biolink-model.yaml

id: "https://biolink.github.io/biolink-model/ontology/biolink.ttl"
name: biolink model
description: >-
  Entity and association taxonomy and datamodel for life-sciences data
license: https://creativecommons.org/publicdomain/zero/1.0/

prefixes:
  biolink: http://bioentity.io/vocab/
  OBAN: http://purl.org/oban/
  SIO: http://semanticscience.org/resource/SIO_
  wgs: http://www.w3.org/2003/01/geo/wgs84_pos

default_prefix: biolink

default_curi_maps:
  - obo_context
  - monarch_context
  - idot_context
  - semweb_context

id_prefixes:
  - rdf
  - rdfs
  - xsd
  - skos
  - OIO

types:

## Still neeed definition
  phenotype:

  evidence instance:

  chemical formula value:

  identifier type:
    typeof: string
    description: >-
      A string that is intended to uniquely identify a thing
      May be URI in full or compact (CURIE) form

  iri type:
    typeof: string
    description: >-
      An IRI

  label type:
    typeof: string
    description: >-
      A string that provides a human-readable name for a thing

  narrative text:
    typeof: string
    description: >-
      A string that provides a human-readable description of something

  symbol type:
    typeof: string

  chemical formula type:
    typeof: string

  frequency value:
    mappings:
      - UO:0000105

  perecentage frequency value:
    typeof: double
    mappings:
      - UO:0000187

  quotient:
    aliases: ['ratio']
    typeof: double
    mappings:
      - UO:0010006

  unit:
    typeof: string
    mappings:
      - UO:0000000
    id_prefixes:
      - UO
      
  time type:
    typeof: time

  biological sequence:
    typeof: string

slots:

## predicates/relations 

  related to:
    description: >-
      A grouping for any relationship type that holds between any two things
    domain: named thing
    range: named thing
    mappings:
      - owl:topObjectProperty
      - SEMMEDDB:ASSOCIATED_WITH
      
  interacts with:
    description: >-
      holds between any two entities that directly or indirectly interact with each other
    is_a: related to
    in_subset:
      - translator_minimal
    symmetric: true
    mappings:
      - RO:0002434  
      
  physically interacts with:
    is_a: interacts with
    description: >-
      holds between two entities that make physical contact as part of some interaction
    in_subset:
      - translator_minimal
    symmetric: true
    mappings: 
      - WD:P129
      - SEMMEDDB:INTERACTS_WITH  
      
  molecularly interacts with:
    is_a: physically interacts with
    domain: molecular entity
    range: molecular entity
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002436
  
  genetically interacts with:
    is_a: interacts with
    description: >-
      holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality.
    domain: gene
    range: gene
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002435
  
  affects:
    is_a: related to
    description: >-
      describes an entity that has a direct affect on the state or quality of another existing entity.
      Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects risk for' and 'prevents, where the outcome is something that may or may not come to be.
    in_subset:
      - translator_minimal
    mappings:
      - SEMMEDDB:AFFECTS
  
  regulates:
    is_a: affects
    comment: This is a grouping for process-process and entity-entity relations
    mixin: true
    abstract: true
    mappings:
      - WD:P128
    
  positively regulates:
    comment: This is a grouping for process-process and entity-entity relations
    is_a: regulates
    mixin: true
    abstract: true
    
  negatively regulates:
    comment: This is a grouping for process-process and entity-entity relations
    is_a: regulates
    mixin: true
    abstract: true
  
  regulates, process to process:
    is_a: regulates
    domain: occurrent
    range: occurrent
    mappings:
      - RO:0002211
  
  positively regulates, process to process:
    is_a: regulates, process to process
    mixins:
      - positively regulates
    mappings:
      - RO:0002213

  negatively regulates, process to process:
    is_a: regulates, process to process
    mixins:
      - negatively regulates
    mappings:
      - RO:0002212

  regulates, entity to entity:
    aliases: ['activity directly regulates activity of']
    is_a: regulates
    domain: molecular entity
    range: molecular entity
    local_names:
      translator: regulates
      ro: activity directly regulates activity of
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002448

  positively regulates, entity to entity:
    aliases: ['activity directly positively regulates activity of']
    is_a: regulates, entity to entity
    mixins:
      - positively regulates
    local_names:
      translator: positively regulates
      ro: activity directly positively regulates activity of
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002450
      - SEMMEDDB:STIMULATES

  negatively regulates, entity to entity:
    aliases: ['activity directly negatively regulates activity of']
    is_a: regulates, entity to entity
    mixins:
      - negatively regulates
    local_names:
      translator: negatively regulates
      ro: activity directly negatively regulates activity of
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002449
      - SEMMEDDB:INHIBITS

  disrupts:
    is_a: affects
    description: >-
      describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
    in_subset:
      - translator_minimal
    mappings:
      - SEMMEDDB:DISRUPTS
      
  has gene product:
    is_a: related to
    description: >-
      holds between a gene and a transcribed and/or translated product generated from it
    domain: gene
    range: gene product
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002205
      - WD:P688

  homologous to:
    is_a: related to
    aliases: ['in homology relationship with']
    description: >-
      holds between two biological entities that have common evolutionary origin
    comment: typically used to describe homology relationships between genes or gene products
    in_subset:
      - translator_minimal
    mappings:
      - RO:HOM0000001
      - SIO:010302

  paralogous to:
    is_a: homologous to
    description: >-
      a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
    in_subset:
      - translator_minimal
    mappings:
      - RO:HOM0000011

  orthologous to:
    is_a: homologous to
    description: >-
      a homology relationship between entities (typically genes) that diverged after a speciation event.
    in_subset:
      - translator_minimal
    mappings:
      - RO:HOM0000017
      - WD:P684

  xenologous to:
    is_a: homologous to
    description: >-
      a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.
    in_subset:
      - translator_minimal
    mappings:
      - RO:HOM0000018

  coexists with:
    is_a: related to
    description: >-
      holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region
    in_subset:
      - translator_minimal
    mappings:
      - SEMMEDDB:COEXISTS_WITH

  in pathway with:
    description: >-
      holds between two genes or gene products that are part of in the same biological pathway
    is_a: coexists with
    domain: gene or gene product
    range: gene or gene product
    in_subset:
      - translator_minimal

  in complex with:
    description: >-
      holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex
    is_a: coexists with
    domain: gene or gene product
    range: gene or gene product
    in_subset:
      - translator_minimal

  in cell population with:
    description: >-
      holds between two genes or gene products that are expressed in the same cell type or population 
    is_a: coexists with
    domain: gene or gene product
    range: gene or gene product
    in_subset:
      - translator_minimal

  co-localizes with:
    description: >-
      holds between two entities that are observed to be located in the same place.
    is_a: coexists with
    in_subset:
      - translator_minimal
    mappings:
      - RO:00002325

  gene associated with condition:
    is_a: related to
    description: >-
      holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with
    domain: gene
    range: disease or phenotypic feature
    in_subset:
      - translator_minimal
    mappings:
      - WD:P2293

  affects risk for:
    is_a: related to
    description: >-
      holds between two entities where exposure to one entity alters the chance of developing the other 
    in_subset:
      - translator_minimal

  predisposes:
    is_a: affects risk for
    description: >-
      holds between two entities where exposure to one entity increases the chance of developing the other 
    in_subset:
      - translator_minimal
    mappings:
      - SEMMEDDB:PREDISPOSES

  contributes to:
    is_a: related to
    description: >-
      holds between two entities where the occurrence, existence, or activity of one causes or contributes to the occurrence or generation of the other
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002326
      
  causes:
    description: >-
      holds between two entities where the occurrence, existence, or activity of one causes the occurrence or  generation of the other
    is_a: contributes to
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002410
      - SEMMEDDB:CAUSES
      - WD:P1542

