Class: Pathway
URI: base:Pathway
classDiagram
class Pathway
OntologyClass <|-- Pathway
ComputationalProcess <|-- Pathway
Pathway : category
Pathway : description
Pathway : enabled_by
Pathway : has_attribute
Pathway : has_input
Pathway : has_output
Pathway : id
Pathway : in_taxon
Pathway : iri
Pathway : name
Pathway : provided_by
Pathway : type
Pathway : xref
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| description | 0..1 NarrativeText |
a human-readable description of an entity | Entity |
| in_taxon | 0..1 SystemTaxon |
connects an entity to its taxonomic classification | ThingWithTaxon |
| has_output | 0..1 ComputationalProcessOrActivity |
holds between a process and a continuant, where the continuant is an output o... | ComputationalProcessOrActivity |
| xref | 0..* xsd:anyURI |
Alternate CURIEs for a thing | NamedThing |
| has_input | 0..1 ComputationalProcessOrActivity |
holds between a process and a continuant, where the continuant is an input in... | ComputationalProcessOrActivity |
| id | 1..1 NONE |
A unique identifier for an entity | OntologyClass, Entity |
| has_attribute | 0..* Attribute |
connects any entity to an attribute | Entity |
| iri | 0..1 IriType |
An IRI for an entity | Entity |
| type | 0..1 NONE |
Entity | |
| enabled_by | 0..1 SystemEntity |
holds between a process and an entity, where the entity executes the process | ComputationalProcessOrActivity |
| provided_by | 0..* NONE |
The value in this node property represents the knowledge provider that create... | NamedThing |
| category | 0..* CategoryType |
Name of the high level ontology class in which this entity is categorized | Entity |
| name | 0..1 LabelType |
A human-readable name for an attribute or entity | Entity |
Usages
| used by | used in | type | used |
|---|---|---|---|
| ClassToPathwayAssociation | object | range | Pathway |
| OperationalActivityToPathwayAssociation | object | range | Pathway |
| ControlToPathwayAssociation | object | range | Pathway |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/lmodel/base
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | base:Pathway |
| native | base:Pathway |
| exact | WIKIDATA:Q4915012, sumo:pathInSystem |
| narrow | csrc:trusted_path, sumo:ContinuousPath, sumo:ComputerPath |
LinkML Source
Direct
name: pathway
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- WIKIDATA:Q4915012
- sumo:pathInSystem
narrow_mappings:
- csrc:trusted_path
- sumo:ContinuousPath
- sumo:ComputerPath
rank: 1000
is_a: computational process
mixins:
- ontology class
Induced
name: pathway
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- WIKIDATA:Q4915012
- sumo:pathInSystem
narrow_mappings:
- csrc:trusted_path
- sumo:ContinuousPath
- sumo:ComputerPath
rank: 1000
is_a: computational process
mixins:
- ontology class
attributes:
id:
name: id
description: A unique identifier for an entity. Must be either a CURIE shorthand
for a URI or a complete URI
in_subset:
- translator_minimal
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- dct:identifier
- EDAM-DATA:0842
- EFO:id
- REPR:id
- schema:identifier
- SIO:000115
- sumo:Identifier
narrow_mappings:
- dwc:eventID
- dwc:parentEventID
- dwc:identificationID
- dwc:systemID
- CSO:bicm-id
- SIO:000672
- SIO:000674
- ERO:0000044
- ERO:0000480
- NCIT:C94069
- REPR:doi
- SIO:000328
- SIO:000729
- schema:productID
- schema:taxID
- sumo:AccountID
- sumo:AlphaIDString
- sumo:AlphaNumericIDString
- sumo:AgentID
- sumo:CountryID
- sumo:CustomerID
- sumo:currencyCode
- sumo:DistrictID
- sumo:EmployeeID
- sumo:IsoCode
- sumo:LocalizablePlaceID
- sumo:userIDString
- sumo:urlString
- sumo:UniformResourceLocator
- WIKIDATA_PROPERTY:P3743
broad_mappings:
- CSO:catalogue_identifiers
- IAO:0000603
- IAO:0000119
- sumo:identityElement
rank: 1000
identifier: true
alias: id
owner: pathway
domain_of:
- NamedThing
- ontology class
- entity
range: string
required: true
has input:
name: has input
annotations:
canonical_predicate:
tag: canonical_predicate
value: 'True'
opposite_of:
tag: opposite_of
value: has output
description: holds between a process and a continuant, where the continuant is
an input into the process
in_subset:
- translator_minimal
