Biolink-Model
type: Ontology
IAO_0000700: annotation
IAO_0000700: case to entity association mixin
IAO_0000700: cell line to entity association mixin
IAO_0000700: chemical entity or gene or gene product
IAO_0000700: chemical entity or protein or polypeptide
IAO_0000700: chemical entity to entity association mixin
IAO_0000700: chemical or drug or treatment
IAO_0000700: disease or phenotypic feature to entity association mixin
IAO_0000700: disease to entity association mixin
IAO_0000700: entity
IAO_0000700: entity to disease or phenotypic feature association mixin
IAO_0000700: entity to exposure event association mixin
IAO_0000700: entity to outcome association mixin
IAO_0000700: epigenomic entity
IAO_0000700: frequency qualifier mixin
IAO_0000700: gene expression mixin
IAO_0000700: gene grouping mixin
IAO_0000700: gene to entity association mixin
IAO_0000700: genomic entity
IAO_0000700: genotype to entity association mixin
IAO_0000700: macromolecular machine mixin
IAO_0000700: macromolecular machine to entity association mixin
IAO_0000700: mapping collection
IAO_0000700: material sample to entity association mixin
IAO_0000700: model to disease association mixin
IAO_0000700: ontology class
IAO_0000700: organism taxon to entity association
IAO_0000700: outcome
IAO_0000700: pathological entity mixin
IAO_0000700: physical essence or occurrent
IAO_0000700: predicate mapping
IAO_0000700: relationship quantifier
IAO_0000700: subject of investigation
IAO_0000700: thing with taxon
IAO_0000700: variant to entity association mixin
license: https://creativecommons.org/publicdomain/zero/1.0/
ingest date: 3.2.0
generation date: 2023-02-07T19:40:59
metamodel version: 1.7.0
source file: biolink-model.yaml
source file date: 2023-02-07T19:39:37
source file size: 335683

activity
type: Class
subclass of: activity and behavior
subclass of: named thing
definition: An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
narrow match: T056
narrow match: T057
narrow match: T058
narrow match: T062
narrow match: T064
narrow match: T065
narrow match: T066

anatomical entity to anatomical entity ontogenic association
type: Class
subclass of: Restriction
  on class: anatomical entity
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: anatomical entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: anatomical entity to anatomical entity association
definition: 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.

anatomical entity to anatomical entity part of association
type: Class
subclass of: Restriction
  on class: anatomical entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: anatomical entity
  on property: object
  qualified cardinality: 1
subclass of: anatomical entity to anatomical entity association
definition: 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

article
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: volume
subclass of: Restriction
  on class: Uriorcurie
  on property: published in
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: iso abbreviation
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: issue
subclass of: publication

behavior to behavioral feature association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  on class: behavior
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: Restriction
  on class: behavioral feature
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: entity to phenotypic feature association mixin
definition: An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.

behavioral exposure
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
definition: A behavioral exposure is a factor relating to behavior impacting an individual.

behavioral outcome
type: Class
subclass of: outcome
definition: An outcome resulting from an exposure event which is the manifestation of human behavior.

biotic exposure
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
alternative label: bacterial exposure
alternative label: viral exposure
definition: An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).

book
type: Class
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: Restriction
  all values from: String
  on property: type
subclass of: publication
definition: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.

case to phenotypic feature association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: association
subclass of: case to entity association mixin
subclass of: entity to phenotypic feature association mixin
definition: An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.

cell
type: Class
subclass of: anatomical entity

cell line as a model of disease association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  on class: cell line
  on property: subject
  qualified cardinality: 1
subclass of: cell line to disease or phenotypic feature association
subclass of: entity to disease association mixin
subclass of: model to disease association mixin

cellular organism
type: Class
subclass of: organismal entity
subclass of: subject of investigation

chemical affects gene association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: anatomical context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: subject context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: qualified predicate
subclass of: Restriction
  max qualified cardinality: 1
  on class: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: object context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: subject form or variant qualifier
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: subject aspect qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: CausalMechanismQualifierEnum
  on property: causal mechanism qualifier
subclass of: Restriction
  on class: chemical entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: organism taxon
  on property: species context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: subject part qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: object part qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: object aspect qualifier
subclass of: Restriction
  on class: gene or gene product
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: object form or variant qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: ChemicalEntityDerivativeEnum
  on property: subject derivative qualifier
subclass of: association
definition: Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)

chemical entity assesses named thing association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: named thing
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: chemical entity
  on property: subject
  qualified cardinality: 1
subclass of: association

chemical entity or gene or gene product regulates gene association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: chemical entity or gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: association
definition: A regulatory relationship between two genes

chemical gene interaction association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: object part qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: subject form or variant qualifier
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: object context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: subject part qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: subject context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: ChemicalEntityDerivativeEnum
  on property: subject derivative qualifier
subclass of: Restriction
  on class: chemical entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: object form or variant qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: anatomical context qualifier
subclass of: Restriction
  on class: gene or gene product
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: chemical to entity association mixin
definition: describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)

chemical or drug or treatment side effect disease or phenotypic feature association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: chemical or drug or treatment to disease or phenotypic feature association
subclass of: chemical to entity association mixin
subclass of: entity to disease or phenotypic feature association mixin
definition: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.

chemical to chemical derivation association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: chemical entity
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  all values from: macromolecular machine mixin
  on property: catalyst qualifier
subclass of: Restriction
  on class: chemical entity
  on property: subject
  qualified cardinality: 1
subclass of: chemical to chemical association
definition: A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 <<catalyst qualifier P>>

chemical to disease or phenotypic feature association
type: Class
subclass of: Restriction
  on class: disease or phenotypic feature
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: chemical to entity association mixin
subclass of: entity to disease or phenotypic feature association mixin
definition: An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.
narrow match: SIO_000993

chemical to pathway association
type: Class
subclass of: Restriction
  on class: chemical entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: pathway
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: chemical to entity association mixin
definition: An interaction between a chemical entity and a biological process or pathway.

chi squared analysis result
type: Class
subclass of: study result
definition: A result of a chi squared analysis.

clinical finding
type: Class
subclass of: Restriction
  all values from: clinical attribute
  on property: has attribute
subclass of: phenotypic feature
definition: this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations.

clinical measurement
type: Class
subclass of: Restriction
  on class: ontology class
  on property: has attribute type
  qualified cardinality: 1
subclass of: clinical attribute
definition: A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.

clinical trial
type: Class
subclass of: clinical entity

cohort
type: Class
subclass of: study population
subclass of: subject of investigation
definition: A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time.
narrow match: T097
narrow match: T099
narrow match: T100
narrow match: T101

common data element
type: Class
subclass of: information content entity
definition: A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)

complex chemical exposure
type: Class
subclass of: attribute
definition: A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.

complex molecular mixture
type: Class
subclass of: chemical mixture
definition: A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.

concept count analysis result
type: Class
subclass of: study result
definition: A result of a concept count analysis.

contributor association
type: Class
subclass of: Restriction
  on class: information content entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: agent
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  all values from: ontology class
  on property: qualifiers
subclass of: association
definition: Any association between an entity (such as a publication) and various agents that contribute to its realisation

disease or phenotypic feature exposure
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
subclass of: pathological entity mixin
definition: A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.

disease or phenotypic feature outcome
type: Class
subclass of: outcome
definition: Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.

disease or phenotypic feature to genetic inheritance association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: genetic inheritance
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: disease or phenotypic feature to entity association mixin
definition: An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.

disease or phenotypic feature to location association
type: Class
subclass of: Restriction
  on class: anatomical entity
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: disease or phenotypic feature to entity association mixin
definition: An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.

disease to exposure event association
type: Class
subclass of: association
subclass of: disease to entity association mixin
subclass of: entity to exposure event association mixin
definition: An association between an exposure event and a disease.

disease to phenotypic feature association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  on class: phenotypic feature
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  on class: disease
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: association
subclass of: disease to entity association mixin
subclass of: entity to phenotypic feature association mixin
definition: An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.

drug to gene association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: drug to entity association mixin
definition: An interaction between a drug and a gene or gene product.
related match: SIO_001257

drug to gene interaction exposure
type: Class
subclass of: Restriction
  all values from: gene
  on property: has gene or gene product
subclass of: drug exposure
subclass of: gene grouping mixin
definition: drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.

druggable gene to disease association
type: Class
subclass of: Restriction
  all values from: DruggableGeneCategoryEnum
  on property: has evidence
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: entity to disease association mixin
subclass of: gene to disease association
subclass of: gene to entity association mixin

entity to disease association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: FDAApprovalStatusEnum
  on property: FDA approval status
subclass of: association

entity to phenotypic feature association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: FDAApprovalStatusEnum
  on property: FDA approval status
subclass of: association

environmental feature
type: Class
subclass of: planetary entity

environmental food contaminant
type: Class
subclass of: chemical entity
related match: CHEBI_78299

environmental process
type: Class
subclass of: occurrent
subclass of: planetary entity

epidemiological outcome
type: Class
subclass of: outcome
definition: An epidemiological outcome, such as societal disease burden, resulting from an exposure event.
related match: NCIT C19291

event
type: Class
subclass of: named thing
definition: Something that happens at a given place and time.

exon to transcript relationship
type: Class
subclass of: Restriction
  on class: transcript
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: exon
  on property: subject
  qualified cardinality: 1
subclass of: sequence feature relationship
definition: A transcript is formed from multiple exons

exposure event to outcome association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: temporal context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: population of individual organisms
  on property: population context qualifier
subclass of: association
subclass of: entity to outcome association mixin
definition: An association between an exposure event and an outcome.

exposure event to phenotypic feature association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  on class: exposure event
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: association
subclass of: entity to phenotypic feature association mixin
definition: Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.

food
type: Class
subclass of: chemical mixture
definition: A substance consumed by a living organism as a source of nutrition

food additive
type: Class
subclass of: chemical entity
related match: CHEBI_64047

gene as a model of disease association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: entity to disease association mixin
subclass of: gene to disease association
subclass of: model to disease association mixin

gene has variant that contributes to disease association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: subject form or variant qualifier
subclass of: Restriction
  on class: disease
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: gene to disease association

GeneOrGeneProductOrChemicalEntityAspectEnum
type: Class
union of: activity_or_abundance
union of: abundance
union of: activity
union of: expression
union of: synthesis
union of: degradation
union of: cleavage
union of: hydrolysis
union of: metabolic_processing
union of: mutation_rate
union of: stability
union of: folding
union of: localization
union of: transport
union of: secretion
union of: uptake
union of: molecular_modification
union of: acetylation
union of: acylation
union of: alkylation
union of: amination
union of: carbamoylation
union of: ethylation
union of: glutathionylation
union of: glycation
union of: glycosylation
union of: glucuronidation
union of: n_linked_glycosylation
union of: o_linked_glycosylation
union of: hydroxylation
union of: lipidation
union of: farnesylation
union of: geranoylation
union of: myristoylation
union of: palmitoylation
union of: prenylation
union of: methylation
union of: nitrosation
union of: nucleotidylation
union of: phosphorylation
union of: ribosylation
union of: ADP-ribosylation
union of: sulfation
union of: sumoylation
union of: ubiquitination
union of: oxidation
union of: reduction
union of: carboxylation
permissible values: ADP-ribosylation
permissible values: abundance
permissible values: acetylation
permissible values: activity
permissible values: activity_or_abundance
permissible values: acylation
permissible values: alkylation
permissible values: amination
permissible values: carbamoylation
permissible values: carboxylation
permissible values: cleavage
permissible values: degradation
permissible values: ethylation
permissible values: expression
permissible values: farnesylation
permissible values: folding
permissible values: geranoylation
permissible values: glucuronidation
permissible values: glutathionylation
permissible values: glycation
permissible values: glycosylation
permissible values: hydrolysis
permissible values: hydroxylation
permissible values: lipidation
permissible values: localization
permissible values: metabolic_processing
permissible values: methylation
permissible values: molecular_modification
permissible values: mutation_rate
permissible values: myristoylation

gene to expression site association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: ontology class
  on property: quantifier qualifier
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: anatomical entity
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: life stage
  on property: stage qualifier
subclass of: association
definition: An association between a gene and a gene expression site, possibly qualified by stage/timing info.
editorial note: TBD: introduce subclasses for distinction between wild-type and experimental conditions?

gene to gene coexpression association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: life stage
  on property: stage qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: expression site
subclass of: Restriction
  max qualified cardinality: 1
  on class: disease or phenotypic feature
  on property: phenotypic state
subclass of: Restriction
  max qualified cardinality: 1
  on class: ontology class
  on property: quantifier qualifier
subclass of: gene expression mixin
subclass of: gene to gene association
definition: Indicates that two genes are co-expressed, generally under the same conditions.

gene to gene family association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: gene family
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: gene
  on property: subject
  qualified cardinality: 1
subclass of: association
definition: Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships.

gene to gene homology association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: gene or gene product
  on property: object
  qualified cardinality: 1
subclass of: gene to gene association
definition: 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)

gene to gene product relationship
type: Class
subclass of: Restriction
  on class: gene product mixin
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: gene
  on property: subject
  qualified cardinality: 1
subclass of: sequence feature relationship
definition: A gene is transcribed and potentially translated to a gene product

gene to go term association
type: Class
subclass of: Restriction
  on class: ontology class
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: gene
  on property: subject
  qualified cardinality: 1
subclass of: functional association
alternative label: functional association

gene to pathway association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: pathway
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: gene to entity association mixin
definition: An interaction between a gene or gene product and a biological process or pathway.

gene to phenotypic feature association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  on class: phenotypic feature
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: association
subclass of: entity to phenotypic feature association mixin
subclass of: gene to entity association mixin

genome
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: biological entity
subclass of: genomic entity
subclass of: ontology class
subclass of: physical essence
definition: A genome is the sum of genetic material within a cell or virion.

genomic background exposure
type: Class
subclass of: Restriction
  all values from: organism taxon
  on property: in taxon
subclass of: Restriction
  all values from: gene
  on property: has gene or gene product
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: attribute
subclass of: exposure event
subclass of: gene grouping mixin
subclass of: genomic entity
subclass of: ontology class
subclass of: physical essence
subclass of: thing with taxon
definition: A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.

genotype as a model of disease association
type: Class
subclass of: Restriction
  on class: genotype
  on property: subject
  qualified cardinality: 1
subclass of: entity to disease association mixin
subclass of: genotype to disease association
subclass of: model to disease association mixin

genotype to gene association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: gene
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: genotype
  on property: subject
  qualified cardinality: 1
subclass of: association
definition: 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

genotype to genotype part association
type: Class
subclass of: Restriction
  on class: genotype
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: genotype
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: association
definition: Any association between one genotype and a genotypic entity that is a sub-component of it

genotype to phenotypic feature association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: Restriction
  on class: genotype
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: association
subclass of: entity to phenotypic feature association mixin
subclass of: genotype to entity association mixin
definition: Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment

genotype to variant association
type: Class
subclass of: Restriction
  on class: sequence variant
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: genotype
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: association
definition: Any association between a genotype and a sequence variant.

genotypic sex
type: Class
subclass of: biological sex
definition: An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.

geographic exposure
type: Class
subclass of: environmental exposure
subclass of: exposure event
definition: A geographic exposure is a factor relating to geographic proximity to some impactful entity.
narrow match: IceStoremEvent
narrow match: LakeEffectSnowEvent
narrow match: LandslideEvent
narrow match: MarineDenseFogEvent
narrow match: MarineLighteningEvent
narrow match: MarineStrongWindEvent
narrow match: MarineThunderstormWindEvent
narrow match: StormEvent
narrow match: StormSurgeTideEvent
narrow match: StrongWindEvent
narrow match: ThunderstormWindEvent
narrow match: TornadoEvent
narrow match: TropicalDepressionEvent
narrow match: WinterStoremEvent

geographic location at time
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: geographic location
definition: a location that can be described in lat/long coordinates, for a particular time

gross anatomical structure
type: Class
subclass of: anatomical entity
alternative label: organ
alternative label: tissue
narrow match: T018
narrow match: T023
narrow match: T024

haplotype
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: biological entity
subclass of: genomic entity
subclass of: ontology class
subclass of: physical essence
definition: A set of zero or more Alleles on a single instance of a Sequence[VMC]

hospitalization
type: Class
subclass of: clinical intervention

hospitalization outcome
type: Class
subclass of: outcome
definition: An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.

information content entity to named thing association
type: Class
subclass of: Restriction
  on class: named thing
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: named thing
  on property: object
  qualified cardinality: 1
subclass of: association
definition: association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property).

macromolecular complex
type: Class
subclass of: biological entity
subclass of: macromolecular machine mixin
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.

macromolecular machine to biological process association
type: Class
subclass of: Restriction
  on class: biological process
  on property: object
  qualified cardinality: 1
subclass of: functional association
subclass of: macromolecular machine to entity association mixin
definition: 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.

macromolecular machine to cellular component association
type: Class
subclass of: Restriction
  on class: cellular component
  on property: object
  qualified cardinality: 1
subclass of: functional association
subclass of: macromolecular machine to entity association mixin
definition: 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.

macromolecular machine to molecular activity association
type: Class
subclass of: Restriction
  on class: molecular activity
  on property: object
  qualified cardinality: 1
subclass of: functional association
subclass of: macromolecular machine to entity association mixin
definition: 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.

material sample derivation association
type: Class
subclass of: Restriction
  on class: named thing
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: material sample
  on property: subject
  qualified cardinality: 1
subclass of: association
definition: An association between a material sample and the material entity from which it is derived.

material sample to disease or phenotypic feature association
type: Class
subclass of: association
subclass of: entity to disease or phenotypic feature association mixin
subclass of: material sample to entity association mixin
definition: An association between a material sample and a disease or phenotype.

microRNA
type: Class
subclass of: noncoding RNA product

molecular activity to chemical entity association
type: Class
subclass of: Restriction
  on class: chemical entity
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: molecular activity
  on property: subject
  qualified cardinality: 1
subclass of: association
definition: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples

molecular activity to molecular activity association
type: Class
subclass of: Restriction
  on class: molecular activity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: molecular activity
  on property: object
  qualified cardinality: 1
subclass of: association
definition: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples

molecular activity to pathway association
type: Class
subclass of: Restriction
  on class: pathway
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: molecular activity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: association
definition: Association that holds the relationship between a reaction and the pathway it participates in.

