Comparative Data Analysis Ontology
type: Ontology
version IRI: cdao.owl
imports: ontology-metadata.owl
coverage: Comparison of two or more biological entities of the same class when the similarities and differences of the entities are treated explicitly as the product of an evolutionary process of descent with modification.
creator: CDAO Team
description: The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.
subject: comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics
license: http://creativecommons.org/publicdomain/zero/1.0/

has_Character
type: ObjectProperty
sub property of: has
domain: CharacterStateDataMatrix
range: Character
description: This property associates a character data matrix with a character (a column) represented in the matrix.

belongs_to_Edge_as_Child
type: ObjectProperty
sub property of: belongs_to_Edge
inverse of: has_Child_Node
domain: Node
range: DirectedEdge
description: The property links a Node to the Edge it belongs to in the child position.

has_Ancestor
type: ObjectProperty
sub property of: has
inverse of: has_Descendant
type: TransitiveProperty
domain: Node
range: Node
description: The property links a node to any of the other nodes that are its ancestors in a rooted tree.

has_Nucleotide_State
type: ObjectProperty
sub property of: has_State
domain: DesoxiRibonucleotideResidueStateDatum
range: Class
  union of: Generic_State
  union of: DesoxiRibonucleotideResidue
description: This property associates a nucleotide character-state instance with a state value from the domain of nucleotide states.

belongs_to_Edge
type: ObjectProperty
sub property of: belongs_to
domain: Node
range: Edge
description: The property links a Node to one of the edges that are incident on such node.

belongs_to_Character_State_Data_Matrix
type: ObjectProperty
sub property of: belongs_to
domain: Class
  union of: Character
  union of: TU
range: CharacterStateDataMatrix

has_Root
type: ObjectProperty
sub property of: has
inverse of: belongs_to_Tree_as_Root
type: FunctionalProperty
domain: RootedTree
range: Node
description: The property links a rooted tree to the specific node that represents the unique root of the tree.

has_Child
type: ObjectProperty
sub property of: has_Descendant
inverse of: has_Parent
domain: Node
range: Node
property chain axiom: belongs_to_Edge_as_Parent
property chain axiom: has_Child_Node
description: The property links a node to a node that is an immediate descendant in the tree.

has_First_Coordinate_Item
type: ObjectProperty
sub property of: has
domain: CoordinateList
range: Class
  union of: CoordinatePoint
  union of: CoordinateRange
description: The property that relates a coordinate list to the first item in the list.

has_Coordinate
type: ObjectProperty
sub property of: has
domain: CharacterStateDatum
range: DatumCoordinate

belongs_to_Continuous_Character
type: ObjectProperty
sub property of: belongs_to_Character
type: FunctionalProperty
domain: ContinuousStateDatum
range: ContinuousCharacter

has_Datum
type: ObjectProperty
sub property of: has
domain: Class
  union of: Character
  union of: TU
range: CharacterStateDatum
description: This property relates a character to a state datum for the character.

has_Standard_Datum
type: ObjectProperty
sub property of: has_Categorical_Datum
domain: Class
  union of: StandardCharacter
  union of: TU
range: StandardStateDatum

subtree_of
type: ObjectProperty
domain: Network
range: Network
description: This property links two networks where the latter is a substructure of the former

has_Amino_Acid_State
type: ObjectProperty
sub property of: has_State
domain: AminoAcidResidueStateDatum
range: Class
  union of: Generic_State
  union of: AminoAcidResidue
description: This property associates a amino acid character-state instance with a state value from the domain of amino acid states.

is_annotation_of
type: ObjectProperty
inverse of: has_Annotation
domain: CDAOAnnotation
range: Thing

has_RNA_Datum
type: ObjectProperty
sub property of: has_Molecular_Datum

has_Left_State
type: ObjectProperty
sub property of: has_Change_Component
domain: hereditaryChange
range: CharacterStateDomain
description: This property relates a transformation to a 'left' state (the state associated with the 'left' node).

