AF

Nodes

And operator

Labels

• AndOperator
• LogicalOperator
• Glyph

Attributes

• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation
• . -(*)-NECESSARY_STIMULATES-(*)-> BiologicalActivity or Phenotype
• . -(*)-HAS_INPUT-(*)-> BiologicalActivity or Phenotype
• . -(*)-NEGATIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-POSITIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-INFLUENCES-(*)-> BiologicalActivity or Phenotype

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Annotation (SBML style)

Labels

• Annotation

Attributes

• qualifier_uri: str
• qualifier_ns: str
• qualifier: str

Relationships

• . -(1)-HAS_RESOURCE-(*)-> Resource

• [...]-(1)-HAS_ANNOTATION-(*)-> .

Comments

See SBML documentation

Bbox

Labels

• Bbox

Attributes

• x: float
• y: float
• w: float
• h: float

Relationships

• [...]-(1)-HAS_BBOX-(1)-> .

Biological activity

Labels

• BiologicalActivity
• Activity
• Glyph

Attributes

• label: str
• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_UNIT_OF_INFORMATION-(*)-> UnitOfInformation
• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(*)-IS_IN_COMPARTMENT-(1)-> Compartment
• . -(1)-HAS_ANNOTATION-(*)-> Annotation
• . -(*)-NECESSARY_STIMULATES-(*)-> BiologicalActivity or Phenotype
• . -(*)-NEGATIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-POSITIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-INFLUENCES-(*)-> BiologicalActivity or Phenotype

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .
• [...]-(*)-NECESSARY_STIMULATES-(*)-> .
• [...]-(*)-HAS_INPUT-(*)-> .
• [...]-(*)-NEGATIVELY_INFLUENCES-(*)-> .
• [...]-(*)-POSITIVELY_INFLUENCES-(*)-> .
• [...]-(*)-INFLUENCES-(*)-> .

Compartment

Labels

• Compartment
• Glyph

Attributes

• label: str
• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• BiologicalActivity or Phenotype-(*)-IS_IN_COMPARTMENT-(1)-> .
• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Delay

Labels

• DelayOperator
• LogicalOperator
• Glyph

Attributes

• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation
• . -(*)-NECESSARY_STIMULATES-(*)-> BiologicalActivity or Phenotype
• . -(*)-HAS_INPUT-(*)-> BiologicalActivity or Phenotype
• . -(*)-NEGATIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-POSITIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-INFLUENCES-(*)-> BiologicalActivity or Phenotype

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

End

Labels

• End

Attributes

• x: float
• y: float

Relationships

• [...]-(1)-HAS_END-(1)-> .

Influence

Labels

• Influence
• Arc

Attributes

• notes: str
• extension: str
• id: str
• class: ArcClass

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_SOURCE-(1)-> [...]
• . -(1)-HAS_TARGET-(1)-> [...]
• . -(1)-HAS_START-(1)-> Start
• . -(1)-HAS_END-(1)-> End
• . -(1)-HAS_NEXT-(*)-> Next
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• Map-(1)-HAS_ARC-(*)-> .

Label

Labels

• Label

Attributes

• text: str

Relationships

Logic arc

Labels

• LogicArc
• Arc

Attributes

• notes: str
• extension: str
• id: str
• class: ArcClass

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_SOURCE-(1)-> [...]
• . -(1)-HAS_TARGET-(1)-> [...]
• . -(1)-HAS_START-(1)-> Start
• . -(1)-HAS_END-(1)-> End
• . -(1)-HAS_NEXT-(*)-> Next
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• Map-(1)-HAS_ARC-(*)-> .

Map

Labels

• Map

Attributes

• notes: str
• extension: str
• id: str
• language: Language

Relationships

• . -(1)-HAS_GLYPH-(*)-> [...]
• . -(1)-HAS_ARC-(*)-> [...]
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

Negative influence

Labels

• NegativeInfluence
• Influence
• Arc

Attributes

• notes: str
• extension: str
• id: str
• class: ArcClass

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_SOURCE-(1)-> [...]
• . -(1)-HAS_TARGET-(1)-> [...]
• . -(1)-HAS_START-(1)-> Start
• . -(1)-HAS_END-(1)-> End
• . -(1)-HAS_NEXT-(*)-> Next
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• Map-(1)-HAS_ARC-(*)-> .

Next

Labels

• Next

Attributes

• x: float
• y: float
• order: int

Relationships

• [...]-(1)-HAS_NEXT-(*)-> .