mortality outcome
type: Class
subclass of: outcome
definition: An outcome of death from resulting from an exposure event.

named thing associated with likelihood of named thing association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: ontology class
  on property: subject context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: subject aspect qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: ontology class
  on property: object context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: object aspect qualifier
subclass of: association

nucleic acid sequence motif
type: Class
subclass of: biological entity
alternative label: consensus sequence
definition: A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.

nucleosome modification
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: Restriction
  all values from: label type
  on property: synonym
subclass of: biological entity
subclass of: epigenomic entity
subclass of: gene product isoform mixin
subclass of: genomic entity
definition: A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.

observed expected frequency analysis result
type: Class
subclass of: study result
definition: A result of a observed expected frequency analysis.

organism taxon to environment association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: organism taxon
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: named thing
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: organism taxon to entity association

organism taxon to organism taxon interaction
type: Class
subclass of: Restriction
  on class: organism taxon
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: organism taxon
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: associated environmental context
subclass of: organism taxon to organism taxon association
definition: An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens

organism taxon to organism taxon specialization
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: organism taxon
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: organism taxon
  on property: subject
  qualified cardinality: 1
subclass of: organism taxon to organism taxon association
definition: A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo

organism to organism association
type: Class
subclass of: Restriction
  on class: individual organism
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: individual organism
  on property: object
  qualified cardinality: 1
subclass of: association

organismal entity as a model of disease association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  on class: organismal entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: association
subclass of: entity to disease association mixin
subclass of: model to disease association mixin

pairwise molecular interaction
type: Class
subclass of: Restriction
  on class: molecular entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: ontology class
  on property: interacting molecules category
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: molecular entity
  on property: object
  qualified cardinality: 1
subclass of: pairwise gene to gene interaction
definition: An interaction at the molecular level between two physical entities

pathognomonicity quantifier
type: Class
subclass of: specificity quantifier
subclass of: mixin
definition: 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

pathological anatomical exposure
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
definition: An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.

pathological anatomical outcome
type: Class
subclass of: outcome
definition: An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.

pathological anatomical structure
type: Class
subclass of: anatomical entity
subclass of: pathological entity mixin
definition: An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.

pathological process
type: Class
subclass of: biological process
subclass of: pathological entity mixin
definition: A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.
narrow match: T037
narrow match: T046
narrow match: NCIT C19151
narrow match: EFO_0009708

pathological process exposure
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
definition: A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.

pathological process outcome
type: Class
subclass of: outcome
definition: An outcome resulting from an exposure event which is the manifestation of a pathological process.

percentage frequency value
type: Class
subclass of: Double

phenomenon
type: Class
subclass of: named thing
subclass of: occurrent
broad match: T067
broad match: T068
broad match: T070
definition: a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question
narrow match: T034
narrow match: T038
narrow match: T069

phenotypic quality
type: Class
subclass of: organism attribute
alternative label: phenotypic properties
definition: A property of a phenotype
examples: Example(value='weight', description=None)

phenotypic sex
type: Class
subclass of: biological sex
definition: An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.

physiological process
type: Class
subclass of: biological process
subclass of: ontology class
alternative label: physiology
narrow match: T040
narrow match: T042
narrow match: T043
narrow match: T045

population to population association
type: Class
subclass of: Restriction
  on class: population of individual organisms
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: population of individual organisms
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: association
definition: An association between a two populations

posttranslational modification
type: Class
subclass of: Restriction
  all values from: label type
  on property: synonym
subclass of: biological entity
subclass of: gene product isoform mixin
definition: A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.

processed material
type: Class
subclass of: chemical mixture
definition: A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.

protein domain
type: Class
subclass of: Restriction
  all values from: gene
  on property: has gene or gene product
subclass of: biological entity
subclass of: chemical entity or gene or gene product
subclass of: gene grouping mixin
definition: A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.

protein family
type: Class
subclass of: Restriction
  all values from: gene
  on property: has gene or gene product
subclass of: biological entity
subclass of: chemical entity or gene or gene product
subclass of: gene grouping mixin
narrow match: NCIT C20130
narrow match: SIO_001380
narrow match: Q417841

protein isoform
type: Class
subclass of: gene product isoform mixin
subclass of: protein
alternative label: proteoform
definition: Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/

quotient
type: Class
subclass of: Double

RNA product isoform
type: Class
subclass of: gene product isoform mixin
subclass of: RNA product
definition: Represents a protein that is a specific isoform of the canonical or reference RNA

reaction to catalyst association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: object
  qualified cardinality: 1
subclass of: reaction to participant association

reagent targeted gene
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: biological entity
subclass of: genomic entity
subclass of: ontology class
subclass of: physical essence
alternative label: sequence targeting reagent
definition: A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.

relationship type
type: Class
subclass of: ontology class
definition: An OWL property used as an edge label

relative frequency analysis result
type: Class
subclass of: study result
definition: A result of a relative frequency analysis.

sensitivity quantifier
type: Class
subclass of: relationship quantifier
subclass of: mixin

SequenceEnum
type: Class
union of: na
union of: aa
permissible values: aa
permissible values: na

sequence variant modulates treatment association
type: Class
subclass of: Restriction
  on class: treatment
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: sequence variant
  on property: subject
  qualified cardinality: 1
subclass of: association
definition: An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used.
note: An alternate way to model the same information could be via a qualifier

serial
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: issue
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: volume
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: iso abbreviation
subclass of: Restriction
  all values from: String
  on property: type
subclass of: publication
alternative label: journal
definition: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.

siRNA
type: Class
subclass of: noncoding RNA product
alternative label: RNAi
alternative label: small interfering RNA
definition: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.

small molecule
type: Class
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: molecular entity
alternative label: chemical substance
definition: A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).
narrow match: T109
narrow match: T110
narrow match: T111
narrow match: T115
narrow match: T118
narrow match: T119
narrow match: T123
narrow match: T124
narrow match: T125
narrow match: T127
narrow match: T131
narrow match: T196
narrow match: T197
narrow match: CHEBI_59999
narrow match: ChemicalSubstance

snv
type: Class
subclass of: sequence variant
alternative label: single nucleotide polymorphism
alternative label: single nucleotide variant
alternative label: snp
definition: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist

socioeconomic exposure
type: Class
subclass of: Class
  intersection of: Restriction
    all values from: socioeconomic attribute
    on property: has attribute
  intersection of: Restriction
    on property: has attribute
    some values from: socioeconomic attribute
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
definition: A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).

socioeconomic outcome
type: Class
subclass of: outcome
definition: An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event

study
type: Class
subclass of: information content entity
definition: a detailed investigation and/or analysis
narrow match: SIO_000994

study variable
type: Class
subclass of: information content entity
definition: a variable that is used as a measure in the investigation of a study
narrow match: NCIT C142192

taxon to taxon association
type: Class
subclass of: Restriction
  on class: organism taxon
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: organism taxon
  on property: object
  qualified cardinality: 1
subclass of: association

text mining result
type: Class
subclass of: study result
definition: A result of text mining.

transcript to gene relationship
type: Class
subclass of: Restriction
  on class: transcript
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: gene
  on property: object
  qualified cardinality: 1
subclass of: sequence feature relationship
definition: A gene is a collection of transcripts

variant as a model of disease association
type: Class
subclass of: Restriction
  on class: sequence variant
  on property: subject
  qualified cardinality: 1
subclass of: entity to disease association mixin
subclass of: model to disease association mixin
subclass of: variant to disease association

variant to gene expression association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: expression site
subclass of: Restriction
  max qualified cardinality: 1
  on class: life stage
  on property: stage qualifier
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: disease or phenotypic feature
  on property: phenotypic state
subclass of: Restriction
  max qualified cardinality: 1
  on class: ontology class
  on property: quantifier qualifier
subclass of: gene expression mixin
subclass of: variant to gene association
definition: An association between a variant and expression of a gene (i.e. e-QTL)

variant to phenotypic feature association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  on class: sequence variant
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: association
subclass of: entity to phenotypic feature association mixin
subclass of: variant to entity association mixin

variant to population association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  on class: sequence variant
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: Restriction
  on class: population of individual organisms
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: association
subclass of: frequency qualifier mixin
subclass of: frequency quantifier
subclass of: variant to entity association mixin
definition: An association between a variant and a population, where the variant has particular frequency in the population

virus
type: Class
subclass of: organismal entity
subclass of: subject of investigation
definition: A virus is a microorganism that replicates itself as a microRNA and infects the host cell.

animal model available from
type: ObjectProperty
domain: named thing
range: disease or phenotypic feature
sub property of: node property

binds
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: directly physically interacts with
definition: A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.
canonical predicate: True

biological role mixin
type: ObjectProperty
range: String
definition: A role played by the chemical entity or part thereof within a biological context.
narrow match: CHEBI_24432

bonferonni adjusted p value
type: ObjectProperty
domain: association
range: Float
sub property of: adjusted p value
definition: The Bonferroni correction is an adjustment made to P values when several dependent or independent statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni correction, divide the critical P value (α) by the number of comparisons being made. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.
examples: Example(value='0.018', description=None)

broad matches
type: ObjectProperty
range: String
definition: A list of terms from different schemas or terminology systems that have a broader meaning. Such terms often describe a more general concept from different ontological perspectives.

broad synonym
type: ObjectProperty
domain: named thing
range: label type
sub property of: synonym

chemical role mixin
type: ObjectProperty
range: String
definition: A role played by the chemical entity or part thereof within a chemical context.

chemically similar to
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: similar to
definition: holds between one small molecule entity and another that it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
narrow match: CHEBI has functional parent
narrow match: CHEBI has parent hydride
narrow match: CHEBI is conjugate acid of
narrow match: CHEBI is conjugate base of
narrow match: CHEBI is enantiomer of
narrow match: CHEBI is tautomer of
narrow match: NCIT has salt form
canonical predicate: True

chi squared statistic
type: ObjectProperty
domain: association
range: Float
sub property of: association slot
definition: represents the chi-squared statistic computed from observations

clinical modifier qualifier
type: ObjectProperty
domain: association
range: clinical modifier
sub property of: association slot
definition: the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.

coexpressed with
type: ObjectProperty
type: SymmetricProperty
domain: gene or gene product
range: gene or gene product
sub property of: correlated with
definition: holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context.
canonical predicate: True

colocalizes with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: coexists with
definition: holds between two entities that are observed to be located in the same place.
canonical predicate: True

concept count object
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: The number of instances in a dataset/cohort whose records contain the concept in the object slot of an association.

concept count subject
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: The number of instances in a dataset/cohort whose records contain the concept in the subject slot of an association.
examples: Example(value='489', description=None)

concept pair count
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: The number of instances in a dataset/cohort whose records contain both the subject and object concept of an association.
examples: Example(value='1731', description=None)

created with
type: ObjectProperty
domain: dataset
range: String
sub property of: node property

end coordinate
type: ObjectProperty
domain: genomic sequence localization
range: Integer
sub property of: base coordinate
alternative label: end
definition: The position at which the subject genomic entity ends on the chromosome or other entity to which it is located on.

evidence count
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: The number of evidence instances that are connected to an association.

exact matches
type: ObjectProperty
range: String
definition: A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives.

exact synonym
type: ObjectProperty
domain: named thing
range: label type
sub property of: synonym

expected count
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and object concept of an association if the subject and object concepts are independent.

extraction confidence score
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
examples: Example(value='15', description=None)

full name
type: ObjectProperty
domain: named thing
range: label type
sub property of: node property
definition: a long-form human readable name for a thing

genetically interacts with
type: ObjectProperty
type: SymmetricProperty
domain: gene
range: gene
sub property of: interacts with
definition: 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.
canonical predicate: True

has chemical formula
type: ObjectProperty
domain: named thing
range: chemical formula value
sub property of: node property
definition: description of chemical compound based on element symbols

has confidence level
type: ObjectProperty
domain: association
range: confidence level
sub property of: association slot
definition: connects an association to a qualitative term denoting the level of confidence

has constituent
type: ObjectProperty
domain: named thing
range: molecular entity
sub property of: node property
definition: one or more molecular entities within a chemical mixture

has receptor
type: ObjectProperty
domain: exposure event
range: organismal entity
sub property of: node property
definition: the organism or organism part being exposed

has route
type: ObjectProperty
domain: exposure event
range: String
sub property of: node property
definition: the process that results in the stressor coming into direct contact with the receptor
narrow match: has pharmaceutical route
narrow match: SNOMED has dose form intended site
narrow match: SNOMED has route of administration

has stressor
type: ObjectProperty
domain: exposure event
range: String
sub property of: node property
alternative label: has stimulus
definition: the process or entity that the receptor is being exposed to

has supporting study result
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: connects an association to an instance of supporting study result

has topic
type: ObjectProperty
domain: named thing
range: ontology class
sub property of: node property
alternative label: descriptors
alternative label: topic
definition: Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred. See https://github.com/biolink/biolink-model/issues/238

in cell population with
type: ObjectProperty
type: SymmetricProperty
domain: gene or gene product
range: gene or gene product
sub property of: coexists with
definition: holds between two genes or gene products that are expressed in the same cell type or population
canonical predicate: True

in complex with
type: ObjectProperty
type: SymmetricProperty
domain: gene or gene product
range: gene or gene product
sub property of: coexists with
broad match: SIO_010285
definition: holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex
related match: SIO_010497
canonical predicate: True

in linkage disequilibrium with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: holds between two sequence variants, the presence of which are correlated in a population
canonical predicate: True

in pathway with
type: ObjectProperty
type: SymmetricProperty
domain: gene or gene product
range: gene or gene product
sub property of: coexists with
definition: holds between two genes or gene products that are part of in the same biological pathway
related match: SIO_010532
canonical predicate: True

indirectly physically interacts with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: physically interacts with
canonical predicate: True

ln ratio
type: ObjectProperty
domain: association
range: Float
sub property of: association slot
definition: the natural log of the ratio of co-occurrence to expected
examples: Example(value='2.922827136', description=None)

ln ratio confidence interval
type: ObjectProperty
domain: association
range: Float
sub property of: association slot
definition: The 99% confidence interval for the ln_ratio calculation (i.e. the range of values within which the true value has a 99% chance of falling)
examples: Example(value='2.922827136', description=None)

logical interpretation
type: ObjectProperty
domain: association
range: LogicalInterpretationEnum
sub property of: association slot

mechanism of action
type: ObjectProperty
domain: association
range: Boolean
sub property of: association slot
definition: a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes the mechanism of action for a result.

narrow matches
type: ObjectProperty
range: String
definition: A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives.

narrow synonym
type: ObjectProperty
domain: named thing
range: label type
sub property of: synonym

negatively correlated with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: correlated with
definition: A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of one correlates with a decrease or absence of the other).
canonical predicate: True
opposite of: positively correlated with

object location in text
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion
examples: Example(value='15', description=None)

occurs together in literature with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: correlated with
definition: holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider.
canonical predicate: True

opposite of
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).
canonical predicate: True

orthologous to
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: homologous to
definition: a homology relationship between entities (typically genes) that diverged after a speciation event.
canonical predicate: True

paralogous to
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: homologous to
definition: a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
canonical predicate: True

positively correlated with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: correlated with
definition: A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or presence of one correlates with an increase or presence of the other).
canonical predicate: True
opposite of: negatively correlated with

reaction balanced
type: ObjectProperty
domain: association
range: Boolean
sub property of: association slot

related condition
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
canonical predicate: True

related synonym
type: ObjectProperty
domain: named thing
range: label type
sub property of: synonym

relation
type: ObjectProperty
range: String

relative frequency object
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the object concept appears in these same records.

relative frequency object confidence interval
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: The 99% confidence interval for the relative_frequency_object calculation (i.e. the range of values within which the true value has a 99% chance of falling)

relative frequency subject
type: ObjectProperty
domain: association
range: Float
sub property of: association slot
definition: The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the subject concept appears in these same records.
examples: Example(value='0.01840490798', description=None)

relative frequency subject confidence interval
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: The 99% confidence interval for the relative_frequency_subject calculation (i.e. the range of values within which the true value has a 99% chance of falling)

retrieved on
type: ObjectProperty
domain: dataset
range: Date
sub property of: node property

same as
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: exact match
definition: holds between two entities that are considered equivalent to each other
narrow match: external-identifier
canonical predicate: True

sequence variant qualifier
type: ObjectProperty
domain: association
range: sequence variant
sub property of: association slot
definition: a qualifier used in an association with the variant

start coordinate
type: ObjectProperty
domain: genomic sequence localization
range: Integer
sub property of: base coordinate
alternative label: start
definition: The position at which the subject genomic entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 1).

subclass of
type: ObjectProperty
domain: ontology class
range: ontology class
sub property of: related to at concept level
definition: holds between two classes where the domain class is a specialization of the range class
narrow match: has archetype
narrow match: has parent group
narrow match: is presence guidance for
narrow match: has dose form
narrow match: has doseformgroup
narrow match: CHEBI has parent hydride
narrow match: NCIT A11
narrow match: NCIT A14
narrow match: NCIT A16
narrow match: NCIT A3
narrow match: NCIT R36
narrow match: NCIT R42
narrow match: NCIT gene product has chemical classification
narrow match: SNOMED entire anatomy structure of
narrow match: SNOMED has dose form
narrow match: subPropertyOf
canonical predicate: True

subject location in text
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion.
examples: Example(value='15', description=None)

superclass of
type: ObjectProperty
domain: ontology class
range: ontology class
sub property of: related to at concept level
definition: holds between two classes where the domain class is a super class of the range class
narrow match: RB
narrow match: NCIT cdrh parent of
narrow match: NCIT ctcae 5 parent of
narrow match: NCIT subset includes concept
narrow match: OMIM has manifestation
narrow match: SNOMED has basic dose form

supporting data set
type: ObjectProperty
domain: association
range: information resource
sub property of: association slot
definition: A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data).

