Biolink-Model
type: Ontology
license: https://creativecommons.org/publicdomain/zero/1.0/
version: 4.3.9
definition: Entity and association taxonomy and datamodel for life-sciences data

behavioral outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: An outcome resulting from an exposure event which is the manifestation of human behavior.
in scheme: vocab

disease or phenotypic feature outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.
in scheme: vocab

Edge
type: Class
subclass of: ClassDefinition
definition: An edge in a KGX graph, will be superclass for association
in scheme: vocab

epidemiological outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: An epidemiological outcome, such as societal disease burden, resulting from an exposure event.
in scheme: vocab
related match: NCIT C19291

hospitalization outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.
in scheme: vocab

KnowledgeGraph
type: Class
label: knowledge graph
subclass of: Restriction
  min cardinality: 0
  on property: nodes
subclass of: Restriction
  min cardinality: 0
  on property: edges
subclass of: Restriction
  all values from: entity
  on property: nodes
subclass of: Restriction
  all values from: association
  on property: edges
subclass of: Restriction
  min cardinality: 0
  on property: nodes
subclass of: Restriction
  all values from: association
  on property: edges
subclass of: Restriction
  all values from: entity
  on property: nodes
subclass of: Restriction
  min cardinality: 0
  on property: edges
subclass of: ClassDefinition
definition: A knowledge graph is a structured representation of knowledge in the form of a graph, where nodes represent entities or concepts, and edges represent relationships between them. Knowledge graphs are used to organize and connect information from various sources, enabling better understanding, analysis, and reasoning about complex domains.
definition: A knowledge graph represented in KGX format
in scheme: vocab

mapping collection
type: Class
subclass of: Restriction
  all values from: predicate mapping
  on property: predicate mappings
subclass of: Restriction
  min cardinality: 0
  on property: predicate mappings
subclass of: ClassDefinition
definition: A collection of deprecated mappings.
in scheme: vocab

mortality outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: An outcome of death from resulting from an exposure event.
in scheme: vocab

Node
type: Class
subclass of: ClassDefinition
definition: A node in a KGX graph, will be superclass for named thing
in scheme: vocab

pathological anatomical outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.
in scheme: vocab

pathological process outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: An outcome resulting from an exposure event which is the manifestation of a pathological process.
in scheme: vocab

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

socioeconomic outcome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: outcome
subclass of: ClassDefinition
definition: An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event
in scheme: vocab

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
in scheme: vocab

amount or activity decreased by
type: DatatypeProperty
sub property of: related to at instance level
inverse of: decreases amount or activity of
in scheme: vocab

amount or activity increased by
type: DatatypeProperty
sub property of: related to at instance level
inverse of: increases amount or activity of
in scheme: vocab

animal model available from
type: ObjectProperty
range: disease or phenotypic feature
sub property of: node property
in scheme: vocab

binds
type: DatatypeProperty
type: SymmetricProperty
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.
in scheme: vocab
canonical predicate: true

biological role mixin
type: DatatypeProperty
definition: A role played by the chemical entity or part thereof within a biological context.
in scheme: vocab
narrow match: CHEBI_24432

bonferonni adjusted p value
type: DatatypeProperty
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<.
in scheme: vocab

broad matches
type: DatatypeProperty
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.
in scheme: vocab

broad synonym
type: DatatypeProperty
sub property of: synonym
in scheme: vocab

can be carried out by
type: ObjectProperty
domain: occurrent
range: named thing
sub property of: actively involves
inverse of: capable of
in scheme: vocab

caused by
type: DatatypeProperty
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
in scheme: vocab
narrow match: RO_0001022
narrow match: RO_0002608
narrow match: RO_0004019
narrow match: RO_0004020
narrow match: RO_0004028
narrow match: RO_0009501

chembl assay description
type: DatatypeProperty
range: string
definition: Text describing the assay associated with a chemical entity.
in scheme: attributes

chembl binding site comment
type: DatatypeProperty
range: string
definition: Text describing the binding site for a chemical entity.
in scheme: attributes

chembl binding site name
type: DatatypeProperty
range: string
definition: Text indicating the name of the binding site for a chemical entity.
in scheme: attributes

chembl confidence score
type: DatatypeProperty
range: integer
definition: A score defined by ChEMBL that represents the confidence level of a particular drug-target interaction, based on the type and quality of evidence supporting the interaction. The score ranges from 0 to 9, with higher scores indicating stronger evidence for the interaction.
in scheme: attributes

chembl mechanism of action comment
type: DatatypeProperty
range: string
definition: Additional comments regarding the mechanism of action.
in scheme: attributes

chembl mechanism of action description
type: DatatypeProperty
range: string
definition: Text describing the mechanism of action for a chemical entity.
in scheme: attributes

chembl mutation
type: DatatypeProperty
range: string
definition: Text describing mutations associated with a chemical entity.
in scheme: attributes

chembl mutation accession
type: DatatypeProperty
range: string
definition: Accession identifier for a mutation associated with a chemical entity.
in scheme: attributes

chembl selectivity comment
type: DatatypeProperty
range: string
definition: Additional comments regarding the selectivity of the drug.
in scheme: attributes

chemical entity or drug or treatment
type: DatatypeProperty
definition: A union of chemical entities and children, and drug or treatment.
in scheme: vocab

chemical role mixin
type: DatatypeProperty
definition: A role played by the chemical entity or part thereof within a chemical context.
in scheme: vocab

chemically similar to
type: DatatypeProperty
type: SymmetricProperty
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.
in scheme: vocab
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

clinical modifier qualifier
type: ObjectProperty
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.
in scheme: vocab

clinical trial intervention boxed warning
type: DatatypeProperty
domain: association
range: boolean
sub property of: node property
definition: A boolean flag indicating whether a clinical trial intervention has a boxed warning. A boxed warning is the strongest warning that the FDA requires on a prescription drug label. This property should be populated from DailyMed.
in scheme: vocab

clinical trial time perspective
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
definition: The time perspective of a clinical trial as determined by clinicaltrials.gov. The most common values are PROSPECTIVE, RETROSPECTIVE, CROSS_SECTIONAL, or OTHER (most common)..
in scheme: vocab

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.
in scheme: vocab
canonical predicate: true

colocalizes with
type: DatatypeProperty
type: SymmetricProperty
sub property of: coexists with
definition: holds between two entities that are observed to be located in the same place.
in scheme: vocab
canonical predicate: true

completed by
type: DatatypeProperty
sub property of: related to at instance level
inverse of: has completed
in scheme: vocab

concept count object
type: DatatypeProperty
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.
in scheme: vocab

concept count subject
type: DatatypeProperty
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.
in scheme: vocab

concept pair count
type: DatatypeProperty
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.
in scheme: vocab

condition ameliorated by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: affected by
inverse of: ameliorates condition
in scheme: vocab

condition associated with gene
type: ObjectProperty
domain: disease or phenotypic feature
range: gene
sub property of: genetically associated with
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
in scheme: vocab
narrow match: NCIT R176
narrow match: RO_0004000

condition exacerbated by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: affected by
inverse of: exacerbates condition
in scheme: vocab

condition predisposed by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: likelihood affected by
inverse of: predisposes to condition
in scheme: vocab

condition prevented by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: affected by
inverse of: preventative for condition
in scheme: vocab

condition promoted by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: likelihood affected by
inverse of: promotes condition
in scheme: vocab

consumed by
type: ObjectProperty
domain: named thing
range: named thing
sub property of: is input of
inverse of: consumes
in scheme: vocab

contains process
type: DatatypeProperty
sub property of: related to at instance level
inverse of: occurs in
in scheme: vocab

created with
type: DatatypeProperty
domain: dataset
sub property of: node property
in scheme: vocab

dataset download url
type: DatatypeProperty
domain: dataset
sub property of: node property
in scheme: vocab

decreased amount in
type: DatatypeProperty
sub property of: related to at instance level
inverse of: has decreased amount
in scheme: vocab

decreased likelihood associated with
type: DatatypeProperty
sub property of: likelihood associated with
inverse of: associated with decreased likelihood of
in scheme: vocab

develops into
type: DatatypeProperty
sub property of: related to at instance level
inverse of: develops from
in scheme: vocab

dgidb relative drug specificity score
type: DatatypeProperty
range: float
definition: A score defined by DGIdb that quantifies the gene-interaction specificity of a given drug - representing the ratio of average known gene partners for all drugs to the known partners for the given drug. See https://dgidb.org/about/overview/interaction-score.
in scheme: attributes

dgidb relative gene specificity score
type: DatatypeProperty
range: float
definition: A score defined by DGIdb that quantifies the drug-interaction specificity of a given gene - representing the ratio of average known drug partners for all genes to the known partners for the given gene. See https://dgidb.org/about/overview/interaction-score.
in scheme: attributes

disrupted by
type: DatatypeProperty
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.
in scheme: vocab

download url
type: DatatypeProperty
domain: information content entity
sub property of: node property
in scheme: vocab

drug_rep_hub disease area
type: DatatypeProperty
range: string
definition: A term used by Drug Repurposing Hub to describe the disease area associated with a drug.
in scheme: attributes

end coordinate
type: DatatypeProperty
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.
in scheme: vocab

exact matches
type: DatatypeProperty
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.
in scheme: vocab

exact synonym
type: DatatypeProperty
sub property of: synonym
in scheme: vocab

expected count
type: DatatypeProperty
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.
in scheme: vocab

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
in scheme: vocab

gene_fusion_with
type: ObjectProperty
type: SymmetricProperty
domain: gene
range: gene
sub property of: genetically interacts with
definition: holds between two independent genes that have fused through translocation, interstitial deletion, or chromosomal inversion to form a new, hybrid gene. Fusion genes are often implicated in various neoplasms and cancers.
in scheme: vocab
canonical predicate: true

genetic association
type: DatatypeProperty
type: SymmetricProperty
sub property of: associated with
in scheme: vocab

genetic_neighborhood_of
type: ObjectProperty
type: SymmetricProperty
domain: gene
range: gene
sub property of: genetically interacts with
definition: holds between two genes located nearby one another on a chromosome.
in scheme: vocab
canonical predicate: true

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
in scheme: vocab

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

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
in scheme: vocab
narrow match: NCIT disease has molecular abnormality
narrow match: NCIT disease is marked by gene

has catalyst
type: DatatypeProperty
sub property of: has participant
inverse of: catalyzes
in scheme: vocab

has chemical formula
type: DatatypeProperty
range: string
sub property of: node property
definition: description of chemical compound based on element symbols
in scheme: vocab

has confidence level
type: DatatypeProperty
sub property of: association slot
definition: connects an association to a qualitative term denoting the level of confidence
in scheme: vocab

has constituent
type: ObjectProperty
range: molecular entity
sub property of: node property
definition: one or more molecular entities within a chemical mixture
in scheme: vocab

has contraindication
type: ObjectProperty
domain: biological entity
range: chemical or drug or treatment
sub property of: related to at instance level
inverse of: contraindicated in
in scheme: vocab

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

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
in scheme: vocab

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
in scheme: vocab
narrow match: NCIT R178

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

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
in scheme: vocab

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
in scheme: vocab

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
in scheme: vocab

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
in scheme: vocab

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

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
in scheme: vocab

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
in scheme: vocab

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

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

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

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

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
in scheme: vocab

has stressor
type: DatatypeProperty
domain: exposure event
sub property of: node property
alternative label: has stimulus
definition: the process or entity that the receptor is being exposed to
in scheme: vocab

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
in scheme: vocab

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

has topic
type: ObjectProperty
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 scheme: vocab

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
in scheme: vocab
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
in scheme: vocab
related match: SIO_010497
canonical predicate: true

in linkage disequilibrium with
type: DatatypeProperty
type: SymmetricProperty
sub property of: related to at instance level
definition: holds between two sequence variants, the presence of which are correlated in a population
in scheme: vocab
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
in scheme: vocab
related match: SIO_010532
canonical predicate: true

increased amount of
type: DatatypeProperty
sub property of: related to at instance level
inverse of: has increased amount
in scheme: vocab

increased likelihood associated with
type: DatatypeProperty
sub property of: likelihood associated with
inverse of: associated with increased likelihood of
in scheme: vocab

indirectly physically interacts with
type: DatatypeProperty
type: SymmetricProperty
sub property of: physically interacts with
in scheme: vocab
canonical predicate: true

intact confidence value
type: DatatypeProperty
alternative label: intact interaction score
alternative label: intact miscore
definition: A score defined by MI / IntAct that represents the degree of confidence in the existence of a particular interaction by assessing the annotation of that specific interaction in a standards-compliant dataset. The score given to an interaction will increase as the number of experimental evidences supporting that interaction increases. Experimental evidences contribute more highly to the final score than evidences derived by predictive algorithms or literature text-mining methods. Range is 0-1, with higher scores indicated more confidence. See here for details: https://www.ebi.ac.uk/intact/documentation/user-guide#interaction_scoring.
in scheme: attributes

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
in scheme: vocab
mapping relation: RO_0002249

is diagnosed by
type: ObjectProperty
domain: disease or phenotypic feature
range: diagnostic aid
sub property of: related to at instance level
inverse of: diagnoses
in scheme: vocab

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
in scheme: vocab
mapping relation: Q902638

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
in scheme: vocab
note: The CHEBI ID represents a role rather than a predicate

is molecular consequence of
type: DatatypeProperty
domain: ontology class
sub property of: related to at instance level
inverse of: has molecular consequence
in scheme: vocab

is output of
type: ObjectProperty
domain: named thing
range: biological process or activity
sub property of: participates in
inverse of: has output
in scheme: vocab
narrow match: RO_0002354

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
in scheme: vocab

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

ln ratio
type: DatatypeProperty
range: float
sub property of: association slot
definition: the natural log of the ratio of co-occurrence to expected
in scheme: vocab

ln ratio confidence interval
type: DatatypeProperty
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)
in scheme: vocab

location of disease
type: DatatypeProperty
sub property of: related to
inverse of: disease has location
in scheme: vocab

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

mechanism of action
type: DatatypeProperty
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.
in scheme: vocab

member of
type: DatatypeProperty
sub property of: related to at concept level
inverse of: has member
definition: Defines a mereological relation between a item and a collection.
in scheme: vocab

mentioned by
type: DatatypeProperty
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.
in scheme: vocab

missing from
type: DatatypeProperty
sub property of: related to at instance level
inverse of: lacks part
in scheme: vocab

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
in scheme: vocab

models
type: DatatypeProperty
sub property of: related to at instance level
inverse of: model of
in scheme: vocab

models demonstrating benefits for
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: subject of treatment application or study for treatment by
sub property of: tested by preclinical trials of
inverse of: beneficial in models for
in scheme: vocab

narrow matches
type: DatatypeProperty
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.
in scheme: vocab

narrow synonym
type: DatatypeProperty
sub property of: synonym
in scheme: vocab

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).
in scheme: vocab
canonical predicate: true
opposite of: positively correlated with

not completed by
type: DatatypeProperty
sub property of: related to at instance level
inverse of: has not completed
in scheme: vocab

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)
in scheme: vocab

occurs in disease
type: DatatypeProperty
sub property of: related to at instance level
inverse of: disease has basis in
in scheme: vocab

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.
in scheme: vocab
canonical predicate: true

opposite of
type: DatatypeProperty
type: SymmetricProperty
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).
in scheme: vocab
canonical predicate: true

orthologous to
type: DatatypeProperty
type: SymmetricProperty
sub property of: homologous to
definition: a homology relationship between entities (typically genes) that diverged after a speciation event.
in scheme: vocab
canonical predicate: true

paralogous to
type: DatatypeProperty
type: SymmetricProperty
sub property of: homologous to
definition: a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
in scheme: vocab
canonical predicate: true

pharmacologically interacts with
type: ObjectProperty
type: SymmetricProperty
domain: chemical entity
range: chemical entity
sub property of: interacts with
alternative label: drug drug interaction
definition: holds between two pharmacologically active chemicals (typically drugs), where one alters the availability, efficacy, or toxicity of the other in the body when taken simultaneously - typically by altering how the body processes the chemical (pharmacokinetics) or how the chemical acts on the body (pharmacodynamics).
in scheme: vocab
canonical predicate: true

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

plasma membrane part of
type: DatatypeProperty
sub property of: part of
inverse of: has plasma membrane part
in scheme: vocab

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).
in scheme: vocab
canonical predicate: true
opposite of: negatively correlated with

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
in scheme: vocab
narrow match: FMA transforms from
narrow match: RO_0002087
narrow match: RO_0002285

primarily composed of
type: DatatypeProperty
sub property of: related to
inverse of: composed primarily of
in scheme: vocab

produced by
type: DatatypeProperty
sub property of: related to at instance level
inverse of: produces
in scheme: vocab

reaction balanced
type: DatatypeProperty
range: boolean
sub property of: association slot
in scheme: vocab

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

related condition
type: DatatypeProperty
type: SymmetricProperty
sub property of: related to at instance level
in scheme: vocab
canonical predicate: true

related synonym
type: DatatypeProperty
sub property of: synonym
in scheme: vocab

relation
type: DatatypeProperty
in scheme: vocab

relative frequency object
type: DatatypeProperty
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.
in scheme: vocab

relative frequency object confidence interval
type: DatatypeProperty
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)
in scheme: vocab

relative frequency subject
type: DatatypeProperty
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.
in scheme: vocab

relative frequency subject confidence interval
type: DatatypeProperty
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)
in scheme: vocab

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

response associated with
type: DatatypeProperty
sub property of: associated with
inverse of: associated with response to
in scheme: vocab

retrieved on
type: DatatypeProperty
domain: dataset
range: date
sub property of: node property
in scheme: vocab

same as
type: DatatypeProperty
type: SymmetricProperty
sub property of: exact match
definition: holds between two entities that are considered equivalent to each other
in scheme: vocab
narrow match: external-identifier
canonical predicate: true

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

sensitivity decreased by
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: sensitivity affected by
inverse of: decreases sensitivity to
in scheme: vocab

sensitivity increased by
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: related to at instance level
inverse of: increases sensitivity to
in scheme: vocab

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
in scheme: vocab

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

severity qualifier
type: ObjectProperty
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
in scheme: vocab

signor confidence score
type: DatatypeProperty
range: float
definition: A score defined by SIGNOR Lab Diseases that reports confidence level in a curated interaction. Scores are based on four factors: number of supporting publications, occurrence in curated SIGNOR pathways, support in Reactome interaction data, co-mentions in UniProt records. Scores range 0-1, and reflect a relative measure of evidence support, not an absolute probability or statistical confidence measure.
in scheme: attributes

start coordinate
type: DatatypeProperty
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).
in scheme: vocab

superclass of
type: ObjectProperty
domain: ontology class
range: ontology class
sub property of: related to at concept level
inverse of: subclass of
definition: holds between two classes where the domain class is a super class of the range class
in scheme: vocab
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

support graphs
type: DatatypeProperty
sub property of: association slot
definition: A list of knowledge graphs that support the existence of this association.
in scheme: vocab

supporting data set
type: DatatypeProperty
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).
in scheme: vocab

supporting data source
type: DatatypeProperty
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"
in scheme: vocab

supporting study cohort
type: DatatypeProperty
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).
in scheme: vocab

supporting study context
type: DatatypeProperty
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.).
in scheme: vocab

supporting study date range
type: DatatypeProperty
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.
in scheme: vocab

supporting study method description
type: DatatypeProperty
range: anyURI
sub property of: supporting study metadata
definition: A uri or curie pointing to information about the methodology used to generate data supporting an Association.
in scheme: vocab

supporting study method types
type: DatatypeProperty
range: anyURI
sub property of: supporting study metadata
definition: Type(s) of methods that were 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).
in scheme: vocab

supporting study size
type: DatatypeProperty
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).
in scheme: vocab

systematic synonym
type: DatatypeProperty
domain: named thing
range: string
sub property of: node property
definition: more commonly used for gene symbols in yeast
in scheme: vocab

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

temporal interval qualifier
type: DatatypeProperty
sub property of: temporal context qualifier
definition: a constraint of a time interval placed upon the truth value of an association.
in scheme: vocab

tested by clinical trials of
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: subject of treatment application or study for treatment by
sub property of: treated in studies by
inverse of: in clinical trials for
in scheme: vocab

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
in scheme: vocab

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
in scheme: vocab

treatment applications from
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: related to at instance level
sub property of: subject of treatment application or study for treatment by
inverse of: applied to treat
in scheme: vocab

url
type: DatatypeProperty
domain: entity
range: string
sub property of: node property
definition: This slot holds a string representation of a URL for an external resource about the node it is present on. Unlike an 'xref' that is primarily represented by a CURIE, this slot is intended to hold a full URL that can be used to directly access a resource. When linking to an external resource that cannot be represented by a unique CURIE, this slot should be used. However, when the intent is to link to the default URI expansion of a CURIE related to the node it is present on, the xref slot should be used instead.
in scheme: vocab

variant part of
type: DatatypeProperty
sub property of: part of
inverse of: has variant part
in scheme: vocab

version
type: DatatypeProperty
domain: dataset
sub property of: node property
broad match: version
broad match: versionInfo
in scheme: vocab

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

was tested for effect of
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
inverse of: was tested for effect on
in scheme: vocab

xenologous to
type: DatatypeProperty
type: SymmetricProperty
sub property of: homologous to
definition: a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.
in scheme: vocab
canonical predicate: true

annotation
type: Class
subclass of: ClassDefinition
definition: Biolink Model root class for entity annotations.
in scheme: vocab

metabolite
type: Class
subclass of: ChemicalEntityDerivativeEnum
subclass of: PermissibleValue

chemical to entity association mixin
type: Class
subclass of: chemical entity to entity association mixin
definition: An interaction between a chemical entity and another entity
in scheme: vocab

entity to feature or gene qualifiers mixin
type: Class
subclass of: frequency qualifier mixin
definition: Qualifiers for entity to gene associations.
in scheme: vocab

entity to feature or variant qualifiers mixin
type: Class
subclass of: frequency qualifier mixin
definition: Qualifiers for entity to variant associations.
in scheme: vocab

pathognomonicity quantifier
type: Class
subclass of: specificity quantifier
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
in scheme: vocab

sensitivity quantifier
type: Class
subclass of: relationship quantifier
in scheme: vocab

active in
type: ObjectProperty
domain: gene or gene product
range: cellular component
sub property of: related to at instance level
in scheme: vocab
canonical predicate: true

actively involves
type: ObjectProperty
domain: biological process or activity
range: named thing
sub property of: has participant
inverse of: actively involved in
in scheme: vocab

acts upstream of negative effect
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of
in scheme: vocab
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
in scheme: vocab
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
in scheme: vocab
canonical predicate: true

acts upstream of positive effect
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of
in scheme: vocab
canonical predicate: true

ameliorates condition
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects
sub property of: treats
alternative label: ameliorates
alternative label: beneficial for condition
alternative label: therapeutic for condition
definition: Holds between an entity and an existing medical condition (disease or phenotypic feature) where the entity is able to ameliorate symptoms, stabilize progression, or cure the condition.
editorial note: This predicate describes a narrower view of 'treats' - that covers interventions that are beneficial for existing disease, and excludes interventions that prevent/reduce risk of developing a condition in the future.
in scheme: vocab
canonical predicate: true
opposite of: exacerbates condition

applied to treat
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: related to at instance level
sub property of: treats or applied or studied to treat
alternative label: administered to treat
alternative label: given to treat
alternative label: used to treat
definition: Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition.
editorial note: This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions (e.g. here, here, here).
in scheme: vocab
canonical predicate: true

associated with decreased likelihood of
type: DatatypeProperty
sub property of: associated with likelihood of
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.
in scheme: vocab
canonical predicate: true

associated with increased likelihood of
type: DatatypeProperty
sub property of: associated with likelihood of
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.
in scheme: vocab
canonical predicate: true

associated with resistance to
type: ObjectProperty
domain: named thing
range: chemical entity
sub property of: associated with response to
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.
in scheme: vocab
canonical predicate: true

associated with sensitivity to
type: ObjectProperty
domain: named thing
range: chemical entity
sub property of: associated with response to
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.
in scheme: vocab
narrow match: http://snomed.info/id/418038007
canonical predicate: true

