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Class: MacromolecularMachineHasSubstrateAssociation

Description: 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.

Notes: Using macromolecular machine should cover cases of gene-protein conflation.

classDiagram class MacromolecularMachineHasSubstrateAssociation Association <|-- MacromolecularMachineHasSubstrateAssociation MacromolecularMachineHasSubstrateAssociation : adjusted_p_value MacromolecularMachineHasSubstrateAssociation : agent_type MacromolecularMachineHasSubstrateAssociation --|> AgentTypeEnum : agent_type MacromolecularMachineHasSubstrateAssociation : aggregator_knowledge_source MacromolecularMachineHasSubstrateAssociation : category MacromolecularMachineHasSubstrateAssociation : deprecated MacromolecularMachineHasSubstrateAssociation : description MacromolecularMachineHasSubstrateAssociation : elevate_to_prediction MacromolecularMachineHasSubstrateAssociation : evidence_count MacromolecularMachineHasSubstrateAssociation : has_attribute MacromolecularMachineHasSubstrateAssociation --|> Attribute : has_attribute MacromolecularMachineHasSubstrateAssociation : has_confidence_score MacromolecularMachineHasSubstrateAssociation : has_evidence MacromolecularMachineHasSubstrateAssociation --|> InformationContentEntity : has_evidence MacromolecularMachineHasSubstrateAssociation : has_evidence_of_type MacromolecularMachineHasSubstrateAssociation --|> EvidenceType : has_evidence_of_type MacromolecularMachineHasSubstrateAssociation : has_supporting_studies MacromolecularMachineHasSubstrateAssociation --|> Study : has_supporting_studies MacromolecularMachineHasSubstrateAssociation : id MacromolecularMachineHasSubstrateAssociation : iri MacromolecularMachineHasSubstrateAssociation : knowledge_level MacromolecularMachineHasSubstrateAssociation --|> KnowledgeLevelEnum : knowledge_level MacromolecularMachineHasSubstrateAssociation : knowledge_source MacromolecularMachineHasSubstrateAssociation : name MacromolecularMachineHasSubstrateAssociation : negated MacromolecularMachineHasSubstrateAssociation : object MacromolecularMachineHasSubstrateAssociation --|> ChemicalEntityOrProteinOrPolypeptide : object MacromolecularMachineHasSubstrateAssociation : object_category MacromolecularMachineHasSubstrateAssociation --|> OntologyClass : object_category MacromolecularMachineHasSubstrateAssociation : object_category_closure MacromolecularMachineHasSubstrateAssociation --|> OntologyClass : object_category_closure MacromolecularMachineHasSubstrateAssociation : object_closure MacromolecularMachineHasSubstrateAssociation : object_feature_name MacromolecularMachineHasSubstrateAssociation : object_label_closure MacromolecularMachineHasSubstrateAssociation : object_namespace MacromolecularMachineHasSubstrateAssociation : original_object MacromolecularMachineHasSubstrateAssociation : original_predicate MacromolecularMachineHasSubstrateAssociation : original_subject MacromolecularMachineHasSubstrateAssociation : p_value MacromolecularMachineHasSubstrateAssociation : predicate MacromolecularMachineHasSubstrateAssociation : primary_knowledge_source MacromolecularMachineHasSubstrateAssociation : publications MacromolecularMachineHasSubstrateAssociation --|> Publication : publications MacromolecularMachineHasSubstrateAssociation : qualifier MacromolecularMachineHasSubstrateAssociation : qualifiers MacromolecularMachineHasSubstrateAssociation --|> OntologyClass : qualifiers MacromolecularMachineHasSubstrateAssociation : retrieval_source_ids MacromolecularMachineHasSubstrateAssociation --|> RetrievalSource : retrieval_source_ids MacromolecularMachineHasSubstrateAssociation : semmed_agreement_count MacromolecularMachineHasSubstrateAssociation : sources MacromolecularMachineHasSubstrateAssociation --|> RetrievalSource : sources MacromolecularMachineHasSubstrateAssociation : subject MacromolecularMachineHasSubstrateAssociation --|> MacromolecularMachineMixin : subject MacromolecularMachineHasSubstrateAssociation : subject_category MacromolecularMachineHasSubstrateAssociation --|> OntologyClass : subject_category MacromolecularMachineHasSubstrateAssociation : subject_category_closure MacromolecularMachineHasSubstrateAssociation --|> OntologyClass : subject_category_closure MacromolecularMachineHasSubstrateAssociation : subject_closure MacromolecularMachineHasSubstrateAssociation : subject_feature_name MacromolecularMachineHasSubstrateAssociation : subject_label_closure MacromolecularMachineHasSubstrateAssociation : subject_namespace MacromolecularMachineHasSubstrateAssociation : supporting_text MacromolecularMachineHasSubstrateAssociation : timepoint MacromolecularMachineHasSubstrateAssociation : type MacromolecularMachineHasSubstrateAssociation : update_date

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
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
MacromolecularMachineMixin		 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
ChemicalEntityOrProteinOrPolypeptide		 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
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
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
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
MacromolecularMachineHasSubstrateAssociation None
MacromolecularMachineHasSubstrateAssociation None

LinkML Source

name: macromolecular machine has substrate association
description: 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.
notes:
- Using macromolecular machine should cover cases of gene-protein conflation.
examples:
- object:
    subject: NCBIGene:6530
    predicate: biolink:has_substrate
    object: CHEBI:5557
    category: biolink:MacromolecularMachineHasSubstrateAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
- object:
    subject: NCBIGene:50719
    predicate: biolink:has_substrate
    object: UNII:UID84303EL
    category: biolink:MacromolecularMachineHasSubstrateAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
from_schema: https://w3id.org/biolink/vocab/
is_a: association
slot_usage:
  subject:
    name: subject
    range: macromolecular machine mixin
  predicate:
    name: predicate
    subproperty_of: has substrate
  object:
    name: object
    range: chemical entity or protein or polypeptide