precedes
type: ObjectProperty

exclude
type: ObjectProperty

has_Node
type: ObjectProperty
sub property of: has
domain: Edge
range: Node
description: Property that associates to each Edge the Nodes it connects.

nca_node_of
type: ObjectProperty
domain: Node
range: SetOfNodes

has_External_Reference
type: ObjectProperty
domain: TU
range: Thing
comment: Associates a TU to some external taxonomy reference.

has_Coordinate_System
type: ObjectProperty
domain: DatumCoordinate
range: CoordinateSystem
description: This property links a coordinate to the coordinate system it references.

belongs_to_Nucleotide_Character
type: ObjectProperty
sub property of: belongs_to_Character
type: FunctionalProperty
domain: DesoxiRibonucleotideResidueStateDatum
range: DesoxiRibonucleotideResidueCharacter

connects_to
type: ObjectProperty
type: SymmetricProperty

has_Amino_Acid_Datum
type: ObjectProperty
sub property of: has_Molecular_Datum
domain: Class
  union of: AminoAcidResidueCharacter
  union of: TU
range: AminoAcidResidueStateDatum
description: This property relates an amino acid character (a column in a protein sequence alignment) to a state datum for the character (an individual cell in the alignment column).

hereditary_change_of
type: ObjectProperty
range: Character
description: This property relates a type of evolutionary change (an Edge_Transformation) to the character that undergoes the change. The change is a transformation_of the affected character.

has_Compound_Datum
type: ObjectProperty
sub property of: has_Categorical_Datum
domain: Class
  union of: CompoundCharacter
  union of: TU
range: CompoundStateDatum
description: This property relates a compound character (a character with some states that are subdividable) to a state datum for the character.

has_Descendants
type: ObjectProperty
sub property of: has
domain: CommonAncestralNode
range: SetOfNodes

reconciliation_of
type: ObjectProperty
domain: ReconcileTree
range: Tree

belongs_to_Amino_Acid_Character
type: ObjectProperty
sub property of: belongs_to_Character
type: FunctionalProperty
domain: AminoAcidResidueStateDatum
range: AminoAcidResidueCharacter

has_Descendant
type: ObjectProperty
sub property of: has
type: TransitiveProperty
domain: Node
range: Node
description: A property that links a node to any of its descendants in a rooted tree.

has_Continuous_State
type: ObjectProperty
sub property of: has_State
domain: ContinuousStateDatum
range: Continuous
description: This property associates a character-state instance with a state value on a continuous numeric scale.

has_Type
type: ObjectProperty
sub property of: has

belongs_to_Edge_as_Parent
type: ObjectProperty
sub property of: belongs_to_Edge
inverse of: has_Parent_Node
domain: Node
range: DirectedEdge
description: The property links a Node to one of the Edges where the node appears in the parent position (i.e., closer to the root).

has
type: ObjectProperty
inverse of: part_of
description: Generic 'has' property.

has_Parent
type: ObjectProperty
sub property of: has_Ancestor
domain: Node
range: Node
property chain axiom: belongs_to_Edge_as_Child
property chain axiom: has_Parent_Node
description: The property that links a node to its unique parent in a rooted tree.

belongs_to_Compound_Character
type: ObjectProperty
sub property of: belongs_to_Character
domain: CompoundStateDatum
range: CompoundCharacter

homologous_to
type: ObjectProperty
domain: CharacterStateDatum
range: CharacterStateDatum
description: This propery relates different instances of the same character, including the case when the states of the character differ (e.g., large_beak of beak_size_character of TU A is homologous_to small_beak of beak_size_character of TU B).

has_Change_Component
type: ObjectProperty
sub property of: has
domain: hereditaryChange
description: This property relates a transformation to the components that compose it.

has_Categorical_Datum
type: ObjectProperty
sub property of: has_Datum

has_State
type: ObjectProperty
sub property of: has
domain: CharacterStateDatum
range: CharacterStateDomain
description: This property associates a character-state instance with its state value, e.g., a state value expressed in terms of an imported domain ontology.

