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Class: EntityToDiseaseAssociation

Description: An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases.
classDiagram class EntityToDiseaseAssociation Association <|-- EntityToDiseaseAssociation EntityToDiseaseAssociation : adjusted_p_value EntityToDiseaseAssociation : agent_type EntityToDiseaseAssociation --|> AgentTypeEnum : agent_type EntityToDiseaseAssociation : aggregator_knowledge_source EntityToDiseaseAssociation : association_basis_qualifier EntityToDiseaseAssociation --|> AssociationBasisEnum : association_basis_qualifier EntityToDiseaseAssociation : category EntityToDiseaseAssociation : clinical_approval_status EntityToDiseaseAssociation --|> ClinicalApprovalStatusEnum : clinical_approval_status EntityToDiseaseAssociation : deprecated EntityToDiseaseAssociation : description EntityToDiseaseAssociation : effect_size EntityToDiseaseAssociation : effect_type EntityToDiseaseAssociation --|> EffectTypeEnum : effect_type EntityToDiseaseAssociation : elevate_to_prediction EntityToDiseaseAssociation : evidence_count EntityToDiseaseAssociation : FDA_regulatory_approvals EntityToDiseaseAssociation : has_attribute EntityToDiseaseAssociation --|> Attribute : has_attribute EntityToDiseaseAssociation : has_confidence_score EntityToDiseaseAssociation : has_evidence EntityToDiseaseAssociation --|> InformationContentEntity : has_evidence EntityToDiseaseAssociation : has_evidence_of_type EntityToDiseaseAssociation --|> EvidenceType : has_evidence_of_type EntityToDiseaseAssociation : has_supporting_studies EntityToDiseaseAssociation --|> Study : has_supporting_studies EntityToDiseaseAssociation : id EntityToDiseaseAssociation : iri EntityToDiseaseAssociation : knowledge_level EntityToDiseaseAssociation --|> KnowledgeLevelEnum : knowledge_level EntityToDiseaseAssociation : knowledge_source EntityToDiseaseAssociation : max_research_phase EntityToDiseaseAssociation --|> ResearchPhaseEnum : max_research_phase EntityToDiseaseAssociation : name EntityToDiseaseAssociation : negated EntityToDiseaseAssociation : number_of_cases EntityToDiseaseAssociation : object EntityToDiseaseAssociation --|> NamedThing : object EntityToDiseaseAssociation : object_category EntityToDiseaseAssociation --|> OntologyClass : object_category EntityToDiseaseAssociation : object_category_closure EntityToDiseaseAssociation --|> OntologyClass : object_category_closure EntityToDiseaseAssociation : object_closure EntityToDiseaseAssociation : object_feature_name EntityToDiseaseAssociation : object_label_closure EntityToDiseaseAssociation : object_namespace EntityToDiseaseAssociation : original_object EntityToDiseaseAssociation : original_predicate EntityToDiseaseAssociation : original_subject EntityToDiseaseAssociation : p_value EntityToDiseaseAssociation : predicate EntityToDiseaseAssociation : primary_knowledge_source EntityToDiseaseAssociation : publications EntityToDiseaseAssociation --|> Publication : publications EntityToDiseaseAssociation : qualifier EntityToDiseaseAssociation : qualifiers EntityToDiseaseAssociation --|> OntologyClass : qualifiers EntityToDiseaseAssociation : retrieval_source_ids EntityToDiseaseAssociation --|> RetrievalSource : retrieval_source_ids EntityToDiseaseAssociation : semmed_agreement_count EntityToDiseaseAssociation : sources EntityToDiseaseAssociation --|> RetrievalSource : sources EntityToDiseaseAssociation : statistical_significance_qualifier EntityToDiseaseAssociation --|> StatisticalSignificanceQualifierEnum : statistical_significance_qualifier EntityToDiseaseAssociation : stringdb_coexpression_score EntityToDiseaseAssociation : stringdb_combined_score EntityToDiseaseAssociation : stringdb_experimental_score EntityToDiseaseAssociation : subject EntityToDiseaseAssociation --|> NamedThing : subject EntityToDiseaseAssociation : subject_category EntityToDiseaseAssociation --|> OntologyClass : subject_category EntityToDiseaseAssociation : subject_category_closure EntityToDiseaseAssociation --|> OntologyClass : subject_category_closure EntityToDiseaseAssociation : subject_closure EntityToDiseaseAssociation : subject_feature_name EntityToDiseaseAssociation : subject_label_closure EntityToDiseaseAssociation : subject_namespace EntityToDiseaseAssociation : supporting_text EntityToDiseaseAssociation : timepoint EntityToDiseaseAssociation : type EntityToDiseaseAssociation : update_date

