Reactome: A Curated Pathway Database

Attributes of class 'Pathway'

Attribute name Cardinality Value type Allowed classes Attribute origin Value defines instance Db column type
_displayName 1 TEXT N/A DatabaseObject   TEXT
_doRelease 1 OTHER N/A Event   ENUM('TRUE','FALSE')
_timestamp 1 OTHER N/A DatabaseObject   TIMESTAMP
authored + INSTANCE InstanceEdit Event   INTEGER(10) UNSIGNED
compartment + INSTANCE Compartment Event   INTEGER(10) UNSIGNED
created 1 INSTANCE InstanceEdit DatabaseObject   INTEGER(10) UNSIGNED
crossReference + INSTANCE DatabaseIdentifier Event   INTEGER(10) UNSIGNED
definition 1 TEXT N/A Event   TEXT
disease + INSTANCE Disease Event   INTEGER(10) UNSIGNED
doi 1 TEXT N/A Pathway   VARCHAR(64)
edited + INSTANCE InstanceEdit Event   INTEGER(10) UNSIGNED
evidenceType 1 INSTANCE EvidenceType Event   INTEGER(10) UNSIGNED
figure + INSTANCE Figure Event   INTEGER(10) UNSIGNED
goBiologicalProcess 1 INSTANCE GO_BiologicalProcess Event   INTEGER(10) UNSIGNED
hasEvent + INSTANCE Event Pathway ALL INTEGER(10) UNSIGNED
inferredFrom + INSTANCE Event Event   INTEGER(10) UNSIGNED
isCanonical 1 OTHER N/A Pathway   ENUM('TRUE','FALSE')
literatureReference + INSTANCE Publication Event   INTEGER(10) UNSIGNED
modified + INSTANCE InstanceEdit DatabaseObject   INTEGER(10) UNSIGNED
name + TEXT N/A Event   TEXT
normalPathway 1 INSTANCE Pathway Pathway   INTEGER(10) UNSIGNED
orthologousEvent + INSTANCE Event Event   INTEGER(10) UNSIGNED
precedingEvent + INSTANCE Event Event   INTEGER(10) UNSIGNED
relatedSpecies + INSTANCE Species Event   INTEGER(10) UNSIGNED
releaseDate 1 OTHER N/A Event   date
releaseStatus 1 TEXT N/A Event   TEXT
reviewed + INSTANCE InstanceEdit Event   INTEGER(10) UNSIGNED
revised + INSTANCE InstanceEdit Event   INTEGER(10) UNSIGNED
species + INSTANCE Species Event   INTEGER(10) UNSIGNED
stableIdentifier 1 INSTANCE StableIdentifier DatabaseObject   INTEGER(10) UNSIGNED
summation + INSTANCE Summation Event   INTEGER(10) UNSIGNED

Referers of class 'Pathway' instances

Class name Attribute name Cardinality
ReactionCoordinates locatedEvent 1
PathwayCoordinates locatedEvent 1
FailedReaction orthologousEvent +
Pathway orthologousEvent +
Reaction orthologousEvent +
BlackBoxEvent orthologousEvent +
ReactionlikeEvent orthologousEvent +
Event orthologousEvent +
Polymerisation orthologousEvent +
Depolymerisation orthologousEvent +
Pathway hasEvent +
BlackBoxEvent hasEvent +
VertexSearchableTerm termProvider +
Pathway normalPathway 1
BlackBoxEvent templateEvent 1
ConcurrentEventSet concurrentEvents +
Requirement regulatedEntity 1
PositiveRegulation regulatedEntity 1
NegativeGeneExpressionRegulation regulatedEntity 1
Regulation regulatedEntity 1
PositiveGeneExpressionRegulation regulatedEntity 1
NegativeRegulation regulatedEntity 1
PathwayVertex representedInstance 1
FrontPage frontPageItem +
Requirement containedInPathway +
NegativeRegulation containedInPathway +
PositiveGeneExpressionRegulation containedInPathway +
Regulation containedInPathway +
PositiveRegulation containedInPathway +
NegativeGeneExpressionRegulation containedInPathway +
PathwayDiagram representedPathway +
ReactionCoordinates locationContext 1
Pathway precedingEvent +
Reaction precedingEvent +
BlackBoxEvent precedingEvent +
FailedReaction precedingEvent +
Polymerisation precedingEvent +
Depolymerisation precedingEvent +
Event precedingEvent +
ReactionlikeEvent precedingEvent +
FailedReaction inferredFrom +
Pathway inferredFrom +
Reaction inferredFrom +
BlackBoxEvent inferredFrom +
ReactionlikeEvent inferredFrom +
Event inferredFrom +
Depolymerisation inferredFrom +
Polymerisation inferredFrom +
_Deleted replacementInstances +
NegativeRegulation regulator 1
PositiveGeneExpressionRegulation regulator 1
Regulation regulator 1
NegativeGeneExpressionRegulation regulator 1
PositiveRegulation regulator 1
Requirement regulator 1

You can find documentation for the Reactome data model here.

Sidebar on the left shows the hierarchy of Reactome classes. The number of instances of this class is shown in square brackets and is hyperlinked to a page listing all instances in this class.

The main panel shows attributes of the selected class. Own attributes, i.e. the ones which are not inherited from a parent class are indicated in colour.

'+' in 'Cardinality' column indicates that this is a multi-value attribute.

'Value defines instance' column indicates the attributes the values of which determine instance identity and are used to check if an identical instance has been stored in the database already. 'ALL' indicates that that all of the values of a given attribute must be identical while 'ANY' shows that identity of any single value of a given attribute is enough. Of course, if the identity is defined by multiple attributes each of them has to match.