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

beneficial in models for
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: in preclinical trials for
sub property of: treats or applied or studied to treat
definition: Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).
editorial note: This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) .
in scheme: vocab
canonical predicate: true

biomarker for
type: ObjectProperty
domain: chemical entity or gene or gene product
range: disease or phenotypic feature
sub property of: correlated with
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.
in scheme: vocab
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

capable of
type: ObjectProperty
domain: named thing
range: occurrent
sub property of: actively involved in
definition: holds between a physical entity and process or function, where the continuant alone has the ability to carry out the process or function.
in scheme: vocab
narrow match: NCIT R52
narrow match: RO_0002500
canonical predicate: true

catalyzes
type: DatatypeProperty
sub property of: participates in
in scheme: vocab
canonical predicate: true

causes
type: DatatypeProperty
sub property of: contributes to
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
in scheme: vocab
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

close match
type: DatatypeProperty
type: SymmetricProperty
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).
in scheme: vocab
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
canonical predicate: true

composed primarily of
type: DatatypeProperty
sub property of: related to
definition: x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.
in scheme: vocab
canonical predicate: true

consumes
type: ObjectProperty
domain: named thing
range: named thing
sub property of: has input
in scheme: vocab
narrow match: RO_0004009
canonical predicate: true

contraindicated in
type: ObjectProperty
domain: chemical or drug or treatment
range: biological entity
sub property of: related to at instance level
definition: Holds between a substance, procedure, or activity and a medical condition or circumstance, where an authority has established that the substance, procedure, or activity should not be applied as an intervention in patients with the condition or circumstance because it can result in detrimental outcomes.
editorial note: This predicate relates the intervention with a specific disease, phenotype, or other medical circumstance that puts patients at high risk for detrimental outcomes. This may be a different condition from the one that the drug would be used to treat (e.g. pseudoephedrine is contraindicated in people with high-blood pressure as a treatment for nasal congestion), a biological state (e.g. isotretinoin is contraindicated in people who are pregnant as a treatment for acne), or being on a different medication (e.g. aspirin is contraindicated in people taking warfarin as a preventative treatment for stroke).
in scheme: vocab
canonical predicate: true
opposite of: treats

contribution from
type: DatatypeProperty
sub property of: related to at instance level
inverse of: contributes to
in scheme: vocab

dataset count
type: DatatypeProperty
range: integer
sub property of: association slot
definition: The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort.
in scheme: vocab

decreases amount or activity of
type: DatatypeProperty
sub property of: related to at instance level
definition: A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object.
in scheme: vocab

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

derives into
type: DatatypeProperty
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
in scheme: vocab

develops from
type: DatatypeProperty
sub property of: related to at instance level
in scheme: vocab
narrow match: RO_0002207
narrow match: RO_0002225
narrow match: RO_0002226
canonical predicate: true

diagnoses
type: ObjectProperty
domain: diagnostic aid
range: disease or phenotypic feature
sub property of: related to at instance level
definition: a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.
in scheme: vocab
canonical predicate: true

directly physically interacts with
type: DatatypeProperty
type: SymmetricProperty
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).
in scheme: vocab
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: DatatypeProperty
sub property of: related to at instance level
definition: A relation that holds between a disease and an entity where the state of the entity has contribution to the disease.
in scheme: vocab
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: DatatypeProperty
sub property of: related to
definition: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
in scheme: vocab

disrupts
type: DatatypeProperty
sub property of: affects
alternative label: disease causes disruption of
definition: describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
in scheme: vocab
narrow match: RO_0004024
narrow match: RO_0004025
canonical predicate: true
opposite of: enables

editor
type: ObjectProperty
domain: agent
range: publication
sub property of: contributor
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).
in scheme: vocab

enables
type: ObjectProperty
domain: physical entity
range: biological process or activity
sub property of: participates in
definition: holds between a physical entity and a process, where the physical entity executes the process
in scheme: vocab
canonical predicate: true

exacerbates condition
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects
sub property of: promotes condition
alternative label: detrimental for condition
alternative label: exacerbates
broad match: SemMedDBCOMPLICATES
definition: Holds between a substance, procedure, or activity and an existing medical condition (disease or phenotypic feature) where the substance, procedure, or activity worsens some or all aspects of the condition.
in scheme: vocab
canonical predicate: true
opposite of: ameliorates condition

expressed in
type: ObjectProperty
domain: gene or gene product
range: anatomical entity
sub property of: located in
definition: holds between a gene or gene product and an anatomical entity in which it is expressed
in scheme: vocab
narrow match: NCIT R46
narrow match: NCIT R49
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)
in scheme: vocab

gene associated with condition
type: ObjectProperty
domain: gene
range: disease or phenotypic feature
sub property of: genetically associated with
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
in scheme: vocab
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
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
in scheme: vocab
canonical predicate: true

has active ingredient
type: ObjectProperty
domain: drug
range: molecular entity
sub property of: has part
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
in scheme: vocab
mapping relation: RO_0002248
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
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.
in scheme: vocab
canonical predicate: true

has completed
type: DatatypeProperty
sub property of: related to at instance level
definition: holds between an entity and a process that the entity is capable of and has completed
in scheme: vocab
canonical predicate: true
opposite of: has not completed

has decreased amount
type: DatatypeProperty
sub property of: related to at instance level
in scheme: vocab
narrow match: CL has low plasma membrane amount
canonical predicate: true
opposite of: has increased amount

has excipient
type: ObjectProperty
domain: drug
range: molecular entity
sub property of: has part
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
in scheme: vocab
mapping relation: Q902638
canonical predicate: true

has increased amount
type: DatatypeProperty
sub property of: related to at instance level
in scheme: vocab
narrow match: CL has high plasma membrane amount
canonical predicate: true
opposite of: has decreased amount

has manifestation
type: DatatypeProperty
domain: disease
sub property of: related to at instance level
inverse of: manifestation of
in scheme: vocab

has member
type: DatatypeProperty
sub property of: related to at concept level
definition: Defines a mereological relation between a collection and an item.
in scheme: vocab

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

has mode of inheritance
type: ObjectProperty
domain: disease or phenotypic feature
range: genetic inheritance
sub property of: has manifestation
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).
in scheme: vocab
canonical predicate: true

has molecular consequence
type: ObjectProperty
range: ontology class
sub property of: related to at instance level
alternative label: allele has activity
definition: connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583
in scheme: vocab
narrow match: NCIT allele has activity
canonical predicate: true

has not completed
type: DatatypeProperty
sub property of: related to at instance level
definition: holds between an entity and a process that the entity is capable of, but has not completed
in scheme: vocab
canonical predicate: true
opposite of: has completed

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

has phenotype
type: ObjectProperty
domain: biological entity
range: phenotypic feature
sub property of: related to at instance level
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
in scheme: vocab
narrow match: NCIT R89
narrow match: RO_0004022
narrow match: RO_0004029
narrow match: has symptom
canonical predicate: true

has plasma membrane part
type: DatatypeProperty
sub property of: has part
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.
in scheme: vocab
canonical predicate: true

has sequence location
type: ObjectProperty
domain: nucleic acid entity
range: nucleic acid entity
sub property of: related to at instance level
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.
in scheme: vocab
canonical predicate: true

has side effect
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects
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.
in scheme: vocab
canonical predicate: true

has substrate
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: has participant
in scheme: vocab
canonical predicate: true

has variant part
type: DatatypeProperty
sub property of: has part
definition: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it
in scheme: vocab
canonical predicate: true

in clinical trials for
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: studied to treat
sub property of: treats or applied or studied to treat
definition: Holds between an intervention and a medical condition, and reports that a clinical trial is being or has been performed in human patients to test the potential of the intervention to treat the medical condition (e.g. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).
editorial note: This predicate should be used when a source reports a clinical trial where the intervention is being or was interrogated, regardless of the phase of the trial, or its ultimate outcome. Information about phase and outcome can be capture using other modeling elements.
in scheme: vocab
canonical predicate: true

increases amount or activity of
type: DatatypeProperty
sub property of: related to at instance level
definition: A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object.
in scheme: vocab

increases sensitivity to
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: affects sensitivity to
definition: holds between two chemical entities or genes or gene products where the action or effect of one increases the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other
in scheme: vocab
canonical predicate: true
opposite of: decreases sensitivity to

is frameshift variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
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.
in scheme: vocab
canonical predicate: true

is input of
type: ObjectProperty
domain: named thing
range: biological process or activity
sub property of: participates in
inverse of: has input
in scheme: vocab

is missense variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
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.
in scheme: vocab
canonical predicate: true

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

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

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

is splice site variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
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.
in scheme: vocab
canonical predicate: true

is synonymous variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: is sequence variant of
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
in scheme: vocab
canonical predicate: true

lacks part
type: DatatypeProperty
sub property of: related to at instance level
in scheme: vocab
narrow match: CL lacks plasma membrane part
canonical predicate: true
opposite of: has part

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)
in scheme: vocab
narrow match: NCIT Anatomic Structure Has Location Role
narrow match: SNOMED inherent location of

mentions
type: DatatypeProperty
sub property of: related to at instance level
definition: refers to is a relation between one information content entity and the named thing that it makes reference to.
in scheme: vocab
narrow match: SIO_000628

model of
type: DatatypeProperty
sub property of: related to at instance level
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.
in scheme: vocab
narrow match: FOODON_00001301
canonical predicate: true

occurs in
type: DatatypeProperty
sub property of: related to at instance level
definition: holds between a process and a material entity or site within which the process occurs
in scheme: vocab
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

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

predisposes to condition
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects likelihood of
sub property of: promotes condition
alternative label: risk factor for
broad match: SemMedDBPREDISPOSES
definition: Holds between two entities where the presence or application of one increases the chance that the other will come to be.
in scheme: vocab
canonical predicate: true

preventative for condition
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects likelihood of
sub property of: treats
alternative label: prevents
alternative label: prophylactic for
broad match: SemMedDBPREVENTS
definition: Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to prevent it manifesting in the first place.
in scheme: vocab
canonical predicate: true
opposite of: promotes condition

produces
type: DatatypeProperty
sub property of: related to at instance level
definition: holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
in scheme: vocab
narrow match: NCIT R29
narrow match: SNOMED has process output
narrow match: SNOMED specimen procedure of
related match: GOREL_0001010
canonical predicate: true

provider
type: DatatypeProperty
sub property of: contributor
definition: person, group, organization or project that provides a piece of information (e.g. a knowledge association).
in scheme: vocab

publisher
type: ObjectProperty
domain: agent
range: publication
sub property of: contributor
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).
in scheme: vocab

regulates
type: ObjectProperty
domain: physical essence or occurrent
range: physical essence or occurrent
sub property of: affects
sub property of: interacts with
broad match: RO_0002295
broad match: RO_0002332
broad match: RO_0002448
broad match: modulator
broad match: 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.
in scheme: vocab
canonical predicate: true

sensitivity affected by
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: related to at instance level
inverse of: affects sensitivity to
in scheme: vocab

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
in scheme: vocab
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

target for
type: ObjectProperty
domain: gene
range: disease
sub property of: related to at instance level
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
in scheme: vocab
canonical predicate: true

tested by preclinical trials of
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: subject of treatment application or study for treatment by
sub property of: treated in studies by
inverse of: in preclinical trials for
in scheme: vocab

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

translates to
type: ObjectProperty
domain: transcript
range: protein
sub property of: related to at instance level
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)
in scheme: vocab
canonical predicate: true

treated by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: subject of treatment application or study for treatment by
inverse of: treats
in scheme: vocab
narrow match: RO_0002302

was tested for effect on
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
alternative label: was assayed against
alternative label: was experimentally tested against
definition: Reports that the subject was interrogated in an experiment to determine how it may affect the object. 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.
in scheme: vocab
canonical predicate: true

all_some
type: Class
subclass of: LogicalInterpretationEnum
subclass of: PermissibleValue

some_some
type: Class
subclass of: LogicalInterpretationEnum
subclass of: PermissibleValue

accessible dna region
type: Class
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: regulatory region
alternative label: atac-seq accessible region
alternative label: dnase-seq accessible region
definition: A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose
in scheme: vocab

pAC50
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

pEC50
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

pIC50
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

pKd
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

pKi
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

pKoff
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

pKon
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

pXC50
type: Class
subclass of: AffinityParameterEnum
subclass of: PermissibleValue

computational_model
type: Class
subclass of: AgentTypeEnum
subclass of: automated_agent

data_analysis_pipeline
type: Class
subclass of: AgentTypeEnum
subclass of: automated_agent

image_processing_agent
type: Class
subclass of: AgentTypeEnum
subclass of: automated_agent

manual_agent
type: Class
subclass of: AgentTypeEnum
subclass of: PermissibleValue

manual_validation_of_automated_agent
type: Class
subclass of: AgentTypeEnum
subclass of: PermissibleValue

not_provided
type: Class
subclass of: AgentTypeEnum
subclass of: PermissibleValue

text_mining_agent
type: Class
subclass of: AgentTypeEnum
subclass of: automated_agent

anatomical entity has part anatomical entity association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: anatomical entity
  on property: subject
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, that is, the subject is has the object entity as a part (the expected predicate is "biolink:has_part" or suitable predicate slots inheriting from it, i.e., "biolink:has_plasma_membrane_part", "biolink:has_variant_part", etc.). This includes relationships between cells and cellular components, between issues and cells, whole organisms and tissues.
in scheme: vocab

anatomical entity part of anatomical entity association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anatomical entity
  on property: subject
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
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, that is, the subject is a part of the object entity (the expected predicate is "biolink:part_of" or suitable predicate slots inheriting from it, i.e., "biolink:plasma_membrane_part_of", "biolink:variant_part_of", etc.). This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms.
in scheme: vocab

anatomical entity to anatomical entity ontogenic association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anatomical entity
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
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.
in scheme: vocab

discovery_and_development_phase
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_accelerated_approval
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_breakthrough_therapy
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_clinical_research_phase
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_clinical_research_phase_1
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_clinical_research_phase_2
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_clinical_research_phase_3
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_clinical_research_phase_4
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_fast_track
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_post_market_safety_review
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_priority_review
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

fda_review_phase_4
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

post_approval_withdrawal
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

preclinical_research_phase
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

regular_fda_approval
type: Class
subclass of: ApprovalStatusEnum
subclass of: PermissibleValue

bacterium
type: Class
subclass of: organismal entity
definition: A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile.
in scheme: vocab

behavior to behavioral feature association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: behavior
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: behavioral feature
  on property: object
subclass of: association
definition: An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.
in scheme: vocab

behavioral exposure
type: Class
subclass of: exposure event
definition: A behavioral exposure is a factor relating to behavior impacting an individual.
in scheme: vocab

equal_to
type: Class
subclass of: BinaryRelationEnum
subclass of: PermissibleValue

greater_than
type: Class
subclass of: BinaryRelationEnum
subclass of: PermissibleValue

less_than
type: Class
subclass of: BinaryRelationEnum
subclass of: PermissibleValue

biological process or activity to anatomical entity association
type: Class
subclass of: Restriction
  all values from: biological process or activity
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: association
definition: An association between a biological process or activity and an anatomical entity.
in scheme: vocab

biological process or activity to biological process or activity association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: biological process or activity
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: biological process or activity
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: association
definition: Classification relationship between biological processes or activities (e.g. coupling of two molecular activities; assignment of molecular activity to a pathway; implicating a pathway in a biological process; etc.)
in scheme: vocab

biological process or activity to gene or gene product or gene family association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene or gene product or gene family
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: biological process or activity
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: association
definition: Relationship between a biological processor activity (e.g. molecular activity, biological process or pathway) to gene or gene product or gene family.
in scheme: vocab

biotic exposure
type: Class
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).
in scheme: vocab

book
type: Class
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: type
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.
in scheme: vocab

case to disease association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: case to entity association mixin
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: onset qualifier
subclass of: Restriction
  all values from: disease
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: onset qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: onset
  on property: onset qualifier
subclass of: association
definition: An association between a Case (patient) and a Disease
in scheme: vocab

case to gene association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: case to entity association mixin
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: association
definition: Association between a Case and a Gene (e.g., indicating a gene of interest for the case)
in scheme: vocab

case to phenotypic feature association
type: Class
subclass of: Restriction
  all values from: onset
  on property: onset qualifier
subclass of: Restriction
  max cardinality: 1
  on property: negated
subclass of: Restriction
  all values from: boolean
  on property: negated
subclass of: Restriction
  min cardinality: 0
  on property: onset qualifier
subclass of: Restriction
  max cardinality: 1
  on property: onset qualifier
subclass of: Restriction
  min cardinality: 0
  on property: negated
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: Restriction
  on property: mixins
  some values from: case to entity association mixin
subclass of: association
definition: An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.
in scheme: vocab

case to variant association
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: has zygosity
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: zygosity
  on property: has zygosity
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: has zygosity
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: sequence variant
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: case to entity association mixin
subclass of: association
definition: Association between a Case and a Genetic Variant
in scheme: vocab

causal gene to disease association
type: Class
subclass of: Restriction
  all values from: disease
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: gene to entity association mixin
subclass of: Restriction
  all values from: string
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: Datatype
    intersection of: string
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^HP:\d{7}$
  on property: allelic requirement
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: allelic requirement
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: allelic requirement
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: association
in scheme: vocab

ADP-ribosylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

acetylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

adduction
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: covalent_binding

allosteric_antagonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: antagonism

ampylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

antibody_agonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: agonism

antibody_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

antisense_oligonucleotide_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

atpase_activation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

biased_agonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: agonism

binding
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

biphasic_allosteric_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: mixed_allosteric_modulation

carboxylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

catalytic_activity
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

chaperone_mediated_stabilization
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: stabilization

chelation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

chemical_modification
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

cleavage
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

cofactor
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: positive_modulation

competitive_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

crosslinking
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: covalent_binding

de-ADP-ribosylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

deacetylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

deglycosylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

degradation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

demethylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

deneddylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

dephosphorylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

destabilization
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

desumoylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

deubiquitination
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

disruption
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

disuphide_binding
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: covalent_binding

exogenous_gene
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

exogenous_protein
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

feedback_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

gating_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

glycosylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

gtpase_activation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

guanyl_nucleotide_exchange
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: activation

hydrolysis
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

hydroxylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

induction
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: positive_modulation

inverse_agonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

irreversible_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

isomerization
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

mixed_agonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

molecular_channel_blockage
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

molecular_channel_opening
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: activation

monoubiquitination
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: ubiquitination

multitarget_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

myristoylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: lipidation

neddylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

negative_allosteric_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: noncompetitive_inhibition

negative_gene_editing_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

non_competitive_antagonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: antagonism

opening
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

oxidation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

oxidoreduction
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

palmitoylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: lipidation

partial_agonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: agonism

phosphorylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

polyubiquitination
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: ubiquitination

positive_allosteric_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: activation

post_transcriptional_regulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

potentiation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: positive_modulation

reduction
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

release
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

relocalization
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

rna_interference_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

s_nitrosylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

sequestration
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

signaling_mediated_control
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

stimulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: activation

sulfation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

sumoylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

suppression
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

transcriptional_regulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

transglutamination
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: covalent_binding

translational_regulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

trimethylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: methylation

tyrosination
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

vaccine_antigen
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: immune_system_modulation

cell
type: Class
subclass of: anatomical entity
in scheme: vocab

cell line as a model of disease association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  on property: mixins
  some values from: model to disease association mixin
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: cell line
  on property: subject
subclass of: cell line to disease or phenotypic feature association
in scheme: vocab

cell line to entity association mixin
type: Class
subclass of: Mixin
definition: An relationship between a cell line and another entity
in scheme: vocab

chemical affects gene association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: evidence count
subclass of: Restriction
  min cardinality: 0
  on property: dgidb interaction score
subclass of: Restriction
  all values from: anyURI
  on property: supporting documents
subclass of: Restriction
  min cardinality: 0
  on property: supporting documents
subclass of: Restriction
  min cardinality: 0
  on property: evidence count
subclass of: Restriction
  max cardinality: 1
  on property: dgidb evidence score
subclass of: Restriction
  min cardinality: 0
  on property: dgidb evidence score
subclass of: Restriction
  max cardinality: 1
  on property: dgidb interaction score
subclass of: Restriction
  all values from: integer
  on property: dgidb evidence score
subclass of: Restriction
  all values from: float
  on property: dgidb interaction score
subclass of: Restriction
  all values from: integer
  on property: evidence count
subclass of: chemical affects biological entity 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.)
in scheme: vocab

chemical entity assesses named thing association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: chemical entity
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: association
in scheme: vocab

chemical entity or gene or gene product regulates gene association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  all values from: chemical entity or gene or gene product
  on property: subject
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: association
definition: A regulatory relationship between two genes
in scheme: vocab

chemical entity to biological process association
type: Class
subclass of: Restriction
  all values from: biological process
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: organism taxon
  on property: species context qualifier
subclass of: Restriction
  all values from: chemical entity
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: species context qualifier
subclass of: Restriction
  all values from: string
  on property: anatomical context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: species context qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: anatomical context qualifier
subclass of: association
definition: An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process.
in scheme: vocab

chemical entity to chemical derivation association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: catalyst qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: macromolecular machine mixin
  on property: catalyst qualifier
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: chemical entity
  on property: object
subclass of: Restriction
  all values from: chemical entity
  on property: subject
subclass of: chemical entity to chemical entity 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
in scheme: vocab

chemical entity to disease or phenotypic feature association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: disease or phenotypic feature
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: clinical approval status
subclass of: Restriction
  max cardinality: 1
  on property: max research phase
subclass of: Restriction
  all values from: ResearchPhaseEnum
  on property: max research phase
subclass of: Restriction
  all values from: ClinicalApprovalStatusEnum
  on property: clinical approval status
subclass of: Restriction
  max cardinality: 1
  on property: clinical approval status
subclass of: Restriction
  min cardinality: 0
  on property: max research phase
subclass of: Restriction
  on property: mixins
  some values from: entity to disease or phenotypic feature association mixin
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: association
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.
in scheme: vocab
narrow match: SIO_000993

