AMBIT RESTful web services: an implementation of the OpenTox application programming interface.
AMBIT RESTful web services: an implementation of the OpenTox application programming interface.
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DOI：
10.1186/1758-2946-3-18
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发表时间：
2011-05-16
影响因子：
8.6
通讯作者：
Jeliazkov V
中科院分区：
文献类型：
--
作者：
Jeliazkova N;Jeliazkov V
AMBIT Web 服务包是 OpenTox 应用程序编程接口的几个现有独立实现之一，是根据表述性状态传输 (REST) 架构的原则构建的。开源预测毒理学框架由 EC FP7 OpenTox 项目的合作伙伴开发，旨在提供对毒性数据和预测模型以及验证程序的统一访问。这是通过以下方式实现的：i) 基于通用 OWL-DL 本体的信息模型 ii) 相关本体的链接； iii) 数据和算法，可通过标准化 REST Web 服务接口获得，其中每个化合物、数据集或预测方法都有一个唯一的网址，用于检索其资源描述框架 (RDF) 表示形式，或启动相关计算。 AMBIT Web 服务包是作为 AMBIT 模块的扩展而开发的，增加了创建（定量）结构-活性关系 (QSAR) 模型的能力，并提供了 OpenTox API 兼容接口。 W3C 资源描述框架中数据和处理资源的表示有助于将资源集成为关联数据。通过上传具有化学结构和任意属性集的数据集，它们可以自动以多种格式在线提供。这些服务为多种描述符计算、机器学习和相似性搜索算法以及适用性域和毒性预测模型提供统一的接口。所有用于预测化合物毒理学危害的 Toxtree 模块也集成在该软件包中。处理的复杂性和多样性被简化为简单的范例“从网址读取数据，执行处理，写入网址”。该在线服务可以轻松运行预测，无需安装任何软件，还可以共享在线数据集和模型。可下载的网络应用程序允许研究人员为特定目的并在合适的位置设置任意数量的服务实例。这些服务可以用作处理资源密集型任务和数据共享的分布式框架，也可以根据具体需求以完全独立的方式使用。通过 OpenTox API 公开功能的优点是无缝互操作性，不仅在单个 Web 应用程序中，而且在分布式服务网络中也是如此。最后但并非最不重要的一点是，这些服务为构建 Web 混搭、具有友好 GUI 的最终用户应用程序以及将功能嵌入现有工作流系统提供了基础。
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.