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- RO:0002233
close_mappings:
- RO:0002352
narrow_mappings:
- LOINC:has_fragments_for_synonyms
- LOINC:has_system
- RO:0002590
- RO:0004009
rank: 1000
is_a: has participant
domain: occurrent
multivalued: true
inherited: true
alias: has_input
owner: pathway
domain_of:
- computational process or activity
range: computational process or activity
has output:
name: has output
annotations:
canonical_predicate:
tag: canonical_predicate
value: 'True'
opposite_of:
tag: opposite_of
value: has input
description: holds between a process and a continuant, where the continuant is
an output of the process
in_subset:
- translator_minimal
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- RO:0002234
close_mappings:
- RO:0002353
- RO:0002354
narrow_mappings:
- RO:0002296
- RO:0002297
- RO:0002299
- RO:0002588
- RO:0004008
rank: 1000
is_a: has participant
domain: occurrent
multivalued: true
inherited: true
alias: has_output
owner: pathway
domain_of:
- computational process or activity
range: computational process or activity
enabled by:
name: enabled by
annotations:
opposite_of:
tag: opposite_of
value: prevented by
description: holds between a process and an entity, where the entity executes
the process
in_subset:
- translator_minimal
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- RO:0002333
rank: 1000
is_a: has participant
domain: computational process or activity
multivalued: true
inherited: true
alias: enabled_by
owner: pathway
domain_of:
- computational process or activity
inverse: enables
range: system entity
in taxon:
name: in taxon
annotations:
canonical_predicate:
tag: canonical_predicate
value: 'True'
description: connects an entity to its taxonomic classification. Only certain
kinds of entities can be taxonomically classified; see 'thing with taxon'
in_subset:
- translator_minimal
from_schema: https://w3id.org/lmodel/base
aliases:
- instance of
- is system source of subclasses
- system has class
- class found in system
- subclasses has system source
exact_mappings:
- RO:0002162
- WIKIDATA_PROPERTY:P703
narrow_mappings:
- RO:0002160
rank: 1000
is_a: related to at instance level
domain: thing with taxon
multivalued: true
inherited: true
alias: in_taxon
owner: pathway
domain_of:
- thing with taxon
range: system taxon
provided by:
name: provided by
description: 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.
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- pav:providedBy
- WIKIDATA:Q68974939
rank: 1000
is_a: node property
domain: named thing
multivalued: true
alias: provided_by
owner: pathway
domain_of:
- named thing
range: string
xref:
name: xref
description: Alternate CURIEs for a thing
in_subset:
- translator_minimal
from_schema: https://w3id.org/lmodel/base
aliases:
- dbxref
- Dbxref
- DbXref
exact_mappings:
- WIKIDATA:Q1302249
narrow_mappings:
- dwc:identificationReferences
- gr:relatedWebService
- NCIT:hasDbXref
rank: 1000
is_a: node property
domain: named thing
multivalued: true
alias: xref
owner: pathway
domain_of:
- named thing
- publication
- class
- subclasses mixin
range: uriorcurie
iri:
name: iri
description: An IRI for an entity. This is determined by the id using expansion
rules.
comments:
- see also https://url.spec.whatwg.org/#goals
in_subset:
- translator_minimal
- samples
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- rr:IRI
- WIKIDATA_PROPERTY:P854
- WIKIDATA:Q424583
- XAPI:IRI
close_mappings:
- NCIT:C165071
- sumo:UniformResourceLocator
related_mappings:
- dwc:usewithiri
narrow_mappings:
- RO:0002617
rank: 1000
alias: iri
owner: pathway
domain_of:
- attribute
- entity
range: iri type
category:
name: category
description: "Name of the high level ontology class in which this entity is categorized.\
\ Corresponds to the label for the base entity type class.\n * In a neo4j database\
\ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\
\ be a base model class URI.\nThis field is multi-valued. It should include\
\ values for ancestors of the base class\nIn an RDF database, nodes will typically\
\ have an rdf:type triples. This can be to the most specific base class, or\
\ potentially to a class more specific than something in base."