Not operator

Labels

• NotOperator
• LogicalOperator
• Glyph

Attributes

• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation
• . -(*)-NECESSARY_STIMULATES-(*)-> BiologicalActivity or Phenotype
• . -(*)-HAS_INPUT-(*)-> BiologicalActivity or Phenotype
• . -(*)-NEGATIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-POSITIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-INFLUENCES-(*)-> BiologicalActivity or Phenotype

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Or operator

Labels

• OrOperator
• LogicalOperator
• Glyph

Attributes

• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation
• . -(*)-NECESSARY_STIMULATES-(*)-> BiologicalActivity or Phenotype
• . -(*)-HAS_INPUT-(*)-> BiologicalActivity or Phenotype
• . -(*)-NEGATIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-POSITIVELY_INFLUENCES-(*)-> BiologicalActivity or Phenotype
• . -(*)-INFLUENCES-(*)-> BiologicalActivity or Phenotype

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Phenotype

Labels

• Phenotype
• Activity
• Glyph

Attributes

• label: str
• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_UNIT_OF_INFORMATION-(*)-> UnitOfInformation
• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(*)-IS_IN_COMPARTMENT-(1)-> Compartment
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .
• [...]-(*)-NECESSARY_STIMULATES-(*)-> .
• [...]-(*)-HAS_INPUT-(*)-> .
• [...]-(*)-NEGATIVELY_INFLUENCES-(*)-> .
• [...]-(*)-POSITIVELY_INFLUENCES-(*)-> .
• [...]-(*)-INFLUENCES-(*)-> .

Port

Labels

• Port

Attributes

• id: str
• x: float
• y: float

Relationships

• [...]-(1)-HAS_PORT-(*)-> .
• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .

Positive influence

Labels

• PositiveInfluence
• Influence
• Arc

Attributes

• notes: str
• extension: str
• id: str
• class: ArcClass

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_SOURCE-(1)-> [...]
• . -(1)-HAS_TARGET-(1)-> [...]
• . -(1)-HAS_START-(1)-> Start
• . -(1)-HAS_END-(1)-> End
• . -(1)-HAS_NEXT-(*)-> Next
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• Map-(1)-HAS_ARC-(*)-> .

Resource (inside SBML style annotation)

Labels

• Resource

Attributes

• id: str
• uri: str
• collection_ns: str

Relationships

• Annotation-(1)-HAS_RESOURCE-(*)-> .

Comments

See SBML documentation

Start

Labels

• Start

Attributes

• x: float
• y: float

Relationships

• [...]-(1)-HAS_START-(1)-> .

Submap

Labels

• Submap
• Glyph

Attributes

• label: str
• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_TERMINAL-(*)-> Terminal
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Tag

Labels

• Tag
• Glyph

Attributes

• label: str
• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Terminal

Labels

• Terminal
• AuxilliaryUnit
• Glyph

Attributes

• label: str
• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• Submap-(1)-HAS_TERMINAL-(*)-> .
• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Unit of information

Labels

• UnitOfInformation
• AuxilliaryUnit
• Glyph

Attributes

• prefix: str
• value: str
• type: EntityType (AF only)
• notes: str
• extension: str
• id: str
• class: GlyphClass
• clone: bool
• clone_label: str
• compartmentOrder: float
• oritentation: Orientation

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_BBOX-(1)-> Bbox
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• BiologicalActivity or Phenotype-(1)-HAS_UNIT_OF_INFORMATION-(*)-> .
• [...]-(1)-HAS_SOURCE-(1)-> .
• [...]-(1)-HAS_TARGET-(1)-> .
• Map-(1)-HAS_GLYPH-(*)-> .

Unknown influence

Labels

• UnknownInfluence
• Influence
• Arc

Attributes

• notes: str
• extension: str
• id: str
• class: ArcClass

Relationships

• . -(1)-HAS_PORT-(*)-> Port
• . -(1)-HAS_SOURCE-(1)-> [...]
• . -(1)-HAS_TARGET-(1)-> [...]
• . -(1)-HAS_START-(1)-> Start
• . -(1)-HAS_END-(1)-> End
• . -(1)-HAS_NEXT-(*)-> Next
• . -(1)-HAS_ANNOTATION-(*)-> Annotation

• Map-(1)-HAS_ARC-(*)-> .

