Reactome: A Curated Pathway Database

Attributes of class 'Pathway'

Attribute name Cardinality Value type Allowed classes Attribute origin Value defines instance Db column type
DB_ID 1 INTERNAL_ID N/A DatabaseObject   INTEGER(10) UNSIGNED
_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
NegativeRegulation containedInPathway +
PositiveGeneExpressionRegulation containedInPathway +
PositiveRegulation containedInPathway +
Requirement containedInPathway +
NegativeGeneExpressionRegulation containedInPathway +
Regulation containedInPathway +
BlackBoxEvent templateEvent 1
Regulation regulatedEntity 1
NegativeGeneExpressionRegulation regulatedEntity 1
PositiveRegulation regulatedEntity 1
Requirement regulatedEntity 1
PositiveGeneExpressionRegulation regulatedEntity 1
NegativeRegulation regulatedEntity 1
_Deleted replacementInstances +
VertexSearchableTerm termProvider +
ReactionCoordinates locatedEvent 1
PathwayCoordinates locatedEvent 1
Pathway inferredFrom +
Depolymerisation inferredFrom +
Reaction inferredFrom +
BlackBoxEvent inferredFrom +
FailedReaction inferredFrom +
Event inferredFrom +
Polymerisation inferredFrom +
ReactionlikeEvent inferredFrom +
ConcurrentEventSet concurrentEvents +
ReactionlikeEvent orthologousEvent +
BlackBoxEvent orthologousEvent +
Event orthologousEvent +
FailedReaction orthologousEvent +
Polymerisation orthologousEvent +
Reaction orthologousEvent +
Depolymerisation orthologousEvent +
Pathway orthologousEvent +
FrontPage frontPageItem +
PathwayDiagram representedPathway +
Pathway hasEvent +
BlackBoxEvent hasEvent +
Regulation regulator 1
NegativeGeneExpressionRegulation regulator 1
PositiveGeneExpressionRegulation regulator 1
NegativeRegulation regulator 1
Requirement regulator 1
PositiveRegulation regulator 1
Pathway precedingEvent +
Depolymerisation precedingEvent +
Reaction precedingEvent +
FailedReaction precedingEvent +
Event precedingEvent +
Polymerisation precedingEvent +
BlackBoxEvent precedingEvent +
ReactionlikeEvent precedingEvent +
PathwayVertex representedInstance 1
Pathway normalPathway 1
ReactionCoordinates locationContext 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.