Jump to main content or area navigation.

Contact Us

Computational Toxicology Research Program

DSSTox Glossary

red triangle bullet graphic CAS
red triangle bullet graphic CRD
red triangle bullet graphic DSSTox File Name
red triangle bullet graphic DOP File
red triangle bullet graphic DOP3D File
red triangle bullet graphic InChI
red triangle bullet graphic Field
red triangle bullet graphic FTP
red triangle bullet graphic Log File
red triangle bullet graphic Record
red triangle bullet graphic SDF
red triangle bullet graphic SMILES
red triangle bullet graphic Source
red triangle bullet graphic Source SDF Download Page
red triangle bullet graphic Standard Chemical Fields
red triangle bullet graphic Standard Toxicity Fields
red triangle bullet graphic Source-Specific Fields
red triangle bullet graphic User

 

CAS Refers to Chemical Abstracts Service Registry Number (http://www.cas.org/ exit EPA), 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.
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
DSSTox File Name  
Back to top list.Return to Top
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
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

Back to top list.Return to Top

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
Log File

Back to top list.Return to Top

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

ms word document icon View Sample DSSTox Log File
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
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
SMILES

Back to top list.Return to Top

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
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.
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
Standard Toxicity Fields

Back to top list.Return to Top

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
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.
User  

Back to top list.
Return to Top
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

Jump to main content.