$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/
  sio: http://semanticscience.org/resource/
  edam: http://edamontology.org/
  evs: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#

$graph:

- name: hostSchema
  type: record
  fields:
    host_species:
        type: string
        jsonldPredicate:
          _id: http://www.ebi.ac.uk/efo/EFO_0000532
    host_id:
        type: string
        jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_000115
    host_common_name:
        type: string?
        jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/NOMEN_0000037
    host_sex:
        type: string
        jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/PATO_0000047
    host_age:
        type: int?
        jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/PATO_0000011
    host_age_unit:
        type: string?
        jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/UO_0000036
    host_health_status:
        type: string?
        jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
    host_treatment:
      type: string?
      jsonldPredicate:
          _id: http://www.ebi.ac.uk/efo/EFO_0000727
    host_vaccination:
      type: string?
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/VO_0000001
    additional_host_information:
      type: string?
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_001167

- name: sampleSchema
  type: record
  fields:
    collector_name:
      type: string
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/OBI_0001895
    collecting_institution:
      type: string
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_001167
    specimen_source:
      type: string?
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/OBI_0001479
    collection_date:
      type: string?
      jsonldPredicate:
          _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
    collection_location:
      type: string?
      jsonldPredicate:
        _id: http://purl.obolibrary.org/obo/GAZ_00000448
    sample_storage_conditions:
      type: string?
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/OBI_0001472
    additional_collection_information:
      type: string?
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_001167
    sample_id:
      type: string
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_000115
    source_database_accession:
      type: string?
      jsonldPredicate:
          _id: http://edamontology.org/data_2091

- name: virusSchema
  type: record
  fields:
    virus_species:
      type: string?
      jsonldPredicate:
          _id: http://edamontology.org/data_1875
    virus_strain:
      type: string?
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_010055

- name: technologySchema
  type: record
  fields:
    sample_sequencing_technology:
      type: string
      jsonldPredicate:
        _id: http://purl.obolibrary.org/obo/OBI_0600047
    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:
      type: string
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_000116
    submitter_date:
      type: string
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/NCIT_C94162
    submitter_address:
      type: string?
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_000172
    originating_lab:
      type: string
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/NCIT_C37984
    lab_address:
      type: string?
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/OBI_0600047
    provider_sample_id:
      type: string?
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/NCIT_C37900
    submitter_sample_id:
      type: string?
      jsonldPredicate:
          _id: http://www.ebi.ac.uk/efo/EFO_0001741
    authors:
      type: string?
      jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/NCIT_C42781
    submitter_id:
      type: string?
      jsonldPredicate:
          _id: http://semanticscience.org/resource/SIO_000115

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