name: koza-graph-schema
id: https://w3id.org/monarch-initiative/koza/graph-schema
imports:
- linkml:types
prefixes:
  biolink: https://w3id.org/biolink/vocab/
  dct: http://purl.org/dc/terms/
  linkml: https://w3id.org/linkml/
  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
  rdfs: http://www.w3.org/2000/01/rdf-schema#
default_prefix: https://w3id.org/monarch-initiative/koza/graph-schema/
default_range: string
slots:
  FDA_adverse_event_level:
    exact_mappings:
    - biolink:FDA_adverse_event_level
    slot_uri: biolink:FDA_adverse_event_level
    range: string
  agent_type:
    exact_mappings:
    - biolink:agent_type
    slot_uri: biolink:agent_type
    range: string
  aggregator_knowledge_source:
    exact_mappings:
    - biolink:aggregator_knowledge_source
    slot_uri: biolink:aggregator_knowledge_source
    range: string
    multivalued: true
  available_from:
    exact_mappings:
    - biolink:available_from
    slot_uri: biolink:available_from
    range: string
    multivalued: true
  broad_synonym:
    exact_mappings:
    - biolink:broad_synonym
    slot_uri: biolink:broad_synonym
    range: string
    multivalued: true
  category:
    exact_mappings:
    - biolink:category
    slot_uri: biolink:category
    range: uriorcurie
  clinical_approval_status:
    exact_mappings:
    - biolink:clinical_approval_status
    slot_uri: biolink:clinical_approval_status
    range: string
  deprecated:
    exact_mappings:
    - biolink:deprecated
    slot_uri: biolink:deprecated
    range: boolean
  description:
    exact_mappings:
    - biolink:description
    slot_uri: dct:description
    range: string
  disease_context_qualifier:
    exact_mappings:
    - biolink:disease_context_qualifier
    slot_uri: biolink:disease_context_qualifier
    range: uriorcurie
  disease_context_qualifier_category: {}
  disease_context_qualifier_closure:
    multivalued: true
  disease_context_qualifier_closure_label:
    multivalued: true
  disease_context_qualifier_label: {}
  disease_context_qualifier_namespace: {}
  evidence_count:
    range: integer
  exact_synonym:
    exact_mappings:
    - biolink:exact_synonym
    slot_uri: biolink:exact_synonym
    range: string
    multivalued: true
  file_source:
    description: Source file stem injected by koza at load time.
    range: string
    multivalued: false
  frequency_qualifier:
    exact_mappings:
    - biolink:frequency_qualifier
    slot_uri: biolink:frequency_qualifier
    range: string
  frequency_qualifier_category: {}
  frequency_qualifier_label: {}
  frequency_qualifier_namespace: {}
  full_name:
    exact_mappings:
    - biolink:full_name
    slot_uri: biolink:full_name
    range: string
  grouping_key: {}
  has_attribute:
    exact_mappings:
    - biolink:has_attribute
    slot_uri: biolink:has_attribute
    range: uriorcurie
    multivalued: true
  has_biological_sex:
    exact_mappings:
    - biolink:has_biological_sex
    slot_uri: biolink:has_biological_sex
    range: uriorcurie
  has_confidence_score:
    exact_mappings:
    - biolink:has_confidence_score
    slot_uri: biolink:has_confidence_score
    range: float
  has_count:
    exact_mappings:
    - biolink:has_count
    slot_uri: biolink:has_count
    range: integer
  has_descendant:
    multivalued: true
  has_descendant_count:
    range: integer
  has_descendant_label:
    multivalued: true
  has_evidence:
    exact_mappings:
    - biolink:has_evidence
    slot_uri: biolink:has_evidence
    range: uriorcurie
    multivalued: true
  has_gene:
    exact_mappings:
    - biolink:has_gene
    slot_uri: biolink:has_gene
    range: uriorcurie
    multivalued: true
  has_percentage:
    exact_mappings:
    - biolink:has_percentage
    slot_uri: biolink:has_percentage
    range: double
  has_phenotype:
    multivalued: true
  has_phenotype_closure:
    multivalued: true
  has_phenotype_closure_label:
    multivalued: true
  has_phenotype_count:
    range: integer
  has_phenotype_label:
    multivalued: true
  has_quotient:
    exact_mappings:
    - biolink:has_quotient
    slot_uri: biolink:has_quotient
    range: double
  has_total:
    exact_mappings:
    - biolink:has_total
    slot_uri: biolink:has_total
    range: integer
  id:
    exact_mappings:
    - biolink:id
    slot_uri: biolink:id
    range: string
  in_taxon:
    exact_mappings:
    - biolink:in_taxon
    slot_uri: biolink:in_taxon
    range: uriorcurie
  in_taxon_label:
    exact_mappings:
    - biolink:in_taxon_label
    slot_uri: biolink:in_taxon_label
    range: string
  iri:
    exact_mappings:
    - biolink:iri
    slot_uri: biolink:iri
    range: uriorcurie
  knowledge_level:
    exact_mappings:
    - biolink:knowledge_level
    slot_uri: biolink:knowledge_level
    range: string
  medic_application_numbers:
    multivalued: true
  medic_approval_date: {}
  medic_approval_status_raw: {}
  medic_approved_authorities:
    multivalued: true
  medic_approved_jurisdictions:
    multivalued: true
  medic_assertion_flags:
    multivalued: true
  medic_claim_relation: {}
  medic_co_administered_with:
    multivalued: true
  medic_disease_context:
    multivalued: true
  medic_disease_context_ids:
    multivalued: true
  medic_earliest_approval_date: {}
  medic_is_allergen:
    range: boolean
  medic_is_diagnostic_agent:
    range: boolean
  medic_jurisdiction: {}
  medic_marketing_status_usa: {}
  medic_mention_id: {}
  medic_object_mention_id: {}
  medic_pair_confidence:
    range: float
  medic_pair_n_assertions:
    range: integer
  medic_pair_reliability: {}
  medic_registration_numbers:
    multivalued: true
  medic_reliability: {}
  medic_source: {}
  medic_stub:
    range: boolean
  medic_subject_mention_id: {}
  medic_supporting_text_truncated:
    range: boolean
  name:
    exact_mappings:
    - biolink:name
    slot_uri: rdfs:label
    range: string
  namespace: {}
  narrow_synonym:
    exact_mappings:
    - biolink:narrow_synonym
    slot_uri: biolink:narrow_synonym
    range: string
    multivalued: true
  negated:
    exact_mappings:
    - biolink:negated
    slot_uri: biolink:negated
    range: boolean
  object:
    exact_mappings:
    - biolink:object
    slot_uri: rdf:object
    range: uriorcurie
  object_aspect_qualifier:
    exact_mappings:
    - biolink:object_aspect_qualifier
    slot_uri: biolink:object_aspect_qualifier
    range: string
  object_category:
    exact_mappings:
    - biolink:object_category
    slot_uri: biolink:object_category
    range: uriorcurie
  object_closure:
    multivalued: true
  object_closure_label:
    multivalued: true
  object_label: {}
  object_location_in_text:
    multivalued: true
  object_namespace: {}
  object_specialization_qualifier:
    exact_mappings:
    - biolink:object_specialization_qualifier
    slot_uri: biolink:object_specialization_qualifier
    range: uriorcurie
  object_taxon: {}
  object_taxon_label: {}
  onset_qualifier:
    exact_mappings:
    - biolink:onset_qualifier
    slot_uri: biolink:onset_qualifier
    range: uriorcurie
  onset_qualifier_category: {}
  onset_qualifier_label: {}
  onset_qualifier_namespace: {}
  original_object:
    exact_mappings:
    - biolink:original_object
    slot_uri: biolink:original_object
    range: string
  original_predicate:
    exact_mappings:
    - biolink:original_predicate
    slot_uri: biolink:original_predicate
    range: uriorcurie
  original_subject:
