Changes between Version 4 and Version 5 of WikiStart


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Timestamp:
11/14/13 20:27:10 (9 years ago)
Author:
thomas
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  • WikiStart

    v4 v5  
    1 = Welcome to the !ChemoTyper Development Wiki = 
     1= Welcome to ChemoTyper = 
    22 
    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. 
     4 
     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 
     10 
     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). 
     12 
     13ChemoTyper can be downloaded free-of-charge for public use. 
     14 
     15Link: Download ChemoTyper application (Windows XP/Vista/7) 
     16 
     17== CSRML Reference Library Implementation == 
     18 
     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. 
     24 
     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. 
     30 
     31The CSRML reference library implementation can be downloaded free-of-charge for public use. 
     32 
     33Link: Download CSRML reference library implementation (Windows ZIP file) 
     34 
     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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