OpenTox ToxPredict screencast

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• published: 16 May 2010
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Welcome to this OpenTox screencast, demonstrating and teaching some basic ToxPredict software features. ToxPredict (http://toxpredict.org/) estimates the chemical hazard of chemical structures. It relies on OpenTox API-v1.1 compliant RESTful webservices. Users can either search the OpenTox prototype database, which includes currently quality labelled data for thousands of REACH-relevant chemicals, grouped in datasets, or upload their own chemical structure data. ToxPredict provides access to 14 ready to use models, addressing 13 different endpoints. The ToxCreate sister application allows more advanced users to train new OpenTox models. In order to enter your ToxPredict workflow press the GO! Button. ToxPredicts Graphical User Interface includes three main areas: 1) A navigation bar at the top of the screen, which enables users to find their way through the application workflow; 2) The navigation bar is followed by a short contextual help section, providing specific details for the current step being executed; 3) And finally, an input/output section for specifying queries and displaying results is situated at the bottom of the screen. In the first step of your ToxPredict workflow you are invited to select the structure(s) for which you would like to apply some OpenTox model(s). The Search, Draw and Upload tabs provide different ways for structure selection: • Search: In the Search tab you can enter any free text, including but not limited to CAS registry number, EINECS number, SMILES, InChI, chemical name, or any other keyword; ToxPredict will automatically recognize the intended search type and return zero, one or more hits, depending on the search type, the information currently available in the OpenTox database and the selected preferred number of hits; • Draw: You can draw a chemical structure in the built-in editor and perform exact structure or substructure search, or structural similarity based search; ToxPredict will return zero, one or more hits, depending on the search type, the information currently available in the OpenTox database and the selected preferred number of hits; • Upload: You can upload your own dataset(s); ToxPredict accepts SDF, MOL, CSV and RDF input file formats, among many others. Once you have entered your query string, chemical structure drawing or file name for upload you should press NEXT to proceed to the following step of your ToxPredict workflow. For the sake of this presentation we will model the properties of a specific compound (2-(4-methylphenylpropanal), a flavour and fragrance agent) by drawing its structure in the structure diagram editor to define the query and proceed to the following step. In the second step you can browse the list of chemicals, which have been found to correspond to the query, defined in the first step. We can see the structure of the chemicals on the left hand side of the screen and some further details like CAS registry number, EINECS number, IUPAC name, synonyms and quality label. In case that you are satisfied with this list you can proceed to the following step by clicking the NEXT button. Otherwise you could go back to the first step of the workflow and define a different query. The following screen lists the available OpenTox models that could be selected for estimating various properties for each of the query chemicals along with the corresponding endpoints. In this case Ill select all available models and proceed to the following step. In this step the selected models are applied to all query chemicals and you can follow the processing progress, which is refreshed automatically every 30 seconds. You could also proceed with a manual refresh in order to check whether the processing has already been completed. After the processing has been completed, you can go to the last step of the ToxPredict workflow to get the detailed results for the selected models and compounds, displayed in a web page and also available for download as a SDF file, which is convenient for further automatic processing. As you can see in the results section, 2 alerts for carcinogenicity and mutagenicity are raised for 2-(4-methylphenylpropanal), according to the ToxTree: Benigni/Bossa rules for carcinogenicity and mutagenicity. Furthermore, the Cramer rules model indicates that the chemical falls in Class I (these are substances with simple chemical structures and for which efficient modes of metabolism exist, suggesting a low order of oral toxicity). According to the ToxTree: Skin irritation model the compound is either irritating or corrosive to skin. And finally, an alert for Schiff base formation is identified, which means that theoretically this chemical can be skin sensitizer. We could conclude this analysis by making the observation that this substance might need some further investigation, because several models indicate that it might be potentially hazardous. Thank you for your attention!