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

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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.