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

新的DNA测序技术导致了个体科学家、基因组测序项目和元基因组学项目提交的序列数据库中的大量新数据。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。这启发了用于编码蛋白质序列的自动注释的新工具的开发。这一领域最成功的发展之一是产生了所谓的蛋白质‘特征’，即能够根据新确定的序列所属的蛋白质家族和/或它们所包含的结构或功能结构域来表征新确定的序列的诊断方法。蛋白质签名方法已经被一些数据库采用，其中十个顶级资源被整合到InterPro数据库中。InterPro及其配套的蛋白质分析软件工具InterProScan现在是世界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面临着缺乏资金支持的问题。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。进入的数据量呈指数级增长，数据库现在很难及时向公众提供数据，同时保持必要的高标准数据质量。此外，随着它们变得越来越流行，以及用户需求的增加，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，而且要成为新技术的早期采用者。这项提议旨在通过采用新技术来加强和进一步开发InterPro及其源数据库来解决这些问题。它的目标是简化生产流程，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。随着联盟活动及其协调更加正规化，我们将更有效地利用资源和分担任务，以确保数据库的长期可持续性。我们的具体目标是：-简化数据生产程序，以便能够更快地周转时间发布数据；-开发和整合新的注释工具和标准，使限速注释步骤更快、更容易，并共享注释等任务，以消除工作中的冗余；-密切合作，改进蛋白质匹配的质量保证程序；-协调InterProScan和其他基于HMM的数据库升级到最新的HMer版本；-改进InterProScan蛋白质结构域查找软件；-开发数据库连接和数据交换的新技术；以及-扩展Web界面的功能，以更好地满足用户社区的需求。对InterProScan和蛋白质配对程序的计划改进将提高蛋白质功能分类的质量和速度；简化生产程序将使数据库能够在新的蛋白质结构域和家族可用时立即向公众公布。新技术将促进不同数据库之间更容易地建立联系，并将使公众能够访问来自不同来源的数据。它们还将通过改进对数据的程序化访问，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应对不断增加的新数据洪流，并以更定期的发布向公众开放。最终，这些改进将使InterPro及其合作伙伴更容易和更高效地进行维护，为更可持续的未来铺平道路，并增加它们对科学界的好处和有用性。

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.