models_metadata.yml.hmp

# THIS FILE CAN BE AUTO-GENERATED (minus descriptions) USING util/generated_models_metadata_yml.py

metadata_mapping:
# This section configures the following areas:
# 1) UI - The autocomplete mapping for adding facets on the search page
# 2) API - Fields for Aggregations class in models.py
# 3) API - Converting UI facet/field names to Neo4j cypher

  # subject props
  subtype:
      cypher_field: "subject.subtype"
      description: "The subtype of the study"
      doc_type: "cases"
      field: "subject subtype"
      type: "string"

  project_subtype:
      cypher_field: "subject.project_subtype"
      description: "The subtype of the project"
      doc_type: "cases"
      field: "subject project subtype"
      type: "string"

  id:
      cypher_field: "subject.id"
      description: "The subject's UUID"
      doc_type: "cases"
      field: "subject ID"
      type: "string"

  rand_subject_id:
      cypher_field: "subject.rand_subject_id"
      description: "The subject's per-study ID (can view in individual sample page)"
      doc_type: "cases"
      field: "subject study ID"
      type: "string"

  project_id:
      cypher_field: "subject.project_id"
      description: ""
      doc_type: "cases"
      field: "subject project ID"
      type: "string"

  race:
      cypher_field: "subject.race"
      description: "The subject's race/ethnicity"
      doc_type: "cases"
      field: "subject race"
      type: "string"

  project_name:
      cypher_field: "subject.project_name"
      description: "The name of the project within which the sequencing was organized"
      doc_type: "cases"
      field: "subject project name"
      type: "string"

  gender:
      cypher_field: "subject.gender"
      description: "The subject's sex"
      doc_type: "cases"
      field: "subject gender"
      type: "string"

  # sample props
  geo_loc_name:
      cypher_field: "sample.geo_loc_name"
      description: "The geographical origin of the sample as defined by the country or sea name followed by specific region name"
      doc_type: "cases"
      field: "sample geo location name"
      type: "string"

  subtype:
      cypher_field: "sample.subtype"
      description: "The subtype of the sample"
      doc_type: "cases"
      field: "sample subtype"
      type: "string"

  study_subtype:
      cypher_field: "sample.study_subtype"
      description: "The subtype of the study"
      doc_type: "cases"
      field: "sample study subtype"
      type: "string"

  env_package:
      cypher_field: "sample.env_package"
      description: "Controlled vocabulary of MIGS/MIMS environmental packages"
      doc_type: "cases"
      field: "sample environmental package"
      type: "string"

  id:
      cypher_field: "sample.id"
      description: "The iHMP ID of the sample"
      doc_type: "cases"
      field: "sample id"
      type: "string"

  study_center:
      cypher_field: "sample.study_center"
      description: "The study's sequencing center"
      doc_type: "cases"
      field: "sample study center"
      type: "string"

  study_srp_id:
      cypher_field: "sample.study_srp_id"
      description: "NCBI Sequence Read Archive (SRA) project ID"
      doc_type: "cases"
      field: "sample study SRP ID"
      type: "string"

  study_name:
      cypher_field: "sample.study_name"
      description: "The name of the study"
      doc_type: "cases"
      field: "sample study name"
      type: "string"

  visit_subtype:
      cypher_field: "sample.visit_subtype"
      description: "The subtype of the visit"
      doc_type: "cases"
      field: "sample visit subtype"
      type: "string"

  visit_id:
      cypher_field: "sample.visit_id"
      description: "The identifier used by the sequence center to uniquely identify the visit"
      doc_type: "cases"
      field: "sample visit ID"
      type: "string"

  study_description:
      cypher_field: "sample.study_description"
      description: "A longer description of the study"
      doc_type: "cases"
      field: "sample study description"
      type: "string"

  study_contact:
      cypher_field: "sample.study_contact"
      description: "The study's primary contact at the sequencing center"
      doc_type: "cases"
      field: "sample study contact"
      type: "string"

  body_site:
      cypher_field: "sample.body_site"
      description: "Body site from which the sample was obtained using the FMA ontology"
      doc_type: "cases"
      field: "sample body site"
      type: "string"

