FunPDBe - enhancing structural and functional annotation of macromolecular structure data in the PDB by collaboration and integration

生命科学领域的快速技术和科学进步导致生物数据的数量和多样性呈指数级增长。这彻底改变了生命科学研究，并将其转变为数据驱动的科学领域。这种转变也影响了我们对生命分子（如蛋白质）三维结构的理解。大分子的结构可以为生物过程的功能机制提供重要的见解。这些结构数据存档在蛋白质数据库（PDB）中，这是生物医学领域最古老的数据档案之一。PDB成立于1971年，现在包含超过120，000个大分子结构。PDB由一个全球合作组织wwPDB管理，欧洲蛋白质数据库（PDBe）是该组织的创始成员。wwPDB合作伙伴接受由世界各地的科学家确定的新的大分子结构，并通过对这些新存放的条目进行注释来解释这些结构的分布方式。就大分子的生物学背景而言，这种注释是有限的。将这些数据与其他生物信息和预测注释相结合，可以帮助我们提高对生命和疾病过程的理解，帮助设计新的药物分子，或者了解遗传变异对健康和疾病的影响。将PDB中的大分子结构数据与提供生物学背景的增值注释相结合，可以加速使用这些信息来改进工业生物技术，英国拥有世界领先的结构生物信息学社区，多年来开发了许多数据分析工具和数据资源，为大分子结构数据添加生物背景和增值注释，PDB。虽然这些资源得到了很好的利用，但如果解决信息碎片化和缺乏描述注释信息的标准的问题，则可以进一步提高它们的使用率。FunPDBe旨在通过标准化功能注释的共享方式来解决这些问题，并随后实现一个中央数据资源，将PDB中的数据与英国领先的结构生物信息学数据资源中的注释结合在一起。在项目期间开发的基础设施将允许集成来自地球仪的其他数据资源的注释，这些注释最初未参与该项目。该项目还将提供对这一丰富数据的统一访问。FunPDBe将提高可持续性，确保注释安全存档，在可预见的未来可以访问，消除重复工作，从而保护开发专业参与数据资源的工作和投资。因此，FunPDBe将成为一个独特的，开放的全球资源，并有助于确保英国在未来的结构计算生物学中的领导地位。我们的目标将通过以下具体活动来实现。一系列研讨会，为英国结构生物信息学社区建立一个开放论坛2。使用为不同数据类型定义的标准在FunPDBe资源中识别和导入结构和功能注释。3.分析和验证不同预测算法提供的注释4.定义和实施数据收集和整合的协议和机制5.使用数据标准提供统一的数据访问机制;确定和创建有用的代表性数据集，以支持研究人员群体6。编写培训材料并举办培训讲习班

Rapid technological and scientific advances in the field of life sciences have resulted in exponential increase in the amount and diversity of biological data. This has revolutionised life-science research and transformed it into a data driven scientific field. This transformation is also affecting our understanding of three-dimensional structures of molecules of life such as proteins. Structures of macromolecules can provide great insights into the functional mechanism of biological processes. These structural data are archived in the Protein Data Bank (PDB), one of the oldest data archives in the biomedical field. PDB was established in 1971 and now contains more than 120,000 structures of macromolecules. PDB is managed by a worldwide collaboration, wwPDB, of which Protein Data Bank in Europe (PDBe) is a founding member. The wwPDB partners accept new macromolecular structures determined by scientists across the world and standardise the way these are distributed by carrying out annotation of these newly deposited entries. This annotation is limited as far as the biological context of the macromolecule is concerned. Integrating these data with other biological information and predicted annotations can help improve our understanding of life and disease processes, help design new drug molecules, or understand the effects of genetic variation on health and disease. Combining the macromolecular structure data in the PDB with value-added annotations that provide biological context can accelerate the use of this information in improving industrial biotechnology, agricultural products and human health.The UK has world leading structural bioinformatics community that has over the years developed many data analysis tools and data resources to add biological context and value added annotations to macromolecular structure data available in the PDB. Although these resources are well used, their usage can be further improved if the issues of fragmentation of information and lack of standards for describing the annotation information are addressed. FunPDBe, is designed to address these issues by standardising the way functional annotations can be shared and by subsequently implementing a central data resource that brings together the data from the PDB with the annotations from the leading UK-based structural bioinformatics data resources.. The infrastructure developed during the project will allow integration of annotations from other data resources from around the globe, not initially involved in this project. The project will also provide uniform access to this enriched data. FunPDBe will improve sustainability, ensuring that the annotations are archived safely, are accessible for the foreseeable future, remove duplication of effort and thus protect the work and investment that has gone into developing the specialised participating data resources. Thus, FunPDBe will become a unique, open global resource, and help secure the UK's leading role in structural computational biology into the future. Our goal will be achieved through following specific activities -1. A series of workshops to establish an open forum for the UK structural bioinformatics community2. Identify and import structural and functional annotations in the FunPDBe resource using standards defined for the different data types.3. Analyse and validate annotations provided by different prediction algorithms4. Define and implement protocols and mechanisms for data collection and integration5. Provide uniform data access mechanisms using the data standards; identify and create useful representative datasets to support researcher community6. Develop training materials and deliver training workshops