Data hierarchy

All data imported into G-nom is stored in a hierarchy originating the the NCBI Taxonomy. Each genome assembly is linked to a species with a unique NCBI Taxonomy ID. G-nom uses an internal copy of the NCBI taxdump as a reference which is updated automatically every two weeks (system administrators can adjust this service interval).

flowchart TD
    Genus --> A@{ shape: processes, label: "Species" }
    A@{ shape: processes, label: "Species" } --> B@{ shape: processes, label: "Assemblies" }
    B@{ shape: processes, label: "Assemblies" } --> Genome
    B@{ shape: processes, label: "Assemblies" } --> C@{ shape: processes, label: "Mappings" }
    B@{ shape: processes, label: "Assemblies" } --> D@{ shape: processes, label: "Annotations" }
    B@{ shape: processes, label: "Assemblies" } --> E@{ shape: processes, label: "Analyses" }

Additional data referencing or analysing the genome assembly can be imported. This includes genomic annotations and mappings as well as BUSCO, fCAT and taXaminer analyses. All entities presented in the diagram have additional metadata associated with them which is handled by G-nom automatically. In some cases e.g. species, additional hand-curated data such as Descriptions, Images or Geodata can be added using the taxon editor and will be displayed on the assembly page.

Warning

Currently, the taxon Editor only supports editing species-level taxa.

All data at or below assembly level is access-controlled, allowing users to decide who can read / edit their imported data.