Adding Rhesus Macaque to the Alliance

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Summary We propose to incorporate the rhesus macaque (Macaca mulatta) genome into the Alliance of Genome Resources (Alliance). This one-year project would serve two main purposes. First, it will bring a non-human primate into the Alliance, which will deeply connect knowledge about this important research organism to other research organisms and provide useful features for the macaque research community. Second, it will provide preliminary results and a path forward for a robust knowledgebase project for other non-human primates to be associated with the Alliance. It will also serve as a proof of principle for the Alliance’s agility and scalability. In collaboration with an existing and already interested resource, mGAP (the Macaque Genotype and Phenotype Resource), we will systematically bring information about this macaque genome and genetics into the Alliance. Starting with existing macaque resources (e.g., mGAP for variants, phenotypes, and disease connections) as well as generic resources (NCBI for genome; GOC for Gene annotations; BioGrid/IMEX for molecular interactions; Reactome; OMIM). The Oregon National Primate Research Center (ONPRC) has been interested in joining the Alliance for five years, and we are now ready to engage fully. In particular, the Alliance is well on its way to having an extensible persistent store with a rich-data model handling variants, disease annotations; gene expression; GO annotations; interactions and so forth. We will populate these with macaque data over the year. As the macaque data are incorporated, we will provide for macaque the full suite of features available on the current Alliance site, and others as they become available. Specifically, we will provide a macaque landing page with community-specific content; a community forum; gene pages for all macaque genes; orthology calls for protein-coding genes; an interactive table of variants; disease annotations; a JBrowse2 instance that will visualize variants as well as gene structure models; automated descriptions of gene function that will head each gene page; table of Gene Ontology (GO) annotations; pathways from Reactome and GO-CAM; gene expression; and molecular interactions. Together this will provide a useful resource to the growing non-human primate genome biology community and its connection with a broader set of biomedical researchers.