Embracing new technologies to streamline improve and sustain InterPro and its contributing databases

新的DNA测序技术导致了大量的新数据被提交到序列数据库中，这些数据是由个体科学家、基因组测序项目和宏基因组学项目提交的。这些序列进入数据库时很少或根本没有注释，限制了它们对科学界的有用性。这激发了对编码蛋白序列进行自动注释的新工具的开发。该领域最成功的发展之一是所谓的蛋白质“特征”的产生，即能够根据它们所属的蛋白质家族和/或它们包含的结构或功能域来表征新确定序列的诊断方法。蛋白质标记方法已被许多数据库采用，其中10种顶级资源已集成到InterPro数据库中。InterPro及其配套的蛋白质分析软件工具InterProScan是目前世界上领先的蛋白质功能分类资源之一。然而，尽管取得了成功，InterPro及其合作伙伴目前仍受到缺乏资金支持的困扰。维持和改进这种规模的数据库所需的资金数额往往被低估。输入数据的数量呈指数级增长，数据库现在努力及时地向公众提供数据，同时保持必要的高数据质量标准。此外，随着它们变得越来越流行，用户需求增加，这些核心数据库承受着越来越大的压力，不仅要跟上不断增长的数据量和不断增长的社区需求，而且要成为新兴技术的早期采用者。本提案旨在通过采用新技术来增强和进一步发展InterPro及其源数据库来解决这些问题。它旨在简化生产流程，以提供更定期的数据发布，并更好地应对不断增加的数据量。透过更正式的联盟活动和协调，我们会更有效地利用资源和分担任务，以确保资料库的长期可持续发展。具体而言，我们的目标是：-简化数据生产程序，以加快发布数据的周转时间；-开发和集成新的注释工具和标准，使限速注释步骤更快，更容易，并共享任务，如注释，以消除冗余的努力；-密切合作，改进蛋白质匹配的质量保证程序；协调将InterProScan和其他基于hmm的数据库升级到最新的HMMer版本；-改进InterProScan蛋白结构域查找软件；-利用数据库连接和数据交换的新技术；扩展Web界面的功能，以更好地满足用户群体的需求。计划对InterProScan和蛋白质匹配程序的改进将提高蛋白质功能分类的质量和速度；简化生产过程将使数据库能够在新的蛋白质结构域和家族可用时尽快向公众提供。新技术将促进不同数据库之间更容易的联系，并将向公众提供获取不同来源数据的途径。它们还将通过提供对数据的改进的程序化访问，为更复杂的分析打开大门。此外，这些新的流程和技术将使InterPro及其成员数据库能够处理不断增加的新数据洪流，并使公众能够更定期地访问这些数据。最终，这些改进将使InterPro及其合作伙伴更容易、更有效地维护，为更可持续的未来铺平道路，并增加他们对科学界的利益和有用性。

New DNA sequencing technologies have led to a flood of new data in sequence databases being submitted by individual scientists, genome sequencing projects and metagenomics projects. These sequences enter the databases with little or no annotation, limiting their usefulness to the scientific community. This has inspired the development of new tools for automatic annotation of the encoded protein sequences. One of the most successful developments in this area has been in the production of so-called protein 'signatures', diagnostic methods that are able to characterise newly-determined sequences in terms of the protein families to which they belong and/or the structural or functional domains they contain. Protein signature approaches have been adopted by a number of databases, and ten of the top such resources are integrated into the InterPro database. InterPro, and its accompanying protein analysis software tool, InterProScan, is now one of the leading protein functional classification resources in the world. However, despite its success, InterPro and its partners are currently suffering from a lack of financial support. The level of funding required to maintain and improve a database of this size is often underestimated. The amount of incoming data is increasing exponentially, and databases now struggle to provide their data to the public in a timely way, while at the same time maintaining the necessary high standards of data quality. Moreover, as they become more popular, and user demands increase, these core databases endure mounting pressure not only to keep up with the expanding volume of data and growing community requirements, but also to be early adopters of newly emerging technologies. This proposal aims to resolve these issues by embracing new technologies to enhance and further develop InterPro and its source databases. It aims to streamline production processes both to provide more regular data releases and to better cope with increased volumes of data. With more formalised Consortium activities and coordination thereof, we will make more efficient use of resources and share tasks to ensure long-term sustainability of the databases. Specifically we aim to: - Streamline data production procedures to enable a faster turn-around time for releasing the data; - Develop and integrate new annotation tools and standards to make the rate-limiting annotation step quicker and easier, and share tasks, such as annotation, to remove redundancy in effort; - Work closely together to improve quality-assurance procedures for protein matches; - Coordinate the upgrade of InterProScan and other HMM-based databases to the latest HMMer version; - Improve the InterProScan protein domain-finding software; - Exploit new technologies for database linking and data exchange; and - Extend the functionality of the Web interface to better meet the needs of the user community. The planned improvements to InterProScan and the protein match procedures will improve the quality, as well as the speed of protein functional classification; streamlining the production processes will enable the databases to get new protein domains and families out to the public as soon as they become available. New technologies will facilitate easier linking between different databases, and will provide the public with access to data from different sources. They will also open the door to more complex analyses, by providing improved programmatic access to the data. In addition, these new processes and technologies will allow InterPro and its member databases to cope with the ever-increasing flood of new data and make it accessible to the public in more regular releases. Ultimately, these improvements will make InterPro and its partners easier and more efficient to maintain, paving the way to a more sustainable future and increasing their benefit and usefulness to the scientific community.