OpenTox Use Cases and Knowledge Café Groups

Below I post a summary of the OpenTox Predictive Toxicology Use Cases we will discuss during the Knowledge Café sessions at the workshop in Rome 10-11 September 2009 on Satisfying REACH Requirements in Predictive Toxicology. 

Guidance

The group of names indicate the starting discussion group for each use case for each session.  We will also have a rotation so that participants can join a second use case discussion in each session.  The Moderator will introduce the use case and guide the discussion, and summarise progress for the second rotation, and during the final group discussion.  The Reporter for each group is marked with an asterisk (*) and will assume the role of documenting the progress of the discussion for adding to use case documentation.  Whereas other participants can rotate tables, the Moderator and Reporter stay at the same table during a session.  The use cases will be subject to further documentation and peer review post-workshop.

Use Cases and Groups

Thursday morning, 10th September

1.      Run a Collaborative in silico in vitro Predictive Toxicology Project

Short Name: Collaboration

Moderator: Barry Hardy

Discussion Group:

Andreas Sutter, Antonio Conto, Micha Rautenberg*, Paola Gramatica, Sunil Chawla, Willie Peijnenburg

2.      Integration of multiple data sources and resources for a predictive toxicology model

Short Name: Integration

Moderator: Nina Jeliaskova

Discussion Group:

Andrew Worth, Bob Diderich, David Bower, Fabian Buchwald*, Indira Ghosh, Olga Tcheremenskaia, Sylvain Bintein

3.      Create a consensus-based predictive model

Short Name: Consensus

Moderator: Stefan Kramer

Discussion Group:

Alex Tropsha, Alexey Zakharov, Andreas Maunz*, Elena Fioravanzo, Joanna Jaworska, Pantelis Sopasakis

4.      Given a chemical structure, predict an endpoint

Short Name: Predict

Moderator David Gallagher

Discussion Group:

Andreas Karwath, Antreas Afantitis*, Arianna Bassan, Barun Bhatarai, Christoph Helma, Georgia Melagraki, Olga Raevskaja

5.      Read Across for Chronic Toxicity

Short Name: Read Across

Moderator: Sylvia Escher

Discussion Group:

Maurizio Colombo, Oleg Raevsky, Richard Beger, Romualdo Benigni, Stephanie Ringeissen, Vedrin Jeliazkov*, Vladimir Poroikov

6.      Validate an SVM model

Short Name: Validate

Moderator: Harry Sarimveis

Discussion Group:

Ester Papa, Evgueni Kolossov, Lothar Richter, Martin Gütlein*, Tobias Girschick

Thursday afternoon, 10th September

1.      Generate a safety prediction from a metabolomics dataset

Short Name: Metabolomics

Moderator: Stefan Kramer

Discussion Group:

David Bower, Elena Fioravanzo, Richard Beger, Lothar Richter*, Stephanie Ringeissen, Alexey Zakharov

2.      Given a set of in vitro data predict in vivo data (Descriptor Selection Approach)

Short Name: Descriptor

Moderator: Vladimir Poroikov

Discussion Group:

Alex Tropsha, Andreas Sutter, Antreas Afantitis, Barun Bhatarai, Harry Sarimveis*, Romualdo Benigni

3.      Given a set of in vitro data predict in vivo data (Bayesian Net Approach)

Short Name: Bayesian

Moderator:  Paola Gramatica

Discussion Group:

Andreas Maunz, Barry Hardy*, Georgia Melagraki, Joanna Jaworska, Nina Jeliazkova, Oleg Raevsky

4.      Decision tree to decide whether substances can be assessed by the TTC approach

Short Name:  Decision Tree

Moderator: Vedrin Jeliazkov

Discussion Group:

Bob Diderich, Ester Papa, Olga Raevskaja, Olga Tcheremenskaia, Pantelis Sopasakis*, Sylvia Escher, Tobias Girschick