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
clinical_approval_status:
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. 		0..1
ClinicalApprovalStatusEnum		 direct
max_research_phase:
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. 		0..1
ResearchPhaseEnum		 direct
FDA_regulatory_approvals:
Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536). 		*
String		 direct
number_of_cases:
The number of cases in a study or clinical trial, primarily used in conversion of drug approval data. 		0..1
Integer		 direct
subject:
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. 		1
NamedThing		 Association
predicate:
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 		1
Uriorcurie		 Association
object:
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. 		1
NamedThing		 Association
negated:
if set to true, then the association is negated i.e. is not true 		0..1
Boolean		 Association
qualifier:
grouping slot for all qualifiers on an edge. useful for testing compliance with association classes 		0..1
String		 Association
qualifiers:
connects an association to qualifiers that modify or qualify the meaning of that association 		*
OntologyClass		 Association
publications:
One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement. 		*
Publication		 Association
sources:
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). 		*
RetrievalSource		 Association
has_evidence_of_type:
Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology. 		*
EvidenceType		 Association
has_evidence:
Connects an association to detailed information providing supporting evidence. 		*
InformationContentEntity		 Association
knowledge_source:
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. 		0..1
String		 Association
primary_knowledge_source:
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. 		0..1
String		 Association
aggregator_knowledge_source:
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. 		*
String		 Association
knowledge_level:
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. 		1
KnowledgeLevelEnum		 Association knowledge_assertion, prediction, statistical_association
agent_type:
Describes the high-level category of agent who originally generated a statement of knowledge or other type of information. 		1
AgentTypeEnum		 Association manual_agent, automated_agent, computational_model, text_mining_agent
timepoint:
a point in time 		0..1
TimeType		 Association
original_subject:
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. 		0..1
String		 Association
original_predicate:
used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
Uriorcurie		 Association
original_object:
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. 		0..1
String		 Association
subject_feature_name:
Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene 		0..1
String		 Association
object_feature_name:
Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease 		0..1
String		 Association
subject_category:
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. 		0..1
OntologyClass		 Association biolink:Gene
object_category:
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. 		0..1
OntologyClass		 Association biolink:Disease
subject_closure:
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. 		*
String		 Association
object_closure:
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. 		*
String		 Association ['MONDO:0000167', 'MONDO:0005395']
subject_category_closure:
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. 		*
OntologyClass		 Association ['biolink:Gene', 'biolink:NamedThing']
object_category_closure:
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. 		*
OntologyClass		 Association ['biolink:Disease', 'biolink:NamedThing']
subject_namespace:
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. 		0..1
String		 Association NCBIGene
object_namespace:
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. 		0..1
String		 Association MONDO
subject_label_closure:
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. 		*
String		 Association ['BRCA1']
object_label_closure:
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. 		*
String		 Association breast cancer, cancer
retrieval_source_ids:
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. 		*
RetrievalSource		 Association
p_value:
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. 		0..1
Float		 Association
adjusted_p_value:
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<. 		0..1
Float		 Association
statistical_significance_qualifier:
A statement qualifier that categorizes an association's evidence by statistical significance into coarse bands, as a categorical companion to the numeric 'p value' and 'adjusted p value' slots. It applies only to assessments derived from a quantitative significance statistic (raw p-value, multiple-testing-adjusted p-value, or q-value/FDR), and MUST NOT encode ordinal study-stage, evidence-tier, or confidence-level labels (e.g. clinical trial phases) that are not statistical-significance statements. 		0..1
StatisticalSignificanceQualifierEnum		 Association very_strongly_significant, strongly_significant, significant, suggestive, not_significant
effect_size:
A quantitative measure of the magnitude and direction of an effect or association between the subject and object of an edge, as estimated by a statistical method. The specific metric used (e.g. Cohen's d, odds ratio, Pearson's r) is indicated by the companion 'effect type' slot. 		0..1
Float		 Association
effect_type:
Specifies the statistical metric or method used to compute the numeric value in the companion 'effect size' slot. This disambiguates the effect size value, which is otherwise uninterpretable without knowing the metric (e.g. Cohen's d vs. odds ratio vs. Pearson's r). 		0..1
EffectTypeEnum		 Association cohens_d, odds_ratio, pearsons_r
supporting_text:
The segment of text from a document that supports the mined assertion. 		*
String		 Association Here, we report two new cases of rivaroxaban-induced hepatitis.
has_supporting_studies:
Studies that produced information used as evidence to generate the knowledge expressed in an Association. 		*
Study		 Association
update_date:
date on which an entity was updated. This can be applied to nodes or edges 		0..1
Date		 Association
has_confidence_score:
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. 		0..1
Float		 Association
stringdb_combined_score:
A confidence score assigned by STRING representing the estimated likelihood that two proteins are functionally associated, based on the probabilistic integration of all available evidence channels (e.g., curated databases, experiments, co-expression, evolutionary evidence, and text mining). Higher scores indicate greater confidence in the existence of a biologically meaningful functional association. 		0..1
Float		 Association
stringdb_experimental_score:
A confidence score assigned by STRING representing the estimated likelihood that two proteins are functionally associated based solely on experimental evidence, including laboratory measurements of physical interactions or protein associations. Higher scores indicate stronger experimental support for a biological association between the proteins. 		0..1
Float		 Association
stringdb_coexpression_score:
A confidence score assigned by STRING representing the estimated likelihood that two proteins are functionally associated based solely on evidence that their encoding genes exhibit correlated expression patterns across one or more transcriptomic datasets. Higher scores indicate stronger support for a biological association inferred from gene co-expression. 		0..1
Float		 Association
elevate_to_prediction:
A boolean flag indicating whether a clinical trial finding should be elevated to a prediction. 		0..1
Boolean		 Association
evidence_count:
The number of evidence instances that are connected to an association. 		0..1
Integer		 Association
semmed_agreement_count:
The number of times this concept has been asserted in the SemMedDB literature database. 		0..1
Integer		 Association
association_basis_qualifier:
A statement-level qualifier used with the 'associated with' predicate (or one of its subpredicates) to indicate the biological, clinical, or statistical basis of the asserted association. Use this qualifier when no more specific predicate exists to capture the intended meaning of the association. 		0..1
AssociationBasisEnum		 Association
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 Entity
iri:
An IRI for an entity. This is determined by the id using expansion rules. 		0..1
IriType		 Entity
category:
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} 		*
Uriorcurie		 Entity
type:
rdf:type of biolink:Association should be fixed at rdf:Statement 		*
String		 Entity
name:
A human-readable name for an attribute or entity. 		0..1
LabelType		 Entity
description:
a human-readable description of an entity 		0..1
NarrativeText		 Entity
has_attribute:
connects any entity to an attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