has_Left_Node
type: ObjectProperty
sub property of: has_Change_Component
domain: hereditaryChange
range: Node
description: This property relates a transformation to a 'left' node (the node that has the 'left' state).

has_Right_State
type: ObjectProperty
sub property of: has_Change_Component
domain: hereditaryChange
range: CharacterStateDomain
description: This property relates a transformation to a 'right' state (the state associated with the 'right' node).

represents_TU
type: ObjectProperty
inverse of: represented_by_Node
type: FunctionalProperty
domain: Node
range: TU
description: This property relates a TU or taxonomic unit (typically associated with character data) to a phylogenetic history (Tree).

exclude_Node
type: ObjectProperty
sub property of: exclude
range: Node

has_Compound_State
type: ObjectProperty
sub property of: has_State
domain: CompoundStateDatum
range: Class
  union of: Generic_State
  union of: Compound
description: This property associates a compound character-state instance with its compound state value.

belongs_to
type: ObjectProperty
equivalent property: part_of
domain: Thing
range: Thing
description: Generic property that links a concept to another concept it is a constituent of. The property is a synonym of part_of.

belongs_to_TU
type: ObjectProperty
sub property of: belongs_to
type: FunctionalProperty
domain: CharacterStateDatum
range: TU
description: This property relates a character-state datum to its TU.

belongs_to_Network
type: ObjectProperty
sub property of: belongs_to
domain: Class
  union of: Edge
  union of: Node
range: Network

has_Annotation
type: ObjectProperty
sub property of: has
domain: Thing
range: CDAOAnnotation

part_of
type: ObjectProperty

has_Nucleotide_Datum
type: ObjectProperty
sub property of: has_Molecular_Datum
domain: Class
  union of: DesoxiRibonucleotideResidueCharacter
  union of: TU
range: DesoxiRibonucleotideResidueStateDatum
description: This property relates a nucleotide character (a column in a nucleotide alignment) to a state datum for the character (an individual cell in the alignment column).

represented_by_Node
type: ObjectProperty
domain: TU
range: Node
description: This property relates a TU to a node that represents it in a network.

has_Remaining_Coordinate_List
type: ObjectProperty
sub property of: has
domain: CoordinateList
range: CoordinateList
description: The property that relates a coordinate list to the item in the list beyond the first item.

has_Element
type: ObjectProperty
sub property of: has
domain: SetOfThings

exclude_Subtree
type: ObjectProperty
sub property of: exclude
range: Subtree

belongs_to_Tree
type: ObjectProperty
sub property of: belongs_to
domain: Class
  union of: Edge
  union of: Node
range: Tree

has_Parent_Node
type: ObjectProperty
sub property of: has_Node
type: FunctionalProperty
domain: DirectedEdge
range: Node
description: Associates to a Directed Edge the Node that is in the parent position in the edge (i.e., the node touched by the edge and closer to the root of the tree)

has_Lineage_node
type: ObjectProperty
sub property of: has
domain: Lineage
range: Node

belongs_to_Tree_as_Root
type: ObjectProperty
sub property of: belongs_to
domain: Node
range: Tree

has_Hereditary_Change
type: ObjectProperty
sub property of: has
domain: Edge
range: hereditaryChange

belongs_to_Character
type: ObjectProperty
sub property of: belongs_to
type: FunctionalProperty
domain: CharacterStateDatum
range: Character

has_Molecular_Datum
type: ObjectProperty
sub property of: has_Categorical_Datum
domain: Class
  union of: MolecularCharacter
  union of: TU
range: MolecularStateDatum

has_Continuous_Datum
type: ObjectProperty
sub property of: has_Datum
domain: Class
  union of: ContinuousCharacter
  union of: TU
range: ContinuousStateDatum
description: This property relates a continuous character to a state datum for the character.

has_TU
type: ObjectProperty
sub property of: has
domain: CharacterStateDataMatrix
range: TU
description: This property associates a character data matrix with a TU (a row) represented in the matrix.

