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

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.