supporting data source
type: ObjectProperty
domain: association
range: information resource
sub property of: association slot
definition: An Information Resource from which data was retrieved and subsequently used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data).
editorial note: For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The "primary knowledge source" for this edge is "infores:icees-asthma". A "supporting data source" for this KP- generated knowledge is "infores:unc-cdw-health." The "aggregator knowledge source" for this data is "infores:aragorn-ara"

supporting document type
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result.
examples: Example(value='Journal Article', description=None)

supporting document year
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: The document year (typically the publication year) for the supporting document used in a Text Mining Result.
examples: Example(value='1999', description=None)

supporting study cohort
type: ObjectProperty
domain: association
range: String
sub property of: supporting study metadata
definition: A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria).

supporting study context
type: ObjectProperty
domain: association
range: String
sub property of: supporting study metadata
definition: A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.).

supporting study date range
type: ObjectProperty
domain: association
range: String
sub property of: supporting study metadata
definition: The date range over which data was collected in a study that provided evidence for an Association.

supporting study method description
type: ObjectProperty
domain: association
range: Uriorcurie
sub property of: supporting study metadata
definition: A uri or curie pointing to information about the methodology used to generate data supporting an Association.

supporting study method type
type: ObjectProperty
domain: association
range: Uriorcurie
sub property of: supporting study metadata
definition: A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of experimental assay, or statistical calculation, or computational analysis).

supporting study size
type: ObjectProperty
domain: association
range: Integer
sub property of: supporting study metadata
definition: The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a clinical study).

supporting text
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: The segment of text from a document that supports the mined assertion.
examples: Example(value='The administration of 50g/ml bupivacaine promoted maximum breast cancer.', description=None)

supporting text section type
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text.
examples: Example(value='Introduction', description=None)

temporal interval qualifier
type: ObjectProperty
domain: association
range: time type
sub property of: temporal context qualifier
definition: a constraint of a time interval placed upon the truth value of an association.

update date
type: ObjectProperty
domain: named thing
range: Date
sub property of: node property
definition: date on which an entity was updated. This can be applied to nodes or edges

version
type: ObjectProperty
domain: dataset
range: String
sub property of: node property
broad match: ingest date
broad match: versionInfo

version of
type: ObjectProperty
domain: dataset version
range: dataset summary
sub property of: node property

xenologous to
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: homologous to
definition: a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.
canonical predicate: True

systematic synonym
type: ObjectProperty
domain: named thing
range: label type
sub property of: node property
definition: more commonly used for gene symbols in yeast

administrative entity
type: Class
subclass of: named thing

behavior
type: Class
subclass of: activity and behavior
subclass of: biological process
subclass of: ontology class
narrow match: T041
narrow match: T054
narrow match: T055

behavioral feature
type: Class
subclass of: phenotypic feature
definition: A phenotypic feature which is behavioral in nature.

book chapter
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: volume
subclass of: Restriction
  on class: Uriorcurie
  on property: published in
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: chapter
subclass of: publication

case
type: Class
subclass of: individual organism
subclass of: subject of investigation
alternative label: patient
alternative label: proband
definition: An individual (human) organism that has a patient role in some clinical context.

cell line to disease or phenotypic feature association
type: Class
subclass of: Restriction
  on class: disease or phenotypic feature
  on property: subject
  qualified cardinality: 1
subclass of: association
subclass of: cell line to entity association mixin
subclass of: entity to disease or phenotypic feature association mixin
definition: 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.

chemical exposure
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
definition: A chemical exposure is an intake of a particular chemical entity.

chemical formula value
type: Class
subclass of: Restriction
  on data range: string
  on property: value
  qualified cardinality: 1
editorial note: Should be implemented as a stronger type

chemical or drug or treatment to disease or phenotypic feature association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: FDAIDAAdverseEventEnum
  on property: FDA adverse event level
subclass of: association
subclass of: chemical to entity association mixin
subclass of: entity to disease or phenotypic feature association mixin
definition: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.

clinical course
type: Class
subclass of: clinical attribute
definition: The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual

clinical intervention
type: Class
subclass of: clinical entity

clinical modifier
type: Class
subclass of: clinical attribute
definition: Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects

coding sequence
type: Class
subclass of: nucleic acid entity

confidence level
type: Class
subclass of: information content entity
definition: Level of confidence in a statement

drug exposure
type: Class
subclass of: chemical exposure
subclass of: exposure event
alternative label: drug dose
alternative label: drug intake
alternative label: medication intake
broad match: SIO_001005
definition: A drug exposure is an intake of a particular drug.

drug to entity association mixin
type: Class
subclass of: Restriction
  on class: drug
  on property: subject
  qualified cardinality: 1
subclass of: chemical entity to entity association mixin
subclass of: mixin
definition: An interaction between a drug and another entity

DruggableGeneCategoryEnum
type: Class
union of: tclin
union of: tbio
union of: tchem
union of: tdark
permissible values: tbio
permissible values: tchem
permissible values: tclin
permissible values: tdark

environmental exposure
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: attribute
subclass of: exposure event
definition: A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants.

exon
type: Class
subclass of: nucleic acid entity
definition: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.

FDA adverse event level
type: ObjectProperty
domain: association
range: FDAIDAAdverseEventEnum
sub property of: association slot

gene family
type: Class
subclass of: Restriction
  all values from: gene
  on property: has gene or gene product
subclass of: biological entity
subclass of: chemical entity or gene or gene product
subclass of: gene grouping mixin
alternative label: orthogroup
alternative label: protein family
definition: any grouping of multiple genes or gene products related by common descent
narrow match: NCIT C20130
narrow match: SIO_001380
narrow match: Q417841

genotype to disease association
type: Class
subclass of: Restriction
  on class: named thing
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  on class: named thing
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: association
subclass of: entity to disease association mixin
subclass of: genotype to entity association mixin
note: TODO decide no how to model pathogenicity

geographic location
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: longitude
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: latitude
subclass of: planetary entity
definition: a location that can be described in lat/long coordinates

LogicalInterpretationEnum
type: Class
union of: some_some
union of: all_some
union of: inverse_all_some
permissible values: all_some
permissible values: some_some
permissible values: inverse_all_some

mapping collection
type: Class
subclass of: Restriction
  all values from: predicate mapping
  on property: predicate mappings
definition: A collection of deprecated mappings.

molecular mixture
type: Class
subclass of: chemical mixture
definition: A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.

organism attribute
type: Class
subclass of: attribute
definition: describes a characteristic of an organismal entity.

pairwise gene to gene interaction
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: gene to gene association
definition: 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)
narrow match: ProteinProteinInteraction

polypeptide
type: Class
subclass of: biological entity
subclass of: chemical entity or gene or gene product
subclass of: chemical entity or protein or polypeptide
alternative label: amino acid entity
definition: A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.
narrow match: T087
narrow match: T116
narrow match: SO_0000104

reaction to participant association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: ReactionDirectionEnum
  on property: reaction direction
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: stoichiometry
subclass of: Restriction
  on class: molecular entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: ReactionSideEnum
  on property: reaction side
subclass of: chemical to chemical association

sequence association
type: Class
subclass of: association
definition: An association between a sequence feature and a nucleic acid entity it is localized to.

specificity quantifier
type: Class
subclass of: relationship quantifier
subclass of: mixin

study population
type: Class
subclass of: population of individual organisms
definition: A group of people banded together or treated as a group as participants in a research study.

symbol type
type: Class
subclass of: String

treatment
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: Restriction
  all values from: drug
  on property: has drug
subclass of: Restriction
  all values from: device
  on property: has device
subclass of: Restriction
  all values from: procedure
  on property: has procedure
subclass of: chemical or drug or treatment
subclass of: exposure event
subclass of: named thing
alternative label: medical action
alternative label: medical intervention
broad match: MAXO_0000058
definition: A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures

variant to disease association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  on class: named thing
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: named thing
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: association
subclass of: entity to disease association mixin
subclass of: variant to entity association mixin
note: TODO decide no how to model pathogenicity

variant to gene association
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: gene
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: variant to entity association mixin
definition: An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)

active in
type: ObjectProperty
domain: gene or gene product
range: cellular component
sub property of: related to at instance level
inverse of: has active component
canonical predicate: True

acts upstream of negative effect
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of
inverse of: has negative upstream actor
canonical predicate: True

acts upstream of or within negative effect
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of or within
inverse of: has negative upstream or within actor
canonical predicate: True

acts upstream of or within positive effect
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of or within
inverse of: has positive upstream or within actor
canonical predicate: True

acts upstream of positive effect
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of
inverse of: has positive upstream actor
canonical predicate: True

address
type: ObjectProperty
domain: named thing
range: String
sub property of: node property
definition: the particulars of the place where someone or an organization is situated. For now, this slot is a simple text "blob" containing all relevant details of the given location for fitness of purpose. For the moment, this "address" can include other contact details such as email and phone number(?).

adjusted p value
type: ObjectProperty
domain: association
range: Float
sub property of: p value
definition: The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.

adverse event of
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: affected by
inverse of: has adverse event

affiliation
type: ObjectProperty
domain: agent
range: Uriorcurie
sub property of: node property
definition: a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.

aggregator knowledge source
type: ObjectProperty
domain: association
range: information resource
sub property of: knowledge source
definition: An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.
editorial note: For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The "primary knowledge source" for this edge is "infores:icees-asthma". A "supporting data source" for this KP- generated knowledge is "infores:unc-cdw-health." The "aggregator knowledge source" for this data is "infores:aragorn-ara"

amount or activity decreased by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: decreases amount or activity of

amount or activity increased by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: increases amount or activity of

assesses
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: is assessed by
alternative label: was assayed against
definition: The effect of a thing on a target was interrogated in some assay. A relationship between some perturbing agent (usually a chemical compound) and some target entity, where the affect of the perturbing agent on the target entity was interrogated in a particular assay. The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type of biological entity.
canonical predicate: True

associated environmental context
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: An attribute that can be applied to an association where the association holds between two entities located or occurring in a particular environment. For example, two microbial taxa may interact in the context of a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure. # TODO: add examples of values for this property.

associated with decreased likelihood of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: associated with likelihood of
inverse of: decreased likelihood associated with
definition: Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is less probable.
canonical predicate: True

associated with increased likelihood of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: associated with likelihood of
inverse of: increased likelihood associated with
definition: Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is more probable.
canonical predicate: True

associated with resistance to
type: ObjectProperty
domain: named thing
range: chemical entity
sub property of: associated with
inverse of: resistance associated with
definition: A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of resistance to treatment by the chemical.
canonical predicate: True

associated with sensitivity to
type: ObjectProperty
domain: named thing
range: chemical entity
sub property of: associated with
inverse of: sensitivity associated with
broad match: PATO_0000085
definition: A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of sensitivity to treatment by the chemical.
narrow match: http://snomed.info/id/418038007
canonical predicate: True

author
type: ObjectProperty
domain: agent
range: publication
sub property of: contributor
inverse of: has author
definition: an instance of one (co-)creator primarily responsible for a written work

authors
type: ObjectProperty
domain: publication
range: String
sub property of: node property
definition: connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as "surname, firstname initial.". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.

available from
type: ObjectProperty
domain: named thing
range: DrugAvailabilityEnum
sub property of: node property

biomarker for
type: ObjectProperty
domain: chemical entity or gene or gene product
range: disease or phenotypic feature
sub property of: correlated with
inverse of: has biomarker
broad match: RO_0002607
definition: holds between a measurable chemical 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.
narrow match: NCIT R47
narrow match: NCIT genetic biomarker related to
narrow match: NCIT is molecular abnormality of disease
narrow match: Orphanet_465410
canonical predicate: True

can be carried out by
type: ObjectProperty
domain: occurrent
range: occurrent
sub property of: actively involves
inverse of: capable of

capable of
type: ObjectProperty
domain: occurrent
range: occurrent
sub property of: actively involved in
inverse of: can be carried out by
definition: holds between a physical entity and process or function, where the continuant alone has the ability to carry out the process or function.
narrow match: NCIT R52
narrow match: RO_0002500
canonical predicate: True

catalyst qualifier
type: ObjectProperty
domain: association
range: macromolecular machine mixin
sub property of: association slot
definition: a qualifier that connects an association between two causally connected entities (for example, two chemical entities, or a chemical entity in that changes location) and the gene product, gene, or complex that enables or catalyzes the change.

catalyzes
type: ObjectProperty
domain: nucleic acid entity
range: molecular activity
sub property of: participates in
inverse of: has catalyst
canonical predicate: True

caused by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: contribution from
inverse of: causes
alternative label: disease caused by disruption of
alternative label: disease has basis in dysfunction of
alternative label: realized in response to
alternative label: realized in response to stimulus
definition: holds between two entities where the occurrence, existence, or activity of one is caused by the occurrence or generation of the other
narrow match: RO_0001022
narrow match: RO_0002608
narrow match: RO_0004019
narrow match: RO_0004020
narrow match: RO_0004028
narrow match: RO_0009501

causes
type: ObjectProperty
domain: named thing
range: named thing
sub property of: contributes to
inverse of: caused by
broad match: RO_0002410
broad match: RO_0002506
definition: holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other
narrow match: has physiologic effect
narrow match: GOREL_0000040
narrow match: MONDO disease causes feature
narrow match: MONDO disease triggers
narrow match: NCIT allele has abnormality
narrow match: NCIT biological process has result biological process
narrow match: NCIT chemical or drug has physiologic effect
narrow match: NCIT chemical or drug initiates biological process
narrow match: NCIT chromosome mapped to disease
narrow match: NCIT disease has normal tissue origin
narrow match: NCIT process initiates biological process
narrow match: RO_0002256
narrow match: RO_0002315
narrow match: RO_0002507
narrow match: RO_0002509
narrow match: RO_0004001
narrow match: SNOMED causative agent of
narrow match: SNOMED has realization
narrow match: in response to
narrow match: Orphanet_317343
narrow match: Orphanet_317344
narrow match: Orphanet_317346
narrow match: Orphanet_410295
narrow match: Orphanet_410296
canonical predicate: True
opposite of: prevents

chapter
type: ObjectProperty
domain: book chapter
range: String
sub property of: node property
definition: chapter of a book

close match
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at concept level
definition: a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity).
narrow match: classified as
narrow match: SY
narrow match: has quantified form
narrow match: CHEBI is enantiomer of
narrow match: CHEBI is tautomer of
narrow match: hasDbXref
narrow match: xref
canonical predicate: True

completed by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: has completed

composed primarily of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to
inverse of: primarily composed of
definition: x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.
canonical predicate: True

condition associated with gene
type: ObjectProperty
domain: gene
range: disease or phenotypic feature
sub property of: genetic association
inverse of: gene associated with condition
alternative label: disease associated with gene
definition: holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products
narrow match: NCIT R176

consumed by
type: ObjectProperty
domain: occurrent
range: biological process or activity
sub property of: is input of
inverse of: consumes

consumes
type: ObjectProperty
domain: biological process or activity
range: occurrent
sub property of: has input
inverse of: consumed by
narrow match: RO_0004009
canonical predicate: True

contains process
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: occurs in

contraindicated for
type: ObjectProperty
domain: drug
range: disease or phenotypic feature
sub property of: related to at instance level
inverse of: has contraindication
definition: Holds between a drug and a disease or phenotype, such that a person with that disease should not be treated with the drug.
canonical predicate: True
opposite of: treats

creation date
type: ObjectProperty
domain: named thing
range: Date
sub property of: node property
alternative label: publication date
definition: date on which an entity was created. This can be applied to nodes or edges

decreased amount in
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: has decreased amount

decreased likelihood associated with
type: ObjectProperty
domain: named thing
range: named thing
sub property of: likelihood associated with
inverse of: associated with decreased likelihood of

decreases amount or activity of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: amount or activity decreased by
definition: A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object.

decreases response to
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: affects response to
inverse of: response decreased by
definition: holds between two chemical entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other
narrow match: decreases response to substance
canonical predicate: True
opposite of: increases response to

develops from
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: develops into
narrow match: RO_0002207
narrow match: RO_0002225
narrow match: RO_0002226
canonical predicate: True

develops into
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: develops from

diagnoses
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: related to at instance level
inverse of: is diagnosed by
definition: a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.
canonical predicate: True

directly physically interacts with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: physically interacts with
broad match: RO_0002578
broad match: SIO_000203
definition: A causal mechanism mediated by a direct contact between the effector and target entities (this contact may be weak or strong, transient or stable).
narrow match: affects binding
narrow match: chelator
narrow match: pharos.nih.govdrug targets
narrow match: interaction typescofactor
canonical predicate: True

disease has basis in
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: occurs in disease
definition: A relation that holds between a disease and an entity where the state of the entity has contribution to the disease.
narrow match: MONDO disease has basis in accumulation of
narrow match: MONDO disease has basis in development of
canonical predicate: True

disease has location
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to
inverse of: location of disease
definition: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.

disrupted by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: affected by
inverse of: disrupts
definition: describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another.

disrupts
type: ObjectProperty
domain: named thing
range: named thing
sub property of: affects
inverse of: disrupted by
alternative label: disease causes disruption of
definition: describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
narrow match: RO_0004024
narrow match: RO_0004025
canonical predicate: True
opposite of: enables

distribution download url
type: ObjectProperty
domain: dataset distribution
range: String
sub property of: node property

drug regulatory status world wide
type: ObjectProperty
range: String
alternative label: max phase
definition: An agglomeration of drug regulatory status worldwide. Not specific to FDA.
narrow match: clinically tested approved unknown phase
narrow match: clinically tested suspended phase 0
narrow match: clinically tested suspended phase 1
narrow match: clinically tested suspended phase 1 or phase 2
narrow match: clinically tested suspended phase 2
narrow match: clinically tested suspended phase 2 or phase 3
narrow match: clinically tested suspended phase 3
narrow match: clinically tested terminated phase 0
narrow match: clinically tested terminated phase 1
narrow match: clinically tested terminated phase 1 or phase 2
narrow match: clinically tested terminated phase 2
narrow match: clinically tested terminated phase 2 or phase 3
narrow match: clinically tested terminated phase 3
narrow match: clinically tested withdrawn phase 0
narrow match: clinically tested withdrawn phase 1
narrow match: clinically tested withdrawn phase 1 or phase 2
narrow match: clinically tested withdrawn phase 2
narrow match: clinically tested withdrawn phase 2 or phase 3
narrow match: clinically tested withdrawn phase 3
narrow match: NCIT R172
narrow match: NCIT regimen has accepted use for disease

editor
type: ObjectProperty
domain: agent
range: publication
sub property of: contributor
inverse of: has editor
definition: editor of a compiled work such as a book or a periodical (newspaper or an academic journal). Note that in the case of publications which have a containing "published in" node property, the editor association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the editorial agent of the encompassing publication (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).

