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

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.