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

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.