chemical entity to pathway association
type: Class
subclass of: Restriction
  all values from: pathway
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: chemical entity
  on property: subject
subclass of: association
definition: An interaction between a chemical entity and a biological process or pathway.
in scheme: vocab

chemical gene interaction association
type: Class
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: object part qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: anatomical context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object context qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  all values from: integer
  on property: dgidb evidence score
subclass of: Restriction
  min cardinality: 0
  on property: subject part qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object form or variant qualifier
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: object context qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: dgidb interaction score
subclass of: Restriction
  min cardinality: 0
  on property: dgidb evidence score
subclass of: Restriction
  max cardinality: 1
  on property: subject part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object part qualifier
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: object part qualifier
subclass of: Restriction
  all values from: ChemicalEntityDerivativeEnum
  on property: subject derivative qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  all values from: float
  on property: dgidb interaction score
subclass of: Restriction
  max cardinality: 1
  on property: object context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: dgidb evidence score
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: causal mechanism qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject context qualifier
subclass of: Restriction
  all values from: chemical entity
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: CausalMechanismQualifierEnum
  on property: causal mechanism qualifier
subclass of: Restriction
  min cardinality: 0
  on property: has affinity
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: object form or variant qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: object form or variant qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: subject context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: causal mechanism qualifier
subclass of: Restriction
  all values from: affinity measurement
  on property: has affinity
subclass of: Restriction
  min cardinality: 0
  on property: anatomical context qualifier
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: dgidb interaction score
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: subject part qualifier
subclass of: association
broad match: SIO_001257
definition: describes an 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)
in scheme: vocab

chemical or drug or treatment adverse event association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: FDAIDAAdverseEventEnum
  on property: FDA adverse event level
subclass of: Restriction
  min cardinality: 0
  on property: FDA adverse event level
subclass of: Restriction
  on property: mixins
  some values from: entity to feature or disease qualifiers mixin
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: FDA adverse event level
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: entity to disease or phenotypic feature association mixin
subclass of: association
definition: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an untoward medical occurrence that happens during treatment, whether or not considered related to the treatment.
in scheme: vocab

chemical or drug or treatment side effect association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: entity to feature or disease qualifiers mixin
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: entity to disease or phenotypic feature association mixin
subclass of: association
definition: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an unintended, but predictable, secondary effect of the treatment.
in scheme: vocab

chemical or drug or treatment to disease or phenotypic feature association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: entity to feature or disease qualifiers mixin
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: entity to disease or phenotypic feature association mixin
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: association
definition: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the chemical or treatment is used to treat, or is being studied to treat, the disease or phenotypic feature.
in scheme: vocab

analog_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: modified_form

dominant_negative_variant_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: non_loss_of_function_variant_form

gain_of_function_variant_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: non_loss_of_function_variant_form

loss_of_function_variant_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: genetic_variant_form

mutant_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: genetic_variant_form

snp_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: polymorphic_form

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

fda_approved_for_condition
type: Class
subclass of: ClinicalApprovalStatusEnum
subclass of: approved_for_condition

not_provided
type: Class
subclass of: ClinicalApprovalStatusEnum
subclass of: PermissibleValue

off_label_use
type: Class
subclass of: ClinicalApprovalStatusEnum
subclass of: not_approved_for_condition

post_approval_withdrawal
type: Class
subclass of: ClinicalApprovalStatusEnum
subclass of: not_approved_for_condition

clinical finding
type: Class
subclass of: Restriction
  all values from: clinical attribute
  on property: has attribute
subclass of: Restriction
  min cardinality: 0
  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.
in scheme: vocab

clinical measurement
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: has attribute type
subclass of: Restriction
  all values from: Thing
  on property: has attribute type
subclass of: Restriction
  max cardinality: 1
  on property: has attribute type
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.
in scheme: vocab

adult
type: Class
subclass of: ClinicalTrialAgeStageEnum
subclass of: PermissibleValue

child
type: Class
subclass of: ClinicalTrialAgeStageEnum
subclass of: PermissibleValue

older_adult
type: Class
subclass of: ClinicalTrialAgeStageEnum
subclass of: PermissibleValue

ACTIVE_NOT_RECRUITING
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

APPROVED_FOR_MARKETING
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

AVAILABLE
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

COMPLETED
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

ENROLLING_BY_INVITATION
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

NOT_YET_RECRUITING
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

NO_LONGER_AVAILABLE
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

RECRUITING
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

SUSPENDED
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

TEMPORARILY_NOT_AVAILABLE
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

TERMINATED
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

UNKNOWN
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

WITHDRAWN
type: Class
subclass of: ClinicalTrialStatusEnum
subclass of: PermissibleValue

cohort
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: study population
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.
in scheme: vocab
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)
in scheme: vocab

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

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.
in scheme: vocab

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

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

contributor association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: Thing
  on property: qualifiers
subclass of: Restriction
  all values from: information content entity
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: agent
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: qualifiers
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: association
definition: Any association between an entity (such as a publication) and various agents that contribute to its realisation
in scheme: vocab

correlated gene to disease association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: string
  on property: subject form or variant qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: disease
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: allelic requirement
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: diseases confidence score
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: z score
subclass of: Restriction
  all values from: float
  on property: z score
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: allelic requirement
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  on property: mixins
  some values from: gene to entity association mixin
subclass of: Restriction
  all values from: Datatype
    intersection of: string
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^HP:\d{7}$
  on property: allelic requirement
subclass of: Restriction
  min cardinality: 0
  on property: diseases confidence score
subclass of: Restriction
  max cardinality: 1
  on property: z score
subclass of: Restriction
  all values from: float
  on property: diseases confidence score
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: association
in scheme: vocab

downregulated
type: Class
subclass of: DirectionQualifierEnum
subclass of: decreased

upregulated
type: Class
subclass of: DirectionQualifierEnum
subclass of: increased

disease associated with response to chemical entity association
type: Class
subclass of: Restriction
  all values from: ResponseEnum
  on property: response context qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: chemical entity
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: response context qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: disease
  on property: subject
subclass of: Restriction
  all values from: ResponseTargetEnum
  on property: response target context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: response context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: response target context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: response target context qualifier
subclass of: association
definition: A statistical association between a disease and a chemical entity where the chemical entity has a therapeutic or adverse effect on the disease progression, symptoms or outcomes in a patient, cell line, or any model system.
in scheme: vocab

disease or phenotypic feature exposure
type: Class
subclass of: Restriction
  on property: mixins
  some values from: pathological entity mixin
subclass of: exposure event
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.
in scheme: vocab

disease or phenotypic feature to genetic inheritance association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: disease or phenotypic feature to entity association mixin
subclass of: Restriction
  all values from: genetic inheritance
  on property: object
subclass of: association
definition: An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.
in scheme: vocab

disease or phenotypic feature to location association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: disease or phenotypic feature to entity association mixin
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: association
definition: An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.
in scheme: vocab

disease to exposure event association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: entity to exposure event association mixin
subclass of: Restriction
  on property: mixins
  some values from: disease to entity association mixin
subclass of: association
definition: An association between an exposure event and a disease.
in scheme: vocab

disease to phenotypic feature association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: onset
  on property: onset qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: disease
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: onset qualifier
subclass of: Restriction
  on property: mixins
  some values from: frequency quantifier
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: Restriction
  max cardinality: 1
  on property: onset qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: disease to entity association mixin
subclass of: Restriction
  all values from: phenotypic feature
  on property: object
subclass of: association
definition: An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.
in scheme: vocab

over_the_counter
type: Class
subclass of: DrugAvailabilityEnum
subclass of: PermissibleValue

prescription
type: Class
subclass of: DrugAvailabilityEnum
subclass of: PermissibleValue

absorption_through_the_skin
type: Class
subclass of: DrugDeliveryEnum
subclass of: PermissibleValue

inhalation
type: Class
subclass of: DrugDeliveryEnum
subclass of: PermissibleValue

intramuscular_injection
type: Class
subclass of: DrugDeliveryEnum
subclass of: injection

intravenous_injection
type: Class
subclass of: DrugDeliveryEnum
subclass of: injection

oral
type: Class
subclass of: DrugDeliveryEnum
subclass of: PermissibleValue

subcutaneous_injection
type: Class
subclass of: DrugDeliveryEnum
subclass of: injection

drug label
type: Class
subclass of: publication
broad match: C41203
definition: a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc.
in scheme: vocab

drug to entity association mixin
type: Class
subclass of: chemical entity to entity association mixin
definition: An interaction between a drug and another entity
in scheme: vocab

drug to gene association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: drug to entity association mixin
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: association
definition: An interaction between a drug and a gene or gene product.
in scheme: vocab
related match: SIO_001257

drug to gene interaction exposure
type: Class
subclass of: Restriction
  on property: mixins
  some values from: gene grouping mixin
subclass of: drug exposure
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.
in scheme: vocab

tbio
type: Class
subclass of: DruggableGeneCategoryEnum
subclass of: PermissibleValue

tchem
type: Class
subclass of: DruggableGeneCategoryEnum
subclass of: PermissibleValue

tclin
type: Class
subclass of: DruggableGeneCategoryEnum
subclass of: PermissibleValue

tdark
type: Class
subclass of: DruggableGeneCategoryEnum
subclass of: PermissibleValue

druggable gene to disease association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: druggable gene category
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: druggable gene category
subclass of: Restriction
  on property: mixins
  some values from: gene to entity association mixin
subclass of: Restriction
  all values from: DruggableGeneCategoryEnum
  on property: druggable gene category
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: gene to disease association
in scheme: vocab

entity to disease association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: number of cases
subclass of: Restriction
  max cardinality: 1
  on property: max research phase
subclass of: Restriction
  all values from: ResearchPhaseEnum
  on property: max research phase
subclass of: Restriction
  min cardinality: 0
  on property: FDA regulatory approvals
subclass of: Restriction
  min cardinality: 0
  on property: clinical approval status
subclass of: Restriction
  all values from: string
  on property: FDA regulatory approvals
subclass of: Restriction
  min cardinality: 0
  on property: number of cases
subclass of: Restriction
  min cardinality: 0
  on property: max research phase
subclass of: Restriction
  max cardinality: 1
  on property: clinical approval status
subclass of: Restriction
  all values from: string
  on property: number of cases
subclass of: Restriction
  all values from: ClinicalApprovalStatusEnum
  on property: clinical approval status
subclass of: association
in scheme: vocab

entity to exposure event association mixin
type: Class
subclass of: Mixin
definition: An association between some entity and an exposure event.
in scheme: vocab

entity to outcome association mixin
type: Class
subclass of: Mixin
definition: An association between some entity and an outcome
in scheme: vocab

entity to phenotypic feature association
type: Class
subclass of: Restriction
  all values from: string
  on property: FDA regulatory approvals
subclass of: Restriction
  max cardinality: 1
  on property: clinical approval status
subclass of: Restriction
  all values from: ClinicalApprovalStatusEnum
  on property: clinical approval status
subclass of: Restriction
  min cardinality: 0
  on property: clinical approval status
subclass of: Restriction
  min cardinality: 0
  on property: max research phase
subclass of: Restriction
  max cardinality: 1
  on property: number of cases
subclass of: Restriction
  all values from: ResearchPhaseEnum
  on property: max research phase
subclass of: Restriction
  max cardinality: 1
  on property: max research phase
subclass of: Restriction
  min cardinality: 0
  on property: number of cases
subclass of: Restriction
  all values from: string
  on property: number of cases
subclass of: Restriction
  min cardinality: 0
  on property: FDA regulatory approvals
subclass of: association
in scheme: vocab

environmental feature
type: Class
subclass of: planetary entity
in scheme: vocab

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

environmental process
type: Class
subclass of: Restriction
  on property: mixins
  some values from: occurrent
subclass of: planetary entity
in scheme: vocab

epigenomic entity
type: Class
subclass of: Mixin
in scheme: vocab

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

evidence
type: Class
subclass of: information content entity
definition: Dereferences detailed evidence that supports an association
in scheme: vocab

exon to transcript relationship
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: exon
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: transcript
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: sequence feature relationship
definition: A transcript is formed from multiple exons
in scheme: vocab

exposure event to outcome association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: entity to outcome association mixin
subclass of: Restriction
  max cardinality: 1
  on property: temporal context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: population context qualifier
subclass of: Restriction
  all values from: population of individual organisms
  on property: population context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: population context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: temporal context qualifier
subclass of: Restriction
  all values from: string
  on property: temporal context qualifier
subclass of: association
definition: An association between an exposure event and an outcome.
in scheme: vocab

exposure event to phenotypic feature association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: exposure event
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: association
definition: Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.
in scheme: vocab

life_threatening_adverse_event
type: Class
subclass of: FDAIDAAdverseEventEnum
subclass of: PermissibleValue

serious_adverse_event
type: Class
subclass of: FDAIDAAdverseEventEnum
subclass of: PermissibleValue

suspected_adverse_reaction
type: Class
subclass of: FDAIDAAdverseEventEnum
subclass of: PermissibleValue

unexpected_adverse_event
type: Class
subclass of: FDAIDAAdverseEventEnum
subclass of: PermissibleValue

feature or disease qualifiers to entity mixin
type: Class
subclass of: frequency qualifier mixin
definition: Qualifiers for disease or phenotype to entity associations.
in scheme: vocab

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

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

fungus
type: Class
subclass of: cellular organism
definition: A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).
in scheme: vocab
narrow match: FOODON_03315605
narrow match: NCBITaxon_1670606

gene affects chemical association
type: Class
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: subject part qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  all values from: string
  on property: subject derivative qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object part qualifier
subclass of: Restriction
  min cardinality: 0
  on property: species context qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: subject context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: causal mechanism qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object part qualifier
subclass of: Restriction
  min cardinality: 0
  on property: anatomical context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object derivative qualifier
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  all values from: organism taxon
  on property: species context qualifier
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject direction qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: subject context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object context qualifier
subclass of: Restriction
  all values from: CausalMechanismQualifierEnum
  on property: causal mechanism qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: anatomical context qualifier
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: object form or variant qualifier
subclass of: Restriction
  all values from: chemical entity
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: object context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object form or variant qualifier
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: object part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: species context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object context qualifier
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: causal mechanism qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: ChemicalEntityDerivativeEnum
  on property: object derivative qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: object form or variant qualifier
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: subject form or variant qualifier
subclass of: association
definition: Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)
in scheme: vocab

gene as a model of disease association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: model to disease association mixin
subclass of: gene to disease association
in scheme: vocab

gene family to gene or gene product or gene family association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: gene family
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene
  on property: subject
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: association
definition: Relationship between a gene family and a contained gene or gene product or gene family.
in scheme: vocab

gene has variant that contributes to disease association
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: string
  on property: subject form or variant qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: disease
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: gene to disease association
in scheme: vocab

ADP-ribosylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

absorption
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

acetylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

activity
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: activity_or_abundance

acylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

adenyl_nucleotide_exchange
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_interaction

aggregation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

alkylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

amination
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

carbamoylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

carboxylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

degradation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

ethylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

expression
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: abundance

farnesylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

folding
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

geranoylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

glucuronidation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

glutathionylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

glycation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

glycosylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

guanyl_nucleotide_exchange
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_interaction

hydrolysis
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: cleavage

hydroxylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

interaction
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

isomerization
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

lipidation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

localization
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

metabolic_processing
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

methylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

mutation_rate
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

myristoylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

n_linked_glycosylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

nitrosation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

nucleotidylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

o_linked_glycosylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

oxidation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

palmitoylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

phosphorylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

prenylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

reduction
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

release
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

ribosylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

secretion
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: transport

splicing
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

stability
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

sulfation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

sumoylation
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

synthesis
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: abundance

ubiquitination
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: molecular_modification

uptake
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: transport

3_prime_utr
type: Class
subclass of: GeneOrGeneProductOrChemicalPartQualifierEnum
subclass of: PermissibleValue

5_prime_utr
type: Class
subclass of: GeneOrGeneProductOrChemicalPartQualifierEnum
subclass of: PermissibleValue

enhancer
type: Class
subclass of: GeneOrGeneProductOrChemicalPartQualifierEnum
subclass of: PermissibleValue

exon
type: Class
subclass of: GeneOrGeneProductOrChemicalPartQualifierEnum
subclass of: PermissibleValue

intron
type: Class
subclass of: GeneOrGeneProductOrChemicalPartQualifierEnum
subclass of: PermissibleValue

polya_tail
type: Class
subclass of: GeneOrGeneProductOrChemicalPartQualifierEnum
subclass of: PermissibleValue

promoter
type: Class
subclass of: GeneOrGeneProductOrChemicalPartQualifierEnum
subclass of: PermissibleValue

gene or gene product or gene family to anatomical entity association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: gene or gene product or gene family
  on property: subject
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: association
definition: An association between a gene or gene product or gene family and an anatomical entity.
in scheme: vocab

gene or gene product or gene family to biological process or activity association
type: Class
subclass of: Restriction
  all values from: biological process or activity
  on property: object
subclass of: Restriction
  all values from: gene or gene product or gene family
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: association
definition: Relationship between a gene or gene product or gene family to a specified biological process or activity (e.g. molecular activity, biological process or pathway).
in scheme: vocab

gene regulates gene association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: species context qualifier
subclass of: Restriction
  all values from: organism taxon
  on property: species context qualifier
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: species context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: object aspect qualifier
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: association
definition: Describes a regulatory relationship between two genes or gene products.
in scheme: vocab

biolink:associated_with
type: Class
subclass of: GeneToDiseasePredicateEnum
subclass of: PermissibleValue

biolink:contributes_to
type: Class
subclass of: GeneToDiseasePredicateEnum
subclass of: PermissibleValue

gene to expression site association
type: Class
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: stage qualifier
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: stage qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object specialization qualifier
subclass of: Restriction
  all values from: life stage
  on property: stage qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: object specialization qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: quantifier qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: ontology class
  on property: quantifier qualifier
subclass of: Restriction
  max cardinality: 1
  on property: quantifier qualifier
subclass of: Restriction
  all values from: anyURI
  on property: object specialization 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?
in scheme: vocab

gene to gene coexpression association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: gene expression mixin
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: gene to gene association
definition: Indicates that two genes are co-expressed, generally under the same conditions.
in scheme: vocab

gene to gene family association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: gene
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: gene family
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
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.
in scheme: vocab

gene to gene homology association
type: Class
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
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)
in scheme: vocab

gene to gene product relationship
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene
  on property: subject
subclass of: Restriction
  all values from: gene product mixin
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: sequence feature relationship
definition: A gene is transcribed and potentially translated to a gene product
in scheme: vocab

gene to go term association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: ontology class
  on property: object
subclass of: Restriction
  all values from: gene
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: functional association
alternative label: functional association
in scheme: vocab

gene to pathway association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: gene to entity association mixin
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: pathway
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: association
definition: An interaction between a gene or gene product and a biological process or pathway.
in scheme: vocab

gene to phenotypic feature association
type: Class
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: phenotypic feature
  on property: object
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: subject form or variant qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: Restriction
  all values from: GeneToPhenotypicFeaturePredicateEnum
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: allelic requirement
subclass of: Restriction
  all values from: Datatype
    intersection of: string
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^HP:\d{7}$
  on property: allelic requirement
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  on property: mixins
  some values from: gene to entity association mixin
subclass of: Restriction
  max cardinality: 1
  on property: allelic requirement
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: association
in scheme: vocab
narrow match: SIO_000983
narrow match: DiseaseGeneAssociation
note: NCIT:R176 refers to the inverse relationship
note: for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype
note: if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.

biolink:associated_with
type: Class
subclass of: GeneToPhenotypicFeaturePredicateEnum
subclass of: PermissibleValue

biolink:causes
type: Class
subclass of: GeneToPhenotypicFeaturePredicateEnum
subclass of: PermissibleValue

biolink:contributes_to
type: Class
subclass of: GeneToPhenotypicFeaturePredicateEnum
subclass of: PermissibleValue

biolink:has_phenotype
type: Class
subclass of: GeneToPhenotypicFeaturePredicateEnum
subclass of: PermissibleValue

genome
type: Class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: biological entity
definition: A genome is the sum of genetic material within a cell or virion.
in scheme: vocab

genomic background exposure
type: Class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  on property: mixins
  some values from: gene grouping mixin
subclass of: Restriction
  on property: mixins
  some values from: thing with taxon
subclass of: exposure event
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.
in scheme: vocab

genotype as a model of disease association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: genotype
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: model to disease association mixin
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: genotype to disease association
in scheme: vocab

genotype to gene association
type: Class
subclass of: Restriction
  all values from: genotype
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
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
in scheme: vocab

genotype to genotype part association
type: Class
subclass of: Restriction
  all values from: genotype
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: genotype
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: association
definition: Any association between one genotype and a genotypic entity that is a sub-component of it
in scheme: vocab

genotype to phenotypic feature association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: genotype
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: genotype to entity association mixin
subclass of: association
definition: Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment
in scheme: vocab

genotype to variant association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: genotype
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: sequence variant
  on property: object
subclass of: association
definition: Any association between a genotype and a sequence variant.
in scheme: vocab

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.
in scheme: vocab

geographic exposure
type: Class
subclass of: environmental exposure
definition: A geographic exposure is a factor relating to geographic proximity to some impactful entity.
in scheme: vocab
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 cardinality: 1
  on property: timepoint
subclass of: Restriction
  min cardinality: 0
  on property: timepoint
subclass of: Restriction
  all values from: string
  on property: timepoint
subclass of: geographic location
definition: a location that can be described in lat/long coordinates, for a particular time
in scheme: vocab