enables
type: ObjectProperty
domain: physical entity
range: biological process or activity
sub property of: participates in
inverse of: enabled by
definition: holds between a physical entity and a process, where the physical entity executes the process
canonical predicate: True
opposite of: prevents

end interbase coordinate
type: ObjectProperty
domain: genomic sequence localization
range: Integer
sub property of: interbase coordinate
definition: The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.
opposite of: start interbase coordinate

exacerbates
type: ObjectProperty
domain: biological entity
range: disease or phenotypic feature
sub property of: affects
inverse of: is exacerbated by
broad match: SemMedDBCOMPLICATES
definition: A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
canonical predicate: True

expressed in
type: ObjectProperty
domain: gene or gene product
range: anatomical entity
sub property of: located in
inverse of: expresses
definition: holds between a gene or gene product and an anatomical entity in which it is expressed
narrow match: NCIT R46
narrow match: NCIT R49
canonical predicate: True

expresses
type: ObjectProperty
domain: anatomical entity
range: gene or gene product
sub property of: location of
inverse of: expressed in
alternative label: anatomy expresses gene
definition: holds between an anatomical entity and gene or gene product that is expressed there

format
type: ObjectProperty
domain: information content entity
range: String
sub property of: node property

gene associated with condition
type: ObjectProperty
domain: disease or phenotypic feature
range: gene
sub property of: genetic association
inverse of: condition associated with gene
broad match: GENO_0000840
broad match: GENO_0000841
definition: holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with
narrow match: NCIT R175
narrow match: NCIT R38
narrow match: NCIT R48
canonical predicate: True

gene product of
type: ObjectProperty
domain: gene product mixin
range: gene
sub property of: related to at instance level
inverse of: has gene product
definition: definition x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of thatf process is either y or something that is ribosomally translated from x
canonical predicate: True

genome build
type: ObjectProperty
domain: genomic sequence localization
range: StrandEnum
sub property of: sequence localization attribute
definition: The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens.

has active component
type: ObjectProperty
domain: cellular component
range: gene or gene product
sub property of: related to at instance level
inverse of: active in

has active ingredient
type: ObjectProperty
domain: drug
range: molecular entity
sub property of: has part
inverse of: is active ingredient of
definition: holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component
canonical predicate: True
opposite of: is excipient of

has adverse event
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects
inverse of: adverse event of
alternative label: adverse effect
definition: An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment with a therapeutic agent. Adverse events may be caused by something other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or diseases temporally associated with the treatment, whether or not considered related to the treatment. Adverse events are unintended effects that occur when a medication is administered correctly.
canonical predicate: True

has author
type: ObjectProperty
domain: publication
range: agent
sub property of: has contributor
inverse of: author

has biomarker
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical entity or gene or gene product
sub property of: correlated with
inverse of: biomarker for
definition: holds between a disease or phenotypic feature and a measurable chemical entity that is used as an indicator of the presence or state of the disease or feature. # metabolite
narrow match: NCIT disease has molecular abnormality
narrow match: NCIT disease is marked by gene

has catalyst
type: ObjectProperty
domain: molecular activity
range: nucleic acid entity
sub property of: has participant
inverse of: catalyzes

has chemical role
type: ObjectProperty
domain: named thing
range: chemical role
sub property of: related to at concept level
definition: A role is particular behaviour which a chemical entity may exhibit.

has completed
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: completed by
definition: holds between an entity and a process that the entity is capable of and has completed
canonical predicate: True
opposite of: has not completed

has contraindication
type: ObjectProperty
domain: disease or phenotypic feature
range: drug
sub property of: related to at instance level
inverse of: contraindicated for

has decreased amount
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: decreased amount in
narrow match: CL has low plasma membrane amount
canonical predicate: True
opposite of: has increased amount

has device
type: ObjectProperty
domain: named thing
range: device
sub property of: node property
definition: connects an entity to one or more (medical) devices

has drug
type: ObjectProperty
domain: named thing
range: drug
sub property of: node property
definition: connects an entity to one or more drugs

has editor
type: ObjectProperty
domain: publication
range: agent
sub property of: has contributor
inverse of: editor

has excipient
type: ObjectProperty
domain: drug
range: molecular entity
sub property of: has part
inverse of: is excipient of
definition: holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component
canonical predicate: True

has frameshift variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: has sequence variant
inverse of: is frameshift variant of
alternative label: splice acceptor variant
alternative label: splice donor variant
alternative label: splice region variant

has gene
type: ObjectProperty
domain: named thing
range: gene
sub property of: has gene or gene product
definition: connects an entity associated with one or more genes

has gene product
type: ObjectProperty
domain: gene
range: gene product mixin
sub property of: related to at instance level
inverse of: gene product of
definition: holds between a gene and a transcribed and/or translated product generated from it
narrow match: NCIT R178

has increased amount
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: increased amount of
narrow match: CL has high plasma membrane amount
canonical predicate: True
opposite of: has decreased amount

has member
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at concept level
inverse of: member of
definition: Defines a mereological relation between a collection and an item.

has metabolite
type: ObjectProperty
domain: molecular entity
range: molecular entity
sub property of: derives into
inverse of: is metabolite of
definition: holds between two molecular entities in which the second one is derived from the first one as a product of metabolism
note: The CHEBI ID represents a role rather than a predicate
canonical predicate: True

has missense variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: has sequence variant
inverse of: is missense variant of

has mode of inheritance
type: ObjectProperty
domain: disease or phenotypic feature
range: genetic inheritance
sub property of: has manifestation
inverse of: mode of inheritance of
definition: Relates a disease or phenotypic feature to its observed genetic segregation and assumed associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).
canonical predicate: True

has molecular consequence
type: ObjectProperty
domain: named thing
range: ontology class
sub property of: related to at instance level
inverse of: is molecular consequence of
alternative label: allele has activity
definition: connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583
narrow match: NCIT allele has activity
canonical predicate: True

has nearby variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: has sequence variant
inverse of: is nearby variant of
alternative label: 3 prime UTR variant
alternative label: 5 prime UTR premature start codon gain variant
alternative label: 5 prime UTR variant
alternative label: intron variant
alternative label: non coding transcript exon variant

has negative upstream actor
type: ObjectProperty
domain: biological process
range: gene or gene product
sub property of: has upstream actor
inverse of: acts upstream of negative effect

has negative upstream or within actor
type: ObjectProperty
domain: biological process
range: gene or gene product
sub property of: has upstream or within actor
inverse of: acts upstream of or within negative effect

has non coding variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: has sequence variant
inverse of: is non coding variant of

has nonsense variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: has sequence variant
inverse of: is nonsense variant of

has not completed
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: not completed by
definition: holds between an entity and a process that the entity is capable of, but has not completed
canonical predicate: True
opposite of: has completed

has numeric value
type: ObjectProperty
domain: quantity value
range: Double
definition: connects a quantity value to a number

has nutrient
type: ObjectProperty
domain: chemical entity
range: chemical entity
sub property of: has food component
inverse of: nutrient of
definition: one or more nutrients which are growth factors for a living organism
canonical predicate: True

has phenotype
type: ObjectProperty
domain: biological entity
range: phenotypic feature
sub property of: related to at instance level
inverse of: phenotype of
alternative label: disease presents symptom
broad match: NCIT R108
broad match: NCIT R115
definition: 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). In SNOMEDCT, disorders with keyword 'characterized by' should translate into this predicate.
editorial note: check the range
narrow match: NCIT R89
narrow match: RO_0004022
narrow match: has symptom
canonical predicate: True

has plasma membrane part
type: ObjectProperty
domain: named thing
range: named thing
sub property of: has part
inverse of: plasma membrane part of
definition: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
canonical predicate: True

has positive upstream actor
type: ObjectProperty
domain: biological process
range: gene or gene product
sub property of: has upstream actor
inverse of: acts upstream of positive effect

has positive upstream or within actor
type: ObjectProperty
domain: biological process
range: gene or gene product
sub property of: has upstream or within actor
inverse of: acts upstream of or within positive effect

has predisposing factor
type: ObjectProperty
domain: named thing
range: named thing
sub property of: risk affected by
inverse of: predisposes

has procedure
type: ObjectProperty
domain: named thing
range: procedure
sub property of: node property
definition: connects an entity to one or more (medical) procedures

has provider
type: ObjectProperty
domain: information content entity
range: agent
sub property of: has contributor
inverse of: provider

has publisher
type: ObjectProperty
domain: publication
range: agent
sub property of: has contributor
inverse of: publisher

has qualitative value
type: ObjectProperty
domain: attribute
range: named thing
definition: connects an attribute to a value

has quantitative value
type: ObjectProperty
domain: attribute
range: quantity value
definition: connects an attribute to a value
narrow match: SNOMED has concentration strength numerator value
narrow match: SNOMED has presentation strength denominator value
narrow match: SNOMED has presentation strength numerator value

has sequence location
type: ObjectProperty
domain: nucleic acid entity
range: nucleic acid entity
sub property of: related to at instance level
inverse of: sequence location of
definition: holds between two nucleic acid entities when the subject can be localized in sequence coordinates on the object. For example, between an exon and a chromosome/contig.
canonical predicate: True

has side effect
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects
inverse of: is side effect of
alternative label: adverse drug reaction
definition: An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment. Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of the medication.
editorial note: Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative. Aeolus, Sider are both resources that provide side effects.
canonical predicate: True

has splice site variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: has sequence variant
inverse of: is splice site variant of
alternative label: downstream gene variant
alternative label: upstream gene variant

has substrate
type: ObjectProperty
domain: molecular activity
range: chemical entity or gene or gene product
sub property of: has participant
inverse of: is substrate of
canonical predicate: True

has synonymous variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: has sequence variant
inverse of: is synonymous variant of
alternative label: stop gained

has target
type: ObjectProperty
domain: disease
range: gene
sub property of: related to at instance level
inverse of: target for

has taxonomic rank
type: ObjectProperty
domain: named thing
range: taxonomic rank
sub property of: node property

has unit
type: ObjectProperty
domain: quantity value
range: unit
definition: connects a quantity value to a unit
narrow match: SNOMED has concentration strength denominator unit
narrow match: SNOMED has concentration strength numerator unit
narrow match: SNOMED has presentation strength denominator unit
narrow match: SNOMED has presentation strength numerator unit
narrow match: SNOMED has unit of presentation

has variant part
type: ObjectProperty
domain: named thing
range: named thing
sub property of: has part
inverse of: variant part of
definition: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it
canonical predicate: True

has zygosity
type: ObjectProperty
domain: nucleic acid entity
range: zygosity
sub property of: node property

highest FDA approval status
type: ObjectProperty
range: String
definition: Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'

increased amount of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: has increased amount

increased likelihood associated with
type: ObjectProperty
domain: named thing
range: named thing
sub property of: likelihood associated with
inverse of: associated with increased likelihood of

increases amount or activity of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: amount or activity increased by
definition: A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object.

increases response to
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: affects response to
inverse of: response increased by
definition: holds between two chemical entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other
canonical predicate: True
opposite of: decreases response to

interacting molecules category
type: ObjectProperty
domain: association
range: ontology class
sub property of: association slot
examples: Example(value='MI:1048', description='smallmolecule-protein')

iri
type: ObjectProperty
range: iri type
definition: An IRI for an entity. This is determined by the id using expansion rules.

is active ingredient of
type: ObjectProperty
domain: molecular entity
range: drug
sub property of: part of
inverse of: has active ingredient
definition: holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component

is assessed by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: assesses

is diagnosed by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: related to at instance level
inverse of: diagnoses

is exacerbated by
type: ObjectProperty
domain: disease or phenotypic feature
range: biological entity
sub property of: affected by
inverse of: exacerbates

is excipient of
type: ObjectProperty
domain: molecular entity
range: drug
sub property of: part of
inverse of: has excipient
definition: holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component

is frameshift variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
inverse of: has frameshift variant
alternative label: frameshift variant
alternative label: start lost
alternative label: stop lost
definition: holds between a sequence variant and a gene, such the sequence variant causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
canonical predicate: True

is metabolite
type: ObjectProperty
domain: molecular entity
range: Boolean
sub property of: node property
definition: indicates whether a molecular entity is a metabolite

is metabolite of
type: ObjectProperty
domain: molecular entity
range: molecular entity
sub property of: derives from
inverse of: has metabolite
definition: holds between two molecular entities in which the first one is derived from the second one as a product of metabolism
note: The CHEBI ID represents a role rather than a predicate

is missense variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
inverse of: has missense variant
definition: holds between a gene and a sequence variant, such the sequence variant results in a different amino acid sequence but where the length is preserved.
canonical predicate: True

is molecular consequence of
type: ObjectProperty
domain: ontology class
range: named thing
sub property of: related to at instance level
inverse of: has molecular consequence

is nearby variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
inverse of: has nearby variant
definition: holds between a sequence variant and a gene sequence that the variant is genomically close to.
canonical predicate: True

is non coding variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
inverse of: has non coding variant
definition: holds between a sequence variant and a gene, where the variant does not affect the coding sequence
canonical predicate: True

is nonsense variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
inverse of: has nonsense variant
broad match: SO_0002054
definition: holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon
canonical predicate: True

is output of
type: ObjectProperty
domain: occurrent
range: biological process or activity
sub property of: participates in
inverse of: has output

is side effect of
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: affected by
inverse of: has side effect

is splice site variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
inverse of: has splice site variant
definition: holds between a sequence variant and a gene, such the sequence variant is in the canonical splice site of one of the gene's exons.
canonical predicate: True

is substrate of
type: ObjectProperty
domain: chemical entity or gene or gene product
range: molecular activity
sub property of: participates in
inverse of: has substrate

is supplement
type: ObjectProperty
domain: named thing
range: chemical mixture
sub property of: node property

is synonymous variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
inverse of: has synonymous variant
definition: holds between a sequence variant and a gene, such the sequence variant is in the coding sequence of the gene, but results in the same amino acid sequence
canonical predicate: True

is toxic
type: ObjectProperty
domain: named thing
range: Boolean
sub property of: node property

keywords
type: ObjectProperty
domain: publication
range: String
sub property of: node property
definition: keywords tagging a publication

lacks part
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: missing from
narrow match: CL lacks plasma membrane part
canonical predicate: True
opposite of: has part

latitude
type: ObjectProperty
domain: named thing
range: Float
sub property of: node property
definition: latitude

license
type: ObjectProperty
domain: information content entity
range: String
sub property of: node property
narrow match: Property:P275

location of disease
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to
inverse of: disease has location

longitude
type: ObjectProperty
domain: named thing
range: Float
sub property of: node property
definition: longitude

mapped predicate
type: ObjectProperty
range: String
definition: The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.

max tolerated dose
type: ObjectProperty
domain: named thing
range: String
sub property of: node property
definition: The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.

member of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at concept level
inverse of: has member
definition: Defines a mereological relation between a item and a collection.

mentioned by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: mentions
definition: refers to is a relation between one named thing and the information content entity that it makes reference to.

mentions
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: mentioned by
definition: refers to is a relation between one information content entity and the named thing that it makes reference to.
narrow match: SIO_000628

mesh terms
type: ObjectProperty
domain: publication
range: Uriorcurie
sub property of: node property
definition: mesh terms tagging a publication

missing from
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: lacks part

mode of inheritance of
type: ObjectProperty
domain: genetic inheritance
range: disease or phenotypic feature
sub property of: manifestation of
inverse of: has mode of inheritance

model of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: models
definition: holds between a thing and some other thing it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
narrow match: FOODON_00001301
canonical predicate: True

models
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: model of

negated
type: ObjectProperty
domain: association
range: Boolean
sub property of: association slot
definition: if set to true, then the association is negated i.e. is not true

not completed by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: has not completed

nutrient of
type: ObjectProperty
domain: chemical entity
range: chemical entity
sub property of: food component of
inverse of: has nutrient
definition: holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)

object derivative qualifier
type: ObjectProperty
domain: association
range: String
sub property of: derivative qualifier

occurs in
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: contains process
definition: holds between a process and a material entity or site within which the process occurs
narrow match: has imaged location
narrow match: RO_0002231
narrow match: RO_0002232
narrow match: SNOMED has direct procedure site
narrow match: SNOMED has direct site
narrow match: SNOMED has procedure site
narrow match: site of
narrow match: in species
narrow match: SemMedDBOCCURS IN
narrow match: SemMedDBPROCESS OF
canonical predicate: True

occurs in disease
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: disease has basis in

original object
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.

original predicate
type: ObjectProperty
domain: association
range: Uriorcurie
sub property of: association slot
alternative label: original relation
alternative label: relation
definition: used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.

original subject
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.

p value
type: ObjectProperty
domain: association
range: Float
sub property of: association slot
alternative label: unadjusted p value
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.

pages
type: ObjectProperty
domain: publication
range: String
sub property of: node property
definition: page number of source referenced for statement or publication

phase
type: ObjectProperty
domain: coding sequence
range: PhaseEnum
sub property of: sequence localization attribute
definition: The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.

phenotype of
type: ObjectProperty
domain: phenotypic feature
range: biological entity
sub property of: related to at instance level
inverse of: has phenotype

plasma membrane part of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: part of
inverse of: has plasma membrane part

population context qualifier
type: ObjectProperty
domain: association
range: population of individual organisms
sub property of: qualifier
definition: a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.

preceded by
type: ObjectProperty
domain: occurrent
range: occurrent
sub property of: temporally related to
inverse of: precedes
broad match: GENEPIO_0001739
definition: holds between two processes, where the other is completed before the one begins
narrow match: FMA transforms from
narrow match: RO_0002087
narrow match: RO_0002285

precedes
type: ObjectProperty
domain: occurrent
range: occurrent
sub property of: temporally related to
inverse of: preceded by
broad match: Property:P156
definition: holds between two processes, where one completes before the other begins
narrow match: FMA transforms into
narrow match: RO_0002090
narrow match: RO_0002411
narrow match: RO_0002412
canonical predicate: True

predicate mappings
type: ObjectProperty
range: predicate mapping
definition: A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3.