has_Child_Node
type: ObjectProperty
sub property of: has_Node
type: FunctionalProperty
domain: DirectedEdge
range: Node
description: The property associates to a Directed Edge the Node that is in the child position in the edge, i.e., the node touched by the edge and closer to the leaves of the tree.

has_Right_Node
type: ObjectProperty
sub property of: has_Change_Component
domain: hereditaryChange
range: Node
description: This property relates a transformation to a 'right' node (the node that has the 'right' state).

has_Precision
type: DatatypeProperty
range: float

has_Point_Coordinate_Value
type: DatatypeProperty
domain: CoordinatePoint
range: integer

has_Int_Value
type: DatatypeProperty
sub property of: has_Value
range: int

has_Support_Value
type: DatatypeProperty
range: float

has_Value
type: DatatypeProperty

has_Uncertainty_Factor
type: DatatypeProperty
range: float

has_Range_End_Value
type: DatatypeProperty
domain: CoordinateRange
range: integer

has_Float_Value
type: DatatypeProperty
sub property of: has_Value
range: float

has_Range_Start_Value
type: DatatypeProperty
domain: CoordinateRange
range: integer

DesoxiRibonucleotideResidueStateDatum
type: Class
subclass of: MolecularStateDatum

CoordinatePoint
type: Class
subclass of: DatumCoordinate

Lineage
type: Class
subclass of: RootedTree
subclass of: Restriction
  on property: has_Lineage_node
  some values from: Node

Phylo4Tree
type: Class
subclass of: TreeFormat

Network
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has
  all values from: Class
    union of: Edge
    union of: Node

ModelDescription
type: Class
subclass of: CDAOAnnotation
description: Description of a model of transformations.
comment: This is a non-computible description of a model, not the fully specified mathematical model, which typically relates the probability of a transformation to various parameters.

StandardStateDatum
type: Class
subclass of: CategoricalStateDatum

ContinuousCharacterLengthType
type: Class
subclass of: EdgeLengthType

ContinuousCharBayesianLengthType
type: Class
subclass of: ContinuousCharacterLengthType

NEXUSTreeBlock
type: Class
subclass of: TreeFormat

RootedTree
type: Class
subclass of: Tree
subclass of: Restriction
  on property: subtree_of
  all values from: RootedTree
subclass of: Restriction
  on property: has
  all values from: Class
    union of: DirectedEdge
    union of: Node
subclass of: Restriction
  on property: has_Root
  qualified cardinality: 1
  on class: Node
disjoint with: UnrootedTree

Kimura2Parameters
type: Class
subclass of: SubstitutionModel

TreeProcedure
type: Class
subclass of: TreeAnnotation

Generic_State
type: Class
equivalent class: Class
  one of: absent
  one of: unknown
  one of: gap
subclass of: Categorical
description: This concept is tied to the verbally ambiguous 'gap' concept and to the use of a gap character (often the en dash '-') in text representations of sequence alignments. In general, this represents the absence of any positively diagnosed Character-State. As such, the gap may be interpreted as an additional Character-State, as the absence of the Character, or as an unknown value. In some cases it is helpful to separate these.
comment: This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing.

UnrootedSubtree
type: Class
subclass of: Subtree

UnresolvedTree
type: Class
subclass of: Tree

BifurcatingTree
type: Class
equivalent class: FullyResolvedTree
subclass of: Tree

ContinuousStateDatum
type: Class
subclass of: CharacterStateDatum

SubstitutionModel
type: Class
subclass of: ModelDescription

JukesCantor
type: Class
subclass of: SubstitutionModel

DatumCoordinate
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has_Coordinate_System
  qualified cardinality: 1
  on class: CoordinateSystem
description: A positional coordinate giving the source of a character state, used for molecular sequences.
comment: drawing from seqloc categories from NCBI at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML#_Seq-loc:_Locations_on

UnresolvedRootedTree
type: Class
subclass of: RootedTree
subclass of: UnresolvedTree

Branch
type: Class
equivalent class: Edge
description: 'Branch' is the domain-specific synonym for an edge of a (Phylogenetic) Tree or Network. Branches may have properties such as length and degree of support.

