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Course contents

Navigating the OECD QSAR ToolBox

  • For:
    Scientists fully familiar with the concepts and theory of (Q)SAR and read-across
  • Content:
    22 hours of lectures, how-to software guides, software demonstrations and case studies
  • Homework:
    12 quizzes and 19 home assignments using the Toolbox
    • Language:
      English with optional subtitles in French, Spanish, German and Italian
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    Here is what we have covered in
    this course

    This course covers the use of the modules found in the OECD QSAR Toolbox.
    Suitable for scientists who already have a good understanding of the theory of QSAR and read-across.

    If you need learn more about the theory and other useful free software tools, please first complete the
    "    NAMs - Use and application of QSAR and read-across" course before signing up to this course.

    Session 1:
    Introduction to the OECD QSAR ToolBox

    Seminal features of the ToolBox
    Management and development of the ToolBox
    The three interfaces of the ToolBox
    How a general category approach framework is mapped onto the ToolBox category approach workflow

    Learning outcome:
    After the session, the students should be able to understand the use of the ToolBox modules, how each module is related to a specific step in the chemical hazard assessment workflow and in a category approach framework.

    Session 2:
    Input Module

    Overview of the module
    Quality assessment: reliability of the CAS/SMILES relation
    Verify the target identity
    The target identity in the ECHA REACH database

    Software demonstration
    • Input a target chemical
    • Input a list of chemicals
    • Define the target endpoint


    Learning outcome:
    After the session, the students should be able to use the ToolBox Input Module to accomplish some practical tasks such as to input a target chemical, to verify its identity, to input a list of chemicals and to define the target toxicological endpoint.

    Session 3:
    Profiling Module


    Overview of the module

    Groups of profiling schemes: predefined, general mechanistic, endpoint specific, empiric, toxicological and custom
    Documented and simulated metabolism / transformation
    How to choose the relevant profilers

    Software demonstration
    • Profiling chemicals for genotoxicity and skin sensitization


    Learning outcome:
    After the session, the students should be able to understand and use the different types of profiling schemes and with this knowledge, accomplish practical tasks.

    Session 4:
    Data Module

    Overview of the module

    Definition of database versus definition of inventory

    How to choose the relevant databases


    Software demonstration

    • Search the databases with the classical interface
    • Search the databases with the simplified user interface
    • Import a custom database - Vertical import
    • Import a custom database - Horizontal import


    Learning outcome:
    After the session, the students should be able to use the ToolBox Data Module to accomplish some practical tasks such as to collect data from public databases using the classical and the simplified user interface and to create your own custom database.



    Session 5:
    Category Definition Module

    Overview of the module
    Strategies to identify analogues
    How to apply the strategies to identify analogues using the ToolBox profilers
    Evaluation of the analogues in the ToolBox


    Learning outcome:
    After the session, the students should be able to understand the use of the ToolBox Category Definition Module to identify analogues and which are the main sources of uncertainty in read-across that can be addressed by the ToolBox.


    Session 6:
    Data Gap Filling Module

    Overview of the module

    Approaches to predict a missing value for the target chemical

    Software demonstration
    • Read-across: qualitative assessment of the skin sensitisation potential of CAS 3814-55-9
    • Trend analysis: acute aquatic toxicity of CAS 626-89-1

    Learning outcomes:
    After the session, the students should be able to use the ToolBox modules to generate a read-across or a trend analysis prediction accomplishing some basic practical tasks such as to input a target chemical, to define the target toxicological endpoint, to use the profilers to gain knowledge on the mechanism of action of your chemical, to generate an overarching similarity hypothesis, to identify and analyse analogues according to the generated hypothesis, to fill the data gap.

    Session 7:
    Report Module

    Overview of the Module
    Overview of the Report Wizard


    Software demonstration
    • Generate a report

    Learning outcome:

    After the session, the students should be able to understand the use of the ToolBox Report Module and the Report Wizard to generate a report of the hazard assessment performed with the ToolBox.

    Session 8:
    Case Study

    Complete case study for a read-across


    Software demonstration
    • Using the modules in the Toolbox for a step-by-step read-across

    Learning outcome:

    After the session, the students should be able to understand how to use the ToolBox to complete a read-across including the selection of the best analogue(s).

    Tutorial and Software version

    Tutorial
    At the end of the course, you can book a one-to-one tutorial for one hour with the tutor to answer any questions about the material on the course.

    Software version
    This course uses the OECD QSAR Toolbox version 4.6

    We shall endeavour to update our course so it is always current with new releases of the software.

    What can you expect?

    Watch the short video to give you an idea on how the course works
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    5 Star reviews on Trustpilot

    A good guide course for Toolbox users
    I have attended an QSAR workshop and I have learned very much. The course is combined with theory and practice. It is also a great idea to include video record, we can always watch the video when there is a question coming afterwards. Fully recommended for toxicologists.
    Xiuli He, Heel
    OECD Toolbox Training
    The ToxNavigation course on the OECD Toolbox provides a sound foundation on how to operate the toolbox and provides guidance on best practices. Elena is very knowledgeable and provides practical examples on how to predict various hazard endpoints for a molecule of interest. The course is well spaced and easy to follow. I recommend the course to anyone who plans on utilizing the tool for prediction modelling.
    Dieldrich Bermudez, Stepan
    Excellent training on the OECD QSAR toolbox
    Elena's explanation was very clear with a lot of information on the logic and chemistry behind decision making while using ReadAcross. The explanation on the use of the tool was also very good with a practical examples and many questions were addressed very well. The course was very structured and the material and recording were provided in a timely manner by Peter. Overall, this course is highly recommended.
    Arathi Kizhedath, Danone
    Dr Elena Fioravanzo has 30 years experience in cheminformatics and the Managing Director of ToxNavigation - a consultancy utilising the latest methods of computational toxicology to facilitate the chemical risk assessment process.  Elena has presented at many international conferences and has currently 36 papers and 85 posters published.
    Managing Director
    Peter Russell has over 25 years experience in configuring, demonstrating and training scientists in the use of cheminformatics software and database systems.




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