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KGCL Commands.

Example: Rename node.

Class: NodeRename

Command: rename GO:0005635 from 'nuclear envelope' to 'foo bar'

YAML:

id: CHANGE:001
type: NodeRename
old_value: nuclear envelope
new_value: foo bar
about_node: GO:0005635
about_node_representation: curie

Example: Obsolete node.

Class: NodeObsoletion

Command: obsolete GO:0005634

YAML:

id: CHANGE:001
type: NodeObsoletion
about_node: GO:0005634
about_node_representation: curie

Example: Replacement of node after obsoletion.

Class: NodeObsoletionWithDirectReplacement

Command: obsolete GO:0005634 with replacement GO:999

YAML:

id: CHANGE:001
type: NodeObsoletionWithDirectReplacement
about_node: GO:0005634
about_node_representation: curie
has_direct_replacement: GO:999

Example: Addition of a new synonym.

Class: NewSynonym

Command: create exact synonym 'foo' for GO:0005634

YAML:

id: CHANGE:001
type: NewSynonym
new_value: foo
about_node: GO:0005634
about_node_representation: curie
qualifier: exact

Example: Removal of a synonym.

Class: RemoveSynonym

Command: remove synonym 'foo' for GO:0005634

YAML:

id: CHANGE:001
type: RemoveSynonym
old_value: foo
about_node: GO:0005634
about_node_representation: curie

Example: Replace synonym of a node.

Class: SynonymReplacement

Command: change synonym 'cell nucleus' for GO:0005634 to 'cell NUCLEUS'

YAML:

id: CHANGE:001
type: SynonymReplacement
old_value: cell nucleus
new_value: cell NUCLEUS
about_node: GO:0005634
about_node_representation: label

Example: Addition of a node to a subset.

Class: AddNodeToSubset

Command: add GO:0005634 to subset foo

YAML:

id: CHANGE:001
type: AddNodeToSubset
about_node: GO:0005634
about_node_representation: curie
in_subset: foo

Example: Removal of a node from a subset.

Class: RemoveNodeFromSubset

Command: remove GO:0005634 from subset foo

YAML:

id: CHANGE:001
type: RemoveNodeFromSubset
about_node: GO:0005634
about_node_representation: curie
in_subset: foo

Example: Creation of new class.

Class: ClassCreation

Command: create GO:9999999

YAML:

id: CHANGE:001
type: ClassCreation
about_node: GO:9999999
about_node_representation: curie

Example: Creation of new node.

Class: NodeCreation

Command: create node GO:9999999 'foo'

YAML:

id: CHANGE:001
type: NodeCreation
about_node: GO:9999999
about_node_representation: curie
name: foo

Example: Creation of new edge.

Class: EdgeCreation

Command: create edge GO:0005634 BFO:0000050 GO:0009411

YAML:

id: CHANGE:001
type: EdgeCreation
object_type: curie
subject: GO:0005634
predicate: BFO:0000050
object: GO:0009411
subject_type: curie
predicate_type: curie

Example: Place node under another node.

Class: PlaceUnder

Command: create edge GO:0005634 rdfs:subClassOf GO:0009411

YAML:

id: CHANGE:001
type: PlaceUnder
object_type: curie
subject: GO:0005634
predicate: rdfs:subClassOf
object: GO:0009411
subject_type: curie
predicate_type: curie

Example: Change predicate.

Class: PredicateChange

Command: change relationship between GO:0005635 and GO:0005634 from BFO:0000050 to rdfs:subClassOf

YAML:

id: CHANGE:001
type: PredicateChange
old_value: BFO:0000050
new_value: rdfs:subClassOf
old_value_type: curie
new_value_type: curie
about_edge:
  subject: GO:0005635
  predicate: BFO:0000050
  object: GO:0005634
  subject_representation: curie
  predicate_representation: curie
  object_representation: curie

Example: Remove node from under another node.

Class: RemoveUnder

Command: delete edge GO:0005634 rdfs:subClassOf GO:0043231

YAML:

id: CHANGE:001
type: RemoveUnder
object_type: curie
subject: GO:0005634
predicate: rdfs:subClassOf
object: GO:0043231
subject_type: curie
predicate_type: curie

Example: Deletion of an edge.

Class: EdgeDeletion

Command: delete edge GO:0005635 BFO:0000050 GO:0005634

YAML:

id: CHANGE:001
type: EdgeDeletion
object_type: curie
subject: GO:0005635
predicate: BFO:0000050
object: GO:0005634
subject_type: curie
predicate_type: curie

Example: Deepening of a node.

Class: NodeDeepening

Command: deepen GO:0005739 from GO:0043231 to GO:0005634

YAML:

id: CHANGE:001
type: NodeDeepening
old_value: GO:0043231
new_value: GO:0005634
about_edge:
  subject: GO:0005739
  object: GO:0043231
  subject_representation: curie
  object_representation: curie
old_object_type: curie
new_object_type: curie

Example: New definition of a node.

Class: NewTextDefinition

Command: add definition 'this is dummy description' to GO:0005635

YAML:

id: CHANGE:001
type: NewTextDefinition
new_value: this is dummy description
about_node: GO:0005635
about_node_representation: curie

Example: Update defintion of a node.

Class: NodeTextDefinitionChange

Command: change definition of GO:0005635 to 'this is dummy description'

YAML:

id: CHANGE:001
type: NodeTextDefinitionChange
new_value: this is dummy description
about_node: GO:0005635
about_node_representation: curie

Example: Remove definition of a node.

Class: RemoveTextDefinition

Command: remove definition for GO:0005634

YAML:

id: CHANGE:001
type: RemoveTextDefinition
about_node: GO:0005634
about_node_representation: curie