REDfly: The regulatory sequence resource for Drosophila and other insects

我们已经开发了一个独特的资源，REDFly(Fly的法规要素数据库)数据库 转录调控元件，为果蝇和其他物种的基因组提供调控注释 昆虫。调节基因表达的基因组序列-转录顺式调节模块(CRM， 例如“增强子”)和转录因子结合位点(TFBs)--目前没有任何其他主要的 数据库资源。这是一个严重的缺陷，因为CRM在出生缺陷和 慢性病以及正常发育、表型变异和进化。了解以下内容 经过实验验证的CRM和TFBSS对于许多研究领域至关重要，包括口译和 验证大型基因组项目开发的数据，为机器学习CRM提供训练数据- 发现方法、基因组注释、建立基因调控网络模型、研究基因进化 转录调控的基础生物学的许多方面。昆虫标准物质知识 也是开发生物技术方法控制昆虫病媒和用于 消除病原体传播。REDFly包括经过实验验证的CRM和TFBS以及它们的 DNA序列，它们的相关基因，以及它们所指导的表达模式。这是现存的最详细的 后生动物调控元素注释平台，被广泛认为是 监管基因组学领域。只有REDFly集成了所有可用的昆虫顺式调控信息 多个来源提供全面的监管要素集合。这项提案的目标是 是随着识别的CRM和TFBS数量的迅速增加而保持REDly的最新状态，并 更新REDFly网站，以最大限度地提高其对研究社区的效用。研究的重点是：(1)培养。REDFly 随着新研究的发布，将继续保持最新，并将添加有价值的数据和元数据 现有的记录。(2)用户界面。我们将开发更复杂的搜索、显示和下载 能够跟上数据库中现在包含的数据量和类型的急剧增加的步伐。 我们将更新自最初实施以来在十年内过时的软件组件。 (3)数据集成。我们将加强不同数据类型的集成，并为 注释。(4)工作流程。我们将通过改进工作流程来提高我们的管理效率和能力。(5) 本体支持。我们将通过整合最新的本体来改进我们使用生物医学本体的方式- 相关软件，包括本体浏览器和SPARQL查询。拟议的活动意义重大，因为 他们将为多个研究社区提供最新的高价值资源，并增加REDFly的效用 通过添加所需的新特性和功能。REDFly已经证明了它的本质和独特的价值 作为支持假设驱动的经验和计算研究的重要平台 研究领域。通过这里提出的更新和增强，它将极大地增加影响。

We have developed a unique resource, the REDfly (Regulatory Element Database for Fly) database of transcriptional regulatory elements, to provide regulatory annotation for the genome of Drosophila and other insects. The genomic sequences regulating gene expression—transcriptional cis-regulatory modules (CRMs, e.g. “enhancers”) and transcription factor binding sites (TFBSs)—are not currently curated by any other major database resources. This is a serious deficiency as CRMs play critical roles with respect to birth defects and chronic diseases as well as normal development, phenotypic variation, and evolution. Knowledge of experimentally validated CRMs and TFBSs is vital for many areas of research including interpretation and validation of data developed by large-scale genomics projects, providing training data for machine-learning CRM- discovery methods, genome annotation, modeling gene regulatory networks, studying the evolution of gene regulation, and numerous aspects of the basic biology of transcriptional regulation. Knowledge of insect CRMs is also an important step in developing biotechnology methods for control of insect disease vectors and for eliminating pathogen transmission. REDfly includes experimentally verified CRMs and TFBSs along with their DNA sequence, their associated genes, and the expression patterns they direct. It is the most detailed existing platform for metazoan regulatory element annotation and is widely acknowledged as the premier resource in the regulatory genomics arena. Only REDfly integrates all of the available insect cis-regulatory information from multiple sources to provide a comprehensive collection of regulatory elements. The objectives of this proposal are to keep REDfly up to date with the rapidly increasing numbers of CRMs and TFBSs being identified and to update the REDfly site to maximize its utility to the research community. The focus is on: (1) Curation. REDfly will continue to be kept up-to-date as new studies are published, and valuable data and metadata will be added to existing records. (2) User interface. We will develop more sophisticated search, display, and download capabilities to keep pace with the vastly increased amounts and types of data now contained in the database. We will update software components that have become obsolete in the decade since their initial implementation. (3) Data integration. We will increase integration of disparate data types and develop confidence scores for annotations. (4) Workflow. We will increase our curation efficiency and ability through improved workflows. (5) Ontology support. We will improve how we use biomedical ontologies through incorporating the latest ontology- related software, including ontology browsers and SPARQL queries. The proposed activities are significant as they will keep up-to-date a high-value resource for multiple research communities and increase REDfly’s utility by adding needed new features and functions. REDfly has already demonstrated its essential and unique value as an important platform for supporting hypothesis-driven empirical and computational research in multiple research areas. It will have greatly increased impact through the updates and enhancements proposed here.