predisposes
type: ObjectProperty
domain: named thing
range: named thing
sub property of: affects risk for
inverse of: has predisposing factor
definition: holds between two entities where exposure to one entity increases the chance of developing the other
canonical predicate: True
opposite of: prevents

prevented by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: risk affected by
inverse of: prevents
definition: holds between a potential outcome of which the likelihood was reduced by the application or use of an entity.
opposite of: enabled by

prevents
type: ObjectProperty
domain: named thing
range: named thing
sub property of: affects risk for
inverse of: prevented by
definition: holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical entity, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.
narrow match: RO_0002599
canonical predicate: True
opposite of: predisposes

primarily composed of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to
inverse of: composed primarily of

primary knowledge source
type: ObjectProperty
domain: association
range: information resource
sub property of: knowledge source
definition: The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. "aggregator knowledge source" can be used to caputre non-primary sources.
editorial note: For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to the NCATS ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> MolePro --retrieved_from--> ChEMBL --retrieved_from--> ClinicalTrials.gov The "primary knowledge source" for this edge is "infores:clinical-trials-gov". "infores:chembl" and "infores:molecular_data_provider" are listed in the "aggregator knowledge source" property.

produced by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: produces

produces
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: produced by
definition: holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
narrow match: NCIT R29
narrow match: SNOMED has process output
narrow match: SNOMED specimen procedure of
related match: GOREL_0001010
canonical predicate: True

provided by
type: ObjectProperty
domain: named thing
range: String
sub property of: node property
definition: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.

provider
type: ObjectProperty
domain: agent
range: information content entity
sub property of: contributor
inverse of: has provider
definition: person, group, organization or project that provides a piece of information (e.g. a knowledge association).

publications
type: ObjectProperty
domain: association
range: publication
sub property of: supporting documents
alternative label: supporting publications
definition: One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.

publisher
type: ObjectProperty
domain: agent
range: publication
sub property of: contributor
inverse of: has publisher
definition: organization or person responsible for publishing books, periodicals, podcasts, games or software. Note that in the case of publications which have a containing "published in" node property, the publisher association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the publisher agent of the encompassing publication (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).

reaction direction
type: ObjectProperty
domain: association
range: ReactionDirectionEnum
sub property of: association slot
definition: the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)
narrow match: NCIT C42677

reaction side
type: ObjectProperty
domain: association
range: ReactionSideEnum
sub property of: association slot
definition: the side of a reaction being modeled (ie: left or right)

regulated by
type: ObjectProperty
domain: physical essence or occurrent
range: physical essence or occurrent
sub property of: affected by
inverse of: regulates

regulates
type: ObjectProperty
domain: physical essence or occurrent
range: physical essence or occurrent
sub property of: affects
sub property of: interacts with
inverse of: regulated by
broad match: RO_0002295
broad match: RO_0002332
broad match: RO_0002448
broad match: modulator
broad match: Property:P128
definition: A more specific form of affects, that implies the effect results from a biologically evolved control mechanism. Gene-affects-gene relationships will (almost) always involve regulation. Exogenous/environmental chemical-affects-gene relationships are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or possibly one of the 'interacts with' predicates depending on the nature of the interaction.
editorial note: The RO definition of 'directly regulates the activity of' is an exact_mapping here because it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to "RO:0002211" which describes process to process regulation.
canonical predicate: True

resistance associated with
type: ObjectProperty
domain: chemical entity
range: named thing
sub property of: associated with
inverse of: associated with resistance to

response decreased by
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: response affected by
inverse of: decreases response to

response increased by
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: response affected by
inverse of: increases response to

rights
type: ObjectProperty
domain: information content entity
range: String
sub property of: node property

routes of delivery
type: ObjectProperty
range: DrugDeliveryEnum
definition: the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.

sensitivity associated with
type: ObjectProperty
domain: chemical entity
range: named thing
sub property of: associated with
inverse of: associated with sensitivity to

sequence location of
type: ObjectProperty
domain: nucleic acid entity
range: nucleic acid entity
sub property of: related to at instance level
inverse of: has sequence location

source web page
type: ObjectProperty
domain: dataset summary
range: String
sub property of: node property
broad match: has dataset

start interbase coordinate
type: ObjectProperty
domain: genomic sequence localization
range: Integer
sub property of: interbase coordinate
definition: The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).
opposite of: end interbase coordinate

stoichiometry
type: ObjectProperty
domain: association
range: Integer
sub property of: association slot
definition: the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.

strand
type: ObjectProperty
domain: genomic sequence localization
range: StrandEnum
sub property of: sequence localization attribute
definition: The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).

summary
type: ObjectProperty
domain: publication
range: String
sub property of: node property
alternative label: abstract
definition: executive summary of a publication

supporting documents
type: ObjectProperty
domain: association
range: Uriorcurie
sub property of: association slot
definition: One or more referencable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
examples: Example(value='PMID:12345678', description=None)

symbol
type: ObjectProperty
domain: named thing
range: String
sub property of: node property
definition: Symbol for a particular thing

target for
type: ObjectProperty
domain: gene
range: disease
sub property of: related to at instance level
inverse of: has target
definition: A gene is a target of a disease when its products are druggable and when a drug interaction with the gene product could have a therapeutic effect
canonical predicate: True

taxon of
type: ObjectProperty
domain: organism taxon
range: thing with taxon
sub property of: related to at instance level
inverse of: in taxon

trade name
type: ObjectProperty
domain: named thing
range: chemical entity
sub property of: node property

transcribed from
type: ObjectProperty
domain: transcript
range: gene
sub property of: related to at instance level
inverse of: transcribed to
definition: x is transcribed from y if and only if x is synthesized from template y
canonical predicate: True

transcribed to
type: ObjectProperty
domain: gene
range: transcript
sub property of: related to at instance level
inverse of: transcribed from
definition: inverse of transcribed from

translates to
type: ObjectProperty
domain: transcript
range: protein
sub property of: related to at instance level
inverse of: translation of
definition: x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces x (amino acid chain/polypeptide)
canonical predicate: True

translation of
type: ObjectProperty
domain: protein
range: transcript
sub property of: related to at instance level
inverse of: translates to
definition: inverse of translates to

treated by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: is ameliorated by
inverse of: treats
definition: holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition
narrow match: RO_0002302

treats
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: ameliorates
inverse of: treated by
alternative label: indicated for
alternative label: is substance that treats
definition: holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat
narrow match: clinically tested approved unknown phase
narrow match: clinically tested suspended phase 0
narrow match: clinically tested suspended phase 1
narrow match: clinically tested suspended phase 1 or phase 2
narrow match: clinically tested suspended phase 2
narrow match: clinically tested suspended phase 2 or phase 3
narrow match: clinically tested suspended phase 3
narrow match: clinically tested terminated phase 0
narrow match: clinically tested terminated phase 1
narrow match: clinically tested terminated phase 1 or phase 2
narrow match: clinically tested terminated phase 2
narrow match: clinically tested terminated phase 2 or phase 3
narrow match: clinically tested terminated phase 3
narrow match: clinically tested withdrawn phase 0
narrow match: clinically tested withdrawn phase 1
narrow match: clinically tested withdrawn phase 1 or phase 2
narrow match: clinically tested withdrawn phase 2
narrow match: clinically tested withdrawn phase 2 or phase 3
narrow match: clinically tested withdrawn phase 3
narrow match: NCIT regimen has accepted use for disease
narrow match: RO_0002606
narrow match: SNOMED plays role
related match: MONDO disease responds to
canonical predicate: True
opposite of: contraindicated for

variant part of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: part of
inverse of: has variant part

value
type: DatatypeProperty

description
type: ObjectProperty
range: narrative text
alternative label: definition
definition: a human-readable description of an entity
narrow match: Description

has distribution
type: ObjectProperty
domain: dataset version
range: dataset distribution
sub property of: node property

publication type
type: ObjectProperty
range: String
definition: Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.

source logo
type: ObjectProperty
domain: dataset summary
range: String
sub property of: node property

all_some
type: Class

some_some
type: Class

AnatomicalContextQualifierEnum
type: Class

anatomical entity to anatomical entity association
type: Class
subclass of: Restriction
  on class: anatomical entity
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: anatomical entity
  on property: subject
  qualified cardinality: 1
subclass of: association

annotation
type: Class
definition: Biolink Model root class for entity annotations.

case to entity association mixin
type: Class
subclass of: Restriction
  on class: case
  on property: subject
  qualified cardinality: 1
subclass of: mixin
definition: An abstract association for use where the case is the subject

activation
type: Class

agonism
type: Class

antagonism
type: Class

antibody_inhibition
type: Class

binding
type: Class

inducer
type: Class

inhibition
type: Class

inverse_agonism
type: Class

molecular_channel_blockage
type: Class

molecular_channel_opening
type: Class

negative_allosteric_modulation
type: Class

positive_allosteric_modulation
type: Class

potentiation
type: Class

releasing_activity
type: Class

signaling_mediated_control
type: Class

stabilization
type: Class

stimulation
type: Class

transcriptional_regulation
type: Class

cell line
type: Class
subclass of: organismal entity
subclass of: subject of investigation

cell line to entity association mixin
type: Class
subclass of: Restriction
  on class: cell line
  on property: subject
  qualified cardinality: 1
subclass of: mixin
definition: An relationship between a cell line and another entity

ChemicalEntityDerivativeEnum
type: Class
union of: metabolite
permissible values: metabolite

metabolite
type: Class

analog_form
type: Class

gain_of_function_variant_form
type: Class

genetic_variant_form
type: Class

loss_of_function_variant_form
type: Class

modified_form
type: Class

polymorphic_form
type: Class

snp_form
type: Class

chemical role
type: Class
subclass of: attribute
definition: A role played by the molecular entity or part thereof within a chemical context.
examples: Example(value='CHEBI:35469', description=None)

chemical to chemical association
type: Class
subclass of: Restriction
  on class: chemical entity
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: chemical to entity association mixin
definition: A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.

clinical entity
type: Class
subclass of: named thing
definition: Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities

device
type: Class
subclass of: named thing
definition: A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
narrow match: T074
narrow match: T075
narrow match: T122
narrow match: T203
narrow match: SemGroups-v04.txtDEVI

decreased
type: Class

downregulated
type: Class

increased
type: Class

upregulated
type: Class

DrugAvailabilityEnum
type: Class
union of: over_the_counter
union of: prescription
permissible values: over_the_counter
permissible values: prescription

over_the_counter
type: Class

prescription
type: Class

DrugDeliveryEnum
type: Class
union of: inhalation
union of: oral
union of: absorption_through_the_skin
union of: intravenous_injection
permissible values: absorption_through_the_skin
permissible values: inhalation
permissible values: intravenous_injection
permissible values: oral

absorption_through_the_skin
type: Class

inhalation
type: Class

intravenous_injection
type: Class

oral
type: Class

tbio
type: Class

tchem
type: Class

tclin
type: Class

tdark
type: Class

entity to exposure event association mixin
type: Class
subclass of: Restriction
  on class: exposure event
  on property: object
  qualified cardinality: 1
subclass of: mixin
definition: An association between some entity and an exposure event.

entity to feature or disease qualifiers mixin
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: frequency qualifier mixin
subclass of: mixin
definition: Qualifiers for entity to disease or phenotype associations.

entity to outcome association mixin
type: Class
subclass of: Restriction
  on class: outcome
  on property: object
  qualified cardinality: 1
subclass of: mixin
definition: An association between some entity and an outcome

epigenomic entity
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: mixin

evidence type
type: Class
subclass of: information content entity
alternative label: evidence code
definition: Class of evidence that supports an association

discovery_and_development_phase
type: Class

fda_accelerated_approval
type: Class

fda_breakthrough_therapy
type: Class

fda_clinical_research_phase
type: Class

fda_clinical_research_phase_1
type: Class

fda_clinical_research_phase_2
type: Class

fda_clinical_research_phase_3
type: Class

fda_clinical_research_phase_4
type: Class

fda_fast_track
type: Class

fda_post_market_safety_review
type: Class

fda_priority_review
type: Class

fda_review_phase_4
type: Class

post_approval_withdrawal
type: Class

preclinical_research_phase
type: Class

regular_fda_approval
type: Class

FDAIDAAdverseEventEnum
type: Class
union of: life_threatening_adverse_event
union of: serious_adverse_event
union of: suspected_adverse_reaction
union of: unexpected_adverse_event
permissible values: life_threatening_adverse_event
permissible values: serious_adverse_event
permissible values: suspected_adverse_reaction
permissible values: unexpected_adverse_event

life_threatening_adverse_event
type: Class

serious_adverse_event
type: Class

suspected_adverse_reaction
type: Class

unexpected_adverse_event
type: Class

FDA approval status
type: ObjectProperty
domain: association
range: FDAApprovalStatusEnum
sub property of: association slot

frequency quantifier
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: relationship quantifier
subclass of: mixin

ADP-ribosylation
type: Class

abundance
type: Class

acetylation
type: Class

activity
type: Class

activity_or_abundance
type: Class

acylation
type: Class

alkylation
type: Class

amination
type: Class

carbamoylation
type: Class

carboxylation
type: Class

cleavage
type: Class

degradation
type: Class

ethylation
type: Class

expression
type: Class

farnesylation
type: Class

folding
type: Class

geranoylation
type: Class

glucuronidation
type: Class

glutathionylation
type: Class

glycation
type: Class

glycosylation
type: Class

hydrolysis
type: Class

hydroxylation
type: Class

lipidation
type: Class

localization
type: Class

metabolic_processing
type: Class

methylation
type: Class

molecular_modification
type: Class

mutation_rate
type: Class

myristoylation
type: Class

n_linked_glycosylation
type: Class

nitrosation
type: Class

nucleotidylation
type: Class

o_linked_glycosylation
type: Class

oxidation
type: Class

palmitoylation
type: Class

phosphorylation
type: Class

prenylation
type: Class

reduction
type: Class

ribosylation
type: Class

secretion
type: Class

stability
type: Class

sulfation
type: Class

sumoylation
type: Class

synthesis
type: Class

transport
type: Class

ubiquitination
type: Class

uptake
type: Class

3_prime_utr
type: Class

5_prime_utr
type: Class

enhancer
type: Class

exon
type: Class

intron
type: Class

polya_tail
type: Class

promoter
type: Class

iri type
type: Class
subclass of: Uriorcurie

inverse_all_some
type: Class

material sample
type: Class
subclass of: physical entity
subclass of: subject of investigation
alternative label: biosample
alternative label: biospecimen
alternative label: physical sample
alternative label: sample
definition: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]

material sample to entity association mixin
type: Class
subclass of: Restriction
  on class: material sample
  on property: subject
  qualified cardinality: 1
subclass of: mixin
definition: An association between a material sample and something.

narrative text
type: Class
subclass of: String

noncoding RNA product
type: Class
subclass of: RNA product

organism taxon to organism taxon association
type: Class
subclass of: Restriction
  on class: organism taxon
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: organism taxon
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: organism taxon to entity association
definition: A relationship between two organism taxon nodes

PhaseEnum
type: Class
union of: 0
union of: 1
union of: 2
permissible values: 0
permissible values: 1
permissible values: 2

0
type: Class

1
type: Class

2
type: Class

procedure
type: Class
subclass of: activity and behavior
subclass of: named thing
definition: A series of actions conducted in a certain order or manner
narrow match: T059
narrow match: T060
narrow match: T061
narrow match: T063

RNA product
type: Class
subclass of: Restriction
  all values from: label type
  on property: synonym
subclass of: gene product mixin
subclass of: transcript

ReactionDirectionEnum
type: Class
union of: left_to_right
union of: right_to_left
union of: bidirectional
union of: neutral
permissible values: bidirectional
permissible values: left_to_right
permissible values: neutral
permissible values: right_to_left

bidirectional
type: Class

left_to_right
type: Class

neutral
type: Class

right_to_left
type: Class

ReactionSideEnum
type: Class
union of: left
union of: right
permissible values: left
permissible values: right

left
type: Class

right
type: Class

aa
type: Class

na
type: Class

socioeconomic attribute
type: Class
subclass of: attribute
definition: Attributes relating to a socioeconomic manifestation

+
type: Class

-
type: Class

.
type: Class

?
type: Class

taxonomic rank
type: Class
subclass of: ontology class
definition: A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)

unit
type: Class
subclass of: String

zygosity
type: Class
subclass of: attribute

actively involved in
type: ObjectProperty
domain: occurrent
range: molecular activity
sub property of: participates in
inverse of: actively involves
alternative label: involved in
definition: 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
narrow match: RO_0002503
narrow match: by means
narrow match: Orphanet_317348
narrow match: Orphanet_317349
narrow match: Orphanet_327767
canonical predicate: True

actively involves
type: ObjectProperty
domain: molecular activity
range: occurrent
sub property of: has participant
inverse of: actively involved in

ameliorates
type: ObjectProperty
domain: named thing
range: disease or phenotypic feature
sub property of: affects
inverse of: is ameliorated by
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure, clinical intervention) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
canonical predicate: True
opposite of: exacerbates

aspect qualifier
type: ObjectProperty
domain: association
range: String
sub property of: qualifier
definition: Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association.
editorial note: for good examples of aspects in the gene-> chemical space, please see the GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify the gene making the full subject a different ontological type. the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process) the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process) the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity) the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event) the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process) the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality) the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)
examples: Example(value='abundance', description=None)
examples: Example(value='exposure', description=None)
examples: Example(value='expression', description=None)
examples: Example(value='stability', description=None)

base coordinate
type: ObjectProperty
domain: genomic sequence localization
range: Integer
sub property of: sequence localization attribute
alternative label: fully-closed
alternative label: one-based
definition: A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.

