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

生物体的发育和生理是由基因控制的。因此，了解基因的功能以及它们是如何被调节的，对于了解节肢动物的发育、生理和进化是必要的。这样的知识可以帮助我们设计出对付害虫和病媒的策略，例如揭示新的害虫控制靶基因。基因组序列可用于许多生物体，并且整合的基因组数据库允许基因序列的跨物种比较。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，果蝇是节肢动物的唯一代表。通过DFG资助的iBeetle筛选，我们一直在红粉甲虫Tribolium castaneum中使用RNA干扰（RNAi）来生成基因功能的全基因组数据集。这代表了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用于害虫控制的新靶基因的检测。该表型数据集存储并呈现在iBeetle-Base中。除了项目相关数据，iBeetle-Base还提供了对研究社区内外的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，同源性信息和工具，社区链接和资源。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，社区的专家可以为他们感兴趣的基因贡献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，以满足表型数据库的需求。将软件架构更新为微服务，为数据提供开放的API，使其更容易扩展和维护。本体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。此外，我们计划在考虑到社区需求的情况下，用GO术语和其他信息来丰富数据。重要的是，为了使数据库随着该领域不断涌现的新结果而增长，我们希望允许社区添加数据（社区版）。总之，这些措施大大增加了Tribolium社区及其他社区的数据价值。此外，所开发的结构和工具可以用作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。

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.