  biome:
      cypher_field: "sample.biome"
      description: "Biomes are defined based on factors such as plant structures leaf types plant spacing and other factors like climate"
      doc_type: "cases"
      field: "sample biome"
      type: "string"

  collection_date:
      cypher_field: "sample.collection_date"
      description: "time of sampling either as an instance (single point in time) or interval"
      doc_type: "cases"
      field: "sample collection date"
      type: "string"

  visit_visit_number:
      cypher_field: "sample.visit_visit_number"
      description: "A sequential number that is assigned as visits occur for a subject"
      doc_type: "cases"
      field: "sample visit number"
      type: "string"

  body_product:
      cypher_field: "sample.body_product"
      description: "Substance produced by the body e.g. stool mucus where the sample was obtained from"
      doc_type: "cases"
      field: "sample body product"
      type: "string"

  feature:
      cypher_field: "sample.feature"
      description: "Environmental feature level includes geographic environmental features"
      doc_type: "cases"
      field: "sample feature"
      type: "string"

  lat_lon:
      cypher_field: "sample.lat_lon"
      description: "Latitude/longitude in WGS 84 coordinates"
      doc_type: "cases"
      field: "sample latitude longitude"
      type: "string"

  visit_interval:
      cypher_field: "sample.visit_interval"
      description: "The amount of time since the last visit (in days)"
      doc_type: "cases"
      field: "sample visit interval"
      type: "string"

  rel_to_oxygen:
      cypher_field: "sample.rel_to_oxygen"
      description: "Whether the organism is an aerobe or anaerobe"
      doc_type: "cases"
      field: "sample relationship to oxygen"
      type: "string"

  samp_size:
      cypher_field: "sample.samp_size"
      description: "Amount or size of sample (volume mass or area) that was collected"
      doc_type: "cases"
      field: "sample size"
      type: "string"

  samp_mat_process:
      cypher_field: "sample.samp_mat_process"
      description: "Any processing applied to the sample during or after retrieving the sample from environment"
      doc_type: "cases"
      field: "sample material process"
      type: "string"

  material:
      cypher_field: "sample.material"
      description: "Matter that was displaced by the sample before the sampling event"
      doc_type: "cases"
      field: "sample material"
      type: "string"

  samp_collect_device:
      cypher_field: "sample.samp_collect_device"
      description: "The method or device employed for collecting the sample"
      doc_type: "cases"
      field: "sample collection device"
      type: "string"

  visit_date:
      cypher_field: "sample.visit_date"
      description: "Date when the visit occurred"
      doc_type: "cases"
      field: "sample visit date"
      type: "string"

  fecalcal:
      cypher_field: "sample.fecalcal"
      description: "FecalCal result exists if measured for the sample"
      doc_type: "cases"
      field: "sample fecalcal"
      type: "string"

  supersite:
      cypher_field: "sample.supersite"
      description: "Body supersite from which the sample was obtained"
      doc_type: "cases"
      field: "sample supersite"
      type: "string"

  # file props
  format:
      cypher_field: "file.format"
      description: "The format of the file"
      doc_type: "file"
      field: "file format"
      type: "string"

  node_type:
      cypher_field: "file.node_type"
      description: "The node type of the file"
      doc_type: "file"
      field: "file type"
      type: "string"

  id:
      cypher_field: "file.id"
      description: "The iHMP ID of the file"
      doc_type: "file"
      field: "file id"
      type: "string"

  matrix_type:
      cypher_field: "file.matrix_type"
      description: "The type of data used to generate the abundance matrix"
      doc_type: "file"
      field: "file matrix type"
      type: "string"

  annotation_pipeline:
      cypher_field: "file.annotation_pipeline"
      description: "The annotation pipeline used to generate the file"
      doc_type: "file"
      field: "file annotation pipeline"
      type: "string"

  # token props

  # tag props
  term:
      cypher_field: "tag.term"
      description: ""
      doc_type: "file"
      field: "tag term"
      type: "string"


  # user props

  # session props

  # query props