broad match
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at concept level
inverse of: narrow match
definition: a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.
canonical predicate: True
opposite of: narrow match

causal mechanism qualifier
type: ObjectProperty
domain: association
range: CausalMechanismQualifierEnum
sub property of: statement qualifier
definition: A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')

context qualifier
type: ObjectProperty
domain: association
range: String
sub property of: qualifier
definition: Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.
examples: Example(value='cohort x (e.g. a specific population, referenced by an identifier)', description=None)
examples: Example(value='gut microbiome', description=None)

contributes to
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: contribution from
definition: holds between two entities where the occurrence, existence, or activity of one causes or contributes to the occurrence or generation of the other
narrow match: marker mechanism
narrow match: MONDO predisposes towards
narrow match: RO_0002255
narrow match: RO_0003304
canonical predicate: True

contribution from
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: contributes to

derivative qualifier
type: ObjectProperty
domain: association
range: String
sub property of: qualifier
definition: A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’.
examples: Example(value='metabolite', description=None)

derives from
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: derives into
definition: 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
narrow match: CHEBI has functional parent
narrow match: SNOMED has specimen source topography
canonical predicate: True

derives into
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: derives from
alternative label: is normal cell origin of disease
alternative label: may be normal cell origin of disease
definition: 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

direction qualifier
type: ObjectProperty
domain: association
range: String
sub property of: qualifier
definition: Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.
editorial note: the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’ the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’

exact match
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: close match
definition: holds between two entities that have strictly equivalent meanings, with a high degree of confidence
canonical predicate: True

food component of
type: ObjectProperty
domain: chemical entity
range: chemical entity
sub property of: part of
inverse of: has food component
definition: holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)

form or variant qualifier
type: ObjectProperty
domain: association
range: String
sub property of: qualifier
definition: A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’.
editorial note: please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier' terms in the gene->chemical association space. the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’. the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the more specific concept ‘Late Stage forms of Disease X’ the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’ the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’
examples: Example(value='chemical analog', description=None)
examples: Example(value='late stage', description=None)
examples: Example(value='mutation', description=None)
examples: Example(value='severe', description=None)
examples: Example(value='transplant', description=None)

genetic association
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level
canonical predicate: True

has attribute type
type: ObjectProperty
domain: attribute
range: ontology class
definition: connects an attribute to a class that describes it
narrow match: has modality type
narrow match: has view type

has evidence
type: ObjectProperty
domain: association
range: evidence type
sub property of: association slot
definition: connects an association to an instance of supporting evidence

has food component
type: ObjectProperty
domain: chemical entity
range: chemical entity
sub property of: has part
inverse of: food component of
definition: holds between food and one or more chemical entities composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)
canonical predicate: True

has manifestation
type: ObjectProperty
domain: disease
range: named thing
sub property of: related to at instance level
inverse of: manifestation of

interbase coordinate
type: ObjectProperty
domain: genomic sequence localization
range: Integer
sub property of: sequence localization attribute
alternative label: half-open
alternative label: space-based
alternative label: zero-based
definition: A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge.

is ameliorated by
type: ObjectProperty
domain: disease or phenotypic feature
range: named thing
sub property of: affected by
inverse of: ameliorates

is input of
type: ObjectProperty
domain: occurrent
range: biological process or activity
sub property of: participates in
inverse of: has input

iso abbreviation
type: ObjectProperty
domain: publication
range: String
sub property of: node property
definition: Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.

issue
type: ObjectProperty
domain: publication
range: String
sub property of: node property
definition: issue of a newspaper, a scientific journal or magazine for reference purpose

located in
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: location of
definition: 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)
narrow match: at cellular location
narrow match: at tissue
narrow match: in biospecimen
narrow match: has imaging focus
narrow match: BSPO_0000107
narrow match: BSPO_0000108
narrow match: BSPO_0000120
narrow match: BSPO_0000121
narrow match: BSPO_0000122
narrow match: BSPO_0000123
narrow match: BSPO_0000124
narrow match: BSPO_0000125
narrow match: BSPO_0000126
narrow match: BSPO_0001100
narrow match: BSPO_0001101
narrow match: BSPO_0001107
narrow match: BSPO_0015101
narrow match: BSPO_0015102
narrow match: BSPO_0015202
narrow match: FMA has location
narrow match: GOREL_0001004
narrow match: NCIT R100
narrow match: NCIT R145
narrow match: NCIT R155
narrow match: NCIT R156
narrow match: NCIT R165
narrow match: NCIT R166
narrow match: NCIT R167
narrow match: NCIT R168
narrow match: NCIT R169
narrow match: NCIT R170
narrow match: NCIT R171
narrow match: NCIT R40
narrow match: RO_0002303
narrow match: SNOMED has finding site
narrow match: SNOMED has indirect procedure site
narrow match: SNOMED has inherent location
narrow match: in central side of
narrow match: in innermost side of
narrow match: in outermost side of
narrow match: EFO_0000784
canonical predicate: True

location of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: located in
alternative label: site of
definition: holds between material entity or site and a material entity that is located within it (but not considered a part of it)
narrow match: NCIT Anatomic Structure Has Location Role
narrow match: SNOMED inherent location of

manifestation of
type: ObjectProperty
domain: named thing
range: disease
sub property of: related to at instance level
inverse of: has manifestation
broad match: Property:P1557
definition: that part of a phenomenon which is directly observable or visibly expressed, or which gives evidence to the underlying process; used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome
narrow match: SNOMED has definitional manifestation
canonical predicate: True

narrow match
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at concept level
inverse of: broad match
definition: a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.
opposite of: broad match

overlaps
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: holds between entities that overlap in their extents (materials or processes)
narrow match: BSPO_0005001
narrow match: RO_0002100
narrow match: RO_0002102
narrow match: RO_0002433
narrow match: overlaps with
canonical predicate: True

part qualifier
type: ObjectProperty
domain: association
range: String
sub property of: qualifier
definition: defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).
examples: Example(value='polyA tail', description=None)
examples: Example(value='upstream control region', description=None)

physically interacts with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: interacts with
broad match: Property:P129
definition: holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship.
narrow match: drug-interaction
narrow match: FMA adheres to
narrow match: NCIT A7
narrow match: PR non-covalently bound to
canonical predicate: True

published in
type: ObjectProperty
domain: publication
range: Uriorcurie
sub property of: node property
definition: CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal.

qualified predicate
type: ObjectProperty
domain: association
range: String
sub property of: qualifier
definition: Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.
editorial note: to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but doesnt make sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)

qualifiers
type: ObjectProperty
domain: association
range: ontology class
sub property of: association slot
definition: connects an association to qualifiers that modify or qualify the meaning of that association

similar to
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: holds between an entity and some other entity with similar features.
canonical predicate: True

species context qualifier
type: ObjectProperty
domain: association
range: organism taxon
sub property of: statement qualifier
definition: A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.
editorial note: Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs.
examples: Example(value='human', description=None)
examples: Example(value='zebrafish', description=None)

subject direction qualifier
type: ObjectProperty
domain: association
range: DirectionQualifierEnum
sub property of: direction qualifier

temporal context qualifier
type: ObjectProperty
domain: association
range: time type
sub property of: qualifier
definition: a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.

temporally related to
type: ObjectProperty
type: SymmetricProperty
domain: occurrent
range: occurrent
sub property of: related to at instance level
definition: holds between two entities with a temporal relationship
narrow match: RO_0002082
narrow match: RO_0002083
narrow match: RO_0002092
narrow match: RO_0002093
narrow match: RO_0002223
narrow match: RO_0002224
narrow match: RO_0002229
narrow match: RO_0002230
narrow match: RO_0002488
narrow match: RO_0002489
narrow match: RO_0002492
narrow match: RO_0002493
narrow match: RO_0002496
narrow match: RO_0002497
canonical predicate: True

xref
type: ObjectProperty
domain: named thing
range: Uriorcurie
sub property of: node property
alternative label: DbXref
alternative label: Dbxref
alternative label: dbxref
definition: Alternate CURIEs for a thing
narrow match: Dbxref
narrow match: DB Xrefs

has dataset
type: ObjectProperty
domain: dataset version
range: dataset
sub property of: node property

ingest date
type: ObjectProperty
domain: dataset version
range: String
sub property of: node property

activity and behavior
type: Class
subclass of: occurrent
subclass of: mixin
definition: Activity or behavior of any independent integral living, organization or mechanical actor in the world

CausalMechanismQualifierEnum
type: Class
union of: binding
union of: inhibition
union of: antibody_inhibition
union of: antagonism
union of: molecular_channel_blockage
union of: inverse_agonism
union of: negative_allosteric_modulation
union of: agonism
union of: molecular_channel_opening
union of: positive_allosteric_modulation
union of: potentiation
union of: activation
union of: inducer
union of: transcriptional_regulation
union of: signaling_mediated_control
union of: stabilization
union of: stimulation
union of: releasing_activity
permissible values: activation
permissible values: agonism
permissible values: antagonism
permissible values: antibody_inhibition
permissible values: binding
permissible values: inducer
permissible values: inhibition
permissible values: inverse_agonism
permissible values: molecular_channel_blockage
permissible values: molecular_channel_opening
permissible values: negative_allosteric_modulation
permissible values: positive_allosteric_modulation
permissible values: potentiation
permissible values: releasing_activity
permissible values: signaling_mediated_control
permissible values: stabilization
permissible values: stimulation
permissible values: transcriptional_regulation

cellular component
type: Class
subclass of: anatomical entity
alternative label: cell component
alternative label: cell part
broad match: P681
definition: A location in or around a cell

chemical entity or protein or polypeptide
type: Class
subclass of: mixin
definition: A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.

chemical entity to entity association mixin
type: Class
subclass of: Restriction
  on class: chemical entity or gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: mixin
definition: An interaction between a chemical entity and another entity

dataset distribution
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: distribution download url
subclass of: information content entity
definition: an item that holds distribution level information about a dataset.

dataset summary
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: source web page
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: source logo
subclass of: information content entity
definition: an item that holds summary level information about a dataset.

disease or phenotypic feature to entity association mixin
type: Class
subclass of: Restriction
  on class: disease or phenotypic feature
  on property: subject
  qualified cardinality: 1
subclass of: mixin

disease to entity association mixin
type: Class
subclass of: Restriction
  on class: disease
  on property: subject
  qualified cardinality: 1
subclass of: mixin

FDAApprovalStatusEnum
type: Class
union of: discovery_and_development_phase
union of: preclinical_research_phase
union of: fda_clinical_research_phase
union of: fda_review_phase_4
union of: fda_post_market_safety_review
union of: fda_clinical_research_phase_1
union of: fda_clinical_research_phase_2
union of: fda_clinical_research_phase_3
union of: fda_clinical_research_phase_4
union of: fda_fast_track
union of: fda_breakthrough_therapy
union of: fda_accelerated_approval
union of: fda_priority_review
union of: regular_fda_approval
union of: post_approval_withdrawal
permissible values: discovery_and_development_phase
permissible values: fda_accelerated_approval
permissible values: fda_breakthrough_therapy
permissible values: fda_clinical_research_phase
permissible values: fda_clinical_research_phase_1
permissible values: fda_clinical_research_phase_2
permissible values: fda_clinical_research_phase_3
permissible values: fda_clinical_research_phase_4
permissible values: fda_fast_track
permissible values: fda_post_market_safety_review
permissible values: fda_priority_review
permissible values: fda_review_phase_4
permissible values: post_approval_withdrawal
permissible values: preclinical_research_phase
permissible values: regular_fda_approval

frequency qualifier mixin
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: mixin
definition: Qualifier for frequency type associations

gene expression mixin
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: disease or phenotypic feature
  on property: phenotypic state
subclass of: Restriction
  max qualified cardinality: 1
  on class: life stage
  on property: stage qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: ontology class
  on property: quantifier qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: anatomical entity
  on property: expression site
subclass of: mixin
definition: Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs.

gene to disease association
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: frequency value
  on property: frequency qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: severity value
  on property: severity qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: onset
  on property: onset qualifier
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: disease
  on property: object
  qualified cardinality: 1
subclass of: association
subclass of: entity to disease association mixin
subclass of: gene to entity association mixin
note: NCIT:R176 refers to the inverse relationship

gene to gene association
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: gene or gene product
  on property: object
  qualified cardinality: 1
subclass of: association
alternative label: molecular or genetic interaction
definition: abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.

genetic inheritance
type: Class
subclass of: biological entity
alternative label: inheritance
definition: The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.

genotype to entity association mixin
type: Class
subclass of: Restriction
  on class: genotype
  on property: subject
  qualified cardinality: 1
subclass of: mixin

individual organism
type: Class
subclass of: organismal entity
subclass of: subject of investigation
alternative label: organism
definition: An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576
narrow match: Person
narrow match: Q795052

organism taxon to entity association
type: Class
subclass of: Restriction
  on class: organism taxon
  on property: subject
  qualified cardinality: 1
subclass of: mixin
definition: An association between an organism taxon and another entity

pathway
type: Class
subclass of: biological process
subclass of: ontology class
narrow match: GO_0007165
narrow match: SIO_010526

planetary entity
type: Class
subclass of: named thing
definition: Any entity or process that exists at the level of the whole planet

predicate mapping
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: object context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: object derivative qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: CausalMechanismQualifierEnum
  on property: causal mechanism qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: subject derivative qualifier
subclass of: Restriction
  all values from: named thing
  on property: exact match
subclass of: Restriction
  max qualified cardinality: 1
  on class: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: AnatomicalContextQualifierEnum
  on property: anatomical context qualifier
subclass of: Restriction
  all values from: named thing
  on property: broad match
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: qualified predicate
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: mapped predicate
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: object part qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: object aspect qualifier
subclass of: Restriction
  all values from: named thing
  on property: narrow match
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: subject context qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: subject part qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: subject form or variant qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: subject aspect qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: object form or variant qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: organism taxon
  on property: species context qualifier
definition: A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.

protein
type: Class
subclass of: Restriction
  all values from: label type
  on property: synonym
subclass of: gene product mixin
subclass of: polypeptide
broad match: Protein
definition: A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
narrow match: T126
narrow match: T192

sequence feature relationship
type: Class
subclass of: Restriction
  on class: nucleic acid entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: nucleic acid entity
  on property: object
  qualified cardinality: 1
subclass of: association
definition: For example, a particular exon is part of a particular transcript or gene

acts upstream of or within
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of
inverse of: has upstream or within actor
canonical predicate: True

affects response to
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: affects
inverse of: response affected by
canonical predicate: True

affects risk for
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: risk affected by
definition: holds between two entities where exposure to one entity alters the chance of developing the other
canonical predicate: True

anatomical context qualifier
type: ObjectProperty
domain: association
range: AnatomicalContextQualifierEnum
sub property of: statement qualifier
definition: A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).
editorial note: Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs.
examples: Example(value='blood', description=None)
examples: Example(value='cerebral cortext', description=None)

associated with likelihood of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: associated with
inverse of: likelihood associated with
definition: A a relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated, wherein the state or value of one variable predicts the future state or value of the other. E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated with likelihood of a Myocardial Infarction (MI) diagnosis” asserts that the state of having Afib is associated with an increased or decreased likelihood that a patient will later exhibit MI.
canonical predicate: True

enabled by
type: ObjectProperty
domain: biological process or activity
range: physical entity
sub property of: has participant
inverse of: enables
definition: holds between a process and a physical entity, where the physical entity executes the process
opposite of: prevented by

expression site
type: ObjectProperty
domain: association
range: anatomical entity
sub property of: association slot
definition: location in which gene or protein expression takes place. May be cell, tissue, or organ.
examples: Example(value='UBERON:0002037', description='cerebellum')

has output
type: ObjectProperty
domain: biological process or activity
range: occurrent
sub property of: has participant
inverse of: is output of
definition: holds between a process and a continuant, where the continuant is an output of the process
narrow match: NCIT R31
narrow match: OBI_0000299
narrow match: RO_0002296
narrow match: RO_0002297
narrow match: RO_0002298
narrow match: RO_0002299
narrow match: RO_0002588
narrow match: RO_0004008
narrow match: has right element
canonical predicate: True
opposite of: has input

has upstream or within actor
type: ObjectProperty
domain: biological process
range: gene or gene product
sub property of: has upstream actor
inverse of: acts upstream of or within

homologous to
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: similar to
alternative label: in homology relationship with
definition: holds between two biological entities that have common evolutionary origin
narrow match: sexually homologous to
note: typically used to describe homology relationships between genes or gene products
canonical predicate: True

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: holds between any two entities that directly or indirectly interact with each other
editorial note: please use a more specific child predicate of interacts with, either physically interacts with or genetically interacts with.

knowledge source
type: ObjectProperty
domain: association
range: information resource
sub property of: association slot
definition: An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.

likelihood associated with
type: ObjectProperty
domain: named thing
range: named thing
sub property of: associated with
inverse of: associated with likelihood of

object aspect qualifier
type: ObjectProperty
domain: association
range: String
sub property of: aspect qualifier

object direction qualifier
type: ObjectProperty
domain: association
range: DirectionQualifierEnum
sub property of: direction qualifier

object form or variant qualifier
type: ObjectProperty
domain: association
range: String
sub property of: form or variant qualifier

object part qualifier
type: ObjectProperty
domain: association
range: String
sub property of: part qualifier

phenotypic state
type: ObjectProperty
domain: association
range: disease or phenotypic feature
sub property of: association slot
definition: in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.

response affected by
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: affected by
inverse of: affects response to
definition: holds between two chemical entities where the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) of one is affected by the action of the other.

risk affected by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: affects risk for

statement qualifier
type: ObjectProperty
domain: association
range: String
sub property of: qualifier

subject aspect qualifier
type: ObjectProperty
domain: association
range: String
sub property of: aspect qualifier

subject derivative qualifier
type: ObjectProperty
domain: association
range: String
sub property of: derivative qualifier

subject part qualifier
type: ObjectProperty
domain: association
range: String
sub property of: part qualifier

volume
type: ObjectProperty
domain: publication
range: String
sub property of: node property
definition: volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication

ChemicalOrGeneOrGeneProductFormOrVariantEnum
type: Class
union of: genetic_variant_form
union of: modified_form
union of: loss_of_function_variant_form
union of: gain_of_function_variant_form
union of: polymorphic_form
union of: snp_form
union of: analog_form
permissible values: analog_form
permissible values: gain_of_function_variant_form
permissible values: genetic_variant_form
permissible values: loss_of_function_variant_form
permissible values: modified_form
permissible values: polymorphic_form
permissible values: snp_form

clinical attribute
type: Class
subclass of: attribute
definition: Attributes relating to a clinical manifestation

dataset version
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: dataset
  on property: has dataset
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: ingest date
subclass of: Restriction
  max qualified cardinality: 1
  on class: dataset distribution
  on property: has distribution
subclass of: information content entity
definition: an item that holds version level information about a dataset.

