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The eTOX data-sharing project to advance in silico drug-induced toxicity prediction.

Cases M, Briggs K, Steger-Hartmann T, Pognan F, Marc P, Kleinöder T, Schwab CH, Pastor M, Wichard J, Sanz F - Int J Mol Sci (2014)

Bottom Line: The high-quality in vivo preclinical safety data produced by the pharmaceutical industry during drug development, which follows numerous strict guidelines, are mostly not available in the public domain.These safety data are sometimes published as a condensed summary for the few compounds that reach the market, but the majority of studies are never made public and are often difficult to access in an automated way, even sometimes within the owning company itself.The paper describes the efforts undertaken to allow effective data sharing intellectual property (IP) protection and set up of adequate controlled vocabularies) and to establish the database (currently with over 4000 studies contributed by the pharma companies corresponding to more than 1400 compounds).

View Article: PubMed Central - PubMed

Affiliation: Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr. Aiguader 88, Barcelona E-08003, Spain. montserrat.cases@bayer.com.

ABSTRACT
The high-quality in vivo preclinical safety data produced by the pharmaceutical industry during drug development, which follows numerous strict guidelines, are mostly not available in the public domain. These safety data are sometimes published as a condensed summary for the few compounds that reach the market, but the majority of studies are never made public and are often difficult to access in an automated way, even sometimes within the owning company itself. It is evident from many academic and industrial examples, that useful data mining and model development requires large and representative data sets and careful curation of the collected data. In 2010, under the auspices of the Innovative Medicines Initiative, the eTOX project started with the objective of extracting and sharing preclinical study data from paper or pdf archives of toxicology departments of the 13 participating pharmaceutical companies and using such data for establishing a detailed, well-curated database, which could then serve as source for read-across approaches (early assessment of the potential toxicity of a drug candidate by comparison of similar structure and/or effects) and training of predictive models. The paper describes the efforts undertaken to allow effective data sharing intellectual property (IP) protection and set up of adequate controlled vocabularies) and to establish the database (currently with over 4000 studies contributed by the pharma companies corresponding to more than 1400 compounds). In addition, the status of predictive models building and some specific features of the eTOX predictive system (eTOXsys) are presented as decision support knowledge-based tools for drug development process at an early stage.

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Scheme of the eTOXsys architecture.
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ijms-15-21136-f003: Scheme of the eTOXsys architecture.

Mentions: The eTOXsys is a unified software platform integrating the various tools, databases and results achieved during the course of the project. It has been developed by Molecular Networks GmbH. This integrated software system provides access to the predictive models and databases through a uniform user interface to support the hazard identification and risk assessment of drug candidates queried into the system. The system architecture of eTOXsys platform was designed within the consortium during the first two years of the project. The eTOXsys is a web-based system and can be accessed by the end user through a standard web browser. The architecture comprises a decoupled and distributed system in order to take into account the various technologies and methods used by the contributing service providers (databases and predictive models). The services are hosted, provided and maintained by the individual contributing partners who developed the model. The system consists of four main components (Figure 3). The eTOXsys web application facilitates the access to the various services and is provided by the central eTOXsys server to the end user. Furthermore, the eTOXsys server marshals user requests for toxicological endpoint predictions (provided by the prediction services) and database searches (provided by the eTOX database service), collects the results from the corresponding web services and returns them to the end user web application.


The eTOX data-sharing project to advance in silico drug-induced toxicity prediction.

Cases M, Briggs K, Steger-Hartmann T, Pognan F, Marc P, Kleinöder T, Schwab CH, Pastor M, Wichard J, Sanz F - Int J Mol Sci (2014)

Scheme of the eTOXsys architecture.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4264217&req=5

ijms-15-21136-f003: Scheme of the eTOXsys architecture.
Mentions: The eTOXsys is a unified software platform integrating the various tools, databases and results achieved during the course of the project. It has been developed by Molecular Networks GmbH. This integrated software system provides access to the predictive models and databases through a uniform user interface to support the hazard identification and risk assessment of drug candidates queried into the system. The system architecture of eTOXsys platform was designed within the consortium during the first two years of the project. The eTOXsys is a web-based system and can be accessed by the end user through a standard web browser. The architecture comprises a decoupled and distributed system in order to take into account the various technologies and methods used by the contributing service providers (databases and predictive models). The services are hosted, provided and maintained by the individual contributing partners who developed the model. The system consists of four main components (Figure 3). The eTOXsys web application facilitates the access to the various services and is provided by the central eTOXsys server to the end user. Furthermore, the eTOXsys server marshals user requests for toxicological endpoint predictions (provided by the prediction services) and database searches (provided by the eTOX database service), collects the results from the corresponding web services and returns them to the end user web application.

Bottom Line: The high-quality in vivo preclinical safety data produced by the pharmaceutical industry during drug development, which follows numerous strict guidelines, are mostly not available in the public domain.These safety data are sometimes published as a condensed summary for the few compounds that reach the market, but the majority of studies are never made public and are often difficult to access in an automated way, even sometimes within the owning company itself.The paper describes the efforts undertaken to allow effective data sharing intellectual property (IP) protection and set up of adequate controlled vocabularies) and to establish the database (currently with over 4000 studies contributed by the pharma companies corresponding to more than 1400 compounds).

View Article: PubMed Central - PubMed

Affiliation: Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr. Aiguader 88, Barcelona E-08003, Spain. montserrat.cases@bayer.com.

ABSTRACT
The high-quality in vivo preclinical safety data produced by the pharmaceutical industry during drug development, which follows numerous strict guidelines, are mostly not available in the public domain. These safety data are sometimes published as a condensed summary for the few compounds that reach the market, but the majority of studies are never made public and are often difficult to access in an automated way, even sometimes within the owning company itself. It is evident from many academic and industrial examples, that useful data mining and model development requires large and representative data sets and careful curation of the collected data. In 2010, under the auspices of the Innovative Medicines Initiative, the eTOX project started with the objective of extracting and sharing preclinical study data from paper or pdf archives of toxicology departments of the 13 participating pharmaceutical companies and using such data for establishing a detailed, well-curated database, which could then serve as source for read-across approaches (early assessment of the potential toxicity of a drug candidate by comparison of similar structure and/or effects) and training of predictive models. The paper describes the efforts undertaken to allow effective data sharing intellectual property (IP) protection and set up of adequate controlled vocabularies) and to establish the database (currently with over 4000 studies contributed by the pharma companies corresponding to more than 1400 compounds). In addition, the status of predictive models building and some specific features of the eTOX predictive system (eTOXsys) are presented as decision support knowledge-based tools for drug development process at an early stage.

Show MeSH
Related in: MedlinePlus