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

haplotype
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: biological entity
definition: A set of zero or more Alleles on a single instance of a Sequence[VMC]
in scheme: vocab

hospitalization
type: Class
subclass of: clinical intervention
in scheme: vocab

human
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: mammal
definition: A member of the the species Homo sapiens.
in scheme: vocab

icees study result
type: Class
subclass of: Restriction
  all values from: integer
  on property: chi squared dof
subclass of: Restriction
  all values from: float
  on property: fisher exact odds ratio
subclass of: Restriction
  all values from: float
  on property: log odds ratio 95 ci
subclass of: Restriction
  all values from: float
  on property: fisher exact p
subclass of: Restriction
  min cardinality: 0
  on property: fisher exact p
subclass of: Restriction
  max cardinality: 1
  on property: chi squared statistic
subclass of: Restriction
  min cardinality: 0
  on property: chi squared p
subclass of: Restriction
  min cardinality: 0
  on property: log odds ratio
subclass of: Restriction
  all values from: float
  on property: chi squared p
subclass of: Restriction
  all values from: float
  on property: log odds ratio
subclass of: Restriction
  max cardinality: 1
  on property: fisher exact p
subclass of: Restriction
  all values from: integer
  on property: total sample size
subclass of: Restriction
  max cardinality: 1
  on property: chi squared p
subclass of: Restriction
  min cardinality: 0
  on property: chi squared statistic
subclass of: Restriction
  max cardinality: 1
  on property: log odds ratio
subclass of: Restriction
  max cardinality: 1
  on property: total sample size
subclass of: Restriction
  all values from: float
  on property: chi squared statistic
subclass of: Restriction
  min cardinality: 0
  on property: chi squared dof
subclass of: Restriction
  max cardinality: 1
  on property: fisher exact odds ratio
subclass of: Restriction
  min cardinality: 0
  on property: fisher exact odds ratio
subclass of: Restriction
  max cardinality: 1
  on property: chi squared dof
subclass of: Restriction
  min cardinality: 0
  on property: total sample size
subclass of: Restriction
  min cardinality: 0
  on property: log odds ratio 95 ci
subclass of: study result
definition: A study result that represents a result, from a supporting Study, which is specifically associated with an Integrated Clinical and Environmental Exposures Service (ICEES) knowledge assertion.
in scheme: vocab

information content entity to named thing association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: Thing
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
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).
in scheme: vocab

invertebrate
type: Class
subclass of: cellular organism
definition: An animal lacking a vertebral column. This group consists of 98% of all animal species.
in scheme: vocab
related match: NCBITaxon_1767184

journal article
type: Class
subclass of: article
definition: an article, typically presenting results of research, that is published in an issue of a scientific journal.
in scheme: vocab

knowledge_assertion
type: Class
subclass of: KnowledgeLevelEnum
subclass of: PermissibleValue

logical_entailment
type: Class
subclass of: KnowledgeLevelEnum
subclass of: PermissibleValue

not_provided
type: Class
subclass of: KnowledgeLevelEnum
subclass of: PermissibleValue

observation
type: Class
subclass of: KnowledgeLevelEnum
subclass of: PermissibleValue

prediction
type: Class
subclass of: KnowledgeLevelEnum
subclass of: PermissibleValue

statistical_association
type: Class
subclass of: KnowledgeLevelEnum
subclass of: PermissibleValue

text_co_occurrence
type: Class
subclass of: KnowledgeLevelEnum
subclass of: PermissibleValue

log odds analysis result
type: Class
subclass of: study result
definition: A result of a log odds ratio analysis.
in scheme: vocab

inverse_all_some
type: Class
subclass of: LogicalInterpretationEnum
subclass of: PermissibleValue

macromolecular complex
type: Class
subclass of: Restriction
  on property: mixins
  some values from: macromolecular machine mixin
subclass of: biological entity
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.
in scheme: vocab

macromolecular machine has substrate association
type: Class
subclass of: Restriction
  all values from: chemical entity or protein or polypeptide
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: macromolecular machine mixin
  on property: subject
subclass of: association
definition: Describes the relationship between an enzyme (usually a macromolecular complex or gene product) and the molecules it acts on (substrate). The substrate can be a chemical, a polypeptide, or a protein.
editorial note: Using macromolecular machine should cover cases of gene-protein conflation.
in scheme: vocab

macromolecular machine to biological process association
type: Class
subclass of: Restriction
  all values from: biological process
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: macromolecular machine to entity association mixin
subclass of: functional association
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.
in scheme: vocab

macromolecular machine to cellular component association
type: Class
subclass of: Restriction
  all values from: cellular component
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: macromolecular machine to entity association mixin
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: functional association
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.
in scheme: vocab

macromolecular machine to molecular activity association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: macromolecular machine to entity association mixin
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: molecular activity
  on property: object
subclass of: functional association
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.
in scheme: vocab

material sample derivation association
type: Class
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  all values from: material sample
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: association
definition: An association between a material sample and the material entity from which it is derived.
in scheme: vocab

material sample to disease or phenotypic feature association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: entity to disease or phenotypic feature association mixin
subclass of: Restriction
  on property: mixins
  some values from: material sample to entity association mixin
subclass of: association
definition: An association between a material sample and a disease or phenotype.
in scheme: vocab

material sample to entity association mixin
type: Class
subclass of: Mixin
definition: An association between a material sample and something.
in scheme: vocab

microRNA
type: Class
subclass of: noncoding RNA product
in scheme: vocab

molecular activity to chemical entity association
type: Class
subclass of: Restriction
  all values from: chemical entity
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: molecular activity
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
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
in scheme: vocab

molecular activity to molecular activity association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: molecular activity
  on property: object
subclass of: Restriction
  all values from: molecular activity
  on property: subject
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
in scheme: vocab

molecular activity to pathway association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: molecular activity
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: pathway
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: association
definition: Association that holds the relationship between a reaction and the pathway it participates in.
in scheme: vocab

named thing associated with likelihood of named thing association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: object context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: population context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject context qualifier
subclass of: Restriction
  all values from: ontology class
  on property: object context qualifier
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  all values from: string
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: population of individual organisms
  on property: population context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  all values from: ontology class
  on property: subject context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: population context qualifier
subclass of: association
in scheme: vocab

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.
in scheme: vocab

nucleosome modification
type: Class
subclass of: Restriction
  on property: mixins
  some values from: epigenomic entity
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: gene product isoform mixin
subclass of: biological 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.
in scheme: vocab

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

organism taxon to environment association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: organism taxon
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: organism taxon to entity association
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: Thing
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: association
in scheme: vocab

organism taxon to organism taxon interaction
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: associated environmental context
subclass of: Restriction
  min cardinality: 0
  on property: associated environmental context
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: organism taxon
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: associated environmental context
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: organism taxon
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
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
in scheme: vocab

organism taxon to organism taxon specialization
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: organism taxon
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: organism taxon
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: organism taxon to organism taxon association
definition: A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo
in scheme: vocab

organism to organism association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: individual organism
  on property: subject
subclass of: Restriction
  all values from: individual organism
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: association
in scheme: vocab

organismal entity as a model of disease association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: organismal entity
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: model to disease association mixin
subclass of: association
in scheme: vocab

pairwise molecular interaction
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: molecular entity
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: interacting molecules category
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: ontology class
  on property: interacting molecules category
subclass of: Restriction
  max cardinality: 1
  on property: interacting molecules category
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  all values from: molecular entity
  on property: object
subclass of: pairwise gene to gene interaction
definition: An interaction at the molecular level between two physical entities
in scheme: vocab

patent
type: Class
subclass of: publication
definition: a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time.
in scheme: vocab

pathological anatomical exposure
type: Class
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.
in scheme: vocab

pathological anatomical structure
type: Class
subclass of: Restriction
  on property: mixins
  some values from: pathological entity mixin
subclass of: anatomical entity
definition: An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.
in scheme: vocab

pathological process
type: Class
subclass of: Restriction
  on property: mixins
  some values from: pathological entity mixin
subclass of: biological process
definition: A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.
in scheme: vocab
narrow match: T037
narrow match: T046
narrow match: NCIT C19151
narrow match: EFO_0009708

pathological process exposure
type: Class
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.
in scheme: vocab

0
type: Class
subclass of: PhaseEnum
subclass of: PermissibleValue

1
type: Class
subclass of: PhaseEnum
subclass of: PermissibleValue

2
type: Class
subclass of: PhaseEnum
subclass of: PermissibleValue

phenomenon
type: Class
subclass of: Restriction
  on property: mixins
  some values from: occurrent
subclass of: named thing
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
in scheme: vocab
narrow match: T034
narrow match: T038
narrow match: T069

phenotypic feature to disease association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: phenotypic feature to entity association mixin
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: association
in scheme: vocab

phenotypic feature to phenotypic feature association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: Restriction
  on property: mixins
  some values from: phenotypic feature to entity association mixin
subclass of: association
definition: Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.
in scheme: vocab

phenotypic quality
type: Class
subclass of: organism attribute
alternative label: phenotypic properties
definition: A property of a phenotype
in scheme: vocab
mapping relation: PATO_0000001

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.
in scheme: vocab

physiological process
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: biological process
alternative label: physiology
in scheme: vocab
narrow match: T040
narrow match: T042
narrow match: T043
narrow match: T045

plant
type: Class
subclass of: cellular organism
in scheme: vocab

population to population association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: population of individual organisms
  on property: subject
subclass of: Restriction
  all values from: population of individual organisms
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: association
definition: An association between a two populations
in scheme: vocab

posttranslational modification
type: Class
subclass of: Restriction
  on property: mixins
  some values from: gene product isoform mixin
subclass of: biological entity
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.
in scheme: vocab

predicate mapping
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object derivative qualifier
subclass of: Restriction
  min cardinality: 0
  on property: broad match
subclass of: Restriction
  min cardinality: 0
  on property: subject derivative qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject context qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object form or variant qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: species context qualifier
subclass of: Restriction
  all values from: string
  on property: object aspect qualifier
subclass of: Restriction
  all values from: Thing
  on property: narrow match
subclass of: Restriction
  all values from: string
  on property: mapped predicate
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: causal mechanism qualifier
subclass of: Restriction
  all values from: Thing
  on property: broad match
subclass of: Restriction
  max cardinality: 1
  on property: mapped predicate
subclass of: Restriction
  all values from: string
  on property: subject context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: broad match
subclass of: Restriction
  all values from: string
  on property: object form or variant qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object context qualifier
subclass of: Restriction
  all values from: CausalMechanismQualifierEnum
  on property: causal mechanism qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: causal mechanism qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  all values from: Thing
  on property: exact match
subclass of: Restriction
  min cardinality: 0
  on property: exact match
subclass of: Restriction
  max cardinality: 1
  on property: object context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: object context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  all values from: string
  on property: object part qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: exact match
subclass of: Restriction
  min cardinality: 0
  on property: mapped predicate
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: narrow match
subclass of: Restriction
  all values from: string
  on property: object derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: narrow match
subclass of: Restriction
  min cardinality: 0
  on property: object derivative qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object part qualifier
subclass of: Restriction
  all values from: string
  on property: anatomical context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  all values from: organism taxon
  on property: species context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: species context qualifier
subclass of: Restriction
  all values from: string
  on property: subject part qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  all values from: string
  on property: subject derivative qualifier
subclass of: Restriction
  all values from: string
  on property: subject form or variant qualifier
subclass of: Restriction
  min cardinality: 0
  on property: anatomical context qualifier
subclass of: ClassDefinition
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.
in scheme: vocab

preprint publication
type: Class
subclass of: publication
definition: a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal.
in scheme: vocab

process regulates process association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: biological process
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: biological process
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: association
definition: Describes a regulatory relationship between two genes or gene products.
in scheme: vocab

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.
in scheme: vocab

protein domain
type: Class
subclass of: Restriction
  on property: mixins
  some values from: gene grouping mixin
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: biological entity
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.
in scheme: vocab

protein family
type: Class
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: Restriction
  on property: mixins
  some values from: gene grouping mixin
subclass of: biological entity
in scheme: vocab
narrow match: NCIT C20130
narrow match: SIO_001380
narrow match: Q417841

protein isoform
type: Class
subclass of: Restriction
  on property: mixins
  some values from: 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/
in scheme: vocab

RNA product isoform
type: Class
subclass of: Restriction
  on property: mixins
  some values from: gene product isoform mixin
subclass of: RNA product
definition: Represents a protein that is a specific isoform of the canonical or reference RNA
in scheme: vocab

bidirectional
type: Class
subclass of: ReactionDirectionEnum
subclass of: PermissibleValue

left_to_right
type: Class
subclass of: ReactionDirectionEnum
subclass of: PermissibleValue

neutral
type: Class
subclass of: ReactionDirectionEnum
subclass of: PermissibleValue

right_to_left
type: Class
subclass of: ReactionDirectionEnum
subclass of: PermissibleValue

left
type: Class
subclass of: ReactionSideEnum
subclass of: PermissibleValue

right
type: Class
subclass of: ReactionSideEnum
subclass of: PermissibleValue

reaction to catalyst association
type: Class
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: reaction to participant association
in scheme: vocab

reagent targeted gene
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: biological entity
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.
in scheme: vocab

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

clinical_trial_phase_1
type: Class
subclass of: ResearchPhaseEnum
subclass of: clinical_trial_phase

clinical_trial_phase_1_to_2
type: Class
subclass of: ResearchPhaseEnum
subclass of: clinical_trial_phase

clinical_trial_phase_2
type: Class
subclass of: ResearchPhaseEnum
subclass of: clinical_trial_phase

clinical_trial_phase_2_to_3
type: Class
subclass of: ResearchPhaseEnum
subclass of: clinical_trial_phase

clinical_trial_phase_3
type: Class
subclass of: ResearchPhaseEnum
subclass of: clinical_trial_phase

clinical_trial_phase_4
type: Class
subclass of: ResearchPhaseEnum
subclass of: clinical_trial_phase

not_provided
type: Class
subclass of: ResearchPhaseEnum
subclass of: PermissibleValue

pre_clinical_research_phase
type: Class
subclass of: ResearchPhaseEnum
subclass of: PermissibleValue

aggregator_knowledge_source
type: Class
subclass of: ResourceRoleEnum
subclass of: PermissibleValue

primary_knowledge_source
type: Class
subclass of: ResourceRoleEnum
subclass of: PermissibleValue

supporting_data_source
type: Class
subclass of: ResourceRoleEnum
subclass of: PermissibleValue

negative
type: Class
subclass of: ResponseEnum
subclass of: PermissibleValue

therapeutic_response
type: Class
subclass of: ResponseEnum
subclass of: PermissibleValue

cell line
type: Class
subclass of: ResponseTargetEnum
subclass of: PermissibleValue

cohort
type: Class
subclass of: ResponseTargetEnum
subclass of: PermissibleValue

individual
type: Class
subclass of: ResponseTargetEnum
subclass of: PermissibleValue

sample
type: Class
subclass of: ResponseTargetEnum
subclass of: PermissibleValue

aa
type: Class
subclass of: SequenceEnum
subclass of: PermissibleValue

na
type: Class
subclass of: SequenceEnum
subclass of: PermissibleValue

sequence variant modulates treatment association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: treatment
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: sequence variant
  on property: subject
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.
in scheme: vocab
note: An alternate way to model the same information could be via a qualifier

serial
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: issue
subclass of: Restriction
  max cardinality: 1
  on property: volume
subclass of: Restriction
  min cardinality: 0
  on property: volume
subclass of: Restriction
  all values from: string
  on property: issue
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: Restriction
  all values from: string
  on property: type
subclass of: Restriction
  min cardinality: 0
  on property: issue
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  all values from: string
  on property: volume
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  all values from: string
  on property: iso abbreviation
subclass of: Restriction
  min cardinality: 0
  on property: iso abbreviation
subclass of: Restriction
  max cardinality: 1
  on property: iso abbreviation
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.
in scheme: vocab

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.
in scheme: vocab

small molecule
type: Class
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).
in scheme: vocab
narrow match: T109
narrow match: T110
narrow match: T111
narrow match: T115
narrow match: T118
narrow match: T119
narrow match: T124
narrow match: T125
narrow match: T127
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
in scheme: vocab

socioeconomic exposure
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: has attribute
subclass of: Restriction
  all values from: socioeconomic attribute
  on property: has 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).
in scheme: vocab

specificity quantifier
type: Class
subclass of: relationship quantifier
in scheme: vocab

+
type: Class
subclass of: StrandEnum
subclass of: PermissibleValue

-
type: Class
subclass of: StrandEnum
subclass of: PermissibleValue

.
type: Class
subclass of: StrandEnum
subclass of: PermissibleValue

?
type: Class
subclass of: StrandEnum
subclass of: PermissibleValue

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

taxon to taxon association
type: Class
subclass of: Restriction
  all values from: organism taxon
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: organism taxon
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: association
in scheme: vocab

taxonomic rank
type: Class
subclass of: ontology class
definition: A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)
in scheme: vocab
mapping relation: Q427626

text mining study result
type: Class
subclass of: Restriction
  all values from: string
  on property: supporting text
subclass of: Restriction
  max cardinality: 1
  on property: supporting text section type
subclass of: Restriction
  all values from: integer
  on property: supporting document year
subclass of: Restriction
  min cardinality: 0
  on property: subject location in text
subclass of: Restriction
  max cardinality: 1
  on property: supporting document type
subclass of: Restriction
  max cardinality: 1
  on property: extraction confidence score
subclass of: Restriction
  min cardinality: 0
  on property: supporting text
subclass of: Restriction
  all values from: integer
  on property: subject location in text
subclass of: Restriction
  all values from: string
  on property: supporting text section type
subclass of: Restriction
  all values from: integer
  on property: object location in text
subclass of: Restriction
  max cardinality: 1
  on property: supporting document year
subclass of: Restriction
  min cardinality: 0
  on property: supporting document type
subclass of: Restriction
  all values from: float
  on property: extraction confidence score
subclass of: Restriction
  min cardinality: 0
  on property: extraction confidence score
subclass of: Restriction
  min cardinality: 0
  on property: supporting document year
subclass of: Restriction
  min cardinality: 0
  on property: object location in text
subclass of: Restriction
  min cardinality: 0
  on property: supporting text section type
subclass of: Restriction
  all values from: string
  on property: supporting document type
subclass of: study result
definition: A study result that represents information extracted from text using natural language processing techniques. This includes the extracted text, location offsets within the source document, confidence scores, and other metadata related to the text mining process.
in scheme: vocab

transcript to gene relationship
type: Class
subclass of: Restriction
  all values from: transcript
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene
  on property: object
subclass of: sequence feature relationship
definition: A gene is a collection of transcripts
in scheme: vocab

transcription factor binding site
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: regulatory region
alternative label: binding site
alternative label: tf binding site
definition: A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription
in scheme: vocab

variant as a model of disease association
type: Class
subclass of: Restriction
  on property: mixins
  some values from: model to disease association mixin
subclass of: Restriction
  all values from: sequence variant
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: variant to disease association
in scheme: vocab

variant to gene expression association
type: Class
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: gene expression mixin
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: variant to gene association
definition: An association between a variant and expression of a gene (i.e. e-QTL)
in scheme: vocab

variant to phenotypic feature association
type: Class
subclass of: Restriction
  all values from: sequence variant
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to phenotypic feature association mixin
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: variant to entity association mixin
subclass of: association
in scheme: vocab

variant to population association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: has total
subclass of: Restriction
  on property: mixins
  some values from: variant to entity association mixin
subclass of: Restriction
  max cardinality: 1
  on property: has quotient
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: string
  on property: has quotient
subclass of: Restriction
  all values from: string
  on property: has count
subclass of: Restriction
  min cardinality: 0
  on property: has count
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: population of individual organisms
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: sequence variant
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: has quotient
subclass of: Restriction
  on property: mixins
  some values from: frequency qualifier mixin
subclass of: Restriction
  all values from: string
  on property: has total
subclass of: Restriction
  min cardinality: 0
  on property: has total
subclass of: Restriction
  max cardinality: 1
  on property: has count
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: frequency quantifier
subclass of: association
definition: An association between a variant and a population, where the variant has particular frequency in the population
in scheme: vocab

vertebrate
type: Class
subclass of: cellular organism
definition: A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.
in scheme: vocab
related match: NCBITaxon_2662825

virus
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: organismal entity
definition: A virus is a microorganism that replicates itself as a microRNA and infects the host cell.
in scheme: vocab

web page
type: Class
subclass of: publication
definition: a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features.
in scheme: vocab

actively involved in
type: ObjectProperty
domain: named thing
range: biological process or activity
sub property of: participates in
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
in scheme: vocab
narrow match: RO_0002503
narrow match: by means
narrow match: Orphanet_317348
narrow match: Orphanet_317349
narrow match: Orphanet_327767
canonical predicate: true

affiliation
type: DatatypeProperty
domain: agent
range: anyURI
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.
in scheme: vocab

aggregator knowledge source
type: DatatypeProperty
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"
in scheme: vocab

aspect qualifier
type: DatatypeProperty
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)
in scheme: vocab

authors
type: ObjectProperty
domain: publication
range: agent
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.
in scheme: vocab

available from
type: ObjectProperty
range: DrugAvailabilityEnum
sub property of: node property
in scheme: vocab

base coordinate
type: DatatypeProperty
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.
in scheme: vocab

catalyst qualifier
type: ObjectProperty
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.
in scheme: vocab

clinical trial age stage
type: ObjectProperty
domain: clinical trial
range: ClinicalTrialAgeStageEnum
sub property of: node property
definition: The age stage of a clinical trial as determined by clinicaltrials.gov (adult, child, older adult)
in scheme: vocab

clinical trial conditions
type: ObjectProperty
domain: clinical trial
range: disease or phenotypic feature
sub property of: node property
definition: connects a clinical trial to one or more conditions being studied in the trial
in scheme: vocab

clinical trial interventions
type: ObjectProperty
domain: clinical trial
range: clinical intervention
sub property of: node property
definition: connects a clinical trial to one or more interventions being tested in the trial
in scheme: vocab

contributes to
type: DatatypeProperty
sub property of: related to at instance level
definition: holds between two entities where the occurrence, existence, or activity of one contributes to the occurrence or generation of the other
in scheme: vocab
narrow match: marker mechanism
narrow match: MONDO predisposes towards
narrow match: RO_0002255
narrow match: RO_0003304
canonical predicate: true

derivative qualifier
type: DatatypeProperty
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’.
in scheme: vocab

derives from
type: DatatypeProperty
sub property of: related to at instance level
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
in scheme: vocab
narrow match: CHEBI has functional parent
narrow match: SNOMED has specimen source topography
canonical predicate: true

direction qualifier
type: DatatypeProperty
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’
in scheme: vocab

equivalent identifiers
type: DatatypeProperty
range: anyURI
definition: A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources.
in scheme: attributes

form or variant qualifier
type: DatatypeProperty
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’
in scheme: vocab

genetically associated with
type: DatatypeProperty
type: SymmetricProperty
sub property of: associated with
in scheme: vocab
canonical predicate: true
description: Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level

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.
in scheme: vocab
canonical predicate: true

has affinity
type: ObjectProperty
range: affinity measurement
sub property of: association slot
definition: Set of measurements documenting the strength of chemical entity to gene or gene product interactions.
in scheme: vocab

has chemical role
type: ObjectProperty
range: chemical role
sub property of: related to at concept level
definition: A role is particular behaviour which a chemical entity may exhibit.
in scheme: vocab
note: We expect primarily to use CHEBI chemical roles here; however, we are looking for a mapping between CHEBI And ATC codes to support this slot.

has device
type: ObjectProperty
range: device
sub property of: node property
definition: connects an entity to one or more (medical) devices
in scheme: vocab

has drug
type: ObjectProperty
range: drug
sub property of: node property
definition: connects an entity to one or more drugs
in scheme: vocab

has evidence
type: ObjectProperty
range: information content entity
sub property of: association slot
definition: Connects an association to detailed information providing supporting evidence.
in scheme: vocab

has evidence of type
type: ObjectProperty
range: evidence type
sub property of: association slot
definition: Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology.
in scheme: vocab

has food component
type: ObjectProperty
domain: chemical entity
range: chemical entity
sub property of: has part
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)
in scheme: vocab
canonical predicate: true

has gene
type: ObjectProperty
range: gene
sub property of: has gene or gene product
definition: connects an entity associated with one or more genes
in scheme: vocab

has procedure
type: ObjectProperty
range: procedure
sub property of: node property
definition: connects an entity to one or more (medical) procedures
in scheme: vocab

has study results
type: ObjectProperty
domain: study
range: study result
sub property of: association slot
definition: Connects an study to instances of its study result
in scheme: vocab

has supporting studies
type: ObjectProperty
range: study
sub property of: association slot
definition: Studies that produced information used as evidence to generate the knowledge expressed in an Association.
in scheme: vocab

