$base: http://biohackathon.org/bh20-seq-schema
$namespaces:
  sch: https://schema.org/
  efo: http://www.ebi.ac.uk/efo/
  obo: http://purl.obolibrary.org/obo/
$graph:

- name: hostSchema
  type: record
  fields:
    host_species:
        type: string
        jsonldPredicate:
          _id: http://www.ebi.ac.uk/efo/EFO_0000532
    host_id: string
    host_common_name: string?
    host_sex: string?
    host_age: int?
    host_age_unit: string?
    host_health_status: string?
    host_treatment:
      type: string?
      jsonldPredicate:
          _id: http://www.ebi.ac.uk/efo/EFO_0000727
    additional_host_information: string?

- name: sampleSchema
  type: record
  fields:
    collector_name: string
    collecting_institution: string
    specimen_source: string?
    collection_date: string?
    collection_location:
      type: string?
      jsonldPredicate:
        _id: https://schema.org/fromLocation
    sample_storage_conditions: string?
    additional_collection_information: string?

- name: virusSchema
  type: record
  fields:
    virus_species: string?
    virus_strain: string?

- name: technologySchema
  type: record
  fields:
    sample_sequencing_technology:
      type: string
      jsonldPredicate:
        _id: http://www.ebi.ac.uk/efo/EFO_0000532
    sequence_assembly_method:
      type: string?
      jsonldPredicate:
        _id: http://www.ebi.ac.uk/efo/EFO_0002699
    sequencing_coverage:
      type: string?
      jsonldPredicate:
        _id: http://purl.obolibrary.org/obo/FLU_0000848

- name: submitterSchema
  type: record
  fields:
    submitter_name: string
    submitter_address: string?
    originating_lab: string
    lab_address: string?
    provider_sample_id: string?
    submitter_sample_id: string?
    authors: string?
    submitter_id: string?

- name: MainSchema
  type: record
  documentRoot: true
  fields:
    host: hostSchema
    sample: sampleSchema
    virus: virusSchema?
    technology: technologySchema
    submitter: submitterSchema
    sequencefile:
      doc: The subject (eg the fasta/fastq file) that this metadata describes
      type: string?
      jsonldPredicate:
        _id: "@id"
        _type: "@id"