from_schema: https://w3id.org/lmodel/base
rank: 1000
is_a: type
domain: entity
multivalued: true
designates_type: true
alias: category
owner: pathway
domain_of:
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
- entity
is_class_field: true
range: category type
required: true
pattern: ^base:\d+$
type:
name: type
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- dct:type
- IAO:0000219
- NCIT:C25284
- schema:type
- SWO:type
- sumo:Class
- WIKIDATA:Q21146257
- WIKIDATA_PROPERTY:P427
narrow_mappings:
- CTRL:DataType
- CTRL:SemanticType
- dwc:measurementType
- GR:typeOfGood
- IAO:0000411
- sumo:hardwareType
- WIKIDATA:Q190087
broad_mappings:
- SIO:000011
- RO:0002473
- IAO:0006011
rank: 1000
slot_uri: rdf:type
alias: type
owner: pathway
domain_of:
- entity
range: string
name:
name: name
description: A human-readable name for an attribute or entity.
in_subset:
- translator_minimal
- samples
from_schema: https://w3id.org/lmodel/base
aliases:
- label
- display name
- title
exact_mappings:
- CSO:named_entity
- gr:name
- OM:name
- REPR:name
- schema:name
- SIO:000116
- sumo:Name
- WIKIDATA_PROPERTY:P2561
close_mappings:
- IAO:0000111
- IAO:0000118
- skos:altLabel
- sumo:originalTitle
narrow_mappings:
- AML:hasAttributeName
- dct:title
- NCIT:P386
- WIKIDATA_PROPERTY:P1476
- rr:column
- rr:tableName
- schema:recordLabel
broad_mappings:
- CSO:named_entity
rank: 1000
slot_uri: rdfs:label
alias: name
owner: pathway
domain_of:
- NamedThing
- attribute
- entity
- assembly mixin
range: label type
description:
name: description
description: a human-readable description of an entity
in_subset:
- translator_minimal
from_schema: https://w3id.org/lmodel/base
aliases:
- definition
exact_mappings:
- dct:description
- IAO:0000115
- schema:description
- skos:definitions
- sumo:NarrativeText
- WIKIDATA:Q1200750
close_mappings:
- sumo:Descriptor
narrow_mappings:
- csrc:architecture_description
- CSO:architecture_description
- CSO:concept_description
- CSO:shape_description
- OM:longcomment
rank: 1000
slot_uri: dct:description
alias: description
owner: pathway
domain_of:
- NamedThing
- entity
range: narrative text
has attribute:
name: has attribute
description: connects any entity to an attribute
in_subset:
- samples
from_schema: https://w3id.org/lmodel/base
exact_mappings:
- AML:hasAttribute
- CTRL:hasParameter
- ssn:hasProperty
- SIO:000008
close_mappings:
- sumo:hasVariable
- sumo:property
narrow_mappings:
- AML:hasAttributeName
- AML:hasDescription
- AML:hasICID
- AML:hasName
- AML:hasProject
- AML:hasUnit
- AML:hasSchemaVersion
- AML:hasVersionSUC
- AML:hasWriterVersion
- schema:hasPart
- CDAO:has_Character
- CDAO:has_Root
- CDAO:has_First_Coordinate_Item
- CDAO:has_Coordinate
- CDAO:has_Change_Component
- CDAO:has_Datum
- CDAO:has_Node
- CDAO:has_Annotation
- CDAO:has_Remaining_Coordinate_List
- CDAO:has_State
- CDAO:has_Element
- CTRL:hasApplicationLogic
- CTRL:hasInput
- CTRL:hasMedium
- CTRL:hasOutput
- CTRL:isConnectedTo
- CTRL:isSupervisedBy
- dct:hasPart
- dct:hasFormat
- dct:hasVersion
- EFO:is_executed_in
- EFO:0006351
- geolink:hasAuthoritativeDigitalRepository
- geolink:hasRelatedSample
- geolink:hasAffiliation
- geolink:hasAuthor
- geolink:hasCollector
- geolink:hasContact
