A FAIR community resource for pathogens, hosts and their interactions to enhance global food security and human health

传染性微生物继续给英国农业和食品工业带来重大损失，并日益威胁全球粮食安全、商业和观赏树木健康以及生态系统的恢复力。同样，由于抗菌化合物耐药性的增加以及贸易和旅行的全球化，传染性微生物给英国公共和私人医疗和兽医提供者带来了更大的成本，并威胁到人类和动物的健康和整个生命周期的福祉。有一个实质性的和多样化的英国和国际生物科学研究社区，其需求是由这个资源解决。随着生物科学成为一个日益数据密集的学科，大规模数据分析成为新的规范，建立和维护社区资源，确保数据的可查找性，可访问性，互操作性和可重用性（即是公平的）将使许多不同的生物科学学科受益。近年来，通过应用高通量技术确定生命的分子性质，为病原体的研究（并最终控制）开辟了新的可能性。其中包括基因组测序-揭示决定细胞遗传特性的遗传密码-并扩展到监测生命和疾病不同阶段的不同细胞内容。该FAIR社区资源旨在从病原生物体中捕获广泛的分子信息，并将其与有关感染过程的描述性信息结合起来，包括更具体的分子信息，例如关于感染期间相互作用的病原体和宿主蛋白质，相互作用结果的表型，并标记哪些病原体蛋白质已经被抗感染化学品靶向。关于病原体基因组、基因表达模式和潜在相互作用伙伴的新知识使用Ensembl平台进行存储。Ensembl包含一套用于管理和显示基因组规模数据的综合软件。科学界的成员将越来越多地利用一种新开发的称为PHI-Canto的工具，将关于每种致病物种致病能力所需的经实验验证的基因的新表型知识纳入病原体宿主相互作用（PHI-base）数据库。一个新的策展重点将增加有关以下方面的详细记录：（i）病原体产生的小效应蛋白的库与其在每个宿主物种内的初始靶标之间的分子相互作用，以及（ii）抗感染化学物质的病原体靶标。为了支持正在进行的策展工作，将开发新的通用PHIPO本体（受控定义），以准确描述病原体-宿主相互作用的深度和广度。 通过进一步开发Ensembl基因组、PHI-base和其他关键电子科学数据/信息提供商之间的接口，这将支持基因组和表型数据的联合查询和可视化。我们还将部署新的和现有的工具（图形和非图形），以改善物种间的比较分析和不同大型数据类型的整合，以加快分析并在基因的进化起源、感染过程中重要的突变以及赋予宿主抗性、病原体毒力或抗感染化学品抗性的基因/基因网络方面取得新的发现。我们将继续与大型和活跃的英国研究界在生物科学，以确定他们目前的需求和通过大学/研究所访问新出现的要求，并将进行培训活动，以展示资源的潜在用途。我们将与其他国家的学术和行业科学家合作，参加并在国际会议和研讨会上展示这个公平的社区资源及其用途。

Infectious microbes continue to impose major costs on the UK farming and food industry and increasingly threaten global food security, commercial and ornamental tree health and ecosystem resilience. Similarly, due to the rise in resistance to antimicrobial compounds and increased globalisation of trade and travel, infectious microbes impose ever greater costs on public and private UK medical and veterinary providers and threaten human and animal health and wellbeing across the lifecourse. There is a substantial and diverse UK and international bioscience research community whose needs are addressed by this resource. As the biosciences become an increasingly data-intensive discipline and mega-scale data analyses become the new norm, building and maintaining community resources that ensure the Findability, Accessibility, Interoperability, and Reusability of data (i.e. are FAIR) will benefit many different bioscience disciplines.In recent years, new possibilities for the study (and ultimately control) of pathogens have opened up through the application of high-throughput technologies for determining the molecular nature of life. These include genome sequencing - which reveals the genetic code that determines inherited properties of cells - and extends to monitoring the varied cellular contents at different stages of life and disease. This FAIR community resource is designed to capture broad molecular information from pathogenic organisms, and combine it with descriptive information about the process of infection, including more specific molecular information, e.g. about the pathogen and host proteins that interact during infection, the phenotype of the interaction outcome and flag up which pathogen proteins are already targeted by anti-infective chemicals. The new knowledge on pathogen genomes, patterns of gene expression and potential interacting partner is housed using the Ensembl platform. Ensembl contains a comprehensive suite of software for the management and display of genome-scale data. The new phenotypic knowledge on experimentally verified genes required for the disease-causing abilities of each pathogenic species will increasingly be curated by members of the scientific community into the Pathogen Host Interactions (PHI-base) database using a newly developed tool called PHI-Canto. A new curation focus will increase the details recorded about (i) the molecular interactions between the repertoires of small effector proteins produced by pathogens and their initial targets within each host species, and (ii) the pathogen targets for anti-infective chemistries. To support the ongoing curation efforts, new generic PHIPO ontologies (controlled definitions) will be developed to accurately describe the depth and breadth of pathogen-host interactions. By further developing the interfaces (within and between) Ensembl genomes, PHI-base and other key e-sciences data/ information providers this will support the joint querying and visualisation of genomic and phenotypic data. We will also deploy new and existing tools (graphical and non-graphical) to improve inter-species comparative analysis and the integration of different large data types to speed up analyses and make new discoveries on the evolutionary origin of genes, mutations important in the process of infection and genes/ gene networks conferring host resistance, pathogen virulence or resistance to anti-infective chemicals. We will continue to engage with the large and active UK research community in the biosciences to identify their current needs and emerging requirements through University/Institute visits, and will conduct training activities to demonstrate the potential use of the resource. We will engage with academic and industry based scientists in other countries by attending and presenting this FAIR community resource and its uses at international conferences and workshops.