  treats :
    aliases: ['is substance that treats']
    is_a: affects
    description: >-
      holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat 
    range: disease or phenotypic feature
    in_subset:
      - translator_minimal
    inverse: treated by
    mappings:
      - RO:0002606
      - RO:0003307
      - SEMMEDDB:TREATS
      - WD:P2175

  prevents :
    is_a: affects risk for
    description: >-
      holds between an entity whose application or use reduces the likelihood of a potential outcome. 
      Typically used to associate a chemical substance, exposure, activity, or medical intervention that can prevent
      the onset a disease or phenotypic feature.
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002559
      - SEMMEDDB:PREVENTS

  correlated with:
    is_a: related to
    description: >-
      holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.
    domain: disease or phenotypic feature
    range: molecular entity
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002610

  has biomarker:
    is_a: correlated with
    description: >-
      holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.
    domain: disease or phenotypic feature
    range: molecular entity
    in_subset:
      - translator_minimal
    inverse: biomarker for

  biomarker for:
    is_a: correlated with
    description: >-
      holds between a measurable molecular entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.
    domain: molecular entity
    range: disease or phenotypic feature
    in_subset:
      - translator_minimal
    inverse: has biomarker
    mappings:
      - RO:0002607

  treated by:
    is_a: related to
    description: >-
      holds between a disease or phenotypic feature and a therapeutic process or chemical substance that is used to treat the condition 
    domain: disease or phenotypic feature
    in_subset:
      - translator_minimal
    inverse: treats
    mappings: 
      - RO:0002302
      - WD:P2176

  expressed in:
    is_a: related to
    description: >-
      holds between a gene or gene product and an anatomical entity in which it is expressed
    domain: gene or gene product
    range: anatomical entity
    in_subset:
      - translator_minimal
    inverse: expresses
    mappings:
      - RO:0002206

  expresses:
    is_a: related to
    description: >-
      holds between an anatomical entity and gene or gene product that is expressed there
    domain: anatomical entity
    range: gene or gene product
    in_subset:
      - translator_minimal
    inverse: expressed in
    mappings:
      - RO:0002292

  has phenotype:
    is_a: related to
    description: >-
      holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). 
    domain: biological entity
    range: phenotype
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002200

  occurs in:
    is_a: related to
    description: >-
      holds between a process and a material entity or site within which the process occurs
    in_subset:
      - translator_minimal
    mappings:
      - BFO:0000066
      - SEMMEDDB:OCCURS_IN
      - SEMMEDDB:PROCESS_OF

  located in:
    is_a: related to
    description: >-
      holds between a material entity and a material entity or site within which it is located (but of which it is not considered a part)
    in_subset:
      - translator_minimal
    inverse: location of
    mappings:
      - RO:0001025

  location of:
    is_a: related to
    description: >-
      holds between material entity or site and a material entity that is located within it (but not considered a part of it) 
    in_subset:
      - translator_minimal
    inverse: located in
    mappings:  
      - RO:0001015
      - SEMMEDDB:LOCATION_OF
      - WD:276

  model of:
    is_a: related to
    description: >-
      holds between an entity and some other entity it approximates for purposes of scientific study, in virtue of its exibiting similar features of the studied entity.    
    in_subset:
      - translator_minimal
    mappings:  
      - RO:0003301

  overlaps:
    is_a: related to
    description: >-
      holds between entties that overlap in their extents (materials or processes)
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002131

  has part:
    is_a: overlaps
    description: >-
      holds between wholes and their parts (material entities or processes)
    in_subset:
      - translator_minimal
    inverse: part of
    mappings:
      - BFO:0000051
      - WD:P527

  part of:
    is_a: overlaps
    description: >-
      holds between parts and wholes (material entities or processes)
    in_subset:
      - translator_minimal
    inverse: has part
    mappings:
      - BFO:0000050
      - SEMMEDDB:PART_OF      
      - WD:P361

  has participant:
    is_a: related to
    description: >-
      holds between a process and a continuant, where the continuant is somehow involved in the process 
    domain: occurrent
    in_subset:
      - translator_minimal
    inverse: participates in
    mappings:
     - RO:0000057
     - WD:P2283

  has input:
    is_a: has participant
    description: >-
      holds between a process and a continuant, where the continuant is an input into the process
    domain: occurrent
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002233
      - SEMMEDDB:USES

  participates in:
    is_a: related to
    description: >-
      holds between a continuant and a process, where the continuant is somehow involved in the process
    range: occurrent
    in_subset:
      - translator_minimal
    inverse: has participant
    mappings:
      - RO:0000056

  actively involved in:
    is_a: participates in
    description: >-
      holds between a continuant and a process or function, where the continuant actively contributes to part or all of the process or function it realizes
    range: occurrent
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002331

  capable of:
    is_a: actively involved in
    description: >-
      holds between a continuant and process or function, where the continuant alone has the ability to carry out the process or function. 
    range: occurrent
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002215

  derives into:
    is_a: related to
    description: >-
      holds between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
    in_subset:
      - translator_minimal
    inverse: derives from
    mappings:
      - RO:0001001
      - SEMMEDDB:CONVERTS_TO

  derives from:
    is_a: related to
    description: >-
      holds between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
    in_subset:
      - translator_minimal
    inverse: derives into
    mappings:
      - RO:0001000

  manifestation of:
    is_a: related to
    description: >-
      used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome
    range: disease
    in_subset:
      - translator_minimal
    mappings:
      - SEMMEDDB:MANIFESTATION_OF
      - WD:P1557

  produces:
    is_a: related to
    description: >-
      holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
    in_subset:
      - translator_minimal
    mappings:
      - RO:0003000
      - WD:P1056
      - SEMMEDDB:PRODUCES

  precedes:
    is_a: related to
    description: >-
      holds between two processes, where one completes before the other begins
    domain: occurrent
    range: occurrent
    in_subset:
      - translator_minimal
    mappings:
      - BFO:0000063
      - SEMMEDDB:PRECEDES
      - WD:P156

  same as:
    is_a: related to
    description: >-
      holds between two entities that are considered equivalent to each other
    in_subset:
      - translator_minimal
    mappings:
      - owl:equivalentClass
      - owl:sameAs
      - skos:exactMatch
      - WD:P2888

  subclass of:
    is_a: related to
    description: >-
      holds between two classes where the domain class is a specialization of the range class
    domain: ontology class
    range: ontology class
    in_subset:
      - translator_minimal
    mappings:
      - rdfs:subClassOf
      - SEMMEDDB:IS_A
      - WD:P279
 
## property slots

  node property:
    description: >-
      A grouping for any property that holds between a node and a value
    domain: named thing
    mappings:
      - owl:topAnnotationProperty

  id:
    is_a: node property
    identifier: true
    description: >-
      A unique identifier for a thing.
      Must be either a CURIE shorthand for a URI or a complete URI
    in_subset:
      - translator_minimal
    domain: named thing
    range: identifier type
      
  iri:
    is_a: node property
    description: >-
      An IRI for the node. This is determined by the id using expansion rules.
    in_subset:
      - translator_minimal
    domain: named thing
    range: iri type
  
  name:
    is_a: node property
    aliases: ['label', 'display name']
    domain: named thing
    range: label type
    description: >-
      A human-readable name for a thing
    in_subset:
      - translator_minimal
    mappings:
      - "rdfs:label"
  
  category:
    is_a: node property
    domain: named thing
    range: label type
    description: >-
      Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.
      In a neo4j database this MAY correspond to the neo4j label tag
    is_class_field: true
    in_subset:
      - translator_minimal
    mappings:
      - "rdf:type"
  
  full name:
    is_a: node property
    domain: named thing
    range: label type
    description: >-
      a long-form human readable name for a thing
  