CharacterStateDataMatrixAnnotation
type: Class
subclass of: Class
  intersection of: CDAOAnnotation
  intersection of: Restriction
    on property: is_annotation_of
    some values from: CharacterStateDataMatrix
description: Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.

AncestralNode
type: Class
subclass of: Node
subclass of: Restriction
  on property: has_Descendant
  some values from: Node
subclass of: Restriction
  on property: part_of
  some values from: RootedTree

UnresolvedUnrootedTree
type: Class
subclass of: UnresolvedTree
subclass of: UnrootedTree

UncertainStateDomain
type: Class
subclass of: CharacterStateDomain
subclass of: Restriction
  on property: has_Uncertainty_Factor
  some values from: float

ReconcileTree
type: Class
subclass of: Tree
subclass of: Restriction
  on property: reconciliation_of
  min qualified cardinality: 2
  on class: Tree

Continuous
type: Class
subclass of: CharacterStateDomain
subclass of: Restriction
  on property: has_Value
  cardinality: 1
description: This class describes a continuous value. The link to the actual float value is through the property has_Value. It could have also other properties attached (e.g., has_Precision).

AlignmentProcedure
type: Class
subclass of: CharacterStateDataMatrixAnnotation

Dichotomy
type: Class
equivalent class: Bifurcation
subclass of: AncestralNode
disjoint with: Polytomy

Molecular
type: Class
subclass of: Categorical

ContinuousCharParsimonyLengthType
type: Class
subclass of: ContinuousCharacterLengthType

Categorical
type: Class
subclass of: CharacterStateDomain

CDAOAnnotation
type: Class
subclass of: Thing
description: The base class of annotations in CDAO.
comment: Its possible that this base class should be discarded and that annotations should inherit from an imported base class if one exists.

originationEvent
type: Class
subclass of: Restriction
  on property: belongs_to
  some values from: hereditaryChange

Polytomy
type: Class
equivalent class: Restriction
  on property: belongs_to_Edge_as_Parent
  min cardinality: 3
subclass of: AncestralNode
disjoint with: Bifurcation

PolymorphicStateDomain
type: Class
subclass of: CharacterStateDomain
subclass of: Restriction
  on property: has_Uncertainty_Factor
  has value: 1.0

TreeAnnotation
type: Class
subclass of: Class
  intersection of: CDAOAnnotation
  intersection of: Restriction
    on property: is_annotation_of
    some values from: Tree

Standard
type: Class
subclass of: Categorical

EdgeLength
type: Class
subclass of: EdgeAnnotation
subclass of: Restriction
  on property: has_Type
  some values from: EdgeLengthType
subclass of: Restriction
  on property: has_Value
  some values from: Literal
description: The length of an edge (branch) of a Tree or Network, typically in units of evolutionary changes in character-state per character.
comment: Its possible that this should not be classed as an 'annotation' since it contains data rather than meta-data.

RibonucleotideResidue
type: Class
subclass of: Molecular

Clade
type: Class
equivalent class: HolophyleticGroup
subclass of: Tree

DiscreteCharParsimonyLengthType
type: Class
subclass of: DiscreteCharacterLengthType

MolecularStateDatum
type: Class
subclass of: CategoricalStateDatum

PolyphyleticGroup
type: Class
subclass of: Network
subclass of: Restriction
  on property: exclude_Node
  some values from: Node
disjoint with: MonophyleticGroup

NexusDataBlock
type: Class
subclass of: DataMatrixFormat

BranchingNode
type: Class
equivalent class: Restriction
  on property: belongs_to_Edge_as_Parent
  min cardinality: 2
subclass of: AncestralNode

Compound
type: Class
subclass of: Categorical

CharacterStateDataMatrix
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has_Character
  some values from: Character
subclass of: Restriction
  on property: has
  some values from: CharacterStateDataMatrixAnnotation
subclass of: Restriction
  on property: has_TU
  some values from: TU
description: A matrix of character-state data, typically containing observed data, though in some cases the states in the matrix might be simulated or hypothetical. Synonyms: character Data matrix, character-state matrix