Example values

Slot Name Value
EntityToDiseaseAssociation None
EntityToDiseaseAssociation None
EntityToDiseaseAssociation None
EntityToDiseaseAssociation None

LinkML Source

name: entity to disease association
description: An association between any entity and a disease, capturing clinical context
  such as approval status, research phase, FDA regulatory approvals, and number of
  cases.
examples:
- object:
    subject: CHEBI:50681
    predicate: biolink:in_clinical_trials_for
    object: MONDO:0971091
    category: biolink:EntityToDiseaseAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
- object:
    subject: CHEBI:9150
    predicate: biolink:treats
    object: UMLS:C0520863
    category: biolink:EntityToDiseaseAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
- object:
    subject: CHEBI:28077
    predicate: biolink:applied_to_treat
    object: MONDO:0005011
    category: biolink:EntityToDiseaseAssociation
    knowledge_level: observation
    agent_type: manual_validation_of_automated_agent
- object:
    subject: RXCUI:1367436
    predicate: biolink:contraindicated_in
    object: MONDO:0004981
    category: biolink:EntityToDiseaseAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_validation_of_automated_agent
    publications:
    - a280f164-2833-4f37-96e3-a857c91f77f2
from_schema: https://w3id.org/biolink/vocab/
is_a: association
slots:
- clinical approval status
- max research phase
- FDA regulatory approvals
- number of cases
defining_slots:
- subject
- object