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      AMBIT RESTful web services: an implementation of the OpenTox application programming interface

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      Journal of Cheminformatics

      BioMed Central

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          Abstract

          The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.

          The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. 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 services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

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          Most cited references 9

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          Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics

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            QSAR applicabilty domain estimation by projection of the training set descriptor space: a review.

            As the use of Quantitative Structure Activity Relationship (QSAR) models for chemical management increases, the reliability of the predictions from such models is a matter of growing concern. The OECD QSAR Validation Principles recommend that a model should be used within its applicability domain (AD). The Setubal Workshop report provided conceptual guidance on defining a (Q)SAR AD, but it is difficult to use directly. The practical application of the AD concept requires an operational definition that permits the design of an automatic (computerised), quantitative procedure to determine a models AD. An attempt is made to address this need, and methods and criteria for estimating AD through training set interpolation in descriptor space are reviewed. It is proposed that response space should be included in the training set representation. Thus, training set chemicals are points in n-dimensional descriptor space and m-dimensional model response space. Four major approaches for estimating interpolation regions in a multivariate space are reviewed and compared: range, distance, geometrical, and probability density distribution.
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              Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52.

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                Author and article information

                Journal
                J Cheminform
                Journal of Cheminformatics
                BioMed Central
                1758-2946
                2011
                16 May 2011
                : 3
                : 18
                Affiliations
                [1 ]Ideaconsult Ltd., Angel Kanchev Str 4, Sofia 1000, Bulgaria
                Article
                1758-2946-3-18
                10.1186/1758-2946-3-18
                3120779
                21575202
                Copyright ©2011 Jeliazkova and Jeliazkov; licensee Chemistry Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Software

                Chemoinformatics

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