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

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.