Relationships

HAS_UNIT_OF_INFORMATION

Type

• HAS_UNIT_OF_INFORMATION

Source arity

• 1

Source types

• BiologicalActivity
• Phenotype

Target arity

• 1

Target types

• UnitOfInformation

HAS_PORT

Type

• HAS_PORT

Source arity

• 1

Source types

• OrOperator
• AndOperator
• NotOperator
• DelayOperator
• Compartment
• UnitOfInformation
• Terminal
• BiologicalActivity
• Phenotype
• Submap
• Tag
• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

Target arity

• 1

Target types

• Port

HAS_BBOX

Type

• HAS_BBOX

Source arity

• 1

Source types

• OrOperator
• AndOperator
• NotOperator
• DelayOperator
• Compartment
• UnitOfInformation
• Terminal
• BiologicalActivity
• Phenotype
• Submap
• Tag

Target arity

• 1

Target types

• Bbox

HAS_TERMINAL

Type

• HAS_TERMINAL

Source arity

• 1

Source types

• Submap

Target arity

• 1

Target types

• Terminal

IS_IN_COMPARTMENT

Type

• IS_IN_COMPARTMENT

Source arity

• any

Source types

• BiologicalActivity
• Phenotype

Target arity

• any

Target types

• Compartment

HAS_SOURCE

Type

• HAS_SOURCE

Source arity

• 1

Source types

• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

Target arity

• 1

Target types

• OrOperator
• AndOperator
• NotOperator
• DelayOperator
• Compartment
• UnitOfInformation
• Terminal
• BiologicalActivity
• Phenotype
• Submap
• Tag
• Port

HAS_TARGET

Type

• HAS_TARGET

Source arity

• 1

Source types

• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

Target arity

• 1

Target types

• OrOperator
• AndOperator
• NotOperator
• DelayOperator
• Compartment
• UnitOfInformation
• Terminal
• BiologicalActivity
• Phenotype
• Submap
• Tag
• Port

HAS_START

Type

• HAS_START

Source arity

• 1

Source types

• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

Target arity

• 1

Target types

• Start

HAS_END

Type

• HAS_END

Source arity

• 1

Source types

• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

Target arity

• 1

Target types

• End

HAS_NEXT

Type

• HAS_NEXT

Source arity

• 1

Source types

• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

Target arity

• 1

Target types

• Next

HAS_GLYPH

Type

• HAS_GLYPH

Source arity

• 1

Source types

• Map

Target arity

• 1

Target types

• OrOperator
• AndOperator
• NotOperator
• DelayOperator
• Compartment
• UnitOfInformation
• Terminal
• BiologicalActivity
• Phenotype
• Submap
• Tag

HAS_ARC

Type

• HAS_ARC

Source arity

• 1

Source types

• Map

Target arity

• 1

Target types

• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

HAS_RESOURCE

Type

• HAS_RESOURCE

Source arity

• 1

Source types

• Annotation

Target arity

• 1

Target types

• Resource

HAS_ANNOTATION

Type

• HAS_ANNOTATION

Source arity

• 1

Source types

• Map
• OrOperator
• AndOperator
• NotOperator
• DelayOperator
• Compartment
• UnitOfInformation
• Terminal
• BiologicalActivity
• Phenotype
• Submap
• Tag
• Influence
• UnknownInfluence
• PositiveInfluence
• NegativeInfluence
• LogicArc

Target arity

• 1

Target types

• Annotation

NECESSARY_STIMULATES

Type

• NECESSARY_STIMULATES

Source arity

• any

Source types

• BiologicalActivity
• OrOperator
• AndOperator
• NotOperator
• DelayOperator

Target arity

• any

Target types

• BiologicalActivity
• Phenotype

HAS_INPUT

Type

• HAS_INPUT

Source arity

• any

Source types

• OrOperator
• AndOperator
• NotOperator
• DelayOperator

Target arity

• any

Target types

• BiologicalActivity
• Phenotype

NEGATIVELY_INFLUENCES

Type

• NEGATIVELY_INFLUENCES

Source arity

• any

Source types

• BiologicalActivity
• OrOperator
• AndOperator
• NotOperator
• DelayOperator

Target arity

• any

Target types

• BiologicalActivity
• Phenotype

POSITIVELY_INFLUENCES

Type

• POSITIVELY_INFLUENCES

Source arity

• any

Source types

• BiologicalActivity
• OrOperator
• AndOperator
• NotOperator
• DelayOperator

Target arity

• any

Target types

• BiologicalActivity
• Phenotype

INFLUENCES

Type

• INFLUENCES

Source arity

• any

Source types

• BiologicalActivity
• OrOperator
• AndOperator
• NotOperator
• DelayOperator

Target arity

• any

Target types

• BiologicalActivity
• Phenotype