EuroQSAR2012: BIOCLIPSE-OPENTOX:  Interactive Predictive Toxicology
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EuroQSAR2012: BIOCLIPSE-OPENTOX: Interactive Predictive Toxicology

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Computational predictive toxicology draws knowledge from many independent sources, providing a rich support ...

Computational predictive toxicology draws knowledge from many independent sources, providing a rich support
tool to assess a wide variety of toxicological properties. A key example would be for it to complement
alternative testing methods. The integration of Bioclipse and OpenTox permits toxicity prediction based on the
analysis of chemical structures, and visualization the substructure contributions to the toxicity prediction.
OpenTox [1,2] is a semantic web framework, based on web services, which supports open data exchange and toxicology model building and validation. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The OpenTox services provide unified interfaces to chemical compounds and datasets, several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. OpenTox services could be used in various ways, for example as components in web applications or embedded in existing workflow systems. Despite the workflows flexibility, some users prefer simple user interfaces or software with predefined functionality, while some experts consider scripting languages more convenient for model development than graphical workflow builders. Bioclipse provides convenient solution for both groups of users, offering simultaneously GUI actions, visualisations and scripts.
Bioclipse is a desktop bio- and cheminformatics platform, which combines a rich scriptable and graphical
workbench environment. Bioclipse was recently extended to dynamically discover computational algorithms
exposed via the OpenTox servers [4], using the OpenTox ontology service's SPARQL endpoint. This SPARQL
endpoint functions as a registry of available computational services on the OpenTox network, similar to the role of BioCatalogue. Moreover, when a new descriptor algorithm or model is registered on the OpenTox ontology service, it will automatically be picked up by Bioclipse. Using this approach, Bioclipse has access to the most recent computational services running the latest predictive algorithms and models, while hiding technicalities by reusing a graphics-oriented workbench for the life sciences. The scripting functionality makes it easy to automate data workflows as do workflow applications but the combination with the rich Bioclipse user interface makes it possible at the same time to work with OpenTox interactively.
Bioclipse-OpenTox interoperability for online descriptor calculation and data sharing , as well as accessing
protected OpenTox datasets and calculation procedures via the adopted OpenSSO authenticaiton and
authorisation solution had been demonstrated previous. This work extends the work by demonstrating how to add new models.

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EuroQSAR2012: BIOCLIPSE-OPENTOX:  Interactive Predictive Toxicology EuroQSAR2012: BIOCLIPSE-OPENTOX: Interactive Predictive Toxicology Document Transcript

  • BIOCLIPSE-OPENTOX: INTERACTIVE PREDICTIVE TOXICOLOGY Nina Jeliazkova a, Ola Spjuth b, Egon Willighagen c a) Ideaconsult Ltd., Sofia, Bulgaria, jeliazkova.nina@gmail.com, twitter: @10705013 b) Department of Pharmaceutical Bioinformatics, Uppsala University, Uppsala, Sweden c) Department of Bioinformatics - BiGCaT, Maastricht University, The Netherlands, egon.willighagen@maastrichtuniversity.nl, twitter: @egonwillighagen OpenTox Computational Toxicologist wish list Bioclipse• A semantic web framework, based on web 1. Uniform access to the (online) databases with • A desktop bio- and cheminformatics services [1,2] http://opentox.net experimental data and to computational platform [3] methods• Supports open data exchange and • http://bioclipse.net/ 2. Interactively, graphically explore chemicals toxicology model building and validation • Combines a rich scriptable and graphical 3. See what parts (atoms, fragments) of the Uniform access via molecule trigger toxic responses workbench environment OpenTox web services API 4. Integrate with data analysis methods Visualization 5. Allow reproducibility of the analysis to Chemical structures and Datasets• The representation of data and processing Result: Bioclipse – OpenTox [1-4] resources in W3C Resource Description Framework facilitates integrating the OpenTox web services can be used as: resources as Linked Data. • components in web applications• By uploading datasets with chemical structures and arbitrary set of properties, • components in desktop applications they become automatically available • embedded in existing workflow systems online in several formats.to Computational Components • descriptor calculations • machine learning algorithms The toxicity is often determined by substructures • similarity/structure searching algorithms Scripting, workflows, • applicability domain interactivity • toxicity prediction modelsfor building and publishing Despite the workflows flexibility, somepredictive models users prefer simple user interfaces or software with predefined functionality, 1. Start with an OpenTox dataset: while some experts consider scripting Computational methods discovery languages more convenient for model • Bioclipse dynamically discovers computational development than graphical workflow algorithms exposed via the OpenTox servers [4], builders. using the OpenTox ontology services SPARQL Bioclipse provides convenient solution for endpoint. both groups of users, offering • The SPARQL endpoint functions as a registry of simultaneously GUI actions, visualizations available data and computational services on and scripts. the OpenTox network, similar to the role of BioCatalogue. • When a new descriptor algorithm or model is registered on the OpenTox ontology service, it 2. Launch a machine learning algorithm via Bioclipse JavaScript: will automatically be picked up by Bioclipse. • Using this approach, Bioclipse has access to the most recent computational services running the latest predictive algorithms and models, while hiding technicalities by reusing a graphics- oriented workbench for the life sciences. 3. The result is an online regression or classification model, available via OpenTox web Bioclipse-OpenTox interoperability for service API: Computational toxicology can be online descriptor calculation and data made reproducible using an application sharing , as well as accessing protected programming interface (API) for models OpenTox datasets and calculation and data and scripting. procedures via the adopted OpenSSO authentication and authorization The scripting functionality makes it easy to solution had been demonstrated in [4]. automate data workflows as do workflow Bioclipse scripting was recently extended applications but the combination with the with the ability to build new OpenTox rich Bioclipse user interface makes it models and thus to add new online possible at the same time to work with computational resources. OpenTox interactively.References1) Hardy B., Douglas N., Helma C., Rautenberg M., Jeliazkova N., et al. , Collaborative Development of Predictive Toxicology Applications, Journal of Cheminformatics 2010, 2:72) Jeliazkova N., Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface., Journal of Cheminformatics 2011, 3:18.3) Spjuth, O., Helmus, T., Willighagen, E. L., Kuhn, S., Eklund, M., Wagener, J., Murray-Rust, P., Steinbeck, C., and Wikberg, J. E. S. Bioclipse: an open source workbench for chemo- and bioinformatics.BMC Bioinformatics 2007, 8:59.4) Willighagen, E.L., Jeliazkova, N., Hardy, B., Grafström, R.C., Spjuth, O. Computational toxicology using the OpenTox application programming interface and Bioclipse, BMC Research Notes 2011,4:487.