    exact_mappings:
    - biolink:original_subject
    slot_uri: biolink:original_subject
    range: string
  population_context_qualifier:
    exact_mappings:
    - biolink:population_context_qualifier
    slot_uri: biolink:population_context_qualifier
    range: uriorcurie
  predicate:
    exact_mappings:
    - biolink:predicate
    slot_uri: rdf:predicate
    range: uriorcurie
  primary_knowledge_source:
    exact_mappings:
    - biolink:primary_knowledge_source
    slot_uri: biolink:primary_knowledge_source
    range: string
  provided_by:
    exact_mappings:
    - biolink:provided_by
    slot_uri: biolink:provided_by
    range: string
    multivalued: false
  publications:
    exact_mappings:
    - biolink:publications
    slot_uri: biolink:publications
    range: uriorcurie
    multivalued: true
  qualifier:
    exact_mappings:
    - biolink:qualifier
    slot_uri: biolink:qualifier
    range: string
  qualifiers:
    exact_mappings:
    - biolink:qualifiers
    slot_uri: biolink:qualifiers
    range: uriorcurie
    multivalued: true
  related_synonym:
    exact_mappings:
    - biolink:related_synonym
    slot_uri: biolink:related_synonym
    range: string
    multivalued: true
  same_as:
    multivalued: true
  sex_qualifier:
    exact_mappings:
    - biolink:sex_qualifier
    slot_uri: biolink:sex_qualifier
    range: uriorcurie
  sex_qualifier_category: {}
  sex_qualifier_label: {}
  sex_qualifier_namespace: {}
  sources:
    exact_mappings:
    - biolink:sources
    slot_uri: biolink:sources
    range: RetrievalSource
    multivalued: true
    inlined: true
    inlined_as_list: true
  species_context_qualifier:
    exact_mappings:
    - biolink:species_context_qualifier
    slot_uri: biolink:species_context_qualifier
    range: uriorcurie
  species_context_qualifier_category: {}
  species_context_qualifier_label: {}
  species_context_qualifier_namespace: {}
  stage_qualifier:
    exact_mappings:
    - biolink:stage_qualifier
    slot_uri: biolink:stage_qualifier
    range: uriorcurie
  stage_qualifier_category: {}
  stage_qualifier_label: {}
  stage_qualifier_namespace: {}
  subject:
    exact_mappings:
    - biolink:subject
    slot_uri: rdf:subject
    range: uriorcurie
  subject_category:
    exact_mappings:
    - biolink:subject_category
    slot_uri: biolink:subject_category
    range: uriorcurie
  subject_closure:
    multivalued: true
  subject_closure_label:
    multivalued: true
  subject_form_or_variant_qualifier:
    exact_mappings:
    - biolink:subject_form_or_variant_qualifier
    slot_uri: biolink:subject_form_or_variant_qualifier
  subject_label: {}
  subject_namespace: {}
  subject_taxon: {}
  subject_taxon_label: {}
  subsets:
    exact_mappings:
    - biolink:subsets
    slot_uri: biolink:subsets
    range: string
    multivalued: true
  supporting_text:
    exact_mappings:
    - biolink:supporting_text
    slot_uri: biolink:supporting_text
    range: string
    multivalued: true
  symbol:
    exact_mappings:
    - biolink:symbol
    slot_uri: biolink:symbol
    range: string
  synonym:
    exact_mappings:
    - biolink:synonym
    slot_uri: biolink:synonym
    range: string
    multivalued: true
  synonyms: {}
  temporal_context_qualifier:
    exact_mappings:
    - biolink:temporal_context_qualifier
    slot_uri: biolink:temporal_context_qualifier
    range: time
  type:
    exact_mappings:
    - biolink:type
    slot_uri: rdf:type
    range: string
  xref:
    exact_mappings:
    - biolink:xref
    slot_uri: biolink:xref
    range: uriorcurie
    multivalued: true
classes:
  Association:
    description: Post-closurize edge shape (association + subject/object closure expansion).