RibonucleotideResidueStateDatum
type: Class
subclass of: MolecularStateDatum

TimeCalibratedLengthType
type: Class
subclass of: EdgeLengthType

SetOfNodes
type: Class
subclass of: Class
  intersection of: SetOfThings
  intersection of: Restriction
    on property: has_Element
    all values from: Node

MRCANode
type: Class
subclass of: CommonAncestralNode
subclass of: Restriction
  on property: nca_node_of
  min qualified cardinality: 1
  on class: SetOfThings

FASTADataMatrix
type: Class
subclass of: DataMatrixFormat

evolutionaryTransition
type: Class
equivalent class: anageneticChange
subclass of: hereditaryChange
subclass of: Restriction
  on property: has_Left_State
  qualified cardinality: 1
  on class: CharacterStateDomain
subclass of: Restriction
  on property: hereditary_change_of
  qualified cardinality: 1
  on class: Character
subclass of: Restriction
  on property: has_Right_State
  qualified cardinality: 1
  on class: CharacterStateDomain

EdgeLengthType
type: Class
subclass of: Thing

cladogeneticChange
type: Class
subclass of: hereditaryChange

anageneticChange
type: Class
subclass of: hereditaryChange

TUAnnotation
type: Class
subclass of: Class
  intersection of: CDAOAnnotation
  intersection of: Restriction
    on property: is_annotation_of
    some values from: TU

PhyloTree
type: Class
subclass of: TreeFormat

ContinuousCharacter
type: Class
subclass of: Character
subclass of: Restriction
  on property: has_Continuous_Datum
  some values from: ContinuousStateDatum
subclass of: Restriction
  on property: has_Datum
  all values from: ContinuousStateDatum

PHYLIPTree
type: Class
subclass of: TreeFormat

Subtree
type: Class
subclass of: Tree
subclass of: Restriction
  on property: subtree_of
  some values from: Tree

Character
type: Class
subclass of: Restriction
  on property: has_Datum
  some values from: CharacterStateDatum
comment: Traits shown to be relevant for phylogenetic classification

GalledTree
type: Class
subclass of: Network

SpeciesTree
type: Class
subclass of: Tree

TreeFormat
type: Class
subclass of: TreeAnnotation

StandardCharacter
type: Class
subclass of: CategoricalCharacter

AminoAcidResidue
type: Class
subclass of: Molecular
description: This class will be declared equivalent ot the amino acid class description imported

geneDuplication
type: Class
subclass of: cladogeneticChange

CompoundCharacter
type: Class
subclass of: CategoricalCharacter
subclass of: Restriction
  on property: has_Character
  some values from: Character
subclass of: Restriction
  on property: has_Compound_Datum
  some values from: CompoundStateDatum
subclass of: Restriction
  on property: has_Datum
  all values from: CompoundStateDatum
description: A character that could be divided into separate characters but is not due to the non-independence of changes that would result, e.g., as in the case of a subsequence that is either present or absent as a block.

SIMMAPTree
type: Class
subclass of: TreeFormat

CommonAncestralNode
type: Class
subclass of: AncestralNode
subclass of: Class
  union of: BranchingNode
  union of: Restriction
    on property: has_Descendant
    some values from: BranchingNode

NewickTree
type: Class
subclass of: TreeFormat

TimeProportionalLengthType
type: Class
subclass of: EdgeLengthType

DiscreteCharDistanceLengthType
type: Class
subclass of: DiscreteCharacterLengthType

StarTree
type: Class
subclass of: RootedTree
subclass of: Restriction
  on property: has_Child
  all values from: TerminalNode

FullyResolvedUnrootedTree
type: Class
subclass of: BifurcatingTree
subclass of: UnrootedTree

ParaphyleticGroup
type: Class
subclass of: MonophyleticGroup
subclass of: Restriction
  on property: exclude_Subtree
  some values from: Subtree
disjoint with: HolophyleticGroup

geneticEvent
type: Class
subclass of: originationEvent

UnrootedTree
type: Class
subclass of: Tree

CategoricalStateDatum
type: Class
subclass of: CharacterStateDatum

DiscreteCharLikelihoodLengthType
type: Class
subclass of: DiscreteCharacterLengthType

CharacterStateDomain
type: Class
description: The universe of possible states for a particular type of character, e.g., the states of an Amino_Acid character come from the Amino_Acid domain.