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
in scheme: vocab

hgvs nomenclature
type: DatatypeProperty
domain: sequence variant
sub property of: node property
definition: HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued.
in scheme: vocab
note: For more information, please see: https://hgvs-nomenclature.org/stable/background/simple/ and examples: https://hgvs-nomenclature.org/stable/recommendations/summary/.

in preclinical trials for
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: studied to treat
sub property of: treats or applied or studied to treat
definition: Holds between an substance, procedure, or activity and a medical condition, and reports that a pre-clinical study has been performed specifically to test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).
in scheme: vocab
canonical predicate: true

interbase coordinate
type: DatatypeProperty
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.
in scheme: vocab

keywords
type: DatatypeProperty
domain: publication
sub property of: node property
definition: keywords tagging a publication
in scheme: vocab

likelihood affected by
type: DatatypeProperty
sub property of: related to at instance level
inverse of: affects likelihood of
in scheme: vocab

likelihood associated with
type: DatatypeProperty
sub property of: associated with
inverse of: associated with likelihood of
in scheme: vocab

located in
type: ObjectProperty
domain: named thing
range: named thing
sub property of: related to at instance level
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)
in scheme: vocab
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

log odds ratio 95 ci
type: DatatypeProperty
range: float
sub property of: association slot
definition: The ninety-five percent confidence range in which the true log odds ratio for the sample population falls. To calculate the 95% confidence interval (CI) for a log odds ratio (a pair of numbers), you need the standard error (SE) of the log odds ratio. This interval helps you understand the precision of your estimate and whether the association is statistically significant.
in scheme: vocab

manifestation of
type: ObjectProperty
range: disease
sub property of: related to at instance level
broad match: 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
in scheme: vocab
narrow match: SNOMED has definitional manifestation
canonical predicate: true

mesh terms
type: DatatypeProperty
domain: publication
range: anyURI
sub property of: node property
definition: mesh terms tagging a publication
in scheme: vocab

object category closure
type: ObjectProperty
domain: association
range: ontology class
sub property of: association slot
definition: Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

object closure
type: DatatypeProperty
domain: association
sub property of: association slot
definition: Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

object label closure
type: DatatypeProperty
domain: association
range: string
sub property of: association slot
definition: Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

object location in text
type: DatatypeProperty
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
in scheme: vocab

overlaps
type: DatatypeProperty
type: SymmetricProperty
sub property of: related to at instance level
definition: holds between entities that overlap in their extents (materials or processes)
in scheme: vocab
narrow match: BSPO_0005001
narrow match: RO_0002100
narrow match: RO_0002102
narrow match: RO_0002433
narrow match: overlaps with
canonical predicate: true

pages
type: DatatypeProperty
domain: publication
sub property of: node property
definition: page number of source referenced for statement or publication
in scheme: vocab

part qualifier
type: DatatypeProperty
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).
in scheme: vocab

physically interacts with
type: DatatypeProperty
type: SymmetricProperty
sub property of: interacts with
broad match: P129
definition: holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship.
in scheme: vocab
narrow match: drug-interaction
narrow match: FMA adheres to
narrow match: NCIT A7
narrow match: PR non-covalently bound to
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.
in scheme: vocab

provided by
type: DatatypeProperty
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.
in scheme: vocab

publication type
type: DatatypeProperty
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.
in scheme: vocab

publications
type: ObjectProperty
range: publication
sub property of: association slot
alternative label: 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.
in scheme: vocab
note: The notion of a ‘Publication’ is considered broadly to include any document made available for public consumption. It covers journal issues, individual articles, and books - and also things like article pre-prints, white papers, patents, drug labels, web pages, protocol documents, etc.

retrieval source ids
type: ObjectProperty
range: retrieval source
definition: A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.
in scheme: vocab

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.
in scheme: vocab

similar to
type: DatatypeProperty
type: SymmetricProperty
sub property of: related to at instance level
definition: holds between an entity and some other entity with similar features.
in scheme: vocab
canonical predicate: true

source record urls
type: DatatypeProperty
domain: retrieval source
range: anyURI
sub property of: node property
definition: A URL linking to a specific web page or document provided by the source, that contains a record of the knowledge expressed in the Edge. If the knowledge is contained in more than one web page on an Information Resource's site, urls MAY be provided for each.
in scheme: vocab

sources
type: ObjectProperty
range: retrieval source
sub property of: association slot
alternative label: source retrieval provenance
definition: A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org).
in scheme: vocab
note: Note that source retrieval provenance concerns the mechanical retrieval and transformation of data between web accessible information systems. It does not trace the source of knowledge back to specific publications or data sets. And it is not concerned with the reasoning, inference or analysis activities that generate knowledge in the first place (this is instead covered by 'knowledge level' and 'agent type' properties).

specialization qualifier
type: DatatypeProperty
sub property of: qualifier
definition: A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
in scheme: vocab

subject category closure
type: ObjectProperty
domain: association
range: ontology class
sub property of: association slot
definition: Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

subject closure
type: DatatypeProperty
domain: association
sub property of: association slot
definition: Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

subject label closure
type: DatatypeProperty
domain: association
range: string
sub property of: association slot
definition: Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

subject location in text
type: DatatypeProperty
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.
in scheme: vocab

supporting documents
type: DatatypeProperty
range: anyURI
sub property of: association slot
definition: One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
in scheme: vocab

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
in scheme: vocab
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

treated in studies by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: subject of treatment application or study for treatment by
sub property of: treated by
inverse of: studied to treat
in scheme: vocab

upstream resource ids
type: DatatypeProperty
domain: retrieval source
range: anyURI
sub property of: node property
definition: An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.
in scheme: vocab

activity
type: Class
subclass of: Restriction
  on property: mixins
  some values from: 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.
in scheme: vocab
narrow match: T056
narrow match: T057
narrow match: T058
narrow match: T062
narrow match: T064
narrow match: T065
narrow match: T066

administrative entity
type: Class
subclass of: named thing
in scheme: vocab

article
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: volume
subclass of: Restriction
  min cardinality: 1
  on property: published in
subclass of: Restriction
  min cardinality: 0
  on property: issue
subclass of: Restriction
  max cardinality: 1
  on property: iso abbreviation
subclass of: Restriction
  min cardinality: 0
  on property: volume
subclass of: Restriction
  all values from: string
  on property: issue
subclass of: Restriction
  all values from: anyURI
  on property: published in
subclass of: Restriction
  all values from: string
  on property: iso abbreviation
subclass of: Restriction
  min cardinality: 0
  on property: iso abbreviation
subclass of: Restriction
  all values from: string
  on property: volume
subclass of: Restriction
  max cardinality: 1
  on property: issue
subclass of: Restriction
  max cardinality: 1
  on property: published in
subclass of: publication
definition: a piece of writing on a particular topic presented as a stand-alone section of a larger publication
in scheme: vocab

behavior
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: activity and behavior
subclass of: biological process
in scheme: vocab
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.
in scheme: vocab

book chapter
type: Class
subclass of: Restriction
  all values from: anyURI
  on property: published in
subclass of: Restriction
  all values from: string
  on property: chapter
subclass of: Restriction
  max cardinality: 1
  on property: volume
subclass of: Restriction
  all values from: string
  on property: volume
subclass of: Restriction
  max cardinality: 1
  on property: chapter
subclass of: Restriction
  min cardinality: 0
  on property: volume
subclass of: Restriction
  max cardinality: 1
  on property: published in
subclass of: Restriction
  min cardinality: 1
  on property: published in
subclass of: Restriction
  min cardinality: 0
  on property: chapter
subclass of: publication
in scheme: vocab

case
type: Class
subclass of: Restriction
  all values from: biological sex
  on property: has biological sex
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: Restriction
  max cardinality: 1
  on property: has biological sex
subclass of: Restriction
  min cardinality: 0
  on property: has biological sex
subclass of: individual organism
alternative label: patient
alternative label: proband
definition: An individual (human) organism that has a patient role in some clinical context.
in scheme: vocab

allosteric_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

immune_system_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

methylation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

mixed_allosteric_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: allosteric_modulation

noncompetitive_inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

stabilization
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

cell line to disease or phenotypic feature association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: cell line to entity association mixin
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to disease or phenotypic feature association mixin
subclass of: Restriction
  all values from: disease or phenotypic feature
  on property: subject
subclass of: association
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.
in scheme: vocab

chemical affects biological entity association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: causal mechanism qualifier
subclass of: Restriction
  all values from: biological entity
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: subject derivative qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject derivative qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject part qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: species context qualifier
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: object form or variant qualifier
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: species context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object form or variant qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: chemical entity
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  all values from: ChemicalEntityDerivativeEnum
  on property: subject derivative qualifier
subclass of: Restriction
  all values from: organism taxon
  on property: species context qualifier
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: anatomical context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: object part qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: subject context qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: object form or variant qualifier
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalPartQualifierEnum
  on property: subject part qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject part qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object part qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject context qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: anatomical context qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object context qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: object context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object part qualifier
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: causal mechanism qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: CausalMechanismQualifierEnum
  on property: causal mechanism qualifier
subclass of: association
definition: Describes an effect that a chemical has on a biological entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)
in scheme: vocab

chemical entity to entity association mixin
type: Class
subclass of: Mixin
definition: An interaction between a chemical entity and another entity
in scheme: vocab

chemical exposure
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: has quantitative value
subclass of: Restriction
  all values from: quantity value
  on property: has quantitative value
subclass of: exposure event
definition: A chemical exposure is an intake of a particular chemical entity.
in scheme: vocab

polymorphic_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: genetic_variant_form

approved_for_condition
type: Class
subclass of: ClinicalApprovalStatusEnum
subclass of: PermissibleValue

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
in scheme: vocab

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
in scheme: vocab

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
in scheme: vocab

coding sequence
type: Class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: biological entity
in scheme: vocab

decreased
type: Class
subclass of: DirectionQualifierEnum
subclass of: PermissibleValue

increased
type: Class
subclass of: DirectionQualifierEnum
subclass of: PermissibleValue

disease or phenotypic feature to entity association mixin
type: Class
subclass of: Mixin
in scheme: vocab

disease to entity association mixin
type: Class
subclass of: Mixin
in scheme: vocab

drug exposure
type: Class
subclass of: chemical exposure
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.
in scheme: vocab

environmental exposure
type: Class
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.
in scheme: vocab

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

FDA adverse event level
type: ObjectProperty
range: FDAIDAAdverseEventEnum
sub property of: association slot
in scheme: vocab

gene expression mixin
type: Class
subclass of: Mixin
definition: Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs.
in scheme: vocab

cleavage
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

genomic sequence localization
type: Class
subclass of: Restriction
  all values from: PhaseEnum
  on property: phase
subclass of: Restriction
  all values from: nucleic acid entity
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: phase
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  all values from: StrandEnum
  on property: strand
subclass of: Restriction
  max cardinality: 1
  on property: phase
subclass of: Restriction
  all values from: string
  on property: end interbase coordinate
subclass of: Restriction
  all values from: StrandEnum
  on property: genome build
subclass of: Restriction
  min cardinality: 0
  on property: genome build
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: strand
subclass of: Restriction
  min cardinality: 0
  on property: end interbase coordinate
subclass of: Restriction
  max cardinality: 1
  on property: end interbase coordinate
subclass of: Restriction
  max cardinality: 1
  on property: start interbase coordinate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: start interbase coordinate
subclass of: Restriction
  all values from: nucleic acid entity
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: start interbase coordinate
subclass of: Restriction
  min cardinality: 0
  on property: strand
subclass of: Restriction
  max cardinality: 1
  on property: genome build
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.
in scheme: vocab

genotype to disease association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  all values from: Thing
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: genotype to entity association mixin
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: Thing
  on property: subject
subclass of: association
in scheme: vocab
note: TODO decide no how to model pathogenicity

genotype to entity association mixin
type: Class
subclass of: Mixin
in scheme: vocab

geographic location
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: latitude
subclass of: Restriction
  max cardinality: 1
  on property: latitude
subclass of: Restriction
  max cardinality: 1
  on property: longitude
subclass of: Restriction
  all values from: float
  on property: longitude
subclass of: Restriction
  all values from: float
  on property: latitude
subclass of: Restriction
  min cardinality: 0
  on property: longitude
subclass of: planetary entity
definition: a location that can be described in lat/long coordinates
in scheme: vocab

mammal
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: cellular organism
definition: A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex
in scheme: vocab

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.
in scheme: vocab

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

organism taxon to entity association
type: Class
subclass of: Mixin
definition: An association between an organism taxon and another entity
in scheme: vocab

pairwise gene to gene interaction
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
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)
in scheme: vocab
narrow match: ProteinProteinInteraction

phenotypic feature to entity association mixin
type: Class
subclass of: Restriction
  on property: mixins
  some values from: frequency quantifier
subclass of: feature or disease qualifiers to entity mixin
in scheme: vocab

polypeptide
type: Class
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or protein or polypeptide
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: biological entity
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.
in scheme: vocab
narrow match: T087
narrow match: T116
narrow match: SO_0000104

reaction to participant association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: reaction direction
subclass of: Restriction
  min cardinality: 0
  on property: reaction direction
subclass of: Restriction
  max cardinality: 1
  on property: reaction side
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: integer
  on property: stoichiometry
subclass of: Restriction
  all values from: ReactionSideEnum
  on property: reaction side
subclass of: Restriction
  min cardinality: 0
  on property: reaction side
subclass of: Restriction
  all values from: molecular entity
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: stoichiometry
subclass of: Restriction
  all values from: ReactionDirectionEnum
  on property: reaction direction
subclass of: Restriction
  min cardinality: 0
  on property: stoichiometry
subclass of: chemical entity to chemical entity association
in scheme: vocab

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

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

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

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.
in scheme: vocab

treatment
type: Class
subclass of: Restriction
  all values from: device
  on property: has device
subclass of: Restriction
  on property: mixins
  some values from: chemical or drug or treatment
subclass of: Restriction
  all values from: procedure
  on property: has procedure
subclass of: Restriction
  min cardinality: 0
  on property: has device
subclass of: Restriction
  all values from: drug
  on property: has drug
subclass of: Restriction
  min cardinality: 0
  on property: has procedure
subclass of: Restriction
  min cardinality: 0
  on property: has drug
subclass of: exposure event
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
in scheme: vocab

variant to disease association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  on property: mixins
  some values from: variant to entity association mixin
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: entity to disease association mixin
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: Thing
  on property: subject
subclass of: Restriction
  all values from: Thing
  on property: object
subclass of: association
in scheme: vocab
note: TODO decide no how to model pathogenicity

variant to gene association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: gene
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  on property: mixins
  some values from: variant to entity association mixin
subclass of: association
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)
in scheme: vocab

acts upstream of or within
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: acts upstream of
in scheme: vocab
canonical predicate: true

address
type: DatatypeProperty
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(?).
in scheme: vocab

affects sensitivity to
type: ObjectProperty
domain: chemical entity or gene or gene product
range: chemical entity or gene or gene product
sub property of: related to at instance level
definition: holds between two chemical entities or genes or gene products where the action of one affects the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other.
in scheme: vocab
canonical predicate: true

affinity
type: DatatypeProperty
range: float
sub property of: node property
definition: The numerical value describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity is 8.6. Used in conjunction with the affinity parameter slot.
in scheme: vocab

affinity parameter
type: ObjectProperty
range: AffinityParameterEnum
sub property of: node property
definition: The type of parameter describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the 'affinity parameter' is pIC50. Used in conjunction with the 'affinity' slot, within an 'affinity measurement'.
in scheme: vocab

agent type
type: ObjectProperty
domain: association
range: AgentTypeEnum
sub property of: association slot
definition: Describes the high-level category of agent who originally generated a statement of knowledge or other type of information.
editorial note: Note that this property indicates the type of agent who produced a final statement of knowledge, which is often different from the agent oragents who produced information used as evidence to support generation of this knowledge. For example, if a human curator concludes that a particular gene variant causes a medical condition - based on their interpretation of information produced by computational modeling tools, automated data analysis pipelines, and robotic laboratory assay systems - the agent_type for this statement is 'manual agent' - despite all of the evidence being created by automated agents. But if any of these systems is programmed to generate knowledge statements directly and without human assistance, the statement would be attributed to an 'automated_agent'.
in scheme: vocab

associated environmental context
type: DatatypeProperty
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.
in scheme: vocab

associated with likelihood of
type: DatatypeProperty
sub property of: 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 Infraction (MI) diagnosis” asserts that the state of having Afib is associated with an increased or decreased likelihood that a patient will later exhibit MI.
in scheme: vocab
canonical predicate: true

associated with response to
type: DatatypeProperty
sub property of: associated with
definition: A statistical association used to indicate that the object of a statement using this predicate induces a response of some kind in the subject entity. Intentionally broad in definition, this predicate should be used with qualifiers to narrow the type of response (E.g. whether the response is therapeutic, phenotypic, detrimental, resistant, etc. is captured in context, direction, and aspect qualifiers).
in scheme: vocab
note: subject: NCBIGene:2064 # HER2 subject_aspect: Amplification predicate: associated with response to object: CHEBI:10035 # Trastuzumab response_type_qualifier: therapeutic_sensitivity response_direction_qualifer: increased response_target_qualifier: human patient disease_context_qualifier: MONDO:0007254 # breast cancer subject: MONDO:0007254 predicate: associated with response to qualified_predicate: associated with object: CHEBI:10035 # Trastuzumab response_context_qualifier: therapeutic_sensitivity
canonical predicate: true

chapter
type: DatatypeProperty
domain: book chapter
sub property of: node property
definition: chapter of a book
in scheme: vocab

chembl availability type
type: DatatypeProperty
range: string
definition: Text indicating the availability type of the chemical entity.
in scheme: attributes

chembl black box warning
type: DatatypeProperty
range: string
definition: Text describing black box warnings for use of chemicals as therapeutics.
in scheme: attributes

chembl chirality
type: DatatypeProperty
range: string
definition: Tern indicating the chirality of the chemical entity.
in scheme: attributes

chembl drug warning
type: DatatypeProperty
range: string
definition: Text describing warnings for use of chemicals as therapeutics.
in scheme: attributes

chembl natural product
type: DatatypeProperty
range: boolean
definition: Flag indicating if a chemical entity is a natural product.
in scheme: attributes

chembl prodrug
type: DatatypeProperty
range: boolean
definition: Flag indicating if a drug is a prodrug that is active only after being metabolized by the body.
in scheme: attributes

chi squared dof
type: DatatypeProperty
range: integer
sub property of: association slot
definition: Degrees of freedom (dof) in a chi-squared test referring to the number of values in the final calculation of a statistic that are free to vary
in scheme: vocab

chi squared p
type: DatatypeProperty
range: float
sub property of: association slot
definition: The chi-square p-value tells you the probability that the observed differences (or associations) in your data occurred by random chance, assuming the null hypothesis is true.
in scheme: vocab

chi squared statistic
type: DatatypeProperty
range: float
sub property of: association slot
definition: The chi-squared statistic measures how much observed data deviate from expected values under the null hypothesis.
in scheme: vocab

clinical trial age range
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
definition: The age range of a clinical trial as determined by clinicaltrials.gov
in scheme: vocab

clinical trial brief title
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
definition: The brief title of a clinical trial as determined by clinicaltrials.gov
in scheme: vocab

clinical trial enrollment
type: DatatypeProperty
domain: clinical trial
range: integer
sub property of: node property
definition: The enrollment number of a clinical trial as determined by clinicaltrials.gov
in scheme: vocab

clinical trial enrollment type
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
definition: The enrollment type of a clinical trial as determined by clinicaltrials.gov (actual, anticipated, or estimated)
in scheme: vocab

clinical trial intervention model
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
definition: The intervention model of a clinical trial as determined by clinicaltrials.gov. The most common values are SINGLE_GROUP, PARALLEL, CROSSOVER, FACTORIAL, and (null).
in scheme: vocab

clinical trial overall status
type: ObjectProperty
domain: clinical trial
range: ClinicalTrialStatusEnum
sub property of: node property
definition: The overall status of a clinical trial as determined by clinicaltrials.gov
in scheme: vocab

clinical trial phase
type: ObjectProperty
range: ResearchPhaseEnum
sub property of: node property
definition: The phase that a clinical trials study represents
in scheme: vocab

clinical trial primary purpose
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
alternative label: primary purpose
definition: The primary purpose of a clinical trial as determined by clinicaltrials.gov. The most common values are TREATMENT and PREVENTION. Other possible values include BASIC_SCIENCE, SUPPORTIVE_CARE, DIAGNOSTIC, HEALTH_SERVICES_RESEARCH, SCREENING, DEVICE_FEASIBILITY, OTHER, and (null).
in scheme: vocab

clinical trial start date
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
definition: The start date of a clinical trial as determined by clinicaltrials.gov
in scheme: vocab

clinical trial tested intervention
type: DatatypeProperty
domain: clinical trial
range: string
sub property of: node property
definition: Records whether the clinical trials are testing the intervention.
in scheme: vocab

deprecated
type: DatatypeProperty
range: boolean
definition: A boolean flag indicating that an entity is no longer considered current or valid.
in scheme: vocab

description
type: DatatypeProperty
range: string
alternative label: definition
definition: a human-readable description of an entity
in scheme: vocab
narrow match: Description

distribution download url
type: DatatypeProperty
domain: dataset distribution
sub property of: node property
in scheme: vocab

drug regulatory status world wide
type: ObjectProperty
range: ApprovalStatusEnum
alternative label: max phase
definition: An agglomeration of drug regulatory status worldwide. Not specific to FDA.
in scheme: vocab
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

druggable gene category
type: ObjectProperty
range: DruggableGeneCategoryEnum
definition: Classification of druggable genes based on knowledge about drug or small molecule activities.
in scheme: vocab

elevate to prediction
type: DatatypeProperty
range: boolean
sub property of: node property
definition: A boolean flag indicating whether a clinical trial finding should be elevated to a prediction.
in scheme: vocab

end interbase coordinate
type: DatatypeProperty
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.
in scheme: vocab
opposite of: start interbase coordinate

exposure additional condition
type: DatatypeProperty
domain: exposure event
range: string
sub property of: node property
definition: Additional conditions impacting an exposure event.
in scheme: vocab

exposure duration
type: DatatypeProperty
domain: exposure event
range: time
sub property of: node property
definition: Duration of an exposure event.
in scheme: vocab

exposure end age
type: DatatypeProperty
domain: exposure event
range: integer
sub property of: node property
definition: Ending stage of an exposure event.
in scheme: vocab

exposure magnitude
type: DatatypeProperty
domain: exposure event
range: string
sub property of: node property
definition: Magnitude of an exposure event, e.g, parts per million of a toxic chemical.
in scheme: vocab

exposure route
type: DatatypeProperty
domain: exposure event
range: string
sub property of: node property
definition: Route of exposure.
in scheme: vocab

exposure start age
type: DatatypeProperty
domain: exposure event
range: integer
sub property of: node property
definition: Starting age of an exposure event.
in scheme: vocab

exposure type
type: DatatypeProperty
domain: exposure event
range: string
sub property of: node property
definition: Type of exposure
in scheme: vocab

exposure vehicle
type: DatatypeProperty
domain: exposure event
range: string
sub property of: node property
definition: Type of an exposure event.
in scheme: vocab

expression site
type: ObjectProperty
range: anatomical entity
sub property of: association slot
definition: location in which gene or protein expression takes place. May be cell, tissue, or organ.
in scheme: vocab

extraction confidence score
type: DatatypeProperty
range: float
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.
in scheme: vocab

fisher exact odds ratio
type: DatatypeProperty
range: float
sub property of: association slot
definition: The Fisher Exact Test is used to determine whether there is a non-random association between two categorical variables in a 2×2 contingency table, especially when sample sizes are small. The odds ratio (OR) quantifies the strength of that association. OR = 1 implies No association OR > 1 implies Positive association (Group A more likely to have Outcome 1) OR < 1 implies Negative association (Group A less likely to have Outcome 1)
in scheme: vocab

fisher exact p
type: DatatypeProperty
range: float
sub property of: association slot
definition: The Fisher exact p-value tells you the probability of observing a table as extreme as (or more extreme than) your actual data, assuming that the null hypothesis of independence is true. It's most commonly used for 2×2 contingency tables, especially when sample sizes are small or expected counts are low.
in scheme: vocab

format
type: DatatypeProperty
domain: information content entity
sub property of: node property
in scheme: vocab

frequency qualifier
type: DatatypeProperty
range: UO_0000105
sub property of: qualifier
definition: a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject
in scheme: vocab

full name
type: DatatypeProperty
domain: named thing
range: string
sub property of: node property
definition: a long-form human readable name for a thing
in scheme: vocab

gene2phenotype confidence category
type: DatatypeProperty
range: string
definition: A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.
in scheme: attributes

genome build
type: ObjectProperty
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.
in scheme: vocab

has binary relation
type: ObjectProperty
range: BinaryRelationEnum
definition: Qualifies a value context with a mathematical binary relation.
in scheme: vocab

has biological sex
type: ObjectProperty
range: biological sex
definition: The biological sex of the entity (e.g., male or female) regarding a case description from a phenopacket
in scheme: vocab

has confidence score
type: DatatypeProperty
range: float
sub property of: association slot
definition: connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about.
in scheme: vocab

has dataset
type: ObjectProperty
domain: dataset version
range: dataset
sub property of: node property
broad match: source
in scheme: vocab

