Changes between Version 4 and Version 5 of WikiStart

11/14/13 20:27:10 (9 years ago)



  • WikiStart

    v4 v5  
    1 = Welcome to the !ChemoTyper Development Wiki = 
     1= Welcome to ChemoTyper = 
    3 Front page to be written. 
     3The 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. 
     5* Searching for structural alerts for toxicity in chemical structure files 
     6* Filtering of chemical structures according to chemotypes 
     7* Visualization and inspection of chemotypes 
     8* Grouping of chemicals according to chemotypes, and 
     9* Fingerprinting of chemical structure sets against chemotypes 
     11ChemoTyper 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). 
     13ChemoTyper can be downloaded free-of-charge for public use. 
     15Link: Download ChemoTyper application (Windows XP/Vista/7) 
     17== CSRML Reference Library Implementation == 
     19The 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. 
     20CSRML 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 
     21* to read and parse CSRML documents resulting in the programmatic objects representing the CSRML elements, 
     22* to write CSRML objects, e.g., into a file, and 
     23* 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. 
     25The CSRML standard is targeted 
     26* to provide an universal platform of specifying the advanced substructure queries, 
     27* to aid the developers to create GUI-based editors to input substructure queries in CSRML format, 
     28* to support the community and allow the easy exchangeability of the substructure queries between different programs and databases, and 
     29* to encourage the developers to create and distribute the CSRML extensions and software. 
     31The CSRML reference library implementation can be downloaded free-of-charge for public use. 
     33Link: Download CSRML reference library implementation (Windows ZIP file) 
     35== Acknowledgement == 
     36The 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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