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Processing biological literature with customizable Web services supporting interoperable formats

机译：使用支持互操作格式的可定制Web服务处理生物学文献

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Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk.
机译：Web服务已成为互连解决方案以处理大量科学文献的流行手段。这推动了对适用于给定领域并确保Web服务互操作性的高级数据交换格式的研究。在本文中，我们将重点放在生物学领域上，并考虑四种互操作性格式，即BioC，BioNLP，XMI和RDF，它们代表特定于域的和通用的表示形式，并包括完善的和新兴的规范。我们在基于Web的文本挖掘工作台Argo中创建的可定制Web服务的上下文中使用这些格式，该功能具有不断增长的基本分析库和功能，可直接从便捷的图形用户界面构建和部署Web服务。我们演示了Web服务的2种定制：通过从可用分析存储库中构建特定于任务的处理管道，以及通过配置服务以接受并产生输入和输出数据交换格式的组合。我们提供格式的定性评估以及自动分析的定量评估。后者是我们参加第四届BioCreative挑战赛的一部分。在Web服务中内置的用于识别BioC集合中生化概念的分析在10个参与团队中综合得分最高。数据库URL：http：//argo.nactem.ac.uk。

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