Version 8 (modified by thomas, 9 years ago) (diff)


Welcome to the ChemoTyper application

The ChemoTyper application is a tool that allows for searching and highlighting chemical chemotypes (chemical substructures or subgraphs) in datasets of molecules. Typical applications are as following.

  • Searching for structural alerts for toxicity in chemical structure files
  • Filtering of chemical structures according to chemotypes
  • Visualization and inspection of chemotypes
  • Grouping of chemicals according to chemotypes, and
  • Fingerprinting of chemical structure sets against chemotypes

ChemoTyper includes ToxPrint. ToxPrint is a public set of chemotypes developed by Altamira LLC for FDA CFSAN’s CERES project. The ToxPrint contains three basic subsets: generic structural fragments, Ashby-Tennant genotoxic carcinogen rules (1989), cancer TTC categories (Kroes et. al. 2004).

ChemoTyper can be downloaded free-of-charge for public use.

Link: Download ChemoTyper application (Windows XP/Vista/7)

CSRML Reference Library Implementation

The Chemical Subgraphs & Reactions Mark-up Language – CSRML – is a chemical XML language seen as a universal media describing the chemical (sub)structures and its query attributes, as well as the reactions and the transformations' rules. CSRML provides an open-source LGPL-licensed reference library that provides the generic I/O functionality for the CSRML documents. The reference library implementation includes modules

  • to read and parse CSRML documents resulting in the programmatic objects representing the CSRML elements,
  • to write CSRML objects, e.g., into a file, and
  • to validate CSRML content at the basic level, e.g., for checking syntax and semantic features against the language definition expressed by an XML Schema document.

The CSRML standard is targeted

  • to provide an universal platform of specifying the advanced substructure queries,
  • to aid the developers to create GUI-based editors to input substructure queries in CSRML format,
  • to support the community and allow the easy exchangeability of the substructure queries between different programs and databases, and
  • to encourage the developers to create and distribute the CSRML extensions and software.

The CSRML reference library implementation can be downloaded free-of-charge for public use.

Link: Download CSRML reference library implementation (Windows ZIP file)


The ChemoTyper application was developed under a contract from the U.S. FDA, Center for Food Safety and Applied Nutrition (CFSAN), Office of Food Additive Safety. The XML-based substructure (or chemotype) definition language CSRML was co-developed in collaboration with Altamira LLC.

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