RCN: RNA Ontology Consortium (ROC)

这一研究协调网络(RCN)项目支持建立RNA本体论联盟(ROC)，旨在创建一个整合的概念框架--RNA本体论(RO)--用它来了解生物系统中的RNA功能，并推动RNA生物学、化学和基因组学的研究。这将需要整合化学家、分子生物学家、基因学家、信息科学家和结构生物学家的研究范式，进而需要创建一个与RNA功能有关并基于RNA序列、二级和三维结构的通用、动态、可控的词汇(RO)。因此，中华民国的中心目标是确定文献中提到或出现在数据库中的所有RNA基序，就每个基序的定义达成一致，并以结构化的方式将该定义写下来。这是非常及时的，因为关于RNA的知识积累和快速进步。因此，创建RO的目的是(1)整合序列和结构数据库，以及(2)创建强大的软件工具，为实验室科学家带来先进的计算方法。简而言之，这将通过将多样化的信息和数据积累转化为知识来推动RNA科学的发展。为了达到这些目标，中华民国将透过频繁的面对面研讨会，以讨论、辩论及解决疑难的概念问题，促进核糖核酸科学家之间的沟通与合作。这些会议机会将在RNA研究的各个层面创造新的研究方向。在每年的核糖核酸学会会议上，我国的工作小组将汇报进展，并从更广泛的核糖核酸科学家社区获得反馈。该项目的更广泛影响将来自联网活动的有形产品：(1)RNA本体本身，(2)有用的链接数据库，以及(3)强大的集成软件。RO的设立将促进参与RNA科学各个方面的相互重叠的科学家社区之间的交流和合作。此外，RO将为各级科学学生和教师提供清晰的概念，以了解生命的分子基础，以及RNA所发挥的重要作用。整合不同的信息源，创造综合软件和协作工具，将扩大和加强实验室科学家解释其实验数据的能力，以及计算生物学家和基因学家挖掘基因组数据的能力。该项目将借鉴核心小组在构建核糖核酸标记语言RNAML、结构标记语言PDBML、核糖核酸基本分类的全面分类以及SCOR(核糖核酸结构分类)和RiBoweb项目方面的经验。中华民国将与基因本体论和序列本体论社区密切合作，创建与RNA有关的综合本体论，并将使用鲍林格林州立大学托管的服务器在万维网上访问其工作。该联盟得到了核糖核酸协会的支持，以积极促进对其活动的参与，并为其工作寻求广泛投入。积极推动多元化参与的机制，将包括协调人及督导委员会的积极招募，以及透过WWW和RNA学会及相关专业学会的电子邮件名单，传播中华民国的资讯。中华民国鼓励所有有兴趣的科学家参与。

This Research Coordination Network (RCN) project supports the establishment of the RNA Ontology Consortium (ROC), which aims to create an integrating conceptual framework--an RNA Ontology (RO)--with which to understand RNA function in biological systems and to advance research in RNA biology, chemistry and genomics. This will require the integration of the research paradigms of chemists, molecular biologists, genomicists, information scientists and structural biologists, and will in turn require the creation of a common, dynamic, controlled vocabulary (the RO), pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. Thus, the central objective of the ROC is to identify all RNA motifs mentioned in the literature or appearing in databases, to agree upon a definition for each motif and to write that definition down in a structured manner. This is very timely as knowledge about RNA accumulates and progresses rapidly. The purposes for creating the RO are therefore (1) to integrate sequence and structural databases and (2) to create powerful software tools that bring advanced computational methods to the bench scientist. In short, this will advance RNA science by turning diverse information and data accumulation into knowledge. To achieve these aims, ROC will foster communication and promote collaboration among RNA scientists by coordinating frequent face-to-face workshops to discuss, debate, and resolve difficult conceptual issues. These meeting opportunities will create new research directions at various levels of RNA research. At the RNA Society meeting each year, ROC working groups will report progress and obtain feedback from the wider community of RNA scientists. The broader impacts of the project will flow from the tangible products of the networking activities: (1) the RNA Ontology itself, (2) usefully linked databases, and (3) powerfully integrated software. The creation of the RO will facilitate communication and collaboration among the overlapping communities of scientists involved in various aspects of RNA science. Moreover, the RO will provide students and teachers of science at all levels with clear concepts for understanding the molecular basis of life, and the important roles played by RNA. The integration of disparate sources of information and the creation of integrated software and collaboration tools will expand and enhance the ability of bench scientists to interpret their experimental data and of computational biologists and genomicists to mine genomic data. The project will build on the experience of the core group in constructing the RNA mark-up language, RNAML, the structural mark-up language PDBML, a comprehensive classification of basepairing in RNA, as well as SCOR (Structural Classification of RNA) and the Riboweb project. The ROC will work closely with the Gene Ontology and Sequence Ontology communities to create a comprehensive integrated ontology pertaining to RNA and will make its work accessible on the World-Wide Web using servers hosted by Bowling Green State University. The Consortium has the support of the RNA Society to actively foster participation in its activities and to seek broad input for its work. The mechanism for actively promoting diverse participation will include active recruitment by the Coordinator and Steering Committee and dissemination of information regarding the ROC through the WWW and the email lists of the RNA Society and related professional societies. The ROC encourages the participation of all interested scientists.