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

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.