Reactome: A Curated Pathway Database

Attributes of class 'PhysicalEntity'

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   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   TEXT
reviewed + INSTANCE InstanceEdit PhysicalEntity   INTEGER(10) UNSIGNED
revised + INSTANCE InstanceEdit PhysicalEntity   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 'PhysicalEntity' instances

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

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.