Comparative Data Analysis Ontology
type: Ontology
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.
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.
creator: CDAO Team
subject: comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics
rights: http://creativecommons.org/publicdomain/zero/1.0/
version IRI: cdao.owl
imports: ontology-metadata.owl

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

CharacterStateDataMatrix
type: Class
subclass of: Thing
subclass of: cdao resource:arc086eb83
subclass of: cdao resource:arc086eb84
subclass of: cdao resource:arc086eb85
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

Character
type: Class
subclass of: cdao resource:arc086eb101
comment: Traits shown to be relevant for phylogenetic classification

has
type: ObjectProperty
description: Generic 'has' property.

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

DirectedEdge
type: Class
equivalent class: cdao resource:arc086eb146
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: cdao resource:arc086eb152
subclass of: cdao resource:arc086eb153

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

has_Child_Node
type: ObjectProperty
type: FunctionalProperty
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.
domain: DirectedEdge
range: Node
sub property of: has_Node

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

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

has_Nucleotide_State
type: ObjectProperty
description: This property associates a nucleotide character-state instance with a state value from the domain of nucleotide states.
domain: DesoxiRibonucleotideResidueStateDatum
sub property of: has_State
range: cdao resource:arc086eb1

DesoxiRibonucleotideResidueStateDatum
type: Class
subclass of: MolecularStateDatum

has_State
type: ObjectProperty
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.
range: CharacterStateDomain
domain: CharacterStateDatum
sub property of: has

Generic_State
type: Class
equivalent class: cdao resource:arc086eb58
subclass of: Categorical
comment: This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing.
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.

DesoxiRibonucleotideResidue
type: Class
subclass of: Molecular

Edge
type: Class
subclass of: Thing
subclass of: cdao resource:arc086eb118
subclass of: cdao resource:arc086eb119
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.

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

belongs_to_Character_State_Data_Matrix
type: ObjectProperty
range: CharacterStateDataMatrix
sub property of: belongs_to
domain: cdao resource:arc086eb4

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'.

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

RootedTree
type: Class
subclass of: Tree
subclass of: cdao resource:arc086eb52
subclass of: cdao resource:arc086eb56
subclass of: cdao resource:arc086eb57
disjoint with: UnrootedTree

has_Child
type: ObjectProperty
description: The property links a node to a node that is an immediate descendant in the tree.
domain: Node
range: Node
sub property of: has_Descendant
inverse of: has_Parent
property chain axiom: cdao resource:arc086eb7

has_Parent
type: ObjectProperty
description: The property that links a node to its unique parent in a rooted tree.
range: Node
domain: Node
sub property of: has_Ancestor
property chain axiom: cdao resource:arc086eb27

belongs_to_Edge_as_Parent
type: ObjectProperty
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).
range: DirectedEdge
domain: Node
sub property of: belongs_to_Edge
inverse of: has_Parent_Node

has_First_Coordinate_Item
type: ObjectProperty
description: The property that relates a coordinate list to the first item in the list.
domain: CoordinateList
sub property of: has
range: cdao resource:arc086eb9

CoordinateList
type: Class
subclass of: DatumCoordinate

CoordinatePoint
type: Class
subclass of: DatumCoordinate

CoordinateRange
type: Class
subclass of: DatumCoordinate

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

DatumCoordinate
type: Class
subclass of: Thing
subclass of: cdao resource:arc086eb62
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

CharacterStateDatum
type: Class
subclass of: Thing
subclass of: cdao resource:arc086eb116
subclass of: cdao resource:arc086eb117
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.

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

ContinuousStateDatum
type: Class
subclass of: CharacterStateDatum

ContinuousCharacter
type: Class
subclass of: Character
subclass of: cdao resource:arc086eb98
subclass of: cdao resource:arc086eb99

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

has_Datum
type: ObjectProperty
description: This property relates a character to a state datum for the character.
range: CharacterStateDatum
sub property of: has
domain: cdao resource:arc086eb12

has_Standard_Datum
type: ObjectProperty
range: StandardStateDatum
sub property of: has_Categorical_Datum
domain: cdao resource:arc086eb15

StandardStateDatum
type: Class
subclass of: CategoricalStateDatum

has_Categorical_Datum
type: ObjectProperty
sub property of: has_Datum

StandardCharacter
type: Class
subclass of: CategoricalCharacter

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

Network
type: Class
subclass of: Thing
subclass of: cdao resource:arc086eb48

has_Amino_Acid_State
type: ObjectProperty
description: This property associates a amino acid character-state instance with a state value from the domain of amino acid states.
domain: AminoAcidResidueStateDatum
sub property of: has_State
range: cdao resource:arc086eb18