CoordinateList
type: Class
subclass of: DatumCoordinate

GammaDistribution
type: Class
subclass of: SubstitutionModel

DesoxiRibonucleotideResidueCharacter
type: Class
subclass of: MolecularCharacter
subclass of: Restriction
  on property: has_Nucleotide_Datum
  some values from: DesoxiRibonucleotideResidueStateDatum
subclass of: Restriction
  on property: has_Datum
  all values from: DesoxiRibonucleotideResidueStateDatum

CoordinateRange
type: Class
subclass of: DatumCoordinate

ReticulateEvolution
type: Class
subclass of: Network

hereditaryChange
type: Class
subclass of: Restriction
  on property: has_Left_State
  qualified cardinality: 1
  on class: CharacterStateDomain
subclass of: Restriction
  on property: hereditary_change_of
  qualified cardinality: 1
  on class: Character
subclass of: Restriction
  on property: has_Right_State
  qualified cardinality: 1
  on class: CharacterStateDomain

CharacterStateDatum
type: Class
subclass of: Thing
subclass of: Restriction
  on property: belongs_to_TU
  qualified cardinality: 1
  on class: TU
subclass of: Restriction
  on property: belongs_to_Character
  qualified cardinality: 1
  on class: Character
description: The instance of a given character for a given TU. Its state is an object property drawn from a particular character state domain, e.g., the state of an Amino_Acid_State_Datum is an object property drawn from the domain Amino_Acid.

Edge
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has_Annotation
  some values from: EdgeAnnotation
subclass of: Restriction
  on property: has_Node
  qualified cardinality: 2
  on class: Node
description: An edge connecting two nodes in a (Phylogenetic) Tree or Network, also known as a 'branch'. Edges may have attributes such as length, degree of support, and direction. An edge can be a surrogate for a 'split' or bipartition, since each edge in a tree divides the terminal nodes into two sets.

DiscreteCharacterLengthType
type: Class
subclass of: EdgeLengthType

EdgeAnnotation
type: Class
subclass of: Class
  intersection of: CDAOAnnotation
  intersection of: Restriction
    on property: is_annotation_of
    some values from: Edge

FullyResolvedRootedTree
type: Class
subclass of: RootedTree
subclass of: BifurcatingTree
subclass of: Restriction
  on property: has
  all values from: Class
    union of: Dichotomy
    union of: Edge
    union of: TerminalNode

GrafenLengthType
type: Class
subclass of: EdgeLengthType

CoordinateSystem
type: Class
subclass of: Thing
description: A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.

GenBankDataMatrix
type: Class
subclass of: DataMatrixFormat

DataMatrixFormat
type: Class
subclass of: CharacterStateDataMatrixAnnotation

TerminalNode
type: Class
equivalent class: Class
  intersection of: Node
  intersection of: Restriction
    on property: has_Child
    all values from: Class
      complement of: Node
subclass of: Node

RibonucleotideResidueCharacter
type: Class
subclass of: MolecularCharacter
subclass of: Restriction
  on property: has_Datum
  all values from: RibonucleotideResidueStateDatum

Tree
type: Class
subclass of: Network

CategoricalCharacter
type: Class
subclass of: Character

AminoAcidResidueStateDatum
type: Class
subclass of: MolecularStateDatum

PHYLIPDataMatrix
type: Class
subclass of: DataMatrixFormat

ContinuousCharLikelihoodLengthType
type: Class
subclass of: ContinuousCharacterLengthType

