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