  description:
    is_a: node property
    domain: named thing
    range: narrative text
    description: >-
      a human-readable description of a thing
    in_subset:
      - translator_minimal
    mappings:
      - dcterms:description
  
  systematic synonym:
    is_a: node property
    domain: named thing
    range: label type
    description: >-
      more commonly used for gene symbols in yeast
    
  association slot:
    abstract: true
    domain: association
    aliases: ['edge property', 'statement property']
    description: >-
      any slot that relates an association to another entity
    
  subject:
    is_a: association slot
    local_names:
      ga4gh: annotation subject
      neo4j: node with outgoing relationship
    description: >-
      connects an association to the subject of the association.
      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
    required: true
#    range: named thing
    mappings:
      - rdf:subject
      - owl:annotatedSource
      - oban:association_has_subject
      
  object:
    is_a: association slot
    description: >-
      connects an association to the object of the association.
      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
    required: true
#    range: named thing
    local_names:
      ga4gh: descriptor
      neo4j: node with incoming relationship
    mappings:
      - rdf:object
      - owl:annotatedTarget
      - oban:association_has_object

  edge label:
    is_a: association slot
    description: >-
      A high-level grouping for the relationship type. AKA minimal predicate.
      This is analogous to category for nodes. 
    note: in neo4j this corresponds to the relationship type and the convention is for a snake_case label
    range: label type
    required: false

  relation:
    is_a: association slot
    description: >-
      the relationship type by which a subject is connected to an object in an association
    range: relationship type
    required: true
    local_names:
      ga4gh: annotation predicate
      translator: predicate
    mappings:
      - "rdf:predicate"
      - "owl:annotatedProperty"
      - "oban:association_has_predicate"
      
  negated:
    is_a: association slot
    range: boolean
    description: >-
      if set to true, then the association is negated i.e. is not true

  has confidence level:
    is_a: association slot
    range: confidence level
    description: >-
      connects an association to a qualitative term denoting the level of confidence

  has evidence:
    is_a: association slot
    range: evidence instance
    description: >-
      connects an association to an instance of supporting evidence
    mappings:
      - RO:0002558
      
  provided by:
    is_a: association slot
    range: provider
    description: >-
      connects an association to the agent (person, organization or group) that provided it
    mappings:
      - pav:providedBy

  association type:
    is_a: association slot
    range: ontology class
    description: >-
      connects an association to the type of association (e.g. gene to phenotype)
    mappings:
      - rdf:type

  creation date:
    is_a: node property
    range: date
    description: >-
      date on which thing was created. This can be applied to nodes or edges
    mappings:
      - dcterms:created

  update date:
    is_a: node property
    range: date
    description: >-
      date on which thing was updated. This can be applied to nodes or edges
  
  in taxon:
    is_a: related to
    domain: thing with taxon
    range: organism taxon
    description: >-
      connects a thing to a class representing a taxon
    in_subset:
      - translator_minimal
    mappings:
      - RO:0002162
      - WD:P703
      
  latitude:
    is_a: node property
    range: float
    description: >-
      latitude
    mappings:
      - wgs:lat

  longitude:
    is_a: node property
    range: float
    description: >-
      longitude
    mappings:
      - wgs:long

  has chemical formula:
    is_a: node property
    range: chemical formula value
    description: >-
      description of chemical compound based on element symbols
    mappings:
      - WD:P274

  aggregate statistic:
    is_a: node property
    abstract: true
      
  has count:
    description: >-
      number of things with a particular property
    is_a: aggregate statistic
    range: integer

  has total:
    description: >-
      total number of things in a particular reference set
    is_a: aggregate statistic
    range: integer

  has quotient:
    is_a: aggregate statistic
    range: double

  has percentage:
    description: >-
      equivalent to has quotient multiplied by 100
    is_a: aggregate statistic
    range: double

  timepoint:
    is_a: node property
    range: time type
    description: >-
      a point in time

  stage qualifier:
    is_a: association slot
    range: life stage
    path: "object/during"
    description: >-
      stage at which expression takes place

  quantifier qualifier:
    is_a: association slot
    range: ontology class
    description: >-
      A measurable quantity for the object of the association

  qualifiers:
    singular_name: qualifier
    description: >-
      connects an association to qualifiers that modify or qualify the meaning of that association
    local_names:
      ga4gh: annotation qualifier
    is_a: association slot
    multivalued: true
    range: ontology class

  frequency qualifier:
    description: >-
      a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject
    is_a: association slot
    range: frequency value

  severity qualifier:
    description: >-
      a qualifier used in a phenotypic association to state how severe the phenotype is in the subject
    is_a: association slot
    range: severity value

  sex qualifier:
    description: >-
      a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.
    is_a: association slot
    range: biological sex

  onset qualifier:
    description: >-
      a qualifier used in a phenotypic association to state when the phenotype appears is in the subject
    is_a: association slot
    range: onset

  clinical modifier qualifier:
    description: >-
      Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology,
      with respect to severity, laterality, age of onset, and other aspects
    is_a: association slot
    range: clinical modifier

  sequence variant qualifier:
    description: >-
      a qualifier used in an association where the variant
    is_a: association slot
    range: sequence variant
    
  publications:
    singular_name: publication
    description: >-
      connects an association to publications supporting the association
    is_a: association slot
    multivalued: true
    range: publication

  has biological sequence:
    is_a: node property
    description: >-
      connects a genomic feature to its sequence
    range: biological sequence

  has molecular consequence:
    is_a: related to
    description: >-
      connects a sequence variant to a class describing the molecular
      consequence. E.g.  SO:0001583
    range: ontology class

    ## genotypes

  has gene:
    is_a: node property
    description: >-
      connects and entity to a single gene
    range: gene
    
  has zygosity:
    is_a: node property
#    domain: single locus feature complement
    range: zygosity

  filler:
    is_a: node property
    range: named thing
    description: >-
      The value in a property-value tuple

  phase:
    is_a: node property
    description: >-
      TODO

  genome build:
    is_a: node property
    description: >-
      TODO

  interbase coordinate:
    is_a: node property
    description: >-
      TODO

  start interbase coordinate:
    is_a: interbase coordinate

  end interbase coordinate:
    is_a: interbase coordinate
    
classes:

  ## ------
  ## RELATIONSHIP TYPES
  ## ------

  relationship type:
    description: >-
      An OWL property used as an edge label
  

  attribute:
    subclass_of: PATO:0000001
    mixins:
      - ontology class
    description: >-
      A property or characteristic of an entity

  ## ------
  ## THINGS
  ## ------

  biological sex:
    subclass_of: "PATO:0000047"
    is_a: attribute

  phenotypic sex:
    description: >-
      An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.
    subclass_of: "PATO:0001894"
    is_a: biological sex

  genotypic sex:
    description: >-
      An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.
    subclass_of: "PATO:0020000"
    is_a: biological sex

  severity value:
    description: >-
      describes the severity of a phenotypic feature or disease
    is_a: attribute
  
  frequency value:
    description: >-
      describes the frequency of occurrence of an event or condition
    is_a: attribute
  
  clinical modifier:
    description: >-
      Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology,
      with respect to severity, laterality, age of onset, and other aspects
    subclass_of: "HP:0012823"
    is_a: attribute
  
  onset:
    description: >-
      The age group in which manifestations appear
    mappings:
      - "HP:0003674"
    is_a: attribute
  
  relationship quantifier:
    abstract: true
    mixin: true
    
  senstivity quantifier:
    is_a: relationship quantifier
    mixin: true
    
  specificity quantifier:
    is_a: relationship quantifier
    mixin: true
    
  pathognomonicity quantifier:
    is_a: specificity quantifier
    description: >-
      A relationship quantifier between a variant or symptom and a disease, which is
      high when the presence of the feature implies the existence of the disease
    mixin: true
  