    slots:
    - id
    - category
    - subject
    - predicate
    - object
    - FDA_adverse_event_level
    - agent_type
    - aggregator_knowledge_source
    - clinical_approval_status
    - disease_context_qualifier
    - disease_context_qualifier_category
    - disease_context_qualifier_closure
    - disease_context_qualifier_closure_label
    - disease_context_qualifier_label
    - disease_context_qualifier_namespace
    - evidence_count
    - file_source
    - frequency_qualifier
    - frequency_qualifier_category
    - frequency_qualifier_label
    - frequency_qualifier_namespace
    - grouping_key
    - has_attribute
    - has_confidence_score
    - has_count
    - has_evidence
    - has_percentage
    - has_quotient
    - has_total
    - knowledge_level
    - medic_approval_date
    - medic_approval_status_raw
    - medic_assertion_flags
    - medic_claim_relation
    - medic_co_administered_with
    - medic_disease_context
    - medic_disease_context_ids
    - medic_is_allergen
    - medic_is_diagnostic_agent
    - medic_jurisdiction
    - medic_object_mention_id
    - medic_pair_confidence
    - medic_pair_n_assertions
    - medic_pair_reliability
    - medic_reliability
    - medic_source
    - medic_subject_mention_id
    - medic_supporting_text_truncated
    - negated
    - object_aspect_qualifier
    - object_category
    - object_closure
    - object_closure_label
    - object_label
    - object_location_in_text
    - object_namespace
    - object_specialization_qualifier
    - object_taxon
    - object_taxon_label
    - onset_qualifier
    - onset_qualifier_category
    - onset_qualifier_label
    - onset_qualifier_namespace
    - original_object
    - original_predicate
    - original_subject
    - population_context_qualifier
    - primary_knowledge_source
    - provided_by
    - publications
    - qualifier
    - qualifiers
    - sex_qualifier
    - sex_qualifier_category
    - sex_qualifier_label
    - sex_qualifier_namespace
    - sources
    - species_context_qualifier
    - species_context_qualifier_category
    - species_context_qualifier_label
    - species_context_qualifier_namespace
    - stage_qualifier
    - stage_qualifier_category
    - stage_qualifier_label
    - stage_qualifier_namespace
    - subject_category
    - subject_closure
    - subject_closure_label
    - subject_form_or_variant_qualifier
    - subject_label
    - subject_namespace
    - subject_taxon
    - subject_taxon_label
    - supporting_text
    - temporal_context_qualifier
  Entity:
    description: Post-closurize node shape (entity + closure expansion + per-predicate
      aggregations).
    slots:
    - id
    - category
    - name
    - full_name
    - symbol
    - description
    - available_from
    - broad_synonym
    - deprecated
    - exact_synonym
    - file_source
    - has_attribute
    - has_biological_sex
    - has_descendant
    - has_descendant_count
    - has_descendant_label
    - has_gene
    - has_phenotype
    - has_phenotype_closure
    - has_phenotype_closure_label
    - has_phenotype_count
    - has_phenotype_label
    - in_taxon
    - in_taxon_label
    - iri
    - medic_application_numbers
    - medic_approved_authorities
    - medic_approved_jurisdictions
    - medic_earliest_approval_date
    - medic_marketing_status_usa
    - medic_mention_id
    - medic_registration_numbers
    - medic_reliability
    - medic_stub
    - namespace
    - narrow_synonym
    - provided_by
    - related_synonym
    - same_as
    - subsets
    - synonym
    - synonyms
    - type
    - xref
  RetrievalSource:
    attributes:
      category:
        exact_mappings:
        - biolink:category
        range: uriorcurie
        multivalued: true
      id:
        exact_mappings:
        - biolink:id
        range: string
      resource_id:
        exact_mappings:
        - biolink:resource_id
        range: uriorcurie
      resource_role:
        exact_mappings:
        - biolink:resource_role
        range: string
      source_record_urls:
        exact_mappings:
        - biolink:source_record_urls
        range: uriorcurie
        multivalued: true
    class_uri: biolink:RetrievalSource