AminoAcidResidueStateDatum
type: Class
subclass of: MolecularStateDatum

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

is_annotation_of
type: ObjectProperty
domain: CDAOAnnotation
range: Thing

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

has_RNA_Datum
type: ObjectProperty
sub property of: has_Molecular_Datum

has_Molecular_Datum
type: ObjectProperty
range: MolecularStateDatum
sub property of: has_Categorical_Datum
domain: cdao resource:arc086eb41

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

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.

hereditaryChange
type: Class
subclass of: cdao resource:arc086eb113
subclass of: cdao resource:arc086eb114
subclass of: cdao resource:arc086eb115

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

precedes
type: ObjectProperty

exclude
type: ObjectProperty

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

nca_node_of
type: ObjectProperty
range: SetOfNodes
domain: Node

SetOfNodes
type: Class
subclass of: cdao resource:arc086eb86

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

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

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.

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

DesoxiRibonucleotideResidueCharacter
type: Class
subclass of: MolecularCharacter
subclass of: cdao resource:arc086eb111
subclass of: cdao resource:arc086eb112

connects_to
type: ObjectProperty
type: SymmetricProperty

has_Amino_Acid_Datum
type: ObjectProperty
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).
range: AminoAcidResidueStateDatum
sub property of: has_Molecular_Datum
domain: cdao resource:arc086eb21

AminoAcidResidueCharacter
type: Class
subclass of: MolecularCharacter
subclass of: cdao resource:arc086eb144
subclass of: cdao resource:arc086eb145

hereditary_change_of
type: ObjectProperty
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.
range: Character

has_Compound_Datum
type: ObjectProperty
description: This property relates a compound character (a character with some states that are subdividable) to a state datum for the character.
range: CompoundStateDatum
sub property of: has_Categorical_Datum
domain: cdao resource:arc086eb24

CompoundStateDatum
type: Class
subclass of: CategoricalStateDatum

CompoundCharacter
type: Class
subclass of: CategoricalCharacter
subclass of: cdao resource:arc086eb102
subclass of: cdao resource:arc086eb103
subclass of: cdao resource:arc086eb104
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.

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

CommonAncestralNode
type: Class
subclass of: AncestralNode
subclass of: cdao resource:arc086eb105

reconciliation_of
type: ObjectProperty
domain: ReconcileTree
range: Tree

ReconcileTree
type: Class
subclass of: Tree
subclass of: cdao resource:arc086eb70

Tree
type: Class
subclass of: Network

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

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

Continuous
type: Class
subclass of: CharacterStateDomain
subclass of: cdao resource:arc086eb71
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).

has_Type
type: ObjectProperty
sub property of: has

has_Parent_Node
type: ObjectProperty
type: FunctionalProperty
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)
domain: DirectedEdge
range: Node
sub property of: has_Node

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

homologous_to
type: ObjectProperty
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).
domain: CharacterStateDatum
range: CharacterStateDatum

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

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

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

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

has_Compound_State
type: ObjectProperty
description: This property associates a compound character-state instance with its compound state value.
domain: CompoundStateDatum
sub property of: has_State
range: cdao resource:arc086eb29

Compound
type: Class
subclass of: Categorical

part_of
type: ObjectProperty
inverse of: has

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

belongs_to_Network
type: ObjectProperty
range: Network
sub property of: belongs_to
domain: cdao resource:arc086eb32

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

has_Nucleotide_Datum
type: ObjectProperty
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).
range: DesoxiRibonucleotideResidueStateDatum
sub property of: has_Molecular_Datum
domain: cdao resource:arc086eb35

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

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

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

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.

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

Subtree
type: Class
subclass of: Tree
subclass of: cdao resource:arc086eb100

belongs_to_Tree
type: ObjectProperty
range: Tree
sub property of: belongs_to
domain: cdao resource:arc086eb38

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

Lineage
type: Class
subclass of: RootedTree
subclass of: cdao resource:arc086eb47

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

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

MolecularStateDatum
type: Class
subclass of: CategoricalStateDatum

MolecularCharacter
type: Class
subclass of: CategoricalCharacter

has_Continuous_Datum
type: ObjectProperty
description: This property relates a continuous character to a state datum for the character.
range: ContinuousStateDatum
sub property of: has_Datum
domain: cdao resource:arc086eb44

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

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

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_Value
type: DatatypeProperty

has_Support_Value
type: DatatypeProperty
range: float

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

Phylo4Tree
type: Class
subclass of: TreeFormat

TreeFormat
type: Class
subclass of: TreeAnnotation

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.

CategoricalStateDatum
type: Class
subclass of: CharacterStateDatum

ContinuousCharacterLengthType
type: Class
subclass