  frequency quantifier:
    is_a: relationship quantifier
    mixin: true
    slots:
      - has count
      - has total
      - has quotient
      - has percentage
  
  named thing:
    description: "a databased entity or concept/class"
    slots:
      - id
      - name
      - category
    subclass_of: BFO:0000001
    mappings:
      - "UMLSSG:OBJC"
      - WD:Q35120

  biological entity:
    is_a: named thing
    abstract: true
    mappings:
      - WD:Q28845870
        
  ontology class:
    is_a: named thing
    description: "a concept or class in an ontology, vocabulary or thesaurus"
      
  gene ontology class:
    description: >-
      an ontology class that describes a functional aspect of a gene, gene prodoct or complex
    is_a: ontology class
    flags:
      - testing
      
  thing with taxon:
    abstract: true
    mixin: true
    description: >-
      A mixin that can be used on any entity with a taxon
    slots:
      - in taxon
      
  organism taxon:
    is_a: ontology class
    values_from:
      - NCBITaxon
    mappings:
      - WD:Q16521
      
  organismal entity:
    description: >-
      A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities
    abstract: true
    is_a: biological entity
    mappings:
      - WD:Q7239
      
  individual organism:
    mixins:
      - thing with taxon
    is_a: organismal entity
    subclass_of: "NCBITaxon:1"
    mappings:
      - SIO:010000
      - WD:Q795052

  case:
    aliases: ['patient', 'proband']
    is_a: individual organism
    description: >-
      An individual organism that has a patient role in some clinical context.
    
  population of individual organisms:
    local_names:
      ga4gh: population
    mixins:
      - thing with taxon
    is_a: organismal entity
    subclass_of: PCO:0000001
    mappings:
      - SIO:001061
    id_prefixes:
      - ANCESTRO
      
  biosample:
    aliases: ['biospecimen', 'sample']
    mixins:
      - thing with taxon
    is_a: organismal entity
    mappings:
      - SIO:001050
      
  disease or phenotypic feature:
    aliases: ['phenome']
    is_a: biological entity
    description: >-
      Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.
    mixins:
      - thing with taxon
    union_of:
      - disease
      - phenotypic feature
      
  disease:
    aliases: ['condition', 'disorder', 'medical condition']
    is_a: disease or phenotypic feature
    mappings:
      - "MONDO:0000001"
      - "WD:Q12136"
      - SIO:010299
      - UMLSSG:DISO
      
  phenotypic feature:
    aliases: ['sign', 'symptom', 'phenotype', 'trait', 'endophenotype']
    is_a: disease or phenotypic feature
    mappings:
      - "UPHENO:0001001"
      - SIO:010056
      - WD:Q169872
      
  environment:
    aliases: ['environment', 'exposure', 'experimental condition']
    is_a: biological entity
    description: >-
      A feature of the environment of an organism that influences one or more phenotypic features
      of that organism, potentially mediated by genes
    mappings:
      - SIO:000955

  information content entity:
    aliases: ['information', 'information artefact', 'information entity']
    abstract: true
    is_a: named thing
    description: >-
      a piece of information that typically describes some piece of biology or is used as support.
    mappings:
      - "IAO:0000030"
      - "UMLSSG:CONC"
      
  confidence level:
    is_a: information content entity
    description: >-
      Level of confidence in a statement
    values_from:
      - cio
    mappings:
      - "CIO:0000028"
      
  evidence type:
    is_a: information content entity
    aliases: ['evidence code']
    description: >-
      Class of evidence that supports an association
    values_from:
      - eco
    mappings:
      - "ECO:0000000"
      
  publication:
    is_a: information content entity
    aliases: ['reference']
    description: >-
      Any published piece of information. Can refer to a whole publication,
      or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP).
      The scope is intended to be general and include information published on the web as well as journals.
    mappings:
      - "IAO:0000311"

  administrative entity:
    abstract: true
    
  provider:
    is_a: administrative entity
    aliases: ['agent', 'group']
    description: >-
      person, group, organization or project that provides a piece of information
    mappings:
      - UMLSSG:ORGA
      
  molecular entity:
    is_a: biological entity
    mixins:
      - thing with taxon
    aliases: ['bioentity']
    description: "A gene, gene product, small molecule or macromolecule (including protein complex)"
    comment: >-
      Check SIO mapping - also mapped to chemical substance.
    mappings:
      - SIO:010004
      - WD:Q43460564

  chemical substance:
    is_a: molecular entity
    description: >-
      May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex
      material with multiple chemical entities as part
    subclass_of: "CHEBI:24431"
    mappings:
      - "SIO:010004"
      - "UMLSSG:CHEM"
      - "WD:Q79529"
    id_prefixes:
      - CHEMBL.TARGET
      
  drug:
    is_a: chemical substance
    description: >-
      A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
    comment: >-
      The CHEBI ID represents a role rather than a substance
    mappings:
      - WD:Q12140
      - CHEBI:23888
      
  metabolite:
    is_a: chemical substance
    description: >-
      Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.
    comment: >-
      The CHEBI ID represents a role rather than a substance
    mappings:
      - CHEBI:25212
#
#    attribute:
#      subclass_of: PATO:0000001
#      mixins:
#        - ontology class
#      description: >-
#        A property or characteristic of an entity
    
  anatomical entity:
    is_a: organismal entity
    mixins:
      - thing with taxon
    subclass_of: UBERON:0001062
    description: >-
      A subcellular location, cell type or gross anatomical part
    mappings:
      - "UMLSSG:ANAT"
      - SIO:010046
      - WD:Q4936952

  life stage:
    is_a: organismal entity
    mixins:
      - thing with taxon
    subclass_of: UBERON:0000105
    description: >-
      A stage of development or growth of an organism, including post-natal adult stages

  planetary entity:
    is_a: named thing
    description: >-
      Any entity or process that exists at the level of the whole planet
      
  environmental process:
    is_a: planetary entity
    mixins:
      - occurrent
    subclass_of: ENVO:02500000
      
  environmental feature:
    is_a: planetary entity
    subclass_of: ENVO:00002297
      
  clinical entity:
    is_a: named thing
    description: >-
      Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities
      
  clinical trial:
    is_a: clinical entity
      
  clinical intervention:
    is_a: clinical entity
      
  device:
    is_a: named thing
    description: >-
      A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
    mappings:
      - "UMLSSG:DEVI"

  genomic entity:
    is_a: molecular entity
    aliases: ['sequence feature']
    description: >-
      an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)
    slots:
      - has biological sequence
    mappings:
      - "SO:0000110"
      - "UMLSSG:GENE"

  genome:
    is_a: genomic entity
    description: >-
      A genome is the sum of genetic material within a cell or virion.
    mappings:
      - SO:0001026
      - SIO:000984
      - WD:Q7020

  transcript:
    is_a: genomic entity
    description: >-
      An RNA synthesized on a DNA or RNA template by an RNA polymerase
    mappings:
      - SO:0000673
      - SIO:010450

  exon:
    is_a: genomic entity
    description: >-
      A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing
    mappings:
      - SO:0000147
      - SIO:010445
      - WD:Q373027

  coding sequence:
    is_a: genomic entity
    mappings:
      - SO:0000316
      - SIO:001390
      
  macromolecular machine:
    is_a: genomic entity
    union_of:
      - gene
      - gene product
      - macromolecular complex
    description: >-
      A union of gene, gene product, and macromolecular complex.
      These are the basic units of function in a cell. They either carry out individual
      biological activities, or they encode molecules which do this.
    slot_usage:
      name:
        range: symbol type
        description: >-
          genes are typically designated by a short symbol and a full name. We map the symbol to the default display name
          and use an additional slot for full name
      
  gene or gene product:
    is_a: macromolecular machine
    union_of:
      - gene
      - gene product
    description: >-
      a union of genes or gene products.
      Frequently an identifier for one will be used as proxy for another
      
