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
__is_ghost 1 OTHER N/A DatabaseObject   ENUM('TRUE')
_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
Depolymerisation input +
FailedReaction input +
BlackBoxEvent input +
Reaction input +
ReactionlikeEvent input +
Polymerisation input +
Complex entityOnOtherCell +
Reaction entityOnOtherCell +
ReactionlikeEvent entityOnOtherCell +
Polymerisation entityOnOtherCell +
Depolymerisation entityOnOtherCell +
FailedReaction entityOnOtherCell +
BlackBoxEvent entityOnOtherCell +
EntityFunctionalStatus physicalEntity 1
CatalystActivity physicalEntity 1
Reaction output +
ReactionlikeEvent output +
Polymerisation output +
FailedReaction output +
Depolymerisation output +
BlackBoxEvent output +
_Deleted replacementInstances +
Polymerisation requiredInputComponent +
ReactionlikeEvent requiredInputComponent +
Reaction requiredInputComponent +
BlackBoxEvent requiredInputComponent +
Depolymerisation requiredInputComponent +
FailedReaction requiredInputComponent +
CandidateSet hasCandidate +
Complex hasComponent +
DefinedSet inferredTo +
PhysicalEntity inferredTo +
GenomeEncodedEntity inferredTo +
CandidateSet inferredTo +
Polymer inferredTo +
OtherEntity inferredTo +
EntityWithAccessionedSequence inferredTo +
OpenSet inferredTo +
EntitySet inferredTo +
Complex inferredTo +
SimpleEntity inferredTo +
CandidateSet inferredFrom +
GenomeEncodedEntity inferredFrom +
Polymer inferredFrom +
OtherEntity inferredFrom +
PhysicalEntity inferredFrom +
DefinedSet inferredFrom +
EntitySet inferredFrom +
OpenSet inferredFrom +
EntityWithAccessionedSequence inferredFrom +
SimpleEntity inferredFrom +
Complex inferredFrom +
ConcurrentEventSet focusEntity +
NegativeRegulation regulator 1
PositiveRegulation regulator 1
Requirement regulator 1
Regulation regulator 1
VertexSearchableTerm termProvider +
Regulation activeUnit +
Requirement activeUnit +
PositiveRegulation activeUnit +
NegativeRegulation activeUnit +
CatalystActivity activeUnit +
DefinedSet hasMember +
EntitySet hasMember +
OpenSet hasMember +
CandidateSet hasMember +
Polymer repeatedUnit +
EntityVertex representedInstance 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.