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

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.