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

has gene or gene product
type: ObjectProperty
range: gene
sub property of: node property
definition: connects an entity with one or more gene or gene products
in scheme: vocab

has numeric value
type: DatatypeProperty
domain: quantity value
range: double
definition: connects a quantity value to a number
in scheme: vocab

has percentage
type: DatatypeProperty
range: double
sub property of: aggregate statistic
definition: equivalent to has quotient multiplied by 100
in scheme: vocab

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

has taxonomic rank
type: ObjectProperty
range: taxonomic rank
sub property of: node property
in scheme: vocab
mapping relation: P105

has unit
type: DatatypeProperty
domain: quantity value
range: UO_0000000
definition: connects a quantity value to a unit
in scheme: vocab
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 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
in scheme: vocab

highest FDA approval status
type: ObjectProperty
range: ApprovalStatusEnum
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, 'clinical approval status.'
in scheme: vocab

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

in taxon label
type: DatatypeProperty
domain: thing with taxon
range: string
sub property of: node property
definition: The human readable scientific name for the taxon of the entity.
in scheme: vocab
denormalized: true

information content
type: DatatypeProperty
range: float
definition: Information content (IC) value for a term, primarily from Automats.
in scheme: attributes

ingest date
type: DatatypeProperty
domain: dataset version
sub property of: node property
broad match: issued
in scheme: vocab

inheritance
type: ObjectProperty
domain: disease or phenotypic feature
range: genetic inheritance
sub property of: node property
definition: Connects genetic inheritance to a disease or phenotypic feature, as a node property.
in scheme: vocab

interacting molecules category
type: ObjectProperty
range: ontology class
sub property of: association slot
in scheme: vocab

is metabolite
type: DatatypeProperty
domain: molecular entity
range: boolean
sub property of: node property
definition: indicates whether a molecular entity is a metabolite
in scheme: vocab

is supplement
type: DatatypeProperty
domain: chemical mixture
sub property of: node property
in scheme: vocab

is toxic
type: DatatypeProperty
range: boolean
sub property of: node property
in scheme: vocab

knowledge level
type: ObjectProperty
domain: association
range: KnowledgeLevelEnum
sub property of: association slot
alternative label: knowledge type
definition: Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true.
editorial note: The notion of a 'level' of knowledge can in one sense relate to the strength of a statement - i.e. how confident we are that it says something true about our domain of discourse. Here, we can generally consider Assertions to be stronger than Entailments to be stronger than Predictions. But in another sense, 'level' of knowledge can refer to the scope or specificity of what a statement expresses - on a spectrum from context-specific results of a data analysis, to generalized assertions of knowledge or fact. Here, Statistical Associations and Observations represent more foundational statements that are only slightly removed from the data on which they are based (the former reporting the direct results of an analysis in terms of correlations between variables in the data, and the latter describing phenomena that were observed/reported to have occurred).
in scheme: vocab

latitude
type: DatatypeProperty
range: float
sub property of: node property
definition: latitude
in scheme: vocab

license
type: DatatypeProperty
domain: information content entity
sub property of: node property
in scheme: vocab
narrow match: P275

log odds ratio
type: DatatypeProperty
range: float
sub property of: association slot
definition: The natural logarithm of the odds ratio (OR), or the ratio of the odds of an event Y occurring in an exposed group versus the odds of an event Y occurring in a non-exposed group.
in scheme: vocab

longitude
type: DatatypeProperty
range: float
sub property of: node property
definition: longitude
in scheme: vocab

mapped predicate
type: DatatypeProperty
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.
in scheme: vocab

max tolerated dose
type: DatatypeProperty
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.
in scheme: vocab

narrow match
type: DatatypeProperty
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.
in scheme: vocab
opposite of: broad match

object category
type: ObjectProperty
domain: association
range: ontology class
sub property of: association slot
definition: Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

object feature name
type: DatatypeProperty
sub property of: association slot
definition: Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease
in scheme: vocab

object namespace
type: DatatypeProperty
domain: association
range: string
sub property of: association slot
alternative label: object prefix
definition: Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

original object
type: DatatypeProperty
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.
in scheme: vocab

original predicate
type: DatatypeProperty
domain: association
range: anyURI
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.
in scheme: vocab

original subject
type: DatatypeProperty
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.
in scheme: vocab

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.
in scheme: vocab

phenotypic state
type: ObjectProperty
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.
in scheme: vocab

primary knowledge source
type: DatatypeProperty
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 capture 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.
in scheme: vocab

promotes condition
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: affects likelihood of
definition: Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place.
in scheme: vocab
canonical predicate: true
opposite of: preventative for condition

reaction direction
type: ObjectProperty
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.)
in scheme: vocab
narrow match: NCIT C42677

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

resource id
type: DatatypeProperty
domain: retrieval source
range: anyURI
sub property of: node property
definition: The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.
in scheme: vocab

resource role
type: ObjectProperty
domain: retrieval source
range: ResourceRoleEnum
sub property of: node property
definition: The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.
in scheme: vocab

response context qualifier
type: ObjectProperty
range: ResponseEnum
sub property of: context qualifier
definition: a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.
in scheme: vocab

response target context qualifier
type: ObjectProperty
range: ResponseTargetEnum
sub property of: context qualifier
definition: a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material, etc.)
in scheme: vocab

rights
type: DatatypeProperty
domain: information content entity
sub property of: node property
in scheme: vocab

semmed agreement count
type: DatatypeProperty
range: integer
sub property of: association slot
definition: The number of times this concept has been asserted in the SemMedDB literature database.
in scheme: vocab

source logo
type: DatatypeProperty
domain: dataset summary
sub property of: node property
in scheme: vocab

source web page
type: DatatypeProperty
domain: dataset summary
sub property of: node property
broad match: source
in scheme: vocab

start interbase coordinate
type: DatatypeProperty
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).
in scheme: vocab
opposite of: end interbase coordinate

stoichiometry
type: DatatypeProperty
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.
in scheme: vocab

strand
type: ObjectProperty
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).
in scheme: vocab

studied to treat
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: related to at instance level
sub property of: treats or applied or studied to treat
definition: Holds between an substance, procedure, or activity and a medical condition, and reports that one or more scientific study has been performed to specifically test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).
editorial note: Predicates in this hierarchy are used in practice when a source reports performance of a study, but there is not sufficient evidence or demonstrated efficacy against the condition to warrant creating a ‘treats’ assertion edge. Note however that a 'studied to treat' edge may be used as evidence to support creation of a separate 'treats' prediction edge.
in scheme: vocab
canonical predicate: true

subject category
type: ObjectProperty
domain: association
range: ontology class
sub property of: association slot
definition: Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

subject feature name
type: DatatypeProperty
sub property of: association slot
definition: Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene
in scheme: vocab

subject namespace
type: DatatypeProperty
domain: association
range: string
sub property of: association slot
alternative label: subject prefix
definition: Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
in scheme: vocab
denormalized: true

subject specialization qualifier
type: DatatypeProperty
range: anyURI
sub property of: specialization qualifier
definition: A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
in scheme: vocab

summary
type: DatatypeProperty
domain: publication
sub property of: node property
alternative label: abstract
definition: executive summary of a publication
in scheme: vocab

supporting document type
type: DatatypeProperty
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.
in scheme: vocab

supporting document year
type: DatatypeProperty
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.
in scheme: vocab

supporting text section type
type: DatatypeProperty
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.
in scheme: vocab

symbol
type: DatatypeProperty
domain: named thing
sub property of: node property
definition: Symbol for a particular thing
in scheme: vocab

taxon
type: DatatypeProperty
range: anyURI
sub property of: node property
definition: A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology.
in scheme: vocab
note: Note there is also a predicate 'in taxon' that can be used to instantiate an edge between a taxon entity and a thing with taxon entity. This is an acceptable practice for KG construction, but for many applications it is more convenient to use this property slot to directly annotate the taxon on the entity itself.

total sample size
type: DatatypeProperty
range: integer
sub property of: dataset count
definition: The total number of patients or participants within a sample population.
in scheme: vocab

trade name
type: DatatypeProperty
domain: chemical entity
sub property of: node property
in scheme: vocab

treats
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: treats or applied or studied to treat
alternative label: ameliorates or prevents condition
alternative label: indicated for
alternative label: is substance that treats
broad match: treats
broad match: MONDO disease responds to
broad match: SemMedDBTREATS
broad match: P2175
definition: Holds between an intervention (substance, procedure, or activity) and a medical condition (disease or phenotypic feature), and states that the intervention is, in some population(s), able to ameliorate, stabilize, or cure the condition or delay, prevent, or reduce the risk of it manifesting in the first place. ‘Treats’ edges should be asserted (knowledge_level: assertion) only in cases where there is strong supporting evidence - i.e. in some population(s) the intervention is approved for the condition, passed phase 3 or in phase 4 trials for the condition, or is an otherwise established treatment in the medical community (e.g. a widely-accepted or formally recommended off-label use). In the absence of such evidence, weaker predicates should be used in asserted edges (e.g. ‘in clinical trials for’ or ‘beneficial in models of’). ‘Treats’ edges based on weaker or indirect forms of evidence can however be created as predictions (knowledge_level: prediction) and should point to the more foundational asserted edges that support them.
in scheme: vocab
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

update date
type: DatatypeProperty
range: date
sub property of: node property
definition: date on which an entity was updated. This can be applied to nodes or edges
in scheme: vocab

z score
type: DatatypeProperty
range: float
sub property of: association slot
alternative label: normal score
alternative label: standard score
alternative label: z-score
alternative label: z-value
definition: A measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.
in scheme: vocab

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

affinity measurement
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: has binary relation
subclass of: Restriction
  max cardinality: 1
  on property: has binary relation
subclass of: Restriction
  min cardinality: 0
  on property: affinity
subclass of: Restriction
  max cardinality: 1
  on property: affinity parameter
subclass of: Restriction
  max cardinality: 1
  on property: affinity
subclass of: Restriction
  all values from: float
  on property: affinity
subclass of: Restriction
  min cardinality: 0
  on property: affinity parameter
subclass of: Restriction
  all values from: BinaryRelationEnum
  on property: has binary relation
subclass of: Restriction
  all values from: AffinityParameterEnum
  on property: affinity parameter
subclass of: named thing
definition: The type of measurement describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity parameter is pIC50 and the affinity value is 8.6. The binary relation, if given, qualifies the affinity as greater than, less than, or equal.
in scheme: vocab

antagonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: inhibition

lipidation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

ubiquitination
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: molecular_modification

cell line
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: organismal entity
in scheme: vocab

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.
in scheme: vocab

chemical entity to chemical entity association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: chemical entity
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: species context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: organism taxon
  on property: species context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: species context qualifier
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: association
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.
in scheme: vocab

modified_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: PermissibleValue

non_loss_of_function_variant_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: genetic_variant_form

chemical role
type: Class
subclass of: attribute
definition: A role played by the molecular entity or part thereof within a chemical context.
in scheme: vocab

not_approved_for_condition
type: Class
subclass of: ClinicalApprovalStatusEnum
subclass of: PermissibleValue

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
in scheme: vocab
narrow match: T074
narrow match: T075
narrow match: T203
narrow match: SemGroups-v04.txtDEVI

diagnostic aid
type: Class
subclass of: named thing
definition: A device or substance used to help diagnose disease or injury
in scheme: vocab

evidence type
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: named thing
alternative label: evidence code
definition: Class of evidence that supports an association
in scheme: vocab

FDA regulatory approvals
type: DatatypeProperty
range: string
definition: Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536).
in scheme: vocab

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

abundance
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: activity_or_abundance

activity_or_abundance
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

molecular_interaction
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

transport
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

gene or gene product or gene family
type: Class
subclass of: Mixin
definition: A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity (e.g. biological process or anatomical entity)
in scheme: vocab

macromolecular machine to entity association mixin
type: Class
subclass of: Mixin
definition: an association which has a macromolecular machine mixin as a subject
in scheme: vocab

material sample
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: physical entity
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]
in scheme: vocab

noncoding RNA product
type: Class
subclass of: RNA product
in scheme: vocab

organism taxon to organism taxon association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: organism taxon to entity association
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: organism taxon
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: organism taxon
  on property: subject
subclass of: association
definition: A relationship between two organism taxon nodes
in scheme: vocab

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

procedure
type: Class
subclass of: Restriction
  on property: mixins
  some values from: activity and behavior
subclass of: named thing
definition: A series of actions conducted in a certain order or manner
in scheme: vocab
narrow match: T059
narrow match: T060
narrow match: T061
narrow match: T063

RNA product
type: Class
subclass of: Restriction
  on property: mixins
  some values from: gene product mixin
subclass of: transcript
in scheme: vocab

regulatory region
type: Class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: biological entity
alternative label: regulatory element
definition: A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene
in scheme: vocab

relationship quantifier
type: Class
subclass of: Mixin
in scheme: vocab

acts upstream of
type: ObjectProperty
domain: gene or gene product
range: biological process
sub property of: related to at instance level
in scheme: vocab
canonical predicate: true

adjusted p value
type: DatatypeProperty
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<.
in scheme: vocab

affects likelihood of
type: DatatypeProperty
sub property of: related to at instance level
definition: Holds between two entities where the presence or application of one alters the chance that the other will come to be.
editorial note: - This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used for a statistical associations that describe correlations between two feature variables (use predicates in the 'associated with likelihood of' hierarchy here.)
in scheme: vocab
canonical predicate: true

aggregate statistic
type: DatatypeProperty
sub property of: node property
in scheme: vocab

broad match
type: DatatypeProperty
sub property of: related to at concept level
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.
in scheme: vocab
canonical predicate: true
opposite of: narrow match

coexists with
type: DatatypeProperty
type: SymmetricProperty
sub property of: related to at instance level
broad match: SemMedDBCOEXISTS WITH
definition: holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region
in scheme: vocab
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

edges
type: ObjectProperty
range: association
definition: A list of associations between two entities.
in scheme: vocab

exact match
type: DatatypeProperty
type: SymmetricProperty
sub property of: close match
definition: holds between two entities that have strictly equivalent meanings, with a high degree of confidence
in scheme: vocab
canonical predicate: true

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

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

in taxon
type: ObjectProperty
domain: thing with taxon
range: organism taxon
sub property of: related to at instance level
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'
in scheme: vocab
narrow match: RO_0002160
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 or pharmacologically interacts with.
in scheme: vocab

nodes
type: ObjectProperty
range: entity
definition: A list of entities that can be a subject or object of an association
in scheme: vocab

p value
type: DatatypeProperty
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.
in scheme: vocab

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

statement qualifier
type: DatatypeProperty
sub property of: qualifier
definition: A property that qualifies the entirety of the statement made in an association. It applies to both a fully qualified subject and a fully qualified object as well as the predicate and qualified predicate in an association.
in scheme: vocab

supporting text
type: DatatypeProperty
range: string
sub property of: association slot
definition: The segment of text from a document that supports the mined assertion.
in scheme: vocab

temporal context qualifier
type: DatatypeProperty
range: string
sub property of: qualifier
definition: a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.
in scheme: vocab

anatomical entity to anatomical entity association
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anatomical entity
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anatomical entity
  on property: object
subclass of: association
in scheme: vocab

case to entity association mixin
type: Class
subclass of: Mixin
definition: An abstract association for use where the case is the subject
in scheme: vocab

agonism
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: activation

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
in scheme: vocab

clinical intervention
type: Class
subclass of: clinical entity
in scheme: vocab

dataset distribution
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: distribution download url
subclass of: Restriction
  all values from: string
  on property: distribution download url
subclass of: Restriction
  max cardinality: 1
  on property: distribution download url
subclass of: information content entity
definition: an item that holds distribution level information about a dataset.
in scheme: vocab

dataset summary
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: source web page
subclass of: Restriction
  min cardinality: 0
  on property: source logo
subclass of: Restriction
  all values from: string
  on property: source web page
subclass of: Restriction
  max cardinality: 1
  on property: source web page
subclass of: Restriction
  all values from: string
  on property: source logo
subclass of: Restriction
  max cardinality: 1
  on property: source logo
subclass of: information content entity
definition: an item that holds summary level information about a dataset.
in scheme: vocab

injection
type: Class
subclass of: DrugDeliveryEnum
subclass of: PermissibleValue

frequency quantifier
type: Class
subclass of: relationship quantifier
in scheme: vocab

gene product isoform mixin
type: Class
subclass of: gene product 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.
in scheme: vocab

gene to disease association
type: Class
subclass of: Restriction
  all values from: float
  on property: diseases confidence score
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: GeneToDiseasePredicateEnum
  on property: predicate
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: subject form or variant qualifier
subclass of: Restriction
  all values from: string
  on property: gene2phenotype confidence category
subclass of: Restriction
  max cardinality: 1
  on property: diseases confidence score
subclass of: Restriction
  max cardinality: 1
  on property: allelic requirement
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  all values from: disease
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: gene2phenotype confidence category
subclass of: Restriction
  min cardinality: 0
  on property: gene2phenotype confidence category
subclass of: Restriction
  min cardinality: 0
  on property: allelic requirement
subclass of: Restriction
  all values from: Datatype
    intersection of: string
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^HP:\d{7}$
  on property: allelic requirement
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  all values from: GeneOrGeneProductOrChemicalEntityAspectEnum
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  on property: mixins
  some values from: gene to entity association mixin
subclass of: Restriction
  all values from: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  on property: subject form or variant qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: diseases confidence score
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: association
in scheme: vocab
note: NCIT:R176 refers to the inverse relationship
note: for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a disease
note: if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.

gene to gene association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: gene or gene product
  on property: object
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
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.
in scheme: vocab

individual organism
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: organismal entity
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
in scheme: vocab
narrow match: Person
narrow match: Q795052

life stage
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: organismal entity
definition: A stage of development or growth of an organism, including post-natal adult stages
in scheme: vocab
narrow match: HsapDv_0000000

pathway
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: biological process
in scheme: vocab
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
in scheme: vocab

protein
type: Class
subclass of: Restriction
  on property: mixins
  some values from: 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
in scheme: vocab
narrow match: T126
narrow match: T192

quantity value
type: Class
subclass of: Restriction
  all values from: double
  on property: has numeric value
subclass of: Restriction
  max cardinality: 1
  on property: has numeric value
subclass of: Restriction
  all values from: UO_0000000
  on property: has unit
subclass of: Restriction
  min cardinality: 0
  on property: has unit
subclass of: Restriction
  max cardinality: 1
  on property: has unit
subclass of: Restriction
  min cardinality: 0
  on property: has numeric value
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
in scheme: vocab

sequence feature relationship
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: nucleic acid entity
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: nucleic acid entity
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: association
definition: For example, a particular exon is part of a particular transcript or gene
in scheme: vocab

variant to entity association mixin
type: Class
subclass of: Mixin
in scheme: vocab

zygosity
type: Class
subclass of: attribute
in scheme: vocab

context qualifier
type: DatatypeProperty
sub property of: qualifier
definition: Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.
in scheme: vocab

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

knowledge source
type: DatatypeProperty
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.
in scheme: vocab

part of
type: DatatypeProperty
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)
in scheme: vocab
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

sequence localization attribute
type: DatatypeProperty
domain: genomic sequence localization
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.
in scheme: vocab

automated_agent
type: Class
subclass of: AgentTypeEnum
subclass of: PermissibleValue

covalent_binding
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

positive_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

genetic_variant_form
type: Class
subclass of: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subclass of: modified_form

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

dataset version
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: ingest date
subclass of: Restriction
  max cardinality: 1
  on property: has dataset
subclass of: Restriction
  all values from: string
  on property: ingest date
subclass of: Restriction
  all values from: dataset distribution
  on property: has distribution
subclass of: Restriction
  max cardinality: 1
  on property: ingest date
subclass of: Restriction
  min cardinality: 0
  on property: has distribution
subclass of: Restriction
  max cardinality: 1
  on property: has distribution
subclass of: Restriction
  all values from: dataset
  on property: has dataset
subclass of: Restriction
  min cardinality: 0
  on property: has dataset
subclass of: information content entity
definition: an item that holds version level information about a dataset.
in scheme: vocab

entity to feature or disease qualifiers mixin
type: Class
subclass of: frequency qualifier mixin
definition: Qualifiers for entity to disease or phenotype associations.
in scheme: vocab

frequency qualifier mixin
type: Class
subclass of: Mixin
definition: Qualifier for frequency type associations
in scheme: vocab

functional association
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: ontology class
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: macromolecular machine mixin
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
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.
in scheme: vocab

gene grouping mixin
type: Class
subclass of: Mixin
definition: any grouping of multiple genes or gene products
in scheme: vocab

model to disease association mixin
type: Class
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
in scheme: vocab

onset
type: Class
subclass of: clinical course
definition: The age group in which (disease) symptom manifestations appear.
editorial note: This class is in Biolink to support HP ontology annotations which use "onset" (with terms from HP) as an annotation on a disease to phenotypic feature association. This should be the primary use case for this class.
in scheme: vocab

physical entity
type: Class
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: named thing
definition: An entity that has material reality (a.k.a. physical essence).
in scheme: vocab
narrow match: T073

study
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: has study results
subclass of: Restriction
  all values from: study result
  on property: has study results
subclass of: activity
definition: a detailed investigation and/or analysis
in scheme: vocab
narrow match: SIO_000994