5.      Given a chemical generate a REACH risk assessment report (Part 1)

Short Name: REACH report

Moderator:  Andreas Karwath

Discussion Group:

Antonio Conto, Arianna Bassan, David Gallagher*, Indira Ghosh, Micha Rautenberg, Sylvain Bintein, Willie Peijnenburg

6.      Generate a QPRF report

Short Name: QPRF report

Moderator:  Christoph Helma

Discussion Group:

Andrew Worth, Evgueni Kolossov, Fabian Buchwald, Maurizio Colombo, Martin Gütlein*, Sunil Chawla

Friday morning, 11th September

1.      Given a set of chemicals and endpoint(s) prioritise selection of in vitro assays

Short Name: in vitro

Moderator: Barry Hardy

Discussion Group:

Alex Tropsha, Andreas Maunz, Richard Beger, Sylvain Bintein, Tobias Girschick*, Vedrin Jeliazkov, Vladimir Poroikov

2.      Given a chemical generate a REACH risk assessment report (Part 2)

Short Name: REACH report

Moderator: Nina Jeliaskova

Discussion Group:

Alexey Zakharov, Andrew Worth, Joanna Jaworska, Lothar Richter*, Maurizio Colombo, Martin Gütlein

3.      Determine the Applicability Domain of a prediction model

Short Name: Domain

Moderator: Stefan Kramer

Discussion Group:

Andreas Sutter, Arianna Bassan, Christoph Helma*, Evgueni Kolossov, Paola Gramatica, Sunil Chawla

4.      Given a set of endpoint data, develop and store a predictive model

Short Name: Develop

Moderator David Gallagher

Discussion Group:

Antreas Afantitis, Barun Bhatarai, Elena Fioravanzo, Ester Papa, Micha Rautenberg, Olga Raevskaja, Pantelis Sopasakis*

5.      Create a Category for a complex endpoint

Short Name: Category

Moderator: Romualdo Benigni

Discussion Group:

Antonio Conto, Bob Diderich, David Bower, Georgia Melagraki, Olga Tcheremenskaia*,

Willie Peijnenburg

6.      Given set of data for endpoint, develop, internally validate and store multiple predictive models

Short Name: Model

Moderator: Harry Sarimveis

Discussion Group:

Andreas Karwath*, Fabian Buchwald, Indira Ghosh, Oleg Raevsky, Stephanie Ringeissen

Friday afternoon, 11th September

1.      Inclusion of ADME and PBPK properties in OpenTox Framework

Short Name: ADME

Moderator: Vladimir Poroikov

Discussion Group:

Barry Hardy*, David Bower, Oleg Raevsky, Romualdo Benigni

2.      Predict toxicity endpoint using similarity scores

Short Name: Similarity

Moderator: Indira Ghosh

Discussion Group:

Barun Bhatarai, Lothar Richter*, Olga Raevskaja, Olga Tcheremenskaia, Willie Peijnenburg

3.      Given a set of chemicals, select a set of descriptors for modelling an endpoint

Short Name: Select Descriptors

Moderator:  Tobias Girschick

Discussion Group:

Andreas Maunz, Barun Bhatarai, Ester Papa, Evgueni Kolossov, Nina Jeliazkova*, Richard Beger

4.      Generate a QMRF report from OpenTox-based prediction model

Short Name: QMRF Report

Moderator: Vedrin Jeliazkov

Discussion Group:

Andrew Worth, Antonio Conto, David Gallagher*, Micha Rautenberg

5.      Integrate and validate a new algorithm

Short Name: Validate

Moderator:  Andreas Karwath

Discussion Group:

Arianna Bassan, Elena Fioravanzo, Martin Gütlein*, Maurizio Columbo, Stefan Kramer

6.      Compare performance of different models / algorithms

Short Name: Performance

Moderator:  Christoph Helma

Discussion Group:

Alexey Zakharov, Andreas Sutter, Paola Gramatica, Sunil Chawla*, Sylvain Bintein