MolecularCharacter
type: Class
subclass of: CategoricalCharacter

hereditaryPersistance
type: Class
subclass of: Restriction
  on property: belongs_to
  some values from: hereditaryChange

SetOfCharacters
type: Class
subclass of: Class
  intersection of: SetOfThings
  intersection of: Restriction
    on property: has_Element
    all values from: Character

SetOfThings
type: Class
description: The class is used to describe colletions of phylogenetic data elements. Examples include sets of trees for annotating consensus tree provenance, and sets of characters or higher order grouping (e.g., groups of groups of characters) that extends the CharSet block of NEXUS.

Sequence
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has
  some values from: CharacterStateDatum
subclass of: Restriction
  on property: has
  all values from: Restriction
    on property: has_Coordinate
    min qualified cardinality: 1
    on class: DatumCoordinate
description: A set of ordered states, typically the residues in a macromolecular sequence.

speciation
type: Class
equivalent class: cladogenesis
subclass of: cladogeneticChange

cladogenesis
type: Class
subclass of: cladogeneticChange

Bifurcation
type: Class
subclass of: AncestralNode
subclass of: Restriction
  on property: belongs_to_Edge_as_Parent
  cardinality: 2

DiscreteCharBayesianLengthType
type: Class
subclass of: DiscreteCharacterLengthType

TaxonomicLink
type: Class
subclass of: TUAnnotation
description: Link to an externally defined taxonomic hierarchy.

MonophyleticGroup
type: Class
subclass of: Network

molecularRecombination
type: Class
subclass of: recombination

HolophyleticGroup
type: Class
subclass of: MonophyleticGroup

FullyResolvedTree
type: Class
subclass of: Tree

AminoAcidResidueCharacter
type: Class
subclass of: MolecularCharacter
subclass of: Restriction
  on property: has_Amino_Acid_Datum
  some values from: AminoAcidResidueStateDatum
subclass of: Restriction
  on property: has_Datum
  all values from: AminoAcidResidueStateDatum

recombination
type: Class
subclass of: geneticEvent

DesoxiRibonucleotideResidue
type: Class
subclass of: Molecular

RootedSubtree
type: Class
subclass of: RootedTree
subclass of: Subtree

CompoundStateDatum
type: Class
subclass of: CategoricalStateDatum

GapCost
type: Class
subclass of: ModelDescription

TU
type: Class
subclass of: Thing
description: A unit of analysis that may be tied to a node in a tree and to a row in a character matrix. It subsumes the traditional concepts of 'OTU' and 'HTU'.

DirectedEdge
type: Class
equivalent class: Class
  intersection of: Edge
  intersection of: Restriction
    on property: has_Parent_Node
    qualified cardinality: 1
    on class: Node
  intersection of: Restriction
    on property: has_Child_Node
    qualified cardinality: 1
    on class: Node
description: A directed edge. Rooted trees have directed edges. The direction is specified by way of the parent and child relationships of nodes that the edge connects.

Node
type: Class
subclass of: Thing
subclass of: Restriction
  on property: part_of
  some values from: Network
subclass of: Restriction
  on property: belongs_to_Edge_as_Child
  max qualified cardinality: 1
  on class: DirectedEdge

ContinuousCharDistanceLengthType
type: Class
subclass of: ContinuousCharacterLengthType

dA
type: Thing
type: NamedIndividual
type: DesoxiRibonucleotideResidue

absent
type: Thing
type: NamedIndividual
type: Generic_State

unknown
type: Thing
type: NamedIndividual
type: Generic_State

gap
type: Thing
type: NamedIndividual
type: Generic_State

dG
type: Thing
type: NamedIndividual
type: DesoxiRibonucleotideResidue

rU
type: Thing
type: NamedIndividual
type: RibonucleotideResidueStateDatum

dC
type: Thing
type: NamedIndividual
type: DesoxiRibonucleotideResidue

dT
type: Thing
type: NamedIndividual
type: DesoxiRibonucleotideResidue