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