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System Scope and Context

This chapter specifies the boundaries of SILO-LAPIS and describes the interfaces to other systems and users.

  • Configuration and operation: LAPIS is provisioned by the maintainer, who provides a configuration file and operates the instance.
  • Data updates: The maintainer can trigger an update upon which SILO reads data from the disc and stores it internally.
    • Raw data might for example be downloaded from Genbank.
    • Providing correct data will most likely involve some preprocessing (e.g. using Nextstrain) to compute e.g. aligned sequences and insertions.
    • The maintainer needs to make sure that the data is in the correct format.
  • LAPIS can be accessed by the end-user through a REST interface
    • LAPIS has endpoints to fetch the following types of data:
      • Aggregated data: returns how many sequences fulfill the provided filter criteria
      • Amino acid and nucleotide mutations
        • returns a list of mutations (with their proportion and count) which fulfill the provided filter criteria
        • the proportion is relative to all sequences which fulfill the provided criteria
      • Details: returns a list of metadata of the sequences which fulfill the provided criteria
      • Amino acid, aligned and unaligned nucleotide sequences: returns the corresponding sequences which fulfill the provided criteria
    • the provided filter criteria can be a compilation of metadata fields, mutations and insertions.
    • LAPIS offers an OpenAPI specification and a Swagger UI that documents the API.