iBeetle-Base: Building an Interconnected, Interactive and Extendable Repository for Phenotypic Data

iBeetle-Base：构建一个互连、交互式和可扩展的表型数据存储库

• 批准号: 417202192
• 负责人: Professor Dr. Gregor Bucher
• 金额: --
• 依托单位: FIZ Karlsruhe - Leibniz-Institut für Informationsinfrastruktur GmbH (FIZ KA)
• 依托单位国家: 德国
• 项目类别: Research data and software (Scientific Library Services and Information Systems)
• 财政年份: 2018
• 资助国家: 德国
• 起止时间: 2017-12-31 至 2023-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/417202192?language=en
• 关键词: iBeetle; Base; Building; Interconnected; Interactive

The development of an organism and its physiology are governed by genes. Hence, understanding how genes function and how they are regulated is required to understand arthropod development, physiology and evolution. Such knowledge then allows devising strategies to fight insect pests and vectors, for instance revealing novel target genes for pest control. Genomic sequences are available for many organisms and integrated genomic databases allow for cross-species comparisons of gene sequences. However, large scale data on the function of genes (phenotypic data) had been restricted to very few highly established model systems with the fly Drosophila melanogaster being the only representative of arthropods. With the DFG funded iBeetle screen we have been using RNA interference (RNAi) in the red flour beetle Tribolium castaneum to generate a genome wide dataset on gene function. This represents the first large scale phenotypic dataset in any arthropod outside of Drosophila. Indeed, the iBeetle screen has led to the identification of unexpected gene functions and to the detection of novel target genes for pest control. This phenotypic dataset is stored and presented at iBeetle-Base. Beyond project related data iBeetle-Base provides additional information useful for studying gene functions within and outside the community like for instance an integrated genome browser, sequence data, homology information and tools, links and resources for the community. In order to integrate iBeetle-Base (http://ibeetle-base.uni-goettingen.de) with other resources we have established mutual links with FlyBase and we have installed a function where specialists of the community can contribute GO terms for their genes of interest.With this project, we plan to ensure long-term availability, interoperability and extendability of iBeetle-Base fulfilling the need for phenotypic data repositories. Updating the software architecture to microservices providing open APIs for the data, make it easier to extend and to maintain. Integration of ontologies and other measures will allow for interoperability with other data, opening the possibility of cross species comparisons for instance with the fly. Further, we plan to enrich the data with GO terms and other information taking into consideration the needs of the community. Importantly, for the database to grow with the constant flow of new results in the field, we want to allow the community to add data (Community Edition). Together, these measures significantly increase the value of the data for the Tribolium community and beyond. Further, the developed structure and tools can be used as template for other arthropod phenotypic data repositories, the common APIs of which will allow for cross species queries and research.

有机体的发育及其生理是由基因控制的。因此，了解基因的功能和调控机制是了解节肢动物发育、生理和进化的必要条件。这些知识可以用来设计对抗害虫和病媒的策略，例如揭示害虫控制的新靶基因。基因组序列可用于许多生物体，整合的基因组数据库允许跨物种的基因序列比较。然而，关于基因功能的大规模数据（表型数据）仅限于极少数高度建立的模型系统，其中黑腹果蝇是节肢动物的唯一代表。在DFG资助的iBeetle筛选项目中，我们一直在使用RNA干扰（RNAi）技术对红粉甲虫Tribolium castaneum进行研究，以生成基因功能的全基因组数据集。这代表了除果蝇以外任何节肢动物的第一个大规模表型数据集。事实上，iBeetle筛选已经导致了意想不到的基因功能的鉴定和害虫控制的新靶基因的检测。该表型数据集存储在iBeetle-Base。除了项目相关数据之外，iBeetle-Base还提供了对研究社区内外基因功能有用的额外信息，例如集成的基因组浏览器、序列数据、同源信息以及社区的工具、链接和资源。为了整合iBeetle-Base （http://ibeetle-base.uni-goettingen.de）与其他资源，我们与FlyBase建立了相互链接，并安装了一个功能，社区专家可以为他们感兴趣的基因提供GO术语。通过这个项目，我们计划确保iBeetle-Base的长期可用性、互操作性和可扩展性，以满足表型数据存储库的需求。将软件架构更新为为数据提供开放api的微服务，使其更易于扩展和维护。本体论和其他措施的整合将允许与其他数据的互操作性，打开跨物种比较的可能性，例如与苍蝇的比较。此外，考虑到社区的需要，我们计划在数据中加入GO术语和其他信息。重要的是，为了使数据库随着该领域新成果的不断涌现而增长，我们希望允许社区添加数据（社区版）。总之，这些措施显著增加了Tribolium社区和其他社区的数据价值。此外，开发的结构和工具可作为其他节肢动物表型数据库的模板，其通用api将允许跨物种查询和研究。