From data to knowledge / the ONDEX System for integrating Life Sciences data sources

生物科学从不同的专业学科(如遗传学、生物化学、分子生物学)产生许多不同类型的数据。在任何系统生物学项目中，将数据连贯地聚集在一起是一项重大任务。虽然新的生物学辞典数据库和生物学组成部分的分类系统(本体)使连接专家数据库变得更容易，但这只解决了系统生物学家数据集成的部分问题，他们需要更丰富的信息体。例如，有许多不同的方式可以将生物成分联系起来(例如，通过功能、位置、大小)，需要捕获的生物成分以及关于数据来源(历史或来源)的信息在解释时可能很重要。新类型的信息在系统生物学中也很重要，包括对新陈代谢和信息流的生物过程和途径的描述。其中许多是通过从科学文献中提取信息来创建的，以形成系统功能的预测动态模型和模拟的基础。由于系统生物学需要复杂的数据集成和科学文本挖掘，这是生物研究界现成的生物信息学软件无法满足的，因此Rothamsted Research开发了一个原型系统(ONDEX)。该项目将把ONDEX与工作流、图形分析和文本挖掘方面的领先技术结合起来，开发一个强大的专业工具，为系统生物学研究奠定基础。由BBSRC资助的系统生物学中心合作伙伴运营的三个系统生物学研究项目将推动ONDEX的发展，并将验证真正科学问题上的新功能。涉及的生物领域包括：生物能源作物；酵母代谢组模型；以及端粒在衰老中的作用。研究伙伴带来了重要的技术专门知识，将增强ONDEX的新能力，这些能力是其中心的系统生物学家已知的需要的。这些扩展包括：*将数据映射到ONDEX的方法扩展，以扩大可以集成的数据范围，并捕获有关数据的更多信息(元数据)。*最先进的文本挖掘能力，用于从在线文本中提取生物学概念和关系，以使隐藏在科学文献中的新数据能够被提取并构建到模型和数据库中。*扩展以处理许多生物关系中固有的统计不确定性，以便能够使用现代统计推断技术在综合数据集中确定新的关系。*增强复杂关系网络的图形可视化，以容纳新信息并扩展到庞大的数据网络，使人们能够更好地了解新的交互作用，并以更好的方式在高度集成的数据集中查询数据*利用最新的分布式计算技术和科学工作流程来简化、自动化和扩展复杂的集成任务。*扩大与程序员和用户有关的数据接口的范围，以便能够通过互联网共享综合数据集，这些数据集本身就是重要的信息资源。一些行动和工程开发将使ONDEX更容易被生物学家使用，并支持在系统生物学的新领域中的吸收。其中包括新的培训资源、为用户和开发人员举办的讲习班，以及通过外联方案为新的应用程序提供直接帮助。在项目结束时，ONDEX将以精心设计和强大的形式提供给现有用户和新用户，这将更容易被大大扩大的用户和开发人员社区使用，这将使其作为一个开放软件项目长期可持续。

The biological sciences generate many different types of data from different specialist disciplines (e.g. genetics, biochemistry, molecular biology). Bringing data together coherently is a major undertaking in any systems biology project. While new databases of biological thesauri and classification systems (ontologies) for the component parts of biology make it easier to link specialist databases, this only solves part of the problem of data integration for systems biologists who need a much richer body of information. For example, there are many different ways that biological components can be related (e.g. by function, location, size) which needs to be captured and information about the provenance (history or source) of data can be important when it is interpreted. New types of information are also important in systems biology, including descriptions of the biological processes and pathways for metabolism and information flow. Many of these have been created by extracting information from the scientific literature to form the basis for the predictive dynamic models and simulations of system function. Because systems biology has a need for complex data integration and scientific text mining that is not met by readily available bioinformatics software in the biological research community, a prototype system (ONDEX) has been developed by Rothamsted Research. This project will combine ONDEX with leading technologies in workflow, graph analysis and text mining, to develop a powerful and professional tool that will underpin systems biology research. Three systems biology research projects, run by our BBSRC-funded systems biology centre partners, will drive the development of ONDEX and will validate new features on real scientific problems. Biological areas addressed cover: bioenergy crops; yeast metabolome models; and Telomere Function in ageing. The research partners bring important technical expertise that will enhance ONDEX with new capabilities known to be required by systems biologists at their centres. These include: * Extensions to methods that map data into ONDEX to broaden the range of data that can be integrated and capture more of the information about it (the metadata). * State of the art text mining capabilities, for extracting biological concepts and relationships from online text to enable new data buried in the scientific literature to be extracted and structured into models and databases. * Extensions to handle the statistical uncertainty inherent in many biological relationships, to enable new relationships to be identified in the integrated datasets using modern statistical inference techniques. * Enhanced graphical visualisations of the complex network of relationships to accommodate new information and scale to huge data networks, to enable a better understanding of new interactions, and better ways of interrogating the data in a richly integrated dataset * Exploitation of the latest in distributed computing techniques and scientific workflows to simplify, automate and scale the complex task of integration. * Extended range of data interfaces relevant to both programmers and users to enable shared access over the Internet of the integrated datasets, which are important information resources in their own right. A number of actions and engineering developments will make ONDEX easier to use by biologists and support uptake in new areas of systems biology. These include new training resources, workshops for users and developers and providing direct help for new applications through an outreach programme. At the end of the project ONDEX will be delivered in a well-engineered and robust form to existing and new users that will be more readily used by a greatly expanded user and developer community that should make it sustainable in the long term as an open software project.