- geolink:hasContributor
- geolink:hasCollectionEndDate
- geolink:hasCollectionStartDate
- geolink:hasCreator
- geolink:hasDataset
- geolink:hasEditor
- geolink:hasEducator
- geolink:hasFirstAppearance
- geolink:hasIdentifierScheme
- geolink:hasObserver
- geolink:hasObservationArea
- geolink:hasOwner
- geolink:hasParticipant
- geolink:hasParticipationEndTime
- geolink:hasParticipationStartTime
- geolink:hasPart
- geolink:hasPublicationDate
- geolink:hasRegistrationDate
- geolink:hasStartDate
- geolink:hasRepository
- geolink:hasRightsHolder
- geolink:hasScheduler
- geolink:hasTimeStamp
- geolink:hasVendor
- gr:hasBusinessFunction
- gr:hasBrand
- gr:hasCurrency
- gr:hasEligibleQuantity
- gr:hasGlobalLocationNumber
- gr:hasInventoryLevel
- gr:hasManufacturer
- gr:hasMakeAndModel
- gr:hasNext
- gr:hasPrevious
- gr:hasUnitOfMeasurement
- gr:hasValue
- IAO:0000039
- IAO:0000407
- LOINC:has_action_guidance
- LOINC:has_adjustment
- LOINC:has_aggregation_view
- LOINC:has_approach_guidance
- LOINC:has_divisor
- LOINC:has_exam
- LOINC:has_method
- LOINC:has_modality_subtype
- LOINC:has_object_guidance
- LOINC:has_scale
- LOINC:has_suffix
- LOINC:has_time_aspect
- LOINC:has_time_modifier
- LOINC:has_timing_of
- NCIT:is_qualified_by
- NCIT:qualifier_applies_to
- NCIT:has_data_element
- NCIT:role_has_domain
- NCIT:role_has_range
- NCIT:C62618
- OM:hasPhenomenon
- RO:0002002
- RO:0000053
- RO:0000086
- RO:0000087
- RO:0002520
- RO:0002018
- RO:0002017
- RO:0002013
- RO:0002016
- RO:0002025
- RO:0002521
- RO:0002348
- RO:0002566
- RO:0002002
- RO:0002338
- RO:0002339
- RO:0002573
- RO:0009004
- SAN:hasActuatingCapability
- SAN:hasActuatingProperty
- SAN:hasDateTime
- SAN:hasEffect
- SAN:hasWriter
- SIO:000011
- SIO:000586
- SIO:001277
- SIO:000671
- SIO:000312
- SIO:000552
- SIO:000420
- SIO:000253
- SIO:000132
- SIO:000255
- SIO:000008
- SIO:000364
- SIO:000230
- SIO:000235
- SIO:000234
- SIO:000228
- SIO:000229
- SIO:000900
- SIO:000905
- SIO:000221
- SIO:000225
- SIO:000223
- SIO:000217
- SIO:000291
- SIO:000054
- SIO:000059
- SIO:000028
- SIO:000139
- SIO:000772
- SIO:000641
- SIO:000635
- SIO:000066
- SIO:001279
- SIO:000300
- SIO:001278
- SIO:000680
- SIO:000681
- SIO:000679
- SIO:000673
- SIO:000369
- SIO:000053
- SIO:000972
- SIO:000971
- SIO:000273
- SIO:000644
- SIO:000974
- SIO:000553
- SIO:000145
- SWO:0004000
- sosa:hasFeatureOfInterest
- sosa:hasSample
- ssn:hasSubSystem
- ssn:isProxyFor
- ssn-system:hasSystemCapability
- ssn-system:hasSystemProperty
- ssn-system:hasOperatingRange
- ssn-system:hasOperatingProperty
- ssn-system:hasSurvivalRange
- ssn-system:hasSurvivalProperty
- ssn-system:inCondition
- sumo:hasAcrossVariable
- sumo:hasAccount
- sumo:hasAward
- sumo:hasDependency
- sumo:hasDimension
- sumo:hasExpertise
- sumo:hasGUEState
- sumo:hasOccupation
- sumo:hasPurpose
- sumo:hasPurposeForAgent
- sumo:hasSkill
- sumo:hasThroughVariable
- sumo:hasUniform
- sumo:hasVariable
- sumo:holdsRight
- SWO:9001002
- SWO:0004001
- SWO:9000067
- SWO:0004002
- SWO:0000087
- SWO:0000086
- SWO:0004004
- SWO:0000741
- SWO:0004002
- SWO:3000054
- SWO:0004000
rank: 1000
domain: entity
multivalued: true
alias: has_attribute
owner: pathway
domain_of:
- entity
range: attribute