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 correlation is believed to exist, as 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). Note also that this predicate can be used in the absence of a direct statistical analysis, if there is other evidence suggesting that a correlation is likely to exist.
in scheme: vocab
canonical predicate: true

creation date
type: DatatypeProperty
range: date
sub property of: node property
alternative label: date started
alternative label: publication date
definition: date on which an entity was created. This can be applied to nodes or edges
in scheme: vocab

dgidb evidence score
type: DatatypeProperty
range: integer
definition: A score defined by DGIdb that is used to report the amount of evidence supporting a given interaction statement, which is simply the sum of all supporting sources and publications. See https://dgidb.org/about/overview/interaction-score.
in scheme: attributes

dgidb interaction score
type: DatatypeProperty
range: float
definition: A score defined by DGIdb that is used to rank interaction record results in DGIdb, which combines their evidence score (based on total supporting sources and pubs), with their relative gene specificity score and relative drug specificity score. See https://dgidb.org/about/overview/interaction-score.
in scheme: attributes

disease context qualifier
type: ObjectProperty
range: disease
sub property of: context qualifier
definition: A context qualifier representing a disease or condition in which a relationship expressed in an association took place.
in scheme: vocab

diseases confidence score
type: DatatypeProperty
range: float
definition: A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale.
in scheme: attributes

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
in scheme: vocab
opposite of: prevented by

evidence count
type: DatatypeProperty
range: integer
sub property of: association slot
definition: The number of evidence instances that are connected to an association.
in scheme: vocab

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

has part
type: DatatypeProperty
sub property of: overlaps
broad match: contains
broad match: FMA contains
broad match: RO_0001019
definition: holds between wholes and their parts (material entities or processes)
in scheme: vocab
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

has quotient
type: DatatypeProperty
range: double
sub property of: aggregate statistic
in scheme: vocab

has total
type: DatatypeProperty
range: integer
sub property of: aggregate statistic
definition: total number of things in a particular reference set
in scheme: vocab

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

iri
type: DatatypeProperty
range: string
definition: An IRI for an entity. This is determined by the id using expansion rules.
in scheme: vocab

iso abbreviation
type: DatatypeProperty
domain: publication
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.
in scheme: vocab

issue
type: DatatypeProperty
domain: publication
sub property of: node property
definition: issue of a newspaper, a scientific journal or magazine for reference purpose
in scheme: vocab

negated
type: DatatypeProperty
range: boolean
sub property of: association slot
definition: if set to true, then the association is negated i.e. is not true
in scheme: vocab

number of cases
type: DatatypeProperty
sub property of: has count
definition: The number of cases in a study or clinical trial, primarily used in conversion of drug approval data.
in scheme: vocab

object derivative qualifier
type: DatatypeProperty
sub property of: derivative 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’. This qualifier is for the object of an association (or statement).
in scheme: vocab

object specialization qualifier
type: DatatypeProperty
range: anyURI
sub property of: specialization qualifier
definition: A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
in scheme: vocab

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
in scheme: vocab
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: SNOMED has direct device

population context qualifier
type: ObjectProperty
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.
in scheme: vocab

published in
type: DatatypeProperty
domain: publication
range: anyURI
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.
in scheme: vocab

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

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
in scheme: vocab
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

sex qualifier
type: ObjectProperty
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.
in scheme: vocab

stage qualifier
type: ObjectProperty
range: life stage
sub property of: statement qualifier
definition: stage during which gene or protein expression of takes place.
in scheme: vocab

subject of treatment application or study for treatment by
type: ObjectProperty
domain: disease or phenotypic feature
range: chemical or drug or treatment
sub property of: related to at instance level
inverse of: treats or applied or studied to treat
in scheme: vocab

supporting study metadata
type: DatatypeProperty
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.
in scheme: vocab
note: Note that these concrete 'supporting study metadata' slots are used only when a more normalized model that leverages the 'supporting studdies' slot and 'Study' class to link to and describe the Study itself are not possible or preferred, such that this study metadata must be captured directly on the edge.
note: This is an abstract slot that groups a set of concrete slots used to directly attach to an association information about a study that produced evidence used to generate the knowledge expressed in the edge.

activation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: positive_modulation

cellular organism
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: organismal entity
in scheme: vocab

chemical mixture
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: drug regulatory status world wide
subclass of: Restriction
  all values from: ApprovalStatusEnum
  on property: drug regulatory status world wide
subclass of: Restriction
  max cardinality: 1
  on property: is supplement
subclass of: Restriction
  all values from: ApprovalStatusEnum
  on property: highest FDA approval status
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  min cardinality: 0
  on property: drug regulatory status world wide
subclass of: Restriction
  min cardinality: 0
  on property: is supplement
subclass of: Restriction
  all values from: string
  on property: is supplement
subclass of: Restriction
  min cardinality: 0
  on property: highest FDA approval status
subclass of: Restriction
  max cardinality: 1
  on property: highest FDA approval status
subclass of: chemical entity
definition: A chemical mixture is a chemical entity composed of two or more molecular entities.
in scheme: vocab
narrow match: NCIT C20401
narrow match: http://snomed.info/id/49616005

entity to disease or phenotypic feature association mixin
type: Class
subclass of: Mixin
in scheme: vocab

gene product mixin
type: Class
subclass of: gene or gene product
definition: The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules.
in scheme: vocab

gene to entity association mixin
type: Class
subclass of: Mixin
in scheme: vocab

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.
in scheme: vocab

molecular activity
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: has output
subclass of: Restriction
  all values from: molecular entity
  on property: has input
subclass of: Restriction
  on property: mixins
  some values from: occurrent
subclass of: Restriction
  max cardinality: 1
  on property: enabled by
subclass of: Restriction
  min cardinality: 0
  on property: has input
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  all values from: macromolecular machine mixin
  on property: enabled by
subclass of: Restriction
  all values from: molecular entity
  on property: has output
subclass of: Restriction
  max cardinality: 1
  on property: has input
subclass of: Restriction
  min cardinality: 0
  on property: enabled by
subclass of: Restriction
  max cardinality: 1
  on property: has output
subclass of: biological process or activity
alternative label: molecular event
alternative label: molecular function
alternative label: reaction
broad match: T045
definition: An execution of a molecular function carried out by a gene product or macromolecular complex.
in scheme: vocab

physical essence or occurrent
type: Class
subclass of: Mixin
definition: Either a physical or processual entity.
in scheme: vocab

thing with taxon
type: Class
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
in scheme: vocab

affected by
type: DatatypeProperty
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.
in scheme: vocab

affects
type: DatatypeProperty
sub property of: related to at instance level
definition: Describes an entity that has an effect on the state or quality of another existing entity.
editorial note: Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects likelihood of' and 'prevents' where the effect concerns whether or when something may or may not come into existence.
in scheme: vocab
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
related match: pathway
canonical predicate: true

has count
type: DatatypeProperty
range: integer
sub property of: aggregate statistic
definition: number of things with a particular property
in scheme: vocab

has output
type: ObjectProperty
domain: biological process or activity
range: named thing
sub property of: has participant
definition: holds between a process and a continuant, where the continuant is an output of the process
in scheme: vocab
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 participant
type: ObjectProperty
domain: biological process or activity
range: occurrent
sub property of: related to at instance level
definition: holds between a process and a continuant, where the continuant is somehow involved in the process
in scheme: vocab
narrow match: has subject
narrow match: BFO_0000167
narrow match: NCIT process involves gene
narrow match: OBI_0000293
narrow match: RO_0002565
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

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
in scheme: vocab

treats or applied or studied to treat
type: ObjectProperty
domain: chemical or drug or treatment
range: disease or phenotypic feature
sub property of: related to at instance level
definition: Holds between an substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to treat the condition, has been observed to be taken/prescribed in practice with the intent of treating the condition, or has been interrogated in a scientific study that hypothesized an ability to treat the condition (in humans or other biological systems/organisms).
editorial note: This predicate is helpful both as a grouping predicate to aid in searching for broader senses of treating a condition, and as a catch-all for representing sources that are not clear about the sense of treats that is being reported. For example, text-mined statements concerning treatments for disease are based on sentences that can report treatment in any of these different senses and thus require a broader predicate such as this to safely report statement semantics.
in scheme: vocab
canonical predicate: true

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

macromolecular machine mixin
type: Class
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.
in scheme: vocab

clinical_trial_phase
type: Class
subclass of: ResearchPhaseEnum
subclass of: PermissibleValue

has attribute
type: ObjectProperty
domain: entity
range: attribute
definition: connects any entity to an attribute
in scheme: vocab
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: 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 input
type: ObjectProperty
domain: biological process or activity
range: named thing
sub property of: has participant
definition: holds between a process and a continuant, where the continuant is an input into the process
in scheme: vocab
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

is sequence variant of
type: ObjectProperty
domain: sequence variant
range: genomic entity
sub property of: related to at instance level
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
in scheme: vocab
narrow match: P3433
canonical predicate: true

related to at concept level
type: DatatypeProperty
type: SymmetricProperty
sub property of: related to
definition: Represents a relationship held between terminology components that describe the conceptual model of a domain.
in scheme: vocab
canonical predicate: true

synonym
type: DatatypeProperty
domain: named thing
range: string
sub property of: node property
alternative label: alias
definition: Alternate human-readable names for a thing
in scheme: vocab
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
in scheme: vocab

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

entity to phenotypic feature association mixin
type: Class
subclass of: Restriction
  on property: mixins
  some values from: frequency quantifier
subclass of: entity to feature or disease qualifiers mixin
in scheme: vocab

genotype
type: Class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  min cardinality: 0
  on property: has zygosity
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  max cardinality: 1
  on property: has zygosity
subclass of: Restriction
  all values from: zygosity
  on property: has zygosity
subclass of: biological entity
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
in scheme: vocab
note: Consider renaming as genotypic entity

population of individual organisms
type: Class
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: organismal entity
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.
in scheme: vocab

transcript
type: Class
subclass of: biological entity
definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
in scheme: vocab

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 Infraction (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).
in scheme: vocab
narrow match: RO_0004029
narrow match: http://snomed.info/id/47429007
canonical predicate: true

clinical approval status
type: ObjectProperty
range: ClinicalApprovalStatusEnum
sub property of: association slot
definition: The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease.
in scheme: vocab

has biological sequence
type: DatatypeProperty
range: string
sub property of: node property
definition: connects a genomic feature to its sequence
in scheme: vocab

max research phase
type: ObjectProperty
range: ResearchPhaseEnum
sub property of: association slot
definition: The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition.
in scheme: vocab

onset qualifier
type: ObjectProperty
range: onset
sub property of: qualifier
definition: a qualifier used in a phenotypic association to state when the phenotype appears is in the subject.
editorial note: This is in Biolink to support HP ontology annotations which use "onset" (with terms from HP) as an annotation on a disease to phenotypic feature association. Please only use it for this purpose. If the intent is to describe the onset of a disease in the context of a treatment, use object_aspect_qualifier and object_direction_qualifier to capture "delayed onset" or "exacerbated onset" slot.
in scheme: vocab

timepoint
type: DatatypeProperty
range: string
alternative label: duration
definition: a point in time
in scheme: vocab

type
type: DatatypeProperty
domain: entity
in scheme: vocab

volume
type: DatatypeProperty
domain: publication
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
in scheme: vocab

inhibition
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: negative_modulation

negative_modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

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.
in scheme: vocab

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.
in scheme: vocab
narrow match: T184
narrow match: T190
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

retrieval source
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: resource role
subclass of: Restriction
  all values from: anyURI
  on property: upstream resource ids
subclass of: Restriction
  all values from: anyURI
  on property: xref
subclass of: Restriction
  min cardinality: 0
  on property: upstream resource ids
subclass of: Restriction
  all values from: anyURI
  on property: resource id
subclass of: Restriction
  all values from: ResourceRoleEnum
  on property: resource role
subclass of: Restriction
  max cardinality: 1
  on property: resource id
subclass of: Restriction
  min cardinality: 0
  on property: source record urls
subclass of: Restriction
  min cardinality: 1
  on property: resource id
subclass of: Restriction
  all values from: anyURI
  on property: source record urls
subclass of: Restriction
  max cardinality: 1
  on property: resource role
subclass of: Restriction
  min cardinality: 0
  on property: xref
subclass of: information content entity
definition: Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.
in scheme: vocab

entity to disease association mixin
type: Class
subclass of: entity to feature or disease qualifiers mixin
definition: mixin class for any association whose object (target node) is a disease
in scheme: vocab

nucleic acid entity
type: Class
subclass of: Restriction
  on property: mixins
  some values from: thing with taxon
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: molecular entity
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.
in scheme: vocab
narrow match: T086
narrow match: T114

study result
type: Class
subclass of: named thing
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.
in scheme: vocab

xref
type: DatatypeProperty
domain: named thing
range: anyURI
alternative label: DbXref
alternative label: Dbxref
alternative label: dbxref
alternative label: record_url
alternative label: source_record_urls
definition: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
in scheme: vocab
narrow match: Dbxref
narrow match: DB Xrefs

organismal entity
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: has attribute
subclass of: Restriction
  all values from: Thing
  on property: has attribute
subclass of: Restriction
  on property: mixins
  some values from: subject of investigation
subclass of: biological entity
definition: A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities
in scheme: vocab
narrow match: T008

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

allelic requirement
type: DatatypeProperty
range: Datatype
  intersection of: string
  intersection of: Datatype
    on datatype: string
    with restrictions:
      pattern: ^HP:\d{7}$
sub property of: association slot
definition: The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance.
in scheme: vocab
note: This edge property may be used by associations between Genes or SequenceVariants and DiseaseOrPhenotypicFeatures to provide the inheritance pattern and genetic context of the relationship. Terms from the HP mode of inheritance sub-ontology (HP:0000005) should be used in the value of this slot. This slot differs from the predicate "has_mode_of_inheritance", in that the predicate is used to link a disease or phenotype with its general inheritance pattern (how it is typically transmitted from one generation to the next, regardless of the specific genetic variant that is present in an individual or instance).

anatomical context qualifier
type: DatatypeProperty
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.
in scheme: vocab

causal mechanism qualifier
type: ObjectProperty
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')
in scheme: vocab

object form or variant qualifier
type: DatatypeProperty
sub property of: form or variant 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’. This qualifier specifies a change in the object of an association (aka: statement).
in scheme: vocab

object part qualifier
type: DatatypeProperty
sub property of: part 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). This qualifier is for the object of an association (or statement).
in scheme: vocab

subject derivative qualifier
type: DatatypeProperty
sub property of: derivative 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’. This qualifier is for the subject of an association (or statement).
in scheme: vocab

subject part qualifier
type: DatatypeProperty
sub property of: part 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). This qualifier is for the subject of an association (or statement).
in scheme: vocab

entity
type: Class
subclass of: Restriction
  all values from: anyURI
  on property: category
subclass of: Restriction
  all values from: attribute
  on property: has attribute
subclass of: Restriction
  max cardinality: 1
  on property: deprecated
subclass of: Restriction
  all values from: string
  on property: type
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: iri
subclass of: Restriction
  max cardinality: 1
  on property: iri
subclass of: Restriction
  all values from: string
  on property: iri
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: category
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: has attribute
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: deprecated
subclass of: Restriction
  all values from: boolean
  on property: deprecated
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: ClassDefinition
definition: Root Biolink Model class for all things and informational relationships, real or imagined.
in scheme: vocab

attribute
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: iri
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  all values from: quantity value
  on property: has quantitative value
subclass of: Restriction
  all values from: string
  on property: iri
subclass of: Restriction
  all values from: named thing
  on property: has qualitative value
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: has qualitative value
subclass of: Restriction
  all values from: ontology class
  on property: has attribute type
subclass of: Restriction
  max cardinality: 1
  on property: has attribute type
subclass of: Restriction
  min cardinality: 0
  on property: has qualitative value
subclass of: Restriction
  max cardinality: 1
  on property: iri
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: has quantitative value
subclass of: Restriction
  min cardinality: 1
  on property: has attribute type
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: named thing
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.
in scheme: vocab

agent
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: affiliation
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  all values from: anyURI
  on property: affiliation
subclass of: Restriction
  all values from: string
  on property: address
subclass of: Restriction
  max cardinality: 1
  on property: address
subclass of: Restriction
  min cardinality: 0
  on property: address
subclass of: administrative entity
alternative label: group
definition: person, group, organization or project that provides a piece of information (i.e. a knowledge association)
in scheme: vocab
narrow match: T092
narrow match: T093
narrow match: T094
narrow match: T095
narrow match: T096
narrow match: SemGroups-v04.txtORGA

clinical trial
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial tested intervention
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial conditions
subclass of: Restriction
  all values from: ResearchPhaseEnum
  on property: clinical trial phase
subclass of: Restriction
  all values from: string
  on property: clinical trial enrollment type
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial enrollment
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial phase
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial overall status
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial enrollment type
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial brief title
subclass of: Restriction
  all values from: disease or phenotypic feature
  on property: clinical trial conditions
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial interventions
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial age range
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial start date
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial intervention model
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial brief title
subclass of: Restriction
  all values from: string
  on property: clinical trial age range
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial enrollment
subclass of: Restriction
  all values from: string
  on property: clinical trial intervention model
subclass of: Restriction
  min cardinality: 0
  on property: creation date
subclass of: Restriction
  all values from: string
  on property: clinical trial primary purpose
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial primary purpose
subclass of: Restriction
  all values from: string
  on property: clinical trial brief title
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial tested intervention
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial enrollment type
subclass of: Restriction
  all values from: integer
  on property: clinical trial enrollment
subclass of: Restriction
  all values from: clinical intervention
  on property: clinical trial interventions
subclass of: Restriction
  all values from: ClinicalTrialStatusEnum
  on property: clinical trial overall status
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial intervention model
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial phase
subclass of: Restriction
  all values from: string
  on property: clinical trial tested intervention
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial age stage
subclass of: Restriction
  all values from: date
  on property: creation date
subclass of: Restriction
  all values from: ClinicalTrialAgeStageEnum
  on property: clinical trial age stage
subclass of: Restriction
  max cardinality: 1
  on property: clinical trial age range
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial overall status
subclass of: Restriction
  all values from: string
  on property: clinical trial start date
subclass of: Restriction
  max cardinality: 1
  on property: creation date
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial primary purpose
subclass of: Restriction
  min cardinality: 0
  on property: clinical trial start date
subclass of: study
definition: A clinical trial is a research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes.
in scheme: vocab

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

name
type: DatatypeProperty
domain: entity
range: string
alternative label: display name
alternative label: label
alternative label: title
definition: A human-readable name for an attribute or entity.
in scheme: vocab
narrow match: title
narrow match: P1476

object context qualifier
type: DatatypeProperty
sub property of: context qualifier
in scheme: vocab

subject context qualifier
type: DatatypeProperty
sub property of: context qualifier
in scheme: vocab

occurrent
type: Class
subclass of: physical essence or occurrent
definition: A processual entity.
in scheme: vocab

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.
in scheme: vocab
narrow match: T019
narrow match: T020
narrow match: T048
narrow match: T049
narrow match: T191
narrow match: MONDO_0042489

qualifier
type: DatatypeProperty
sub property of: association slot
definition: grouping slot for all qualifiers on an edge. useful for testing compliance with association classes
in scheme: vocab

biological process or activity
type: Class
subclass of: Restriction
  all values from: physical entity
  on property: enabled by
subclass of: Restriction
  all values from: named thing
  on property: has input
subclass of: Restriction
  min cardinality: 0
  on property: enabled by
subclass of: Restriction
  all values from: named thing
  on property: has output
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  max cardinality: 1
  on property: enabled by
subclass of: Restriction
  min cardinality: 0
  on property: has input
subclass of: Restriction
  max cardinality: 1
  on property: has output
subclass of: Restriction
  min cardinality: 0
  on property: has output
subclass of: Restriction
  on property: mixins
  some values from: occurrent
subclass of: Restriction
  max cardinality: 1
  on property: has input
subclass of: biological entity
definition: Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.
in scheme: vocab

molecular entity
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  all values from: boolean
  on property: is metabolite
subclass of: Restriction
  min cardinality: 0
  on property: is metabolite
subclass of: Restriction
  max cardinality: 1
  on property: is metabolite
subclass of: chemical entity
definition: A molecular entity is a chemical entity composed of individual or covalently bonded atoms.
in scheme: vocab
narrow match: T085
narrow match: T088
narrow match: CHEBI_23367
narrow match: MolecularEntity

species context qualifier
type: ObjectProperty
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.
in scheme: vocab

subject direction qualifier
type: ObjectProperty
range: DirectionQualifierEnum
sub property of: direction qualifier
definition: Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement).
in scheme: vocab

biological process
type: Class
subclass of: Restriction
  on property: mixins
  some values from: occurrent
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: biological process or activity
broad match: P682
definition: One or more causally connected executions of molecular functions
in scheme: vocab

information content entity
type: Class
subclass of: Restriction
  all values from: date
  on property: creation date
subclass of: Restriction
  min cardinality: 0
  on property: license
subclass of: Restriction
  min cardinality: 0
  on property: creation date
subclass of: Restriction
  max cardinality: 1
  on property: rights
subclass of: Restriction
  max cardinality: 1
  on property: format
subclass of: Restriction
  max cardinality: 1
  on property: creation date
subclass of: Restriction
  min cardinality: 0
  on property: format
subclass of: Restriction
  min cardinality: 0
  on property: rights
subclass of: Restriction
  max cardinality: 1
  on property: license
subclass of: Restriction
  all values from: string
  on property: format
subclass of: Restriction
  all values from: string
  on property: license
subclass of: Restriction
  all values from: 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.
in scheme: vocab
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

organism taxon
type: Class
subclass of: Restriction
  all values from: taxonomic rank
  on property: has taxonomic rank
subclass of: Restriction
  max cardinality: 1
  on property: has taxonomic rank
subclass of: Restriction
  min cardinality: 0
  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.
in scheme: vocab
narrow match: BiologicalSpecies

exposure event
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: exposure type
subclass of: Restriction
  max cardinality: 1
  on property: exposure additional condition
subclass of: Restriction
  max cardinality: 1
  on property: exposure vehicle
subclass of: Restriction
  min cardinality: 0
  on property: exposure magnitude
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  all values from: string
  on property: exposure vehicle
subclass of: Restriction
  max cardinality: 1
  on property: exposure end age
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  all values from: string
  on property: timepoint
subclass of: Restriction
  min cardinality: 0
  on property: exposure additional condition
subclass of: Restriction
  min cardinality: 0
  on property: exposure duration
subclass of: Restriction
  min cardinality: 0
  on property: exposure start age
subclass of: Restriction
  max cardinality: 1
  on property: exposure start age
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: exposure duration
subclass of: Restriction
  max cardinality: 1
  on property: exposure type
subclass of: Restriction
  all values from: string
  on property: exposure magnitude
subclass of: Restriction
  all values from: integer
  on property: exposure start age
subclass of: Restriction
  all values from: time
  on property: exposure duration
subclass of: Restriction
  all values from: integer
  on property: exposure end age
subclass of: Restriction
  all values from: string
  on property: exposure route
subclass of: Restriction
  max cardinality: 1
  on property: timepoint
subclass of: Restriction
  all values from: string
  on property: exposure type
subclass of: Restriction
  max cardinality: 1
  on property: exposure magnitude
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: timepoint
subclass of: Restriction
  min cardinality: 0
  on property: exposure end age
subclass of: Restriction
  max cardinality: 1
  on property: exposure route
subclass of: Restriction
  all values from: string
  on property: exposure additional condition
subclass of: Restriction
  min cardinality: 0
  on property: exposure vehicle
subclass of: Restriction
  min cardinality: 0
  on property: exposure route
subclass of: named thing
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
in scheme: vocab

