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

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.