| CAS |
Refers to Chemical Abstracts Service Registry Number (http://www.cas.org/  ),
a numerical index for chemical substances that has the general format
000000-00-0. CAS registry numbers, along with the chemical name,
are the most commonly used chemical identifiers employed in public
chemical lists and toxicity databases. The last digit of a CAS No.
represents an error-check code that can be used to verify that the
CAS number is valid. DSSTox files employ strict CAS No. formatting
and error-check codes are verified as a quality control measure. See TestSubstance_CASRN for more information on how CAS are incorporated into DSSTox Data Files.
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| CRD |
A Chemical Relational Database (CRD) application is a specialized
relational database application that imports and exports standard
format SDF files, and that includes both a graphical chemical structure
field in addition to data and text fields. CRDs generally have chemically
intelligent structure-searching functions that allow a user to search
records using generalized structure queries (e.g., based on atoms,
atom and bond type, structural fragments, etc) in addition to searching
across data and text fields. DSSTox does not provide an on-line
CRD capability for searching DSSTox SDF files, but provides information
on a variety of commercial and public CRD application options available
to users.
More on CRDs
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DSSTox
File Name
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Each DSSTox SDF file has a unique file name of the general form:
NAMEID_v1a_#records_ddMmmyy.sdf
The name format adheres to DSSTox standard convention for communicating
the Source NAMEID (e.g., CPDBAS, EPAFHM), version/revision number
(1,2,3/a,b,c, etc.), total number of database records (e.g., 543),
date stamp of file creation (e.g., 10Apr2006), and file type extension
(.sdf). All or part of the DSSTox File Name is used
to name all documentation and data files associated with the main
SDF file(s).
More on DSSTox
File Names
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| DOP File |
The Defined Organic Parent (DOP) file is a specialized SDF file
created for use in Structure-Activity Relationship (SAR) studies.
This file contains only defined organic structures (i.e., no inorganics,
organometallics, or mixtures or unknowns), and is created when the
main SDF file contains chemicals that were tested and are represented
in either salt or complex form. This DOP file represents structures
in their simplified parent form, but otherwise mirrors the content
of the main SDF file and retains information on the tested form
of each chemical. Discontinued 1Mar05. |
| DOP3D File |
This file is identical to the corresponding DOP file, with the
exception of the modified DSSTox_FileName field entry and the Structure
field entry, which in the DOP file contains a two dimensional structure
and in the DOP3D file contains a three dimensional structure. Discontinued 1Mar05. |
| Field
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A field is a delimited sub-section of a CRD file record that can store structural, textual, or numerical information relative to that record. Typically, the structure field is unique in its capacity to store a chemical structure representation, whereas data fields can store numerical or textual data.
More on CRDs |
| FTP |
FTP stands for "File Transfer Protocol" and is a convenient and efficient means for transferring and downloading large data files from the web from a publicly accessible website. Anonymous FTP refers to public FTP access to posted files, where no password or account is needed to access and download files.
FTP Download Instructions |
| InChI |
InChI codes are an XML-based text coding system for chemical structures developed as a collaboration between NIST researchers and IUPAC. InChI codes are unique and capable of representing detailed and nuanced features of chemical structures for robust chemical structure representation. InChI is a public effort and tools for both the generation of InChI codes and the generation of structures from InChI codes are available in the public domain.
More on InChI
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| Log File
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Each DSSTox database (or group of
DSSTox data files sharing the same NAMEID) has a corresponding Log
File, located on the Source SDF Download Page, that documents modifications
or additions to the original DSSTox SDF file(s) leading to subsequent
version and revision updates. In addition, the Log File contains
notes concerning the DSSTox SDF file(s) creation, quality assurance
procedures, and summary counts within chemical data categories.
A single Log File is maintained for DSSTox NAMEID and corresponding
SDF files and all subsequent modifications to those files. See Templates & Sample Files
 View Sample DSSTox Log File
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| Record |
A CRD or SDF file consists of a number of records, usually one
record per chemical structure or experiment. A record typically
consists of a single structure field, followed by a number of data
fields containing numerical and/or textual data pertaining to that
structure. The total number of records in a CRD typically corresponds
to the number of chemical structure entries in the database, although
it is possible for the same structure to be replicated in multiple
records, e.g. corresponding to different experiments of the same
chemical, or different tested forms of the same chemical.
More on CRDs
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| SDF |
SDF stands for Structure Data Format, a standardized textual data
file format developed by MDL, Inc. that is a de facto industry standard
for structure and data import/export in Chemical Relational Database
(CRD) applications. An SDF file stores a chemical structure as a
table of atomic coordinates, bond connections, and bond types, followed
by standard data/text fields associated with that structure. An
SDF file can be opened as a text file by word processing applications,
and is capable of storing an unlimited number of structure/data
records in the same file.
More on SDF
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| SMILES
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SMILES is a simplified chemical notation that allows a user to
represent a primarily 2D chemical structure in linear textual form
for easy entry into a computer application. SMILES notation is commonly
employed in QSAR (Quantitative Structure-Activity Relationship)
modeling applications and in software for prediction of chemical
properties and biological activities. See STRUCTURE_SMILES for more information on how CAS are incorporated into DSSTox Data Files.
More on SMILES
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| Source |
Refers to the person(s) or organization that is the primary author,
creator, and/or host of the data contained in a DSSTox database
or SDF file. The DSSTox Source is identified as the the Main Contact
for toxicity content-related questions or inquiries concerning a
DSSTox database, is generally the senior author of the Main Citation(s)
associated with that database, and is the first author on the DSSTox
citation for that database.
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| Source
SDF Download Page |
This is the main entry page into a
DSSTox database (or group of DSSTox data files sharing the same
NAMEID). It provides a brief description of the database and some
guidance for use, and lists the Main Contact, Main Citation(s),
DSSTox Citation, and Acknowledgements. On this page is a download
table listing the DSSTox SDF file(s) and all accompanying data and
documentation files.
See Templates & Sample Files |
| Standard
Chemical Fields |
Each DSSTox SDF file contains a standard set of chemical information
fields. These include fields for chemical structure, chemical name,
CAS No., SMILES, empirical formula, tested form, substance type,
etc. Such fields are intended to provide a unified chemical information
metric for searching across diverse toxicity databases.
More on DSSTox Standard
Chemical Fields
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| Standard Toxicity Fields
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Each DSSTox SDF file contains a set of standard toxicity information fields, the number of which varies depending on the toxicity content of the database. These include fields for toxicity endpoint, species, study type, etc. Such fields are intended to provide a unified toxicity information metric for searching across diverse toxicity databases.
More on DSSTox Standard Toxicity Fields
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| Source-Specific
Fields |
In DSSTox SDF files, these are data or text fields that are particular
to that DSSTox database, containing information pertaining to toxicity
or biological activity measures of the indicated chemical. These
are in contrast to the Standard Chemical Fields that pertain to
the chemical content of DSSTox databases and are common to all DSSTox
SDF files. All field names are centrally indexed in the DSSTox
Central Field Definition Table, with units of measure and allowable
values indicated.
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User
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This is YOU! or anyone who makes use
of the DSSTox Database Network to obtain information or download
DSSTox SDF files for their personal or corporate use. If you find
this capability useful, please consider publishing a database on
the DSSTox network or otherwise contributing to this community effort.
Support DSSTox Effort
How to Publish
a DSSTox Database
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CAS
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