |                 |                         |                  |
|     |                 | **MLOGP**               |                  |
|     |                 |                         |                  |
|     |                 | **LC50_Note**           |                  |
|     |                 |                         |                  |
|     |                 | **MOA**                 |                  |
|     |                 |                         |                  |
|     |                 | **MOA_MixtureTest**     |                  |
|     |                 |                         |                  |
|     |                 | *                       |                  |
|     |                 | *FishAcuteToxSyndrome** |                  |
|     |                 |                         |                  |
|     |                 | **FishBehaviorTest**    |                  |
+-----+-----------------+-------------------------+------------------+
|     |                 |                         |                  |
+-----+-----------------+-------------------------+------------------+

**Field and Data Counts in Older Versions of DSSTox SDF files:**

<table style="width:100%;">
<colgroup>
<col style="width: 15%" />
<col style="width: 8%" />
<col style="width: 8%" />
<col style="width: 8%" />
<col style="width: 8%" />
<col style="width: 10%" />
<col style="width: 9%" />
<col style="width: 9%" />
<col style="width: 9%" />
<col style="width: 12%" />
</colgroup>
<tbody>
<tr class="odd">
<td rowspan="2"><strong>DSSTox SDF</strong></td>
<td rowspan="2"><strong>Standard Chemical Fields</strong></td>
<td rowspan="2"><strong>Standard Toxicity Fields</strong></td>
<td rowspan="2"><strong>Source-specific fields</strong></td>
<td rowspan="2"><p><strong>Chemical records</strong></p>
<p><strong>total</strong></p></td>
<td colspan="3"><strong>STRUCTURE_ChemicalType:</strong></td>
<td
colspan="2"><strong>STRUCTURE_TestedForm_DefinedOrganic:</strong></td>
</tr>
<tr class="even">
<td><strong>Defined Organic</strong></td>
<td><strong>Inorganic</strong></td>
<td><strong>Organo-metallic</strong></td>
<td><strong>Parent</strong></td>
<td><strong>Salt or complex</strong></td>
</tr>
<tr class="odd">
<td>EPAFHM_v1a</td>
<td>13</td>
<td>0</td>
<td>12</td>
<td>617*</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="even">
<td>EPAFHM_DOP_v1a</td>
<td>15</td>
<td>0</td>
<td>12</td>
<td>610</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td>EPAFHM_v2a</td>
<td>16</td>
<td>3</td>
<td>12</td>
<td>617*</td>
<td>610</td>
<td>1</td>
<td>3</td>
<td>589</td>
<td>15</td>
</tr>
</tbody>
</table>

\*One pair of replicate parent structures (salt or complex) and one pair
of replicate 2D structures (cis and trans) exist in the database.

  --------------------------------------------------------------------------------------------------------------------------------------------------- ---------------- ----------------
  **EPAFHM SDF Content**                                                                                                                              **Totals_v3b**   **Totals_v4a**

  \# Records                                                                                                                                          617              617

  DSSTox Standard Chemical Fields                                                                                                                     18               18

  DSSTox Standard Toxicity Fields                                                                                                                     3                3

  EPAFHM Source Fields                                                                                                                                13               14

  Total \# Fields                                                                                                                                     34               35

  **Chemical Content**                                                                                                                                Counts_v3b       **Counts_v4a**

  **STRUCTURE_ChemicalType**:                                                                                                                                           

  defined organic                                                                                                                                     613              613

  inorganic                                                                                                                                           1                1

  organometallic                                                                                                                                      3                3

  no structure                                                                                                                                        0                0

  **STRUCTURE_TestedForm\_[\                                                                                                                                            
  ]{.underline}DefinedOrganic**[:](../../../../../../../../D:%5Cdsstox_prodfiles_20May2006%5CStandardChemFieldDefTable.html#STRUCTURE_ChemicalType)                    

  parent                                                                                                                                              591              591

  complex                                                                                                                                             11               11

  salt                                                                                                                                                13               13

  salt complex                                                                                                                                        2                2

  **TestSubstance_Description:**                                                                                                                                       

  single chemical compound                                                                                                                            610              609

  defined mixture or formulation                                                                                                                      7                \* (NA)

  undefined mixture                                                                                                                                   0                \* (NA)

  macromolecule                                                                                                                                       0                0

  mixture or formulation                                                                                                                              \* (NA)          8
  --------------------------------------------------------------------------------------------------------------------------------------------------- ---------------- ----------------

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