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Welcome to the ChemoTyper
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 (Ashby, J.; Tennant, R.W., 1988), cancer TTC categories (Kroes, R. et. al. 2004).
Publications about ToxPrint chemotypes, CSRML language, and ChemTyper application
Download the ChemoTyper
ChemoTyper is available for download for registered users.
Please login if you have already an account or register.
The CSRML Reference 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. The CSRML standard is targeted to:
- provide an universal platform of specifying the advanced substructure queries,
- aid the developers to create GUI-based editors to input substructure queries in CSRML format,
- support the community and allow the easy exchangeability of the substructure queries between different programs and databases, and
- encourage the developers to create and distribute the CSRML extensions and software.
Aside the standard XML Schema Definition that establishes the CSRML data structure and XML syntax, an open-source LGPL-licensed reference library that provides the generic I/O functionality for the CSRML documents has been implemented. The reference library implementation contains modules to:
- read and parse CSRML documents resulting in the programmatic objects representing the CSRML elements
- write CSRML objects, e.g., into a file
- 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
Both the XML Schema Definition of CSRML, and the source code of the CSRML reference implementation are released under the GNU Lesser General Public License Version 2.1 and can be downloaded free-of-charge.
Download the Reference Implementation
The source code of the CSRML reference implementation is available for download for registered users.
Please login if you have already an account or register.
Contact
In technical support issues please contact us through: info (at) chemotyper.org
Acknowledgement
The ChemoTyper application was developed by Molecular Networks GmbH, Erlangen, Germany 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, Columbus, OH, USA.
Visit the website of Molecular Networks GmbH and Altamira LLC.