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