functional association
type: Class
subclass of: Restriction
  on class: macromolecular machine mixin
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: ontology class
  on property: object
  qualified cardinality: 1
subclass of: association
definition: An association between a macromolecular machine mixin (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.

gene product isoform mixin
type: Class
subclass of: gene product mixin
subclass of: mixin
definition: 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.

macromolecular machine to entity association mixin
type: Class
subclass of: Restriction
  on class: named thing
  on property: subject
  qualified cardinality: 1
subclass of: mixin
definition: an association which has a macromolecular machine mixin as a subject

pathological entity mixin
type: Class
subclass of: mixin
definition: A pathological (abnormal) structure or process.
narrow match: HP_0000118

physical entity
type: Class
subclass of: named thing
subclass of: physical essence
definition: An entity that has material reality (a.k.a. physical essence).
narrow match: T073

quantity value
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has numeric value
subclass of: Restriction
  max qualified cardinality: 1
  on class: unit
  on property: has unit
subclass of: annotation
definition: A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value

relationship quantifier
type: Class
subclass of: mixin

StrandEnum
type: Class
union of: +
union of: -
union of: .
union of: ?
permissible values: +
permissible values: -
permissible values: .
permissible values: ?

acts upstream of
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: related to at instance level
inverse of: has upstream actor
canonical predicate: True

aggregate statistic
type: ObjectProperty
domain: named thing
range: String
sub property of: node property

category
type: ObjectProperty
domain: entity
range: category type
sub property of: type
definition: 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. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}

coexists with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region
narrow match: has lateral anatomic location
narrow match: has lateral location presence
narrow match: BSPO_0000096
narrow match: BSPO_0000097
narrow match: BSPO_0000098
narrow match: BSPO_0000099
narrow match: BSPO_0000100
narrow match: BSPO_0000102
narrow match: BSPO_0000104
narrow match: BSPO_0000110
narrow match: BSPO_0000113
narrow match: BSPO_0015001
narrow match: BSPO_0015002
narrow match: BSPO_0015003
narrow match: BSPO_0015005
narrow match: BSPO_0015006
narrow match: BSPO_0015007
narrow match: BSPO_0015008
narrow match: BSPO_0015009
narrow match: BSPO_0015012
narrow match: BSPO_0015014
narrow match: BSPO parallel to
narrow match: ENVO_01001307
narrow match: FMA adjacent to
narrow match: FMA afferent to
narrow match: FMA anterior to
narrow match: FMA anteroinferior to
narrow match: FMA anterolateral to
narrow match: FMA anteromedial to
narrow match: FMA anterosuperior to
narrow match: FMA arterial supply of
narrow match: FMA articulates with
narrow match: FMA attaches to
narrow match: FMA bounded by
narrow match: FMA bounds
narrow match: FMA branch of
narrow match: FMA connection type of
narrow match: FMA continuation branch of
narrow match: FMA continuous distally with
narrow match: FMA continuous proximally with
narrow match: FMA corresponds to
narrow match: FMA development type of
narrow match: FMA developmental stage of
narrow match: FMA direct cell shape of
narrow match: FMA direct left of
narrow match: FMA direct right of
narrow match: FMA distal to
narrow match: FMA drains into
narrow match: FMA efferent to
narrow match: FMA external to
narrow match: FMA formed by
narrow match: FMA forms
narrow match: FMA full grown phenotype of
narrow match: FMA fuses with
narrow match: FMA fusion of
narrow match: FMA germ origin of
narrow match: FMA has adherent
narrow match: FMA has arterial supply
narrow match: FMA has branch
narrow match: FMA has connection type
narrow match: FMA has continuation branch
narrow match: FMA has development type
narrow match: FMA has developmental stage
narrow match: FMA has direct cell shape
narrow match: FMA has full grown phenotype
narrow match: FMA has fusion
narrow match: FMA has germ origin
narrow match: FMA has inherent 3d shape
narrow match: FMA has insertion
narrow match: FMA has lymphatic drainage
narrow match: FMA has nerve supply
narrow match: FMA has observed anatomical entity
narrow match: FMA has origin

has input
type: ObjectProperty
domain: biological process or activity
range: occurrent
sub property of: has participant
inverse of: is input of
definition: holds between a process and a continuant, where the continuant is an input into the process
narrow match: has fragments for synonyms
narrow match: has system
narrow match: RO_0002590
narrow match: RO_0004009
narrow match: SNOMED has finding method
narrow match: SNOMED has precondition
narrow match: SNOMED has specimen source identity
narrow match: SNOMED has specimen substance
narrow match: SNOMED uses access device
narrow match: SNOMED uses device
narrow match: SNOMED uses energy
narrow match: SNOMED uses substance
narrow match: has left element
canonical predicate: True
opposite of: has output

has upstream actor
type: ObjectProperty
domain: biological process
range: gene or gene product
sub property of: related to at instance level
inverse of: acts upstream of

object context qualifier
type: ObjectProperty
domain: association
range: String
sub property of: context qualifier

quantifier qualifier
type: ObjectProperty
domain: association
range: ontology class
sub property of: association slot
definition: A measurable quantity for the object of the association
narrow match: measures
narrow match: analyzes
narrow match: measured by
narrow match: property of
narrow match: SemMedDBMEASURES

stage qualifier
type: ObjectProperty
domain: association
range: life stage
sub property of: association slot
definition: stage during which gene or protein expression of takes place.
examples: Example(value='UBERON:0000069', description='larval stage')

subject context qualifier
type: ObjectProperty
domain: association
range: String
sub property of: context qualifier

subject form or variant qualifier
type: ObjectProperty
domain: association
range: String
sub property of: form or variant qualifier

category type
type: Class
subclass of: Uriorcurie

dataset
type: Class
subclass of: information content entity
definition: an item that refers to a collection of data from a data source.

gene to entity association mixin
type: Class
subclass of: Restriction
  on class: gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: mixin

life stage
type: Class
subclass of: organismal entity
definition: A stage of development or growth of an organism, including post-natal adult stages
narrow match: HsapDv_0000000

study result
type: Class
subclass of: information content entity
definition: A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence.
editorial note: The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational analyses, or a larger scale clinical trial or experimental research investigation.

variant to entity association mixin
type: Class
subclass of: Restriction
  on class: sequence variant
  on property: subject
  qualified cardinality: 1
subclass of: mixin

contributor
type: ObjectProperty
domain: agent
range: information content entity
sub property of: related to at instance level
inverse of: has contributor
note: This is a grouping for predicates relating entities to their associated contributors realizing them

has attribute
type: ObjectProperty
domain: entity
range: attribute
definition: connects any entity to an attribute
narrow match: category
narrow match: has structural class
narrow match: has supported concept property
narrow match: has supported concept relationship
narrow match: may be qualified by
narrow match: has action guidance
narrow match: has adjustment
narrow match: has aggregation view
narrow match: has approach guidance
narrow match: has divisor
narrow match: has exam
narrow match: has method
narrow match: has modality subtype
narrow match: has object guidance
narrow match: has scale
narrow match: has suffix
narrow match: has time aspect
narrow match: has time modifier
narrow match: has timing of
narrow match: INO_0000154
narrow match: NCIT R88
narrow match: NCIT eo disease has property or attribute
narrow match: NCIT has data element
narrow match: NCIT has pharmaceutical administration method
narrow match: NCIT has pharmaceutical basic dose form
narrow match: NCIT has pharmaceutical intended site
narrow match: NCIT has pharmaceutical release characteristics
narrow match: NCIT has pharmaceutical state of matter
narrow match: NCIT has pharmaceutical transformation
narrow match: NCIT is qualified by
narrow match: NCIT qualifier applies to
narrow match: NCIT role has domain
narrow match: NCIT role has range
narrow match: OMIM has inheritance type
narrow match: RO_0000053
narrow match: RO_0000086
narrow match: RO_0000087
narrow match: SNOMED has access
narrow match: SNOMED has clinical course
narrow match: SNOMED has count of base of active ingredient
narrow match: SNOMED has dose form administration method
narrow match: SNOMED has dose form release characteristic
narrow match: SNOMED has dose form transformation
narrow match: SNOMED has finding context
narrow match: SNOMED has finding informer
narrow match: SNOMED has inherent attribute
narrow match: SNOMED has intent
narrow match: SNOMED has interpretation
narrow match: SNOMED has laterality
narrow match: SNOMED has measurement method
narrow match: SNOMED has method
narrow match: SNOMED has priority
narrow match: SNOMED has procedure context
narrow match: SNOMED has process duration
narrow match: SNOMED has property
narrow match: SNOMED has revision status
narrow match: SNOMED has scale type
narrow match: SNOMED has severity
narrow match: SNOMED has specimen
narrow match: SNOMED has state of matter
narrow match: SNOMED has subject relationship context
narrow match: SNOMED has surgical approach
narrow match: SNOMED has technique
narrow match: SNOMED has temporal context
narrow match: SNOMED has time aspect
narrow match: SNOMED has units
narrow match: association has object property
narrow match: association has subject property
narrow match: ancestro_0301
narrow match: ancestro_0308
narrow match: EFO is executed in
narrow match: Orphanet C016
narrow match: Orphanet C017
narrow match: has possibly included panel element

has contributor
type: ObjectProperty
domain: information content entity
range: agent
sub property of: related to at instance level
inverse of: contributor

in taxon
type: ObjectProperty
domain: thing with taxon
range: organism taxon
sub property of: related to at instance level
inverse of: taxon of
alternative label: gene found in organism
alternative label: gene product has organism source
alternative label: instance of
alternative label: is organism source of gene product
alternative label: organism has gene
definition: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
narrow match: RO_0002160
canonical predicate: True

sequence localization attribute
type: ObjectProperty
domain: genomic sequence localization
range: String
sub property of: association slot
definition: An attribute that can be applied to a genome sequence localization edge. These edges connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used to ascribe specific positional information and other metadata to the localization. In pragmatic terms this can be thought of as columns in a GFF3 line.

type
type: ObjectProperty
range: String

name
type: ObjectProperty
domain: entity
range: label type
alternative label: display name
alternative label: label
alternative label: title
definition: A human-readable name for an attribute or entity.
narrow match: title
narrow match: Property:P1476

chemical mixture
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: highest FDA approval status
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical mixture
  on property: is supplement
subclass of: Restriction
  all values from: DrugDeliveryEnum
  on property: routes of delivery
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: drug regulatory status world wide
subclass of: chemical entity
definition: A chemical mixture is a chemical entity composed of two or more molecular entities.
narrow match: NCIT C20401
narrow match: http://snomed.info/id/49616005

chemical to entity association mixin
type: Class
subclass of: Restriction
  on class: chemical entity or gene or gene product
  on property: subject
  qualified cardinality: 1
subclass of: chemical entity to entity association mixin
subclass of: mixin
definition: An interaction between a chemical entity and another entity

entity
type: Class
subclass of: Restriction
  all values from: String
  on property: type
subclass of: Restriction
  max qualified cardinality: 1
  on class: label type
  on property: name
subclass of: Restriction
  max qualified cardinality: 1
  on class: narrative text
  on property: description
subclass of: Restriction
  all values from: attribute
  on property: has attribute
subclass of: Restriction
  all values from: category type
  on property: category
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: iri type
  on property: iri
definition: Root Biolink Model class for all things and informational relationships, real or imagined.

entity to disease or phenotypic feature association mixin
type: Class
subclass of: Restriction
  on class: disease or phenotypic feature
  on property: object
  qualified cardinality: 1
subclass of: mixin

gene grouping mixin
type: Class
subclass of: Restriction
  all values from: gene
  on property: has gene or gene product
subclass of: mixin
definition: any grouping of multiple genes or gene products

GeneOrGeneProductOrChemicalPartQualifierEnum
type: Class
union of: 3_prime_utr
union of: 5_prime_utr
union of: polya_tail
union of: promoter
union of: enhancer
union of: exon
union of: intron
permissible values: 3_prime_utr
permissible values: 5_prime_utr
permissible values: enhancer
permissible values: exon
permissible values: intron
permissible values: polya_tail
permissible values: promoter

gene product mixin
type: Class
subclass of: Restriction
  all values from: Uriorcurie
  on property: xref
subclass of: Restriction
  all values from: label type
  on property: synonym
subclass of: gene or gene product
subclass of: mixin
definition: The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules.

model to disease association mixin
type: Class
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: named thing
  on property: subject
  qualified cardinality: 1
subclass of: mixin
definition: 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

population of individual organisms
type: Class
subclass of: organismal entity
subclass of: subject of investigation
definition: A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.

thing with taxon
type: Class
subclass of: Restriction
  all values from: organism taxon
  on property: in taxon
subclass of: mixin
definition: A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes

correlated with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: associated with
definition: A relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated using a correlation analysis method.
editorial note: These concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).
canonical predicate: True

has part
type: ObjectProperty
domain: named thing
range: named thing
sub property of: overlaps
inverse of: part of
broad match: contains
broad match: FMA contains
broad match: RO_0001019
definition: holds between wholes and their parts (material entities or processes)
narrow match: has member
narrow match: has component
narrow match: has ingredient
narrow match: BFO_0000117
narrow match: FMA has constitutional part
narrow match: FMA has member
narrow match: FMA has part
narrow match: FOODON_00001563
narrow match: FOODON_00002420
narrow match: MONDO disease has major feature
narrow match: NCIT R50
narrow match: NCIT complex has physical part
narrow match: RO_0002104
narrow match: RO_0002180
narrow match: RO_0002351
narrow match: RO_0002473
narrow match: RO_0002524
narrow match: RO_0002551
narrow match: SNOMED has component
narrow match: has element in bound
narrow match: has protein in complex
canonical predicate: True
opposite of: lacks part

part of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: overlaps
inverse of: has part
broad match: contained in
broad match: FMA contained in
broad match: RO_0001018
definition: holds between parts and wholes (material entities or processes)
narrow match: component of
narrow match: member of
narrow match: has owning affiliate
narrow match: owning subsection of
narrow match: has supersystem
narrow match: multipart of
narrow match: ingredient of
narrow match: ingredients of
narrow match: precise ingredient of
narrow match: BSPO_0001106
narrow match: BSPO_0001108
narrow match: BSPO_0001113
narrow match: BSPO_0001115
narrow match: CHEBI is substituent group from
narrow match: FMA constitutional part of
narrow match: FMA member of
narrow match: FMA regional part of
narrow match: FMA related developmental entity of
narrow match: MONDO part of progression of disease
narrow match: NCIT R27
narrow match: NCIT R82
narrow match: NCIT is component of chemotherapy regimen
narrow match: RO_0002007
narrow match: RO_0002350
narrow match: RO_0002376
narrow match: RO_0002380
narrow match: RO_0002571
narrow match: RO_0002572
narrow match: RO_0002576
narrow match: SNOMED active ingredient of
narrow match: SNOMED basis of strength substance of
narrow match: SNOMED component of
narrow match: SNOMED direct substance of
narrow match: SNOMED during
narrow match: SNOMED focus of
narrow match: SNOMED has dependent
narrow match: SNOMED part anatomy structure of
narrow match: SNOMED precise active ingredient of
narrow match: UBERON subdivision of
narrow match: layer part of
narrow match: subdivision of
narrow match: trunk part of
narrow match: panel element of
narrow match: panel element of possibly included

related to
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
broad match: topObjectProperty
definition: A relationship that is asserted between two named things
narrow match: RO
narrow match: has mapping qualifier
narrow match: mapped to
narrow match: disease
narrow match: has protein association
narrow match: RQ
narrow match: class code classified by
narrow match: exhibited by
narrow match: has context binding
narrow match: has form
narrow match: larger than
narrow match: owning section of
narrow match: has answer
narrow match: has challenge
narrow match: has evaluation
narrow match: mth has expanded form
narrow match: reformulated to
narrow match: BFO_0000054
narrow match: BTO related to
narrow match: CHEBI is conjugate acid of
narrow match: CHEBI is conjugate base of
narrow match: FMA connected to
narrow match: FMA continuous with
narrow match: FMA homonym of
narrow match: FMA related developmental entity of
narrow match: GOREL_0002005
narrow match: GOREL_0012006
narrow match: IAO_0000136
narrow match: MONDO disease shares features of
narrow match: NCIT disease may have associated disease
narrow match: NCIT human disease maps to eo disease
narrow match: NCIT is abnormal cell of disease
narrow match: NCIT is related to endogenous product
narrow match: PATO reciprocal of
narrow match: RO_0000052
narrow match: RO_0000053
narrow match: RO_0002001
narrow match: RO_0002002
narrow match: RO_0002003
narrow match: RO_0002008
narrow match: RO_0002084
narrow match: RO_0002092
narrow match: RO_0002093
narrow match: RO_0002134
narrow match: RO_0002150
narrow match: RO_0002159
narrow match: RO_0002176
narrow match: RO_0002177
narrow match: RO_0002178
narrow match: RO_0002179
narrow match: RO_0002314
narrow match: RO_0002322
narrow match: RO_0002328
narrow match: RO_0002332
narrow match: RO_0002338
narrow match: RO_0002339
narrow match: RO_0002341
narrow match: RO_0002342
narrow match: RO_0002344
narrow match: RO_0002348
narrow match: RO_0002349
narrow match: RO_0002356
narrow match: RO_0002371
narrow match: RO_0002372
narrow match: RO_0002373
narrow match: RO_0002374
narrow match: RO_0002385
narrow match: RO_0002387
narrow match: RO_0002451
narrow match: RO_0002494
narrow match: RO_0002495
narrow match: RO_0002568
narrow match: RO_0002573

supporting study metadata
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: Information about a study used to generate information used as evidence to support the knowledge expressed in an Association. In practice, data creators should use one of the more specific subtypes of this property.

