Reactome: A Curated Pathway Database

Attributes of class 'PhysicalEntity'

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