  gene:
    is_a: gene or gene product
    aliases: ['locus']
    mappings:
      - "SO:0000704"
      - "SIO:010035"
      - "WD:Q7187"
      - "UMLSSG:GENE"
    id_prefixes:
      - NCBIGene
      - ENSEMBL
      - HGNC
      - MGI
      - ZFIN
      - dictyBase
      - WB
      - SGD
      - PomBase
      
  gene product:
    is_a: gene or gene product
    description: >-
      The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules
    union_of:
      - protein
      - RNA product
    mappings:
      - WD:Q424689
    
  protein:
    is_a: gene product
    aliases: ['polypeptide']
    description: >-
      A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
    mappings:
      - "PR:000000001"
      - "SIO:010043"
      - "WD:Q8054"
    id_prefixes:
      - UniProtKB
      - PR
      - ENSEMBL
    
  gene product isoform:
    is_a: gene product
    description: >-
      This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to
      represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary,
      or it may represent the superclass of all isoforms.
    entity: true
    abstract: true
    
  protein isoform:
    aliases: ['proteoform']
    is_a: protein
    description: >-
      Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/
    mixins:
      - gene product isoform
    id_prefixes:
      - UniProtKB
      - PR
      - ENSEMBL
    
  RNA product:
    is_a: gene product
    mappings:
      - "CHEBI:33697"
      - SIO:010450
      - WD:Q11053
    id_prefixes:
      - RNAcentral
    
  RNA product isoform:
    is_a: RNA product
    description: >-
      Represents a protein that is a specific isoform of the canonical or reference RNA
    mixins:
      - gene product isoform
    id_prefixes:
      - RNAcentral
      
  noncoding RNA product:
    is_a: RNA product
    id_prefixes:
      - RNAcentral
      - NCBIGene
      - ENSEMBL
    subclass_of: SO:0000655
    mappings:
      - SIO:001235
      
  microRNA:
    is_a: noncoding RNA product
    subclass_of: SO:0000276
    mappings:
      - SIO:001397
      - WD:Q310899
    id_prefixes:
      - MIR
        
  macromolecular complex:
    is_a: macromolecular machine
    subclass_of: "GO:0032991"
    mappings:
      - "SIO:010046"
      - WD:Q22325163
    id_prefixes:
      - IntAct
      - GO
      - PR
      - Reactome
      
  gene grouping:
    abstract: true
    mixin: true
    description: >-
      any grouping of multiple genes or gene products

  gene family:
    is_a: molecular entity
    mappings:
      - SIO:001380
      - "NCIT:C20130"
      - WD:Q417841
    mixins:
      - gene grouping
    description: >-
      any grouping of multiple genes or gene products related by common descent
    id_prefixes:
      - PANTHER
      
  zygosity:
    is_a: attribute
    mappings:
      - "GENO:0000133"

  genotype:
    is_a: genomic entity
    description: >-
      An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background
    comment: >-
      Consider renaming as genotypic entity
    slots:
      - has zygosity
    mappings:
      - "GENO:0000536"
      - SIO:001079

  haplotype:
    is_a: genomic entity
    description: >-
      A set of zero or more Alleles on a single instance of a Sequence[VMC]
#    slots:
#      - completeness
    mappings:
      - GENO:0000871
      - VMC:Haplotype

  sequence variant:
    aliases: ['allele']
    local_names:
      agr: allele
    is_a: genomic entity
    description: >-
      An allele that varies in its sequence from what is considered the reference allele at that locus.
    comment: >-
      This class is for modeling the specific state at a locus. A single dbSNP rs ID could correspond to more
      than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)
    mappings:
      - GENO:0000002
      - WD:Q15304597
      - SIO:010277
      - VMC:Allele
    id_prefixes:
      - ClinVar
      - WD
      - CIViC
    alt_descriptions:
      - description: "An enitity that describes a single affected, endogenous allele.  These can be of any type that matches that definition"
        source: AGR
      - description: "A contiguous change at a Location"
        source: VMC
    slots:
      - has gene
    slot_usage:
      has gene:
        multivalued: true
        description: Each allele can be associated with any number of genes
      has biological sequence:
        description: >-
          The state of the sequence w.r.t a reference sequence
      id:
        examples:
          - value: ZFIN:ZDB-ALT-980203-1091
            description: ti282a allele from ZFIN
          - value: ClinVarVariant:17681
            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)

  drug exposure:
    aliases: ['drug intake', 'drug dose']
    is_a: environment
    description: >-
      A drug exposure is an intake of a particular chemical substance
#    slots:
#      - has input
    slot_usage:
      drug:
        range: chemical substance
        required: true
        multivalued: true
    mappings:
      - "ECTO:0000509"
      - SIO:001005

  treatment:
    aliases: ['medical action']
    is_a: environment
    description: >-
      A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures'
    slots:
      - treats
    slot_usage:
      treats:
        range: disease or phenotypic feature
        required: true
      has exposure parts:
        multivalued: true
        range: drug exposure
        required: true
    mappings:
      - "OGMS:0000090"
      - SIO:001398

  geographic location:
    is_a: planetary entity
    description: >-
      a location that can be described in lat/long coordinates
    slots:
      - latitude
      - longitude
    mappings:
      - "UMLSSG:GEOG"
      
  geographic location at time:
    is_a: geographic location
    description: >-
      a location that can be described in lat/long coordinates, for a particular time
    slots:
      - timepoint
      
  ## ------
  ## ASSOCIATIONS
  ## ------
      
  association:
    is_a: information content entity
    description: >-
      A typed association between two entities, supported by evidence
    comment: This is roughly the model used by biolink and ontobio at the moment
    slots:
      - association type
      - subject
      - negated
      - relation
      - object
      - qualifiers
      - publications
      - provided by
    mappings:
      - "OBAN:association"
      - "rdf:Statement"
      - "owl:Axiom"

  genotype to genotype part association:
    is_a: association
    defining_slots:
      - subject
      - object
    description: >-
      Any association between one genotype and a genotypic entity that is a sub-component of it
    slot_usage:
      relation:
        subproperty_of: has variant part
      subject:
        range: genotype
        description: >-
          parent genotype
        definitional: true
      object:
        range: genotype
        description: >-
          child genotype
        definitional: true

  genotype to gene association:
    is_a: association
    defining_slots:
      - subject
      - object
    description: >-
      Any association between a genotype and a gene.
      The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality
    slot_usage:
      relation:
        description: >-
          the relationship type used to connect genotype to gene
      subject:
        range: genotype
        description: >-
          parent genotype
        definitional: true
      object:
        range: gene
        description: >-
          gene implicated in genotype
        definitional: true

  genotype to variant association:
    is_a: association
    defining_slots:
      - subject
      - object
    description: >-
      Any association between a genotype and a sequence variant.
    slot_usage:
      relation:
        description: >-
          the relationship type used to connect genotype to gene
      subject:
        range: genotype
        description: >-
          parent genotype
        definitional: true
      object:
        range: sequence variant
        description: >-
          gene implicated in genotype
        definitional: true

  gene to gene association:
    aliases: ['molecular or genetic interaction']
    abstract: true
    is_a: association
    defining_slots:
      - subject
      - object
    description: >-
      abstract parent class for different kinds of gene-gene or gene product to gene product relationships.
      Includes homology and interaction.
    slot_usage:
      subject:
        range: gene or gene product
        description: >-
          the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary.
          We allow a gene product to stand as proxy for the gene or vice versa
        definitional: true
      object:
        range: gene or gene product
        description: >-
          the object gene in the association. If the relation is symmetric, subject vs object is arbitrary.
          We allow a gene product to stand as proxy for the gene or vice versa
        definitional: true


  gene to gene homology association:
    is_a: gene to gene association
    defining_slots:
      - subject
      - object
      - relation
    description: >-
      A homology association between two genes. May be orthology (in which case the species of subject and object
      should differ) or paralogy (in which case the species may be the same)
    symmetric: true
    slot_usage:
      relation:
        subproperty_of: homologous to
        description: >-
          homology relationship type
        definitional: true


  pairwise interaction association:
    is_a: association
    mixin: true
    abstract: true
    description: >-
      An interaction at the molecular level between two physical entities
    slot_usage:
      subject:
        range: molecular entity
      id:
        description: >-
          identifier for the interaction. This may come from an interaction database such as IMEX.
        examples:
          - value: WB:WBInteraction000538741
        values_from:
          - IMEX
          - BioGRID
      relation:
        subproperty_of: molecularly interacts with
#        range: molecularly interacts with
        values_from:
          - ro
          - mi
        description: "interaction relationship type"
        definitional: true
        examples:
          - value: RO:0002447
            description: the subject molecular phosphorylates the object molecule
      object:
        range: molecular entity
      interacting molecules category:
        # TODO: Is this correct?
        range: ontology class
        subclass_of: "MI:1046"
        examples:
          - value: MI:1048
            description: smallmolecule-protein

  pairwise gene to gene interaction:
    is_a: gene to gene association
    defining_slots:
      - subject
      - object
      - relation
    mixins:
      - pairwise interaction association
    description: >-
      An interaction between two genes or two gene products.
      May be physical (e.g. protein binding) or genetic (between genes).
      May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)
    symmetric: true
    slot_usage:
      relation:
        subproperty_of: molecularly interacts with
        values_from:
          - ro
          - mi
        description: "interaction relationship type"
        definitional: true

  cell line to thing association:
    is_a: association
    defining_slots:
      - subject
    abstract: true
    description: >-
      An relationship between a cell line and another entity
    slot_usage:
      subject:
        range: cell line
        definitional: true

  # TODO: figure out what gives with subject ange
  cell line to disease or phenotypic feature association:
    is_a: association
    mixins:
      - cell line to thing association
      - thing to disease or phenotypic feature association
    description: >-
      An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype
    slot_usage:
      subject:
#        - range: cell line
#        - range: disease or phenotypic feature
        range: disease or phenotypic feature
        
  chemical to thing association:
    is_a: association
    defining_slots:
      - subject
    abstract: true
    description: >-
      An interaction between a chemical entity and another entity
    slot_usage:
      subject:
        range: chemical substance
        description: "the chemical substance or entity that is an interactor"
        definitional: true

  case to thing association:
    is_a: association
    defining_slots:
      - subject
    abstract: true
    description: >-
      An abstract association for use where the case is the subject
    slot_usage:
      subject:
        range: case
        description: "the case (e.g. patient) that has the property"
        definitional: true

  chemical to disease or phenotypic feature association:
    is_a: association
    mappings:
      - SIO:000993
    defining_slots:
      - subject
      - object
    mixins:
      - chemical to thing association
      - thing to disease or phenotypic feature association
    description: >-
      An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to
      or exacerbates the phenotype
    slot_usage:
      object:
        range: disease or phenotypic feature
        description: "the disease or phenotype that is affected by the chemical"
        definitional: true
        
  chemical to pathway association:
    is_a: association
    mappings:
      - SIO:001250
    defining_slots:
      - subject
      - object
    mixins:
      - chemical to thing association
    description: >-
      An interaction between a chemical entity and a biological process or pathway
    slot_usage:
      object:
        range: pathway
        description: "the pathway that is affected by the chemical"
        definitional: true
        
  chemical to gene association:
    is_a: association
    mappings:
      - SIO:001257
    defining_slots:
      - subject
      - object
    mixins:
      - chemical to thing association
    description: >-
      An interaction between a chemical entity and a gene or gene product
    slot_usage:
      object:
        range: gene or gene product
        description: "the gene or gene product that is affected by the chemical"
        definitional: true
        
  biosample to thing association:
    is_a: association
    defining_slots:
      - subject
    abstract: true
    description: >-
      An association between a biosample and something
    slot_usage:
      subject:
        range: biosample
        description: >-
          the biosample being described
        definitional: true
        
  biosample to disease or phenotypic feature association:
    is_a: association
    defining_slots:
      - subject
      - object
    mixins:
      - biosample to thing association
      - thing to disease or phenotypic feature association
    description: >-
      An association between a biosample and a disease or phenotype
        definitional: true

  frequency qualifier:
    mixin: true
    description: >-
      Qualifier for freqency type associations

  entity to feature or disease qualifiers:
    abstract: true
    mixin: true
    is_a: frequency qualifier
    description: >-
      Qualifiers for entity to disease or phenotype associations
    slots:
      - severity qualifier
      - onset qualifier

  entity to phenotypic feature association:
    abstract: true
    defining_slots:
      - object
    is_a: association
    mixins:
      - entity to feature or disease qualifiers
    slot_usage:
      description:
        description: >-
          A description of specific aspects of this phenotype, not otherwise
          covered by the phenotype ontology class
      object:
        range: phenotypic feature
        description: "phenotypic class"
        definitional: true
        values_from: ['upheno', 'hp', 'mp', 'wbphenotypic feature']
        subclass_of: UPHENO:0001001
        examples:
          - value: HP:0002487
            description: Hyperkinesis
          - value: WBPhenotype:0000180 
            description: axon morphology variant
          - value: MP:0001569
            description: abnormal circulating bilirubin level
    slots:
      - sex qualifier

  entity to disease association:
    description: >-
      mixin class for any association whose object (target node) is a disease
    abstract: true
    mixin: true
    is_a: entity to feature or disease qualifiers
    defining_slots:
      - object
    slot_usage:
      object:
        range: disease
        description: "disease"
        definitional: true
        subclass_of: MONDO:0000001
        examples:
          - value: MONDO:0020066
            description: "Ehlers-Danlos syndrome"
      

  disease or phenotypic feature association to thing association:
    abstract: true
    is_a: association
    defining_slots:
      - subject
    slot_usage:
      subject:
        range: disease or phenotypic feature
        description: "disease or phenotype"
        definitional: true
        examples:
          - value: MONDO:0017314
            description: "Ehlers-Danlos syndrome, vascular type"
          - value: MP:0013229
            description: "abnormal brain ventricle size"

  disease or phenotypic feature association to location association:
    is_a: disease or phenotypic feature association to thing association
    description: >-
      An association between either a disease or a phenotypic feature and an anatomical entity,
      where the disease/feature manifests in that site.
    mappings:
      - NCIT:R100
    slot_usage:
      object:
        range: anatomical entity
        description: "anatomical entity in which the disease or feature is found"
        examples:
          - value: UBERON:0002048
            description: "lung"

  thing to disease or phenotypic feature association:
    abstract: true
    is_a: association
    defining_slots:
      - object
    slot_usage:
      object:
        range: disease or phenotypic feature
        description: "disease or phenotype"
        definitional: true
        examples:
          - value: MONDO:0017314
            description: "Ehlers-Danlos syndrome, vascular type"
          - value: MP:0013229
            description: "abnormal brain ventricle size"

  disease to thing association:
    abstract: true
    is_a: association
    defining_slots:
      - subject
    slot_usage:
      subject:
        range: disease
        description: "disease class"
        definitional: true
        values_from: ['mondo', 'omim', 'orphanet', 'ncit', 'doid']
        subclass_of: MONDO:0000001
        examples:
          - value: MONDO:0017314
            description: "Ehlers-Danlos syndrome, vascular type"


  genotype to phenotypic feature association:
    is_a: association
    defining_slots:
      - subject
      - object
    description: >-
      Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype,
      either in isolation or through environment
    mixins:
      - entity to phenotypic feature association
      - genotype to thing association
    slot_usage:
      relation:
        subproperty_of: has phenotype
      subject:
        range: genotype
        description: >-
          genotype that is associated with the phenotypic feature
          
  environment to phenotypic feature association:
    is_a: association
    defining_slots:
      - subject
      - object
    description: >-
      Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype
    mixins:
      - entity to phenotypic feature association
    slot_usage:
      subject:
        range: environment
        definitional: true
          
  disease to phenotypic feature association:
    is_a: association
    defining_slots:
      - subject
      - object
    description: "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way"
    mixins:
      - entity to phenotypic feature association
      - disease to thing association
      
  case to phenotypic feature association:
    is_a: association
    defining_slots:
      - subject
      - object
    description: "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype"
    mixins:
      - entity to phenotypic feature association
      - case to thing association
      
  gene to thing association:
    is_a: association
    defining_slots:
      - subject
    abstract: true
    slot_usage:
      subject:
        range: gene or gene product
        description: "gene that is the subject of the association"

  variant to thing association:
    is_a: association
    local_names:
      ga4gh: variant annotation
    defining_slots:
      - subject
    abstract: true
    mixin: true
    slot_usage:
      subject:
        range: sequence variant
        description: >-
          a sequence variant in which the allele state is associated with some other entity
        examples:
          - value: ClinVar:38077
            description: "ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)"
          - value: ClinGen:CA024716
            description: "chr13:g.32921033G>C (hg19) in ClinGen"
        
  gene to phenotypic feature association:
    is_a: association
    mappings:
      - "http://bio2rdf.org/wormbase_vocabulary:Gene-Phenotype-Association"
    defining_slots:
      - subject
      - object
    mixins:
      - entity to phenotypic feature association
      - gene to thing association
    slot_usage:
      subject:
        range: gene or gene product
        description: "gene in which variation is correlated with the phenotypic feature"
        examples:
          - value: HGNC:2197
            description: "COL1A1 (Human)"
            
  gene to disease association:
    is_a: association
    comment: >-
      NCIT:R176 refers to the inverse relationship
    mappings:
      - SIO:000983
    defining_slots:
      - subject
      - object
    mixins:
      - entity to disease association
      - gene to thing association
    slot_usage:
      subject:
        range: gene or gene product
        description: >-
          gene in which variation is correlated with the disease - may be protective or causative or associative, or as a model

  variant to population association:
    description: >-
      An association between a variant and a population, where the variant has particular frequency in the population
    is_a: association
    defining_slots:
      - subject
      - object
    mixins:
      - variant to thing association
      - frequency quantifier
      - frequency qualifier
    slot_usage:
      subject:
        range: sequence variant
        description: >-
          an allele that has a certain frequency in a given population
        examples:
          - value: "NC_000017.11:g.43051071A>T"
            description: >-
              17:41203088 A/C in gnomad
      object:
        range: population of individual organisms
        description: >-
          the population that is observed to have the frequency
        examples:
          - value: ANCESTRO:0010
            description: African
      has quotient:
        description: >-
          frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency
        examples:
          - value: "0.0001666"
      has count:
        description: >-
          number in object population that carry a particular allele, aka allele count
        examples:
          - value: "4"
            description: 4 individuals in gnomad set
      has total:
        description: >-
          number all populations that carry a particular allele, aka allele number
        examples:
          - value: "24014"
            description: 24014 individuals in gnomad set

  population to population association:
    description: >-
      An association between a two populations
    is_a: association
    defining_slots:
      - subject
      - object
    slot_usage:
      subject:
        range: population of individual organisms
        description: >-
          the population that form the subject of the association
      object:
        range: population of individual organisms
        description: >-
          the population that form the object of the association
      relation:
        description: >-
          A relationship type that holds between the subject and object populations. Standard mereological
          relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships
          can also be used
      
  variant to phenotypic feature association:
    is_a: association
    defining_slots:
      - subject
      - object
    mixins:
      - variant to thing association
      - entity to phenotypic feature association
    slot_usage:
      subject:
        range: sequence variant
        description: >-
          a sequence variant in which the allele state is associated in some way with the phenotype state

  variant to disease association:
    is_a: association
    comment: TODO decide no how to model pathogenicity
    defining_slots:
      - subject
      - object
    mixins:
      - variant to thing association
      - entity to disease association
    slot_usage:
      subject:
        description: >-
          a sequence variant in which the allele state is associated in some way with the disease state
        examples:
          - value: ClinVar:52241
            description: "NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)"
      relation:
        description: >-
          E.g. is pathogenic for
        subproperty_of: related condition
      object:
        description: >-
          a disease that is associated with that variant
        examples:
          - value: MONDO:0016419
            description: hereditary breast cancer
          
  model to disease mixin:
    mixin: true
    abstract: true
    description: >-
      This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some
      features of the disease in a way that is useful for studying the disease outside a patient carrying the disease
    slot_usage:
      subject:
        description: >-
          The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits
          similar features, or a gene that when mutated exhibits features of the disease
      relation:
        subproperty_of: model of
        description: >-
          The relationship to the disease
            
  gene as a model of disease association:
    is_a: gene to disease association
    defining_slots:
      - subject
      - object
      - relation
    mixins:
      - model to disease mixin
      - entity to disease association
    slot_usage:
      subject:
        range: gene or gene product
        description: >-
          A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene,
          or it may be a gene whose mutants recapitulate core features of the disease.
            
  gene has variant that contributes to disease association:
    is_a: gene to disease association
    defining_slots:
      - subject
      - object
      - relation
    slots:
      - sequence variant qualifier
    slot_usage:
      subject:
        range: gene or gene product
        description: >-
          A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene,
          or it may be a gene whose mutants recapitulate core features of the disease.

  genotype to thing association:
    is_a: association
    defining_slots:
      - subject
    abstract: true
    slot_usage:
      subject:
        range: genotype
        description: "genotype that is the subject of the association"
        
  gene to expression site association:
    is_a: association
    defining_slots:
      - subject
      - object
      - relation
    description: >-
      An association between a gene and an expression site, possibly qualified by stage/timing info.
    note: >-
      TBD: introduce subclasses for distinction between wild-type and experimental conditions?
    see_also: "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee"
    slots:
      - stage qualifier
      - quantifier qualifier
    slot_usage:
      subject:
        range: gene or gene product
        description: "gene in which variation is correlated with the phenotypic feature"
      object:
        range: anatomical entity
        description: "location in which the gene is expressed"
        subclass_of: UBERON:0001062
        examples:
          - value: UBERON:0002037
            description: cerebellum
      relation:
        description: "expression relationship"
        subproperty_of: expressed in
      stage qualifier:
        range: life stage
        description: "stage at which the gene is expressed in the site"
        examples:
          - value: UBERON:0000069
            description: larval stage
      quantifier qualifier:
        description: >-
          can be used to indicate magnitude, or also ranking

  sequence variant modulates treatment association:
    is_a: association
    description: >-
      An association between a sequence variant and a treatment or health intervention.
      The treatment object itself encompasses both the disease and the drug used.
    comment: >-
      An alternate way to model the same information could be via a qualifier
    defining_slots:
      - subject
      - object
    abstract: true
    slot_usage:
      subject:
        range: sequence variant
        description: "variant that modulates the treatment of some disease"
      object:
        range: treatment
        description: "treatment whose efficacy is modulated by the subject variant"

  functional association:
    is_a: association
    description: >-
      An association between a macromolecular machine (gene, gene product or complex of gene products) and
      either a molecular activity, a biological process or a cellular location in which a function is executed
    slot_usage:
      subject:
        range: macromolecular machine
#          aliases:
#            bioentity:
#              schema: amigo
        description: "gene, product or macromolecular complex that has the function associated with the GO term"
        examples:
          - value: ZFIN:ZDB-GENE-050417-357
            description: twist1b
      object:
        range: gene ontology class
#          aliases:
#            class:
#              schema: amigo
        description: "class describing the activity, process or localization of the gene product"
        values_from:
          - go
        examples:
          - value: GO:0016301
            description: kinase activity
          - value: GO:0045211
            description: postsynaptic membrane
    