molecular_modification
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: modulation

gene
type: Class
subclass of: Restriction
  on property: mixins
  some values from: gene or gene product
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  max cardinality: 1
  on property: symbol
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  min cardinality: 0
  on property: xref
subclass of: Restriction
  all values from: string
  on property: symbol
subclass of: Restriction
  all values from: anyURI
  on property: xref
subclass of: Restriction
  min cardinality: 0
  on property: symbol
subclass of: biological entity
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.
in scheme: vocab
narrow match: gene

publication
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  all values from: string
  on property: publication type
subclass of: Restriction
  min cardinality: 1
  on property: publication type
subclass of: Restriction
  all values from: anyURI
  on property: mesh terms
subclass of: Restriction
  min cardinality: 0
  on property: mesh terms
subclass of: Restriction
  min cardinality: 0
  on property: xref
subclass of: Restriction
  min cardinality: 0
  on property: pages
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: string
  on property: summary
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: keywords
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: authors
subclass of: Restriction
  all values from: agent
  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: Restriction
  min cardinality: 0
  on property: summary
subclass of: Restriction
  max cardinality: 1
  on property: summary
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  all values from: anyURI
  on property: xref
subclass of: information content entity
definition: Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).
in scheme: vocab
narrow match: T170
narrow match: IAO_0000013

id
type: DatatypeProperty
domain: entity
definition: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
in scheme: vocab

subject form or variant qualifier
type: DatatypeProperty
sub property of: form or variant 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’. This qualifier specifies a change in the subject of an association (aka: statement).
in scheme: vocab

sequence variant
type: Class
subclass of: Restriction
  on property: mixins
  some values from: genomic entity
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: has biological sequence
subclass of: Restriction
  all values from: string
  on property: has biological sequence
subclass of: Restriction
  all values from: gene
  on property: has gene
subclass of: Restriction
  min cardinality: 0
  on property: hgvs nomenclature
subclass of: Restriction
  all values from: string
  on property: hgvs nomenclature
subclass of: Restriction
  min cardinality: 0
  on property: has biological sequence
subclass of: Restriction
  min cardinality: 0
  on property: has gene
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: biological entity
alternative label: allele
definition: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
in scheme: vocab
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)

biological entity
type: Class
subclass of: Restriction
  on property: mixins
  some values from: thing with taxon
subclass of: named thing
alternative label: bioentity
in scheme: vocab
narrow match: T050
narrow match: T129
narrow match: SIO_010046
narrow match: Q28845870

genomic entity
type: Class
subclass of: Mixin
in scheme: vocab
narrow match: T028
narrow match: GENO_0000897

object aspect qualifier
type: DatatypeProperty
sub property of: aspect 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. This qualifier specifies a change in the object of an association (aka: statement).
in scheme: vocab

anatomical entity
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: organismal entity
definition: A subcellular location, cell type or gross anatomical part
in scheme: vocab
narrow match: T031
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

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.
in scheme: vocab

modulation
type: Class
subclass of: CausalMechanismQualifierEnum
subclass of: PermissibleValue

chemical entity
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: chembl prodrug
subclass of: Restriction
  max cardinality: 1
  on property: is toxic
subclass of: Restriction
  min cardinality: 0
  on property: has chemical role
subclass of: Restriction
  max cardinality: 1
  on property: chembl natural product
subclass of: Restriction
  all values from: string
  on property: max tolerated dose
subclass of: Restriction
  min cardinality: 0
  on property: max tolerated dose
subclass of: Restriction
  min cardinality: 0
  on property: chembl drug warning
subclass of: Restriction
  min cardinality: 0
  on property: trade name
subclass of: Restriction
  min cardinality: 0
  on property: routes of delivery
subclass of: Restriction
  on property: mixins
  some values from: physical essence
subclass of: Restriction
  all values from: string
  on property: chembl drug warning
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or protein or polypeptide
subclass of: Restriction
  min cardinality: 0
  on property: chembl chirality
subclass of: Restriction
  all values from: boolean
  on property: is toxic
subclass of: Restriction
  min cardinality: 0
  on property: is toxic
subclass of: Restriction
  on property: mixins
  some values from: chemical entity or gene or gene product
subclass of: Restriction
  max cardinality: 1
  on property: trade name
subclass of: Restriction
  min cardinality: 0
  on property: available from
subclass of: Restriction
  max cardinality: 1
  on property: chembl availability type
subclass of: Restriction
  all values from: string
  on property: trade name
subclass of: Restriction
  max cardinality: 1
  on property: chembl black box warning
subclass of: Restriction
  all values from: chemical role
  on property: has chemical role
subclass of: Restriction
  max cardinality: 1
  on property: chembl chirality
subclass of: Restriction
  min cardinality: 0
  on property: chembl natural product
subclass of: Restriction
  min cardinality: 0
  on property: chembl availability type
subclass of: Restriction
  all values from: boolean
  on property: chembl natural product
subclass of: Restriction
  all values from: string
  on property: chembl chirality
subclass of: Restriction
  max cardinality: 1
  on property: chembl prodrug
subclass of: Restriction
  max cardinality: 1
  on property: max tolerated dose
subclass of: Restriction
  min cardinality: 0
  on property: chembl black box warning
subclass of: Restriction
  all values from: DrugDeliveryEnum
  on property: routes of delivery
subclass of: Restriction
  max cardinality: 1
  on property: chembl drug warning
subclass of: Restriction
  on property: mixins
  some values from: chemical or drug or treatment
subclass of: Restriction
  all values from: DrugAvailabilityEnum
  on property: available from
subclass of: Restriction
  all values from: boolean
  on property: chembl prodrug
subclass of: Restriction
  all values from: string
  on property: chembl black box warning
subclass of: Restriction
  all values from: string
  on property: chembl availability type
subclass of: named thing
broad match: T167
definition: A chemical entity is a physical entity that pertains to chemistry or biochemistry.
in scheme: vocab
narrow match: T123
narrow match: T131
narrow match: Q43460564

molecular_modification
type: Class
subclass of: GeneOrGeneProductOrChemicalEntityAspectEnum
subclass of: PermissibleValue

chemical or drug or treatment
type: Class
subclass of: Mixin
in scheme: vocab

subject aspect qualifier
type: DatatypeProperty
sub property of: aspect 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. This qualifier specifies a change in the subject of an association (aka: statement).
in scheme: vocab

qualified predicate
type: DatatypeProperty
range: anyURI
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. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats 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 does not 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)
in scheme: vocab

object direction qualifier
type: ObjectProperty
range: DirectionQualifierEnum
sub property of: direction qualifier
definition: Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).
in scheme: vocab

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

disease or phenotypic feature
type: Class
subclass of: Restriction
  on property: mixins
  some values from: ontology class
subclass of: Restriction
  min cardinality: 0
  on property: inheritance
subclass of: Restriction
  all values from: genetic inheritance
  on property: inheritance
subclass of: Restriction
  max cardinality: 1
  on property: inheritance
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.
in scheme: vocab
narrow match: T033

ontology class
type: Class
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.
in scheme: vocab
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

association slot
type: DatatypeProperty
domain: association
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
in scheme: vocab

related to at instance level
type: DatatypeProperty
type: SymmetricProperty
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.
in scheme: vocab
canonical predicate: true

node property
type: DatatypeProperty
domain: named thing
definition: A grouping for any property that holds between a node and a value
in scheme: vocab

association
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: subject category closure
subclass of: Restriction
  all values from: retrieval source
  on property: retrieval source ids
subclass of: Restriction
  max cardinality: 1
  on property: original object
subclass of: Restriction
  min cardinality: 0
  on property: object label closure
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: knowledge level
subclass of: Restriction
  all values from: ontology class
  on property: object category closure
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: subject category
subclass of: Restriction
  max cardinality: 1
  on property: object namespace
subclass of: Restriction
  all values from: integer
  on property: semmed agreement count
subclass of: Restriction
  all values from: ontology class
  on property: qualifiers
subclass of: Restriction
  all values from: string
  on property: primary knowledge source
subclass of: Restriction
  min cardinality: 0
  on property: subject closure
subclass of: Restriction
  min cardinality: 0
  on property: subject namespace
subclass of: Restriction
  max cardinality: 1
  on property: object feature name
subclass of: Restriction
  min cardinality: 0
  on property: has supporting studies
subclass of: Restriction
  max cardinality: 1
  on property: primary knowledge source
subclass of: Restriction
  min cardinality: 0
  on property: retrieval source ids
subclass of: Restriction
  all values from: float
  on property: p value
subclass of: Restriction
  max cardinality: 1
  on property: negated
subclass of: Restriction
  all values from: string
  on property: original subject
subclass of: Restriction
  min cardinality: 0
  on property: object category
subclass of: Restriction
  all values from: string
  on property: object feature name
subclass of: Restriction
  max cardinality: 1
  on property: subject feature name
subclass of: Restriction
  all values from: boolean
  on property: negated
subclass of: Restriction
  all values from: string
  on property: object label closure
subclass of: Restriction
  min cardinality: 0
  on property: supporting text
subclass of: Restriction
  max cardinality: 1
  on property: semmed agreement count
subclass of: Restriction
  min cardinality: 1
  on property: agent type
subclass of: Restriction
  max cardinality: 1
  on property: elevate to prediction
subclass of: Restriction
  all values from: float
  on property: has confidence score
subclass of: Restriction
  all values from: string
  on property: object closure
subclass of: Restriction
  all values from: string
  on property: original object
subclass of: Restriction
  all values from: boolean
  on property: elevate to prediction
subclass of: Restriction
  all values from: ontology class
  on property: subject category closure
subclass of: Restriction
  min cardinality: 0
  on property: timepoint
subclass of: Restriction
  min cardinality: 0
  on property: publications
subclass of: Restriction
  min cardinality: 0
  on property: qualifier
subclass of: Restriction
  all values from: string
  on property: subject closure
subclass of: Restriction
  max cardinality: 1
  on property: knowledge source
subclass of: Restriction
  min cardinality: 0
  on property: original predicate
subclass of: Restriction
  all values from: anyURI
  on property: original predicate
subclass of: Restriction
  min cardinality: 0
  on property: adjusted p value
subclass of: Restriction
  max cardinality: 1
  on property: object category
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: object namespace
subclass of: Restriction
  all values from: string
  on property: timepoint
subclass of: Restriction
  min cardinality: 0
  on property: has evidence of type
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: Restriction
  all values from: string
  on property: subject namespace
subclass of: Restriction
  min cardinality: 0
  on property: elevate to prediction
subclass of: Restriction
  max cardinality: 1
  on property: subject namespace
subclass of: Restriction
  min cardinality: 0
  on property: subject feature name
subclass of: Restriction
  all values from: anyURI
  on property: category
subclass of: Restriction
  min cardinality: 0
  on property: object feature name
subclass of: Restriction
  max cardinality: 1
  on property: agent type
subclass of: Restriction
  all values from: integer
  on property: evidence count
subclass of: Restriction
  all values from: AgentTypeEnum
  on property: agent type
subclass of: Restriction
  min cardinality: 0
  on property: category
subclass of: Restriction
  min cardinality: 0
  on property: p value
subclass of: Restriction
  all values from: information content entity
  on property: has evidence
subclass of: Restriction
  all values from: ontology class
  on property: subject category
subclass of: Restriction
  all values from: evidence type
  on property: has evidence of type
subclass of: Restriction
  max cardinality: 1
  on property: evidence count
subclass of: Restriction
  min cardinality: 0
  on property: knowledge source
subclass of: Restriction
  min cardinality: 0
  on property: has confidence score
subclass of: entity
definition: A typed association between two entities, supported by evidence
in scheme: vocab
note: This is roughly the model used by biolink and ontobio at the moment

named thing
type: Class
subclass of: Restriction
  all values from: anyURI
  on property: xref
subclass of: Restriction
  min cardinality: 1
  on property: category
subclass of: Restriction
  all values from: string
  on property: provided by
subclass of: Restriction
  min cardinality: 0
  on property: synonym
subclass of: Restriction
  all values from: string
  on property: synonym
subclass of: Restriction
  all values from: string
  on property: category
subclass of: Restriction
  min cardinality: 0
  on property: xref
subclass of: Restriction
  max cardinality: 1
  on property: full name
subclass of: Restriction
  all values from: anyURI
  on property: taxon
subclass of: Restriction
  min cardinality: 0
  on property: equivalent identifiers
subclass of: Restriction
  min cardinality: 0
  on property: information content
subclass of: Restriction
  min cardinality: 0
  on property: full name
subclass of: Restriction
  max cardinality: 1
  on property: information content
subclass of: Restriction
  all values from: string
  on property: full name
subclass of: Restriction
  all values from: float
  on property: information content
subclass of: Restriction
  min cardinality: 0
  on property: taxon
subclass of: Restriction
  min cardinality: 0
  on property: provided by
subclass of: Restriction
  all values from: anyURI
  on property: equivalent identifiers
subclass of: Restriction
  max cardinality: 1
  on property: taxon
subclass of: entity
definition: a databased entity or concept/class
in scheme: vocab

predicate
type: DatatypeProperty
range: anyURI
sub property of: association slot
definition: 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
in scheme: vocab

category
type: DatatypeProperty
domain: entity
range: anyURI
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}
in scheme: vocab

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.
in scheme: vocab

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.
in scheme: vocab

Restriction
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: disease
  on property: object
on property: mixins
some values from: entity to disease association mixin

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: case
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
on property: mixins
some values from: case to entity association mixin

Restriction
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: organism taxon
  on property: species context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: species context qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: species context qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
on property: mixins
some values from: macromolecular machine to entity association mixin

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  all values from: string
  on property: name
on property: mixins
some values from: macromolecular machine mixin

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: exposure event
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
on property: mixins
some values from: entity to exposure event association mixin

Restriction
subclass of: Restriction
  all values from: gene
  on property: has gene or gene product
subclass of: Restriction
  min cardinality: 0
  on property: has gene or gene product
on property: mixins
some values from: gene grouping mixin

Restriction
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: drug
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
on property: mixins
some values from: drug to entity association mixin

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: disease or phenotypic feature
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
on property: mixins
some values from: disease or phenotypic feature to entity association mixin

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: disease context qualifier
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: disease context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: disease or phenotypic feature
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: subject specialization qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: object specialization qualifier
subclass of: Restriction
  all values from: anyURI
  on property: subject specialization qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object specialization qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject specialization qualifier
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: object specialization qualifier
subclass of: Restriction
  all values from: disease
  on property: disease context qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: anatomical context qualifier
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: string
  on property: anatomical context qualifier
on property: mixins
some values from: entity to disease or phenotypic feature association mixin

Restriction
subclass of: Restriction
  all values from: chemical entity or gene or gene product
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
on property: mixins
some values from: chemical entity to entity association mixin

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: string
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
on property: mixins
some values from: feature or disease qualifiers to entity mixin

Restriction
subclass of: Restriction
  all values from: string
  on property: has biological sequence
subclass of: Restriction
  max cardinality: 1
  on property: has biological sequence
subclass of: Restriction
  min cardinality: 0
  on property: has biological sequence
on property: mixins
some values from: genomic entity

Restriction
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: sex qualifier
subclass of: Restriction
  all values from: phenotypic feature
  on property: object
subclass of: Restriction
  all values from: biological sex
  on property: sex qualifier
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: sex qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
on property: mixins
some values from: entity to phenotypic feature association mixin

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject direction qualifier
subclass of: Restriction
  all values from: string
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: subject direction qualifier
on property: mixins
some values from: entity to feature or variant qualifiers mixin

Restriction
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  all values from: disease
  on property: disease context qualifier
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: disease context qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject direction qualifier
subclass of: Restriction
  all values from: string
  on property: object aspect qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: disease context qualifier
on property: mixins
some values from: entity to feature or disease qualifiers mixin

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: has quotient
subclass of: Restriction
  all values from: double
  on property: has percentage
subclass of: Restriction
  min cardinality: 0
  on property: has quotient
subclass of: Restriction
  all values from: integer
  on property: has count
subclass of: Restriction
  min cardinality: 0
  on property: has count
subclass of: Restriction
  min cardinality: 0
  on property: has total
subclass of: Restriction
  max cardinality: 1
  on property: has percentage
subclass of: Restriction
  max cardinality: 1
  on property: has count
subclass of: Restriction
  all values from: integer
  on property: has total
subclass of: Restriction
  max cardinality: 1
  on property: has total
subclass of: Restriction
  min cardinality: 0
  on property: has percentage
subclass of: Restriction
  all values from: double
  on property: has quotient
on property: mixins
some values from: frequency quantifier

Restriction
subclass of: Restriction
  all values from: disease
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
on property: mixins
some values from: disease to entity association mixin

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: quantifier qualifier
subclass of: Restriction
  min cardinality: 0
  on property: expression site
subclass of: Restriction
  max cardinality: 1
  on property: phenotypic state
subclass of: Restriction
  min cardinality: 0
  on property: quantifier qualifier
subclass of: Restriction
  max cardinality: 1
  on property: stage qualifier
subclass of: Restriction
  max cardinality: 1
  on property: expression site
subclass of: Restriction
  all values from: ontology class
  on property: quantifier qualifier
subclass of: Restriction
  all values from: disease or phenotypic feature
  on property: phenotypic state
subclass of: Restriction
  min cardinality: 0
  on property: phenotypic state
subclass of: Restriction
  all values from: life stage
  on property: stage qualifier
subclass of: Restriction
  all values from: anatomical entity
  on property: expression site
subclass of: Restriction
  min cardinality: 0
  on property: stage qualifier
on property: mixins
some values from: gene expression mixin

Restriction
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: sex qualifier
subclass of: Restriction
  min cardinality: 0
  on property: sex qualifier
subclass of: Restriction
  all values from: phenotypic feature
  on property: subject
subclass of: Restriction
  all values from: biological sex
  on property: sex qualifier
on property: mixins
some values from: phenotypic feature to entity association mixin

Restriction
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: cell line
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
on property: mixins
some values from: cell line to entity association mixin

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  all values from: string
  on property: id
on property: mixins
some values from: ontology class

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 0
  on property: frequency qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: frequency qualifier
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: UO_0000105
  on property: frequency qualifier
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: subject
on property: mixins
some values from: frequency qualifier mixin

Restriction
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: outcome
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
on property: mixins
some values from: entity to outcome association mixin

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: synonym
subclass of: Restriction
  all values from: anyURI
  on property: xref
subclass of: Restriction
  min cardinality: 0
  on property: xref
subclass of: Restriction
  all values from: string
  on property: synonym
on property: mixins
some values from: gene product mixin

Restriction
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: gene or gene product
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
on property: mixins
some values from: gene to entity association mixin

Restriction
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: material sample
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
on property: mixins
some values from: material sample to entity association mixin

Restriction
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: genotype
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
on property: mixins
some values from: genotype to entity association mixin

Restriction
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: organism taxon
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: object
on property: mixins
some values from: organism taxon to entity association

Restriction
subclass of: Restriction
  all values from: organism taxon
  on property: in taxon
subclass of: Restriction
  max cardinality: 1
  on property: in taxon label
subclass of: Restriction
  max cardinality: 1
  on property: in taxon
subclass of: Restriction
  all values from: string
  on property: in taxon label
subclass of: Restriction
  min cardinality: 0
  on property: in taxon label
subclass of: Restriction
  min cardinality: 0
  on property: in taxon
on property: mixins
some values from: thing with taxon

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: chemical entity or gene or gene product
  on property: subject
subclass of: Restriction
  all values from: anyURI
  on property: predicate
on property: mixins
some values from: chemical to entity association mixin

Restriction
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  all values from: named thing
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: object
on property: mixins
some values from: model to disease association mixin

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: has biological sequence
subclass of: Restriction
  max cardinality: 1
  on property: has biological sequence
subclass of: Restriction
  all values from: string
  on property: has biological sequence
on property: mixins
some values from: epigenomic entity

Restriction
subclass of: Restriction
  all values from: sequence variant
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 1
  on property: object
subclass of: Restriction
  all values from: anyURI
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  min cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: predicate
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  all values from: named thing
  on property: object
on property: mixins
some values from: variant to entity association mixin

Restriction
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: object aspect qualifier
subclass of: Restriction
  all values from: string
  on property: object aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: qualified predicate
subclass of: Restriction
  min cardinality: 0
  on property: subject aspect qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object aspect qualifier
subclass of: Restriction
  min cardinality: 0
  on property: object direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: object direction qualifier
subclass of: Restriction
  min cardinality: 0
  on property: subject direction qualifier
subclass of: Restriction
  max cardinality: 1
  on property: subject aspect qualifier
subclass of: Restriction
  all values from: DirectionQualifierEnum
  on property: object direction qualifier
subclass of: Restriction
  all values from: anyURI
  on property: qualified predicate
subclass of: Restriction
  all values from: string
  on property: subject aspect qualifier
on property: mixins
some values from: entity to feature or gene qualifiers mixin

Restriction
min cardinality: 0
on property: primary knowledge source

Restriction
max cardinality: 1
on property: qualifier

Restriction
min cardinality: 0
on property: object closure

Restriction
min cardinality: 1
on property: knowledge level

Restriction
min cardinality: 0
on property: qualifiers

Restriction
max cardinality: 1
on property: subject category

Restriction
min cardinality: 0
on property: aggregator knowledge source

Restriction
max cardinality: 1
on property: subject

Restriction
min cardinality: 0
on property: update date

Restriction
max cardinality: 1
on property: update date

Restriction
max cardinality: 1
on property: object

Restriction
max cardinality: 1
on property: original predicate

Restriction
max cardinality: 1
on property: timepoint

Restriction
min cardinality: 0
on property: semmed agreement count

Restriction
min cardinality: 0
on property: original subject

Restriction
max cardinality: 1
on property: original subject

Restriction
max cardinality: 1
on property: predicate

Restriction
min cardinality: 0
on property: object category closure

Restriction
max cardinality: 1
on property: adjusted p value

Restriction
max cardinality: 1
on property: has confidence score

Restriction
max cardinality: 1
on property: p value

Restriction
min cardinality: 1
on property: object

Restriction
min cardinality: 0
on property: evidence count

Restriction
min cardinality: 0
on property: has evidence

Restriction
min cardinality: 0
on property: original object

Restriction
min cardinality: 0
on property: negated

Restriction
min cardinality: 0
on property: sources

Restriction
min cardinality: 0
on property: subject label closure