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PROPOSED STANDARD TO GREATLY EXPAND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT
Citation:
Williams, C. R. AND A M. Richard. PROPOSED STANDARD TO GREATLY EXPAND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT. Presented at Annual Biomedical Research Conference for Minority Students, Orlando, Florida, 10/29/01 thru 11/02/01.
Description:
PROPOSED ST ANDARD TO GREA TL Y EXP AND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT
The ability to assess the potential toxicity of environmental, pharmaceutical, or industrial chemicals based on chemical structure information is a shared goal of academic, commercial, and government regulatory concerns. Whereas these diverse interests often have different requirements for toxicity assessment, what they share is a need for broad, unrestricted access to existing public toxicity data linked with chemical structure information. The problem, however, is that public sources of toxicity data span diverse toxicity disciplines (e.g. ecotox, cancer, developmental tox), exist in many locations and in many different formats, and most often do not contain chemical structure information. Hence, current sources of toxicity information fail to address the needs of the research and regulatory communities to have flexible and unrestricted structure-searchable access to public toxicity data for use in toxicity screening, model development, or incorporation into chemical toxicity databases. The current project involves development of a distributed structure-searchable public toxicity database network that will enable free public access to toxicity data files, and effectively link knowledgeable toxicity data sources with potential users of this data from other disciplines (such as chemistry , modeling, and computer science). A key requirement of the project was to identify a suitable and universal format for data representation and exchange. After evaluation of various alternative data mining tools and formats a common, standard structure-data file (SDF) format was identified. SDF is a simple text-based format for storing structure and text information that is already being used as an industry standard for exchanging data between chemical relational databases. However, we have found many instances where application vendors have inadvertently corrupted the SDF standard in their exporting functions. The present research is exploring efficient means for generating and distributing SDF files of public toxicity data, as well as identifying and offering feasible solutions for maintaining the integrity of SDF as a standard file format.
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