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Computational Toxicology Research Program

More on Standard Toxicity Fields

DSSTox Standard Toxicity Fields are being incorporated into all DSSTox data files, where applicable. These provide an initial common set of toxicity information fields spanning diverse toxicity databases and, hence, they offer common search metrics to explore diverse toxicity information domains. This page provides a general overview of the objectives, definitions, and features of DSSTox standard toxicity fields.

Main Objectives:

small arrow bullet graphic To promote minimum standards for toxicity study annotation of public chemical toxicity databases
small arrow bullet graphic To provide toxicity field content that will facilitate text searching in conjunction with chemical structure searching across DSSTox SDF files
small arrow bullet graphic To coordinate with other on-going public efforts working to develop and promote use of controlled toxicity vocabularies and ontologies in order to facilitate cross-platform communication and relational database searching (see, e.g., the ToxML standardization effort)

DSSTox Standard Toxicity Fields as of 17February2009:

Future expansion of DSSTox Standard Toxicity Fields:

Note that additional fields, such as Sex, Tissue, Benchmark_Dose, etc. will be considered for addition to the current list as new DSSTox databases containing this information are created. The main criteria for incorporation of new DSSTox Standard Toxicity Fields is the general utility they provide in searching across the diverse content of DSSTox data files. Note that in all cases, standard toxicity field names and content are being coordinated with the public ToxML standardization effort. The latter effort is focused on providing detailed annotation of toxicity experiments and creation of a large sets of controlled vocabulary to describe these. In contrast, the present DSSTox effort has broader objectives. Most often, DSSTox data files are representing only summary toxicity information of use to the Structure-Activity Relationship (SAR) modeling community. In addition, DSSTox databases are typically developed to complement published literature studies or on-line existing databases and, hence, often must conform to existing data terminolgy. Within these competing objectives, however, we will coordinate toxicity vocabulary usage whereever possible with the ToxML standardization effort as we believe that this serves the larger, long-term interests of the modeling and SAR community.

 

Field Name
Allowable Values
Description
Comments
StudyType

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defined text

CPDBAS: Carcinogenicity
DBPCAN: SAR prediction
EPAFHM: Acute Toxicity
FDAMDD: Clinical Reports
NCTRER: Receptor Binding
IRISTR: Human Health Exposure Toxicity Review for Risk Assessment
ARYEXP: microarray
GEOGSE: microarray

Field is used to label all records in the database, generally with the same entry, and is designed to facilitate record identification for cross-database structure searching. Field entry refers to the main type of toxicity study for which data is represented in the database. Field names and content are being coordinated with the public ToxML standardization effort.

Abbreviations in field entries eliminated (June 2007).
Endpoint
 
defined text

CPDBAS
: TD50, Tumor Target Sites
DBPCAN: Carcinogenicity
EPAFHM: LC50
FDAMDD: Maximum Recommended Daily Dose
NCTRER: Estrogen Receptor Relative Binding Affinity
IRISTR: cancer; acute; short-term; sub-chronic; chronic; developmental
Field is used to label all records in the database, generally with the same entry, and is designed to facilitate record identification for cross-database structure searching. Field entry refers to the type of toxicity measure represented within the database. Abbreviations are defined on the main information page for the respective databases and in the corresponding Field Definition File. Field names and content are being coordinated with the public ToxML standardization effort.

Abbreviations in field entries eliminated (June 2007).
Species  

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defined text

CPDBAS
: rat, mouse, hamster, dog, rhesus, cynomolgus, tree shrew, bush baby
DBPCAN:
EPAFHM: fathead minnow
FDAMDD: human
NCTRER: rat
IRISTR: rodent, human, dog, rabbit
Field is used to label all records in the database, generally with the same entry, and is designed to facilitate record identification for cross-database structure searching.

Field entry refers to the species of animal(s) listed in the data file (IRISTR) or record (CPDBAS) and used in the toxicity study or studies. Field is not included in database if the study did not use animals or animal-derived assays, such as a study reporting only SAR predictions (see, e.g., DBPCAN).

Field names and content are being coordinated with the public ToxML standardization effort.
Assay_Target  

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defined text

KIERBL: Rat uterine cytosol (RUC) estrogen receptor (ER)
Field is used to label all records in the database, generally with the same entry, and is designed to facilitate record identification for cross-database structure searching.

Field entry refers to the assay target (tissue and receptor) in the case of receptor-based assays and is intended provide assay-specific annotation for resources such as EPA ACToR and PubChem exit EPA. Field is not included in database if the study did not involve a target receptor-based assay.

Field names and content are being coordinated with the public EPA ACToR and ToxML standardization efforts.

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