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Class: MaterialSampleDerivationAssociation

Description: An association between a material sample and the material entity from which it is derived.
classDiagram class MaterialSampleDerivationAssociation Association <|-- MaterialSampleDerivationAssociation MaterialSampleDerivationAssociation : agent_type MaterialSampleDerivationAssociation --|> AgentTypeEnum : agent_type MaterialSampleDerivationAssociation : aggregator_knowledge_source MaterialSampleDerivationAssociation : category MaterialSampleDerivationAssociation : deprecated MaterialSampleDerivationAssociation : description MaterialSampleDerivationAssociation : has_attribute MaterialSampleDerivationAssociation --|> Attribute : has_attribute MaterialSampleDerivationAssociation : has_evidence MaterialSampleDerivationAssociation --|> EvidenceType : has_evidence MaterialSampleDerivationAssociation : id MaterialSampleDerivationAssociation : iri MaterialSampleDerivationAssociation : knowledge_level MaterialSampleDerivationAssociation --|> KnowledgeLevelEnum : knowledge_level MaterialSampleDerivationAssociation : knowledge_source MaterialSampleDerivationAssociation : name MaterialSampleDerivationAssociation : negated MaterialSampleDerivationAssociation : object MaterialSampleDerivationAssociation --|> NamedThing : object MaterialSampleDerivationAssociation : object_category MaterialSampleDerivationAssociation --|> OntologyClass : object_category MaterialSampleDerivationAssociation : object_category_closure MaterialSampleDerivationAssociation --|> OntologyClass : object_category_closure MaterialSampleDerivationAssociation : object_closure MaterialSampleDerivationAssociation : object_label_closure MaterialSampleDerivationAssociation : object_namespace MaterialSampleDerivationAssociation : original_object MaterialSampleDerivationAssociation : original_predicate MaterialSampleDerivationAssociation : original_subject MaterialSampleDerivationAssociation : predicate MaterialSampleDerivationAssociation : primary_knowledge_source MaterialSampleDerivationAssociation : publications MaterialSampleDerivationAssociation --|> Publication : publications MaterialSampleDerivationAssociation : qualifier MaterialSampleDerivationAssociation : qualifiers MaterialSampleDerivationAssociation --|> OntologyClass : qualifiers MaterialSampleDerivationAssociation : retrieval_source_ids MaterialSampleDerivationAssociation --|> RetrievalSource : retrieval_source_ids MaterialSampleDerivationAssociation : subject MaterialSampleDerivationAssociation --|> MaterialSample : subject MaterialSampleDerivationAssociation : subject_category MaterialSampleDerivationAssociation --|> OntologyClass : subject_category MaterialSampleDerivationAssociation : subject_category_closure MaterialSampleDerivationAssociation --|> OntologyClass : subject_category_closure MaterialSampleDerivationAssociation : subject_closure MaterialSampleDerivationAssociation : subject_label_closure MaterialSampleDerivationAssociation : subject_namespace MaterialSampleDerivationAssociation : timepoint MaterialSampleDerivationAssociation : type

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
subject:
the material sample being described
1..1
MaterialSample
direct
predicate:
derivation relationship
1..1
PredicateType
direct
object:
the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.
1..1
NamedThing
direct
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
0..*
OntologyClass
Association
publications:
One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
0..*
Publication
Association
has_evidence:
connects an association to an instance of supporting evidence
0..*
EvidenceType
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.
0..*
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..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..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_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.
0..*
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.
0..*
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.
0..*
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.
0..*
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.
0..*
String
Association ['BRACA1']
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.
0..*
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.
0..*
RetrievalSource
Association
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
1..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}
0..*
Uriorcurie
Entity
type:
rdf:type of biolink:Association should be fixed at rdf:Statement
0..*
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
0..*
Attribute
Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid.
0..1
Boolean
Entity

LinkML Source

name: material sample derivation association
description: An association between a material sample and the material entity from
  which it is derived.
from_schema: https://w3id.org/biolink/biolink-model
is_a: association
slots:
- subject
- predicate
- object
slot_usage:
  subject:
    name: subject
    description: the material sample being described
    domain_of:
    - association
    - cell line to entity association mixin
    - chemical entity to entity association mixin
    - drug to entity association mixin
    - chemical to entity association mixin
    - case to entity association mixin
    - chemical to chemical association
    - named thing associated with likelihood of named thing association
    - material sample to entity association mixin
    - material sample derivation association
    - disease to entity association mixin
    - entity to exposure event association mixin
    - entity to outcome association mixin
    - frequency qualifier mixin
    - entity to phenotypic feature association mixin
    - disease or phenotypic feature to entity association mixin
    - entity to disease or phenotypic feature association mixin
    - genotype to entity association mixin
    - gene to entity association mixin
    - variant to entity association mixin
    - model to disease association mixin
    - macromolecular machine to entity association mixin
    - organism taxon to entity association
    range: material sample
  object:
    name: object
    description: the material entity the sample was derived from. This may be another
      material sample, or any other material entity, including for example an organism,
      a geographic feature, or some environmental material.
    domain_of:
    - association
    - cell line to entity association mixin
    - chemical entity to entity association mixin
    - drug to entity association mixin
    - chemical to entity association mixin
    - case to entity association mixin
    - chemical to chemical association
    - named thing associated with likelihood of named thing association
    - material sample to entity association mixin
    - material sample derivation association
    - disease to entity association mixin
    - entity to exposure event association mixin
    - entity to outcome association mixin
    - frequency qualifier mixin
    - entity to phenotypic feature association mixin
    - disease or phenotypic feature to entity association mixin
    - entity to disease or phenotypic feature association mixin
    - genotype to entity association mixin
    - gene to entity association mixin
    - variant to entity association mixin
    - model to disease association mixin
    - macromolecular machine to entity association mixin
    - organism taxon to entity association
  predicate:
    name: predicate
    description: derivation relationship
    domain_of:
    - predicate mapping
    - association
    - cell line to entity association mixin
    - chemical entity to entity association mixin
    - drug to entity association mixin
    - chemical to entity association mixin
    - case to entity association mixin
    - chemical to chemical association
    - named thing associated with likelihood of named thing association
    - material sample to entity association mixin
    - material sample derivation association
    - disease to entity association mixin
    - entity to exposure event association mixin
    - entity to outcome association mixin
    - frequency qualifier mixin
    - entity to phenotypic feature association mixin
    - disease or phenotypic feature to entity association mixin
    - entity to disease or phenotypic feature association mixin
    - genotype to entity association mixin
    - gene to entity association mixin
    - variant to entity association mixin
    - model to disease association mixin
    - macromolecular machine to entity association mixin
    - organism taxon to entity association
    subproperty_of: derives from
defining_slots:
- subject
- predicate