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