Reactome: A Curated Pathway Database

Attributes of class 'GenomeEncodedEntity'

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
_timestamp 1 OTHER N/A DatabaseObject   TIMESTAMP
authored 1 INSTANCE InstanceEdit PhysicalEntity   INTEGER(10) UNSIGNED
cellType 1 INSTANCE CellType PhysicalEntity ALL INTEGER(10) UNSIGNED
compartment + INSTANCE EntityCompartment PhysicalEntity ALL INTEGER(10) UNSIGNED
created 1 INSTANCE InstanceEdit DatabaseObject   INTEGER(10) UNSIGNED
crossReference + INSTANCE DatabaseIdentifier PhysicalEntity   INTEGER(10) UNSIGNED
definition 1 TEXT N/A PhysicalEntity   TEXT
disease + INSTANCE Disease PhysicalEntity   INTEGER(10) UNSIGNED
edited + INSTANCE InstanceEdit PhysicalEntity   INTEGER(10) UNSIGNED
figure + INSTANCE Figure PhysicalEntity   INTEGER(10) UNSIGNED
goCellularComponent 1 INSTANCE GO_CellularComponent PhysicalEntity   INTEGER(10) UNSIGNED
inferredFrom + INSTANCE PhysicalEntity PhysicalEntity   INTEGER(10) UNSIGNED
inferredTo + INSTANCE PhysicalEntity PhysicalEntity   INTEGER(10) UNSIGNED
literatureReference + INSTANCE Publication PhysicalEntity   INTEGER(10) UNSIGNED
modified + INSTANCE InstanceEdit DatabaseObject   INTEGER(10) UNSIGNED
name + TEXT N/A PhysicalEntity ANY TEXT
reviewed + INSTANCE InstanceEdit PhysicalEntity   INTEGER(10) UNSIGNED
revised + INSTANCE InstanceEdit PhysicalEntity   INTEGER(10) UNSIGNED
species 1 INSTANCE Taxon
Species
GenomeEncodedEntity ALL INTEGER(10) UNSIGNED
stableIdentifier 1 INSTANCE StableIdentifier DatabaseObject   INTEGER(10) UNSIGNED
summation + INSTANCE Summation PhysicalEntity   INTEGER(10) UNSIGNED
systematicName 1 TEXT N/A PhysicalEntity   TEXT

Referers of class 'GenomeEncodedEntity' instances

Class name Attribute name Cardinality
NegativeGeneExpressionRegulation regulator 1
Requirement regulator 1
PositiveGeneExpressionRegulation regulator 1
NegativeRegulation regulator 1
PositiveRegulation regulator 1
Regulation regulator 1
Complex hasComponent +
OpenSet hasMember +
DefinedSet hasMember +
EntitySet hasMember +
CandidateSet hasMember +
Reaction input +
Polymerisation input +
BlackBoxEvent input +
Depolymerisation input +
FailedReaction input +
ReactionlikeEvent input +
EntityVertex representedInstance 1
BlackBoxEvent output +
Depolymerisation output +
Reaction output +
Polymerisation output +
ReactionlikeEvent output +
FailedReaction output +
CandidateSet hasCandidate +
OpenSet inferredTo +
PhysicalEntity inferredTo +
CandidateSet inferredTo +
SimpleEntity inferredTo +
Complex inferredTo +
GenomeEncodedEntity inferredTo +
EntityWithAccessionedSequence inferredTo +
EntitySet inferredTo +
DefinedSet inferredTo +
Polymer inferredTo +
OtherEntity inferredTo +
Polymer repeatedUnit +
BlackBoxEvent entityOnOtherCell +
Depolymerisation entityOnOtherCell +
Reaction entityOnOtherCell +
Polymerisation entityOnOtherCell +
Complex entityOnOtherCell +
ReactionlikeEvent entityOnOtherCell +
FailedReaction entityOnOtherCell +
BlackBoxEvent requiredInputComponent +
Depolymerisation requiredInputComponent +
Reaction requiredInputComponent +
Polymerisation requiredInputComponent +
ReactionlikeEvent requiredInputComponent +
FailedReaction requiredInputComponent +
EntityFunctionalStatus physicalEntity 1
CatalystActivity physicalEntity 1
VertexSearchableTerm termProvider +
ConcurrentEventSet focusEntity +
GenomeEncodedEntity inferredFrom +
EntityWithAccessionedSequence inferredFrom +
Complex inferredFrom +
SimpleEntity inferredFrom +
CandidateSet inferredFrom +
OpenSet inferredFrom +
PhysicalEntity inferredFrom +
OtherEntity inferredFrom +
Polymer inferredFrom +
EntitySet inferredFrom +
DefinedSet inferredFrom +
CatalystActivity activeUnit +
NegativeGeneExpressionRegulation activeUnit +
PositiveRegulation activeUnit +
Regulation activeUnit +
NegativeRegulation activeUnit +
PositiveGeneExpressionRegulation activeUnit +
Requirement activeUnit +
_Deleted replacementInstances +

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.