DirectionQualifierEnum
type: Class
union of: increased
union of: upregulated
union of: decreased
union of: downregulated
permissible values: decreased
permissible values: downregulated
permissible values: increased
permissible values: upregulated

entity to phenotypic feature association mixin
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has total
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sex
  on property: sex qualifier
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: has count
subclass of: Restriction
  on class: phenotypic feature
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has quotient
subclass of: Restriction
  max qualified cardinality: 1
  on class: Double
  on property: has percentage
subclass of: entity to feature or disease qualifiers mixin
subclass of: frequency quantifier
subclass of: mixin

genotype
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: Restriction
  max qualified cardinality: 1
  on class: zygosity
  on property: has zygosity
subclass of: biological entity
subclass of: genomic entity
subclass of: ontology class
subclass of: physical essence
definition: An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background
note: Consider renaming as genotypic entity

macromolecular machine mixin
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: symbol type
  on property: name
subclass of: mixin
definition: A union of gene locus, 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.

phenotypic feature
type: Class
subclass of: disease or phenotypic feature
alternative label: endophenotype
alternative label: phenotype
alternative label: sign
alternative label: symptom
alternative label: trait
broad match: BFO_0000019
broad match: PATO_0000001
definition: A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.
narrow match: T184
narrow match: APO_0000017
narrow match: FBcv_0001347
narrow match: FYPO_0000001
narrow match: HP_0000118
narrow match: MP_0000001
narrow match: TO_0000387
narrow match: WBPhenotype_0000886
narrow match: XPO_00000000
narrow match: ZP_00000000
narrow match: Q169872
narrow match: Q25203551
examples: Example(value='MP:0001262', description='decreased body weight')

physical essence or occurrent
type: Class
subclass of: mixin
definition: Either a physical or processual entity.

transcript
type: Class
subclass of: nucleic acid entity
definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase.

associated with
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to at instance level
definition: Expresses a relationship between two named things where the relationship is typically generated statistically (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent, 'related to'. This relationship holds between two concepts represented by variables for which a statistical dependence is demonstrated. E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial Infarction (MI)” asserts that having Afib is not statistically independent from whether a patient will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).
narrow match: RO_0004029
narrow match: http://snomed.info/id/47429007
canonical predicate: True

has gene or gene product
type: ObjectProperty
domain: named thing
range: gene
sub property of: node property
definition: connects an entity with one or more gene or gene products

has participant
type: ObjectProperty
domain: biological process or activity
range: occurrent
sub property of: related to at instance level
inverse of: participates in
definition: holds between a process and a continuant, where the continuant is somehow involved in the process
narrow match: has subject
narrow match: BFO_0000167
narrow match: NCIT process involves gene
narrow match: OBI_0000293
narrow match: RO_0004007
narrow match: RO_0004020
narrow match: RO_0004021
narrow match: SNOMED has indirect device
narrow match: SNOMED has procedure device
narrow match: SNOMED has recipient category
narrow match: has participant
narrow match: has bound
narrow match: has compound
narrow match: has element collection
narrow match: has enzyme
narrow match: has nucleic acid
narrow match: has protein
narrow match: has reaction
canonical predicate: True

participates in
type: ObjectProperty
domain: occurrent
range: biological process or activity
sub property of: related to at instance level
inverse of: has participant
definition: holds between a continuant and a process, where the continuant is somehow involved in the process
narrow match: pathway
narrow match: in pathway
narrow match: is given pharmaceutical substance for
narrow match: NCIT R130
narrow match: NCIT R131
narrow match: NCIT R37
narrow match: NCIT R51
narrow match: NCIT R53
narrow match: OBI_0000295
narrow match: RO_0002216
narrow match: RO_0002505
narrow match: RO_0002565
narrow match: SNOMED has direct device

information resource
type: Class
subclass of: information content entity
alternative label: knowledgebase
definition: A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.

affected by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: affects
definition: describes an entity of which the state or quality is affected by another existing entity.

affects
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: affected by
definition: 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.
narrow match: inferred
narrow match: prediction hypothesis
narrow match: GOREL_0001006
narrow match: NCIT R100
narrow match: NCIT R101
narrow match: NCIT R102
narrow match: NCIT R113
narrow match: NCIT R124
narrow match: NCIT R133
narrow match: NCIT R146
narrow match: NCIT R150
narrow match: NCIT R158
narrow match: NCIT R160
narrow match: NCIT R173
narrow match: NCIT R23
narrow match: NCIT R25
narrow match: NCIT R30
narrow match: NCIT R72
narrow match: NCIT gene mapped to disease
narrow match: RO_0002263
narrow match: RO_0002264
narrow match: RO_0002343
narrow match: RO_0002355
narrow match: RO_0002591
narrow match: RO_0002592
narrow match: RO_0012003
narrow match: SNOMED has pathological process
narrow match: UPHENO_0000001
narrow match: is decrease of
narrow match: is increase of
narrow match: SemMedDBADMINISTERED TO
related match: pathway
canonical predicate: True

has sequence variant
type: ObjectProperty
domain: genomic entity
range: sequence variant
sub property of: related to at instance level
inverse of: is sequence variant of

is sequence variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: related to at instance level
inverse of: has sequence variant
alternative label: allelic variant of
alternative label: gene product sequence variation encoded by gene mutant
alternative label: gene product variant of gene product
definition: holds between a sequence variant and a nucleic acid entity
narrow match: P3433
canonical predicate: True

related to at concept level
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to
definition: Represents a relationship held between terminology components that describe the conceptual model of a domain.
canonical predicate: True

sex qualifier
type: ObjectProperty
domain: association
range: biological sex
sub property of: qualifier
definition: a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.

disease
type: Class
subclass of: disease or phenotypic feature
alternative label: condition
alternative label: disorder
alternative label: medical condition
definition: A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
narrow match: T019
narrow match: T020
narrow match: T048
narrow match: T049
narrow match: T190
narrow match: T191
narrow match: MONDO_0042489

drug
type: Class
subclass of: chemical or drug or treatment
subclass of: molecular mixture
subclass of: ontology class
broad match: T121
definition: A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
narrow match: T195
note: The CHEBI ID represents a role rather than a substance

entity to disease association mixin
type: Class
subclass of: Restriction
  on class: disease
  on property: object
  qualified cardinality: 1
subclass of: entity to feature or disease qualifiers mixin
subclass of: mixin
definition: mixin class for any association whose object (target node) is a disease

genomic sequence localization
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: start interbase coordinate
subclass of: Restriction
  max qualified cardinality: 1
  on class: StrandEnum
  on property: genome build
subclass of: Restriction
  max qualified cardinality: 1
  on class: PhaseEnum
  on property: phase
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: end interbase coordinate
subclass of: Restriction
  on class: nucleic acid entity
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  on class: nucleic acid entity
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: StrandEnum
  on property: strand
subclass of: sequence association
broad match: Chromosome
definition: A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.

organismal entity
type: Class
subclass of: Restriction
  all values from: attribute
  on property: has attribute
subclass of: biological entity
subclass of: subject of investigation
definition: A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities

id
type: ObjectProperty
range: String
definition: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI

outcome
type: Class
subclass of: mixin
definition: An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes.

subject of investigation
type: Class
subclass of: mixin
definition: An entity that has the role of being studied in an investigation, study, or experiment

has count
type: ObjectProperty
domain: named thing
range: Integer
sub property of: aggregate statistic
definition: number of things with a particular property

has percentage
type: ObjectProperty
domain: named thing
range: Double
sub property of: aggregate statistic
definition: equivalent to has quotient multiplied by 100

has quotient
type: ObjectProperty
domain: named thing
range: Double
sub property of: aggregate statistic

has total
type: ObjectProperty
domain: named thing
range: Integer
sub property of: aggregate statistic
definition: total number of things in a particular reference set

synonym
type: ObjectProperty
domain: named thing
range: label type
sub property of: node property
alternative label: alias
definition: Alternate human-readable names for a thing
narrow match: has tradename
narrow match: IAO_0000136
narrow match: ancestro_0330
narrow match: altLabel
narrow match: Alias
narrow match: DB Object Synonyms
narrow match: synonyms

biological sex
type: Class
subclass of: attribute

molecular activity
type: Class
subclass of: Restriction
  all values from: molecular entity
  on property: has output
subclass of: Restriction
  all values from: molecular entity
  on property: has input
subclass of: Restriction
  all values from: macromolecular machine mixin
  on property: enabled by
subclass of: biological process or activity
subclass of: occurrent
subclass of: ontology class
alternative label: molecular event
alternative label: molecular function
alternative label: reaction
definition: An execution of a molecular function carried out by a gene product or macromolecular complex.

physical essence
type: Class
subclass of: physical essence or occurrent
subclass of: mixin
definition: Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.

has biological sequence
type: ObjectProperty
domain: named thing
range: biological sequence
sub property of: node property
definition: connects a genomic feature to its sequence

agent
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: label type
  on property: name
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: address
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: Restriction
  all values from: Uriorcurie
  on property: affiliation
subclass of: administrative entity
alternative label: group
definition: person, group, organization or project that provides a piece of information (i.e. a knowledge association)
narrow match: T092
narrow match: T093
narrow match: T094
narrow match: T095
narrow match: T096
narrow match: SemGroups-v04.txtORGA

biological process or activity
type: Class
subclass of: Restriction
  all values from: physical entity
  on property: enabled by
subclass of: Restriction
  all values from: occurrent
  on property: has input
subclass of: Restriction
  all values from: occurrent
  on property: has output
subclass of: biological entity
subclass of: occurrent
subclass of: ontology class
definition: Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.

biological sequence
type: Class
subclass of: String

chemical or drug or treatment
type: Class
subclass of: mixin

onset qualifier
type: ObjectProperty
domain: association
range: onset
sub property of: qualifier
definition: a qualifier used in a phenotypic association to state when the phenotype appears is in the subject

severity qualifier
type: ObjectProperty
domain: association
range: severity value
sub property of: qualifier
definition: a qualifier used in a phenotypic association to state how severe the phenotype is in the subject

timepoint
type: ObjectProperty
range: time type
alternative label: duration
definition: a point in time

nucleic acid entity
type: Class
subclass of: Restriction
  all values from: organism taxon
  on property: in taxon
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: genomic entity
subclass of: molecular entity
subclass of: ontology class
subclass of: physical essence
subclass of: thing with taxon
alternative label: genomic entity
alternative label: sequence feature
definition: A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.
narrow match: T086
narrow match: T114

onset
type: Class
subclass of: clinical course
definition: The age group in which (disease) symptom manifestations appear

severity value
type: Class
subclass of: attribute
definition: describes the severity of a phenotypic feature or disease

frequency qualifier
type: ObjectProperty
domain: association
range: frequency value
sub property of: qualifier
definition: a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject

qualifier
type: ObjectProperty
domain: association
range: String
sub property of: association slot
definition: grouping slot for all qualifiers on an edge. useful for testing compliance with association classes

frequency value
type: Class
subclass of: String

biological process
type: Class
subclass of: biological process or activity
subclass of: occurrent
subclass of: ontology class
broad match: P682
definition: One or more causally connected executions of molecular functions

exposure event
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: ontology class
subclass of: mixin
alternative label: experimental condition
alternative label: exposure
definition: A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes

molecular entity
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is metabolite
subclass of: chemical entity
definition: A molecular entity is a chemical entity composed of individual or covalently bonded atoms.
narrow match: T085
narrow match: T088
narrow match: CHEBI_23367
narrow match: MolecularEntity

time type
type: Class
subclass of: Time

label type
type: Class
subclass of: String

organism taxon
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: taxonomic rank
  on property: has taxonomic rank
subclass of: named thing
alternative label: taxon
alternative label: taxonomic classification
definition: A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.
narrow match: BiologicalSpecies

information content entity
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: license
subclass of: Restriction
  max qualified cardinality: 1
  on class: Date
  on property: creation date
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: format
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: rights
subclass of: named thing
alternative label: information
alternative label: information artefact
alternative label: information entity
definition: a piece of information that typically describes some topic of discourse or is used as support.
narrow match: T077
narrow match: T078
narrow match: T079
narrow match: T080
narrow match: T081
narrow match: T082
narrow match: T089
narrow match: T102
narrow match: T169
narrow match: T171
narrow match: T185
narrow match: SemGroups-v04.txtCONC

publication
type: Class
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: Restriction
  on class: String
  on property: publication type
  qualified cardinality: 1
subclass of: Restriction
  all values from: Uriorcurie
  on property: mesh terms
subclass of: Restriction
  max qualified cardinality: 1
  on class: label type
  on property: name
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: summary
subclass of: Restriction
  all values from: String
  on property: authors
subclass of: Restriction
  all values from: String
  on property: pages
subclass of: Restriction
  all values from: String
  on property: keywords
subclass of: information content entity
definition: Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (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 printed materials, either directly or in one of the Publication Biolink category subclasses.
narrow match: T170
narrow match: IAO_0000013

biological entity
type: Class
subclass of: Restriction
  all values from: organism taxon
  on property: in taxon
subclass of: named thing
subclass of: thing with taxon
alternative label: bioentity
narrow match: T050
narrow match: SIO_010046
narrow match: Q28845870

attribute
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: named thing
  on property: has qualitative value
subclass of: Restriction
  on class: ontology class
  on property: has attribute type
  qualified cardinality: 1
subclass of: Restriction
  all values from: quantity value
  on property: has quantitative value
subclass of: Restriction
  max qualified cardinality: 1
  on class: label type
  on property: name
subclass of: named thing
subclass of: ontology class
definition: A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.

anatomical entity
type: Class
subclass of: organismal entity
subclass of: physical essence
definition: A subcellular location, cell type or gross anatomical part
narrow match: EMAPA_0
narrow match: FBbt_10000000
narrow match: GO_0110165
narrow match: MA_0000001
narrow match: NCIT C12219
narrow match: WBBT_0000100
narrow match: XAO_0000000
narrow match: ZFA_0100000
related match: http://snomed.info/id/123037004

sequence variant
type: Class
subclass of: Restriction
  all values from: gene
  on property: has gene
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: biological entity
subclass of: genomic entity
subclass of: ontology class
subclass of: physical essence
alternative label: allele
definition: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
note: 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)

gene
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: symbol
subclass of: Restriction
  all values from: label type
  on property: synonym
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: biological entity
subclass of: chemical entity or gene or gene product
subclass of: gene or gene product
subclass of: genomic entity
subclass of: ontology class
subclass of: physical essence
broad match: NCIT C45822
definition: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.
narrow match: gene

chemical entity
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: max tolerated dose
subclass of: Restriction
  all values from: chemical role
  on property: has chemical role
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is toxic
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: trade name
subclass of: Restriction
  all values from: DrugAvailabilityEnum
  on property: available from
subclass of: chemical entity or gene or gene product
subclass of: chemical entity or protein or polypeptide
subclass of: chemical or drug or treatment
subclass of: named thing
subclass of: physical essence
definition: A chemical entity is a physical entity that pertains to chemistry or biochemistry.
narrow match: T129
narrow match: Q43460564

chemical entity or gene or gene product
type: Class
subclass of: mixin
definition: A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.

genomic entity
type: Class
subclass of: Restriction
  max qualified cardinality: 1
  on class: biological sequence
  on property: has biological sequence
subclass of: mixin
narrow match: T028
narrow match: GENO_0000897

occurrent
type: Class
subclass of: physical essence or occurrent
subclass of: mixin
definition: A processual entity.

disease or phenotypic feature
type: Class
subclass of: biological entity
alternative label: phenome
definition: 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. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.
narrow match: T033

predicate
type: ObjectProperty
domain: association
range: predicate type
sub property of: association slot
definition: A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.
editorial note: Has a value from the Biolink related_to hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats

predicate type
type: Class
subclass of: Uriorcurie

gene or gene product
type: Class
subclass of: macromolecular machine mixin
subclass of: mixin
definition: A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another

ontology class
type: Class
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: mixin
definition: a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
note: Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
note: This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc
examples: Example(value='UBERON:0000955', description="the class 'brain' from the Uberon anatomy ontology")

association slot
type: ObjectProperty
domain: association
range: String
alternative label: edge property
alternative label: edge qualifier
alternative label: node qualifier
alternative label: statement property
alternative label: statement qualifier
definition: any slot that relates an association to another entity

node property
type: ObjectProperty
domain: named thing
range: String
definition: A grouping for any property that holds between a node and a value

object
type: ObjectProperty
domain: association
range: named thing
sub property of: association slot
definition: 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.

subject
type: ObjectProperty
domain: association
range: named thing
sub property of: association slot
definition: 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.

related to at instance level
type: ObjectProperty
type: SymmetricProperty
domain: named thing
range: named thing
sub property of: related to
definition: Represents a relationship held between two instances of a data classes. Much like an assertion component, in an ABox, these represent facts associated with the conceptual model.
canonical predicate: True

association
type: Class
subclass of: Restriction
  on class: named thing
  on property: object
  qualified cardinality: 1
subclass of: Restriction
  on class: predicate type
  on property: predicate
  qualified cardinality: 1
subclass of: Restriction
  on class: named thing
  on property: subject
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: original object
subclass of: Restriction
  max qualified cardinality: 1
  on class: information resource
  on property: knowledge source
subclass of: Restriction
  all values from: information resource
  on property: aggregator knowledge source
subclass of: Restriction
  all values from: String
  on property: type
subclass of: Restriction
  max qualified cardinality: 1
  on class: Uriorcurie
  on property: original predicate
subclass of: Restriction
  all values from: evidence type
  on property: has evidence
subclass of: Restriction
  max qualified cardinality: 1
  on class: time type
  on property: timepoint
subclass of: Restriction
  all values from: publication
  on property: publications
subclass of: Restriction
  all values from: ontology class
  on property: qualifiers
subclass of: Restriction
  max qualified cardinality: 1
  on class: information resource
  on property: primary knowledge source
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: negated
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: original subject
subclass of: Restriction
  all values from: category type
  on property: category
subclass of: entity
definition: A typed association between two entities, supported by evidence
note: This is roughly the model used by biolink and ontobio at the moment

named thing
type: Class
subclass of: Class
  intersection of: Restriction
    all values from: category type
    on property: category
  intersection of: Restriction
    on property: category
    some values from: category type
subclass of: Restriction
  all values from: String
  on property: provided by
subclass of: Restriction
  all values from: Uriorcurie
  on property: xref
subclass of: entity
definition: a databased entity or concept/class