  macromolecular machine to molecular activity association:
    is_a: functional association
    description: >-
      A functional association between a macromolecular machine (gene, gene product or complex) and
      a molecular activity (as represented in the GO molecular function branch), where the entity
      carries out the activity, or contributes to its execution
    slot_usage:
      object:
        range: molecular activity
          
  macromolecular machine to biological process association:
    is_a: functional association
    description: >-
      A functional association between a macromolecular machine (gene, gene product or complex) and
      a biological process or pathway (as represented in the GO biological process branch), where the entity
      carries out some part of the process, regulates it, or acts upstream of it
    slot_usage:
      object:
        range: biological process

  macromolecular machine to cellular component association:
    is_a: functional association
    description: >-
      A functional association between a macromolecular machine (gene, gene product or complex) and
      a cellular component (as represented in the GO cellular component branch), where the entity
      carries out its function in the cellular component
    slot_usage:
      object:
        range: cellular component
        
  gene to go term association:
    aliases: ['functional association']
    is_a: functional association
    mappings:
      - "http://bio2rdf.org/wormbase_vocabulary:Gene-GO-Association"
    defining_slots:
      - subject
      - object
    slot_usage:
      subject:
        range: molecular entity
#          aliases:
#            bioentity:
#              schema: amigo
        description: "gene, product or macromolecular complex that has the function associated with the GO term"
        examples:
          - value: ZFIN:ZDB-GENE-050417-357
            description: twist1b
      object:
        range: gene ontology class
#          aliases:
#            class:
#              schema: amigo
        description: "class describing the activity, process or localization of the gene product"
        values_from:
          - go
        examples:
          - value: GO:0016301
            description: kinase activity

  ## ------
  ## SEQUENCE FEATURES
  ## ------

  genomic sequence localization:
    is_a: association
    description: >-
      A relationship between a sequence feature and an entity it is localized to. The reference entity may be
      a chromosome, chromosome region or information entity such as a contig
    slot_usage:
      subject:
        aliases: ['sequence feature']
        range: genomic entity  ## todo protein
      object:
        aliases: ['reference']
        range: genomic entity ## typically a chromosomel use monochrom
    slots:
      - start interbase coordinate
      - end interbase coordinate
      - genome build
      - phase
    mappings:
      - faldo:location

  sequence feature relationship:
    is_a: association
    defining_slots:
      - subject
      - object
    description: >-
      For example, a particular exon is part of a particular transcript or gene
    slot_usage:
      subject:
        range: genomic entity  ## todo protein
      object:
        range: genomic entity ## typically a chromosome
    mappings:
      - GMODChado:feature_relationship

  transcript to gene relationship:
    is_a: sequence feature relationship
    defining_slots:
      - subject
      - object
    description: >-
      A gene is a collection of transcripts
    slot_usage:
      subject:
        range: transcript
      object:
        range: gene

  gene to gene product relationship:
    is_a: sequence feature relationship
    defining_slots:
      - subject
      - object
    description: >-
      A gene is transcribed and potentially translated to a gene product
    slot_usage:
      subject:
        range: gene
      object:
        range: gene product
      relation:
        subproperty_of: has gene product

  exon to transcript relationship:
    is_a: sequence feature relationship
    defining_slots:
      - subject
      - object
    description: >-
      A transcript is formed from multiple exons
    slot_usage:
      subject:
        range: exon
      object:
        range: transcript

  gene regulatory relationship:
    is_a: association
    description: >-
      A regulatory relationship between two genes
    slot_usage:
      relation:
        description: >-
          the direction is always from regulator to regulated
      subject:
        range: gene or gene product
        role: regulatory gene
      object:
        range: gene or gene product
        role: regulated gene
  
  anatomical entity to anatomical entity association:
#      schema: gocam
    is_a: association
    defining_slots:
      - subject
      - object
    slot_usage:
      subject:
        range: anatomical entity
      object:
        range: anatomical entity
  
  anatomical entity to anatomical entity part of association:
#      schema: gocam
    is_a: anatomical entity to anatomical entity association
    description: >-
      A relationship between two anatomical entities where the relationship is mereological, i.e
      the two entities are related by parthood. This includes relationships between cellular components
      and cells, between cells and tissues, tissues and whole organisms
    defining_slots:
      - relation
    slot_usage:
      subject:
        range: anatomical entity
        description: >-
          the part
      object:
        range: anatomical entity
        description: >-
          the whole
      relation:
        subproperty_of: part of
  
  anatomical entity to anatomical entity ontogenic association:
    is_a: anatomical entity to anatomical entity association
    description: >-
      A relationship between two anatomical entities where the relationship is ontogenic, i.e
      the two entities are related by development. A number of different relationship types
      can be used to specify the precise nature of the relationship
    defining_slots:
      - relation
    slot_usage:
      subject:
        range: anatomical entity
        description: >-
          the structure at a later time
      object:
        range: anatomical entity
        description: >-
          the structure at an earlier time
      relation:
        subproperty_of: develops from

  occurrent:
    description: >-
      A processual entity
    is_a: named thing
    mappings:
      - "BFO:0000003"

  biological process or activity:
    is_a: biological entity
    description: >-
      Either an individual molecular activity, or a collection of causally connected molecular activities
    union_of:
      - molecular activity
      - biological process
    id_prefixes:
      - GO
      - Reactome

  molecular activity:
    is_a: biological process or activity
    aliases: ['molecular function', 'molecular event', 'reaction']
    mixins:
      - occurrent
    description: >-
      An execution of a molecular function carried out by a gene product or macromolecular complex.
    mappings:
      - "GO:0003674"
    id_prefixes:
      - GO
      - Reactome

  activity and behavior:
    is_a: occurrent
    description: >-
      Activity or behavior of any independent integral living, organization or mechanical actor in the world
    mappings:
      - "UMLSSG:ACTI"

  procedure:
    is_a: occurrent
    description: >-
      A series of actions conducted in a certain order or manner
    mappings:
      - "UMLSSG:PROC"

  phenomenon:
    is_a: occurrent
    description: >-
      a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question
    mappings:
      - "UMLSSG:PHEN"

  biological process:
    is_a: biological process or activity
    mixins:
      - occurrent
    description: >-
      One or more causally connected executions of molecular functions
    mappings:
      - "GO:0008150"
      - SIO:000006
      - WD:Q2996394
    id_prefixes:
      - GO
      - Reactome

  pathway:
    is_a: biological process
    mappings:
      - GO:0007165
      - SIO:010526
      - PW:0000001
      - WD:Q4915012
    id_prefixes:
      - GO
      - Reactome

  physiological process:
    aliases: ['physiology']
    is_a: biological process
    mappings:
      - "UMLSSG:PHYS"
      
  cellular component:
    is_a: anatomical entity
    description: >-
      A location in or around a cell
    mappings:
      - "GO:0005575"
      - SIO:001400
      - WD:Q5058355
    id_prefixes:
      - GO
      
  cell:
    is_a: anatomical entity
    mappings:
      - "GO:0005623"
      - "CL:0000000"
      - "SIO:010001"
      - WD:Q7868
    id_prefixes:
      - CL
      - PO

  cell line:
    is_a: biosample
    mappings:
      - "CLO:0000031"
    id_prefixes:
      - CLO
      
  gross anatomical structure:
    aliases: ['tissue', 'organ']
    is_a: anatomical entity
    mappings:
      - UBERON:0010000
      - SIO:010046
      - WD:Q4936952
    id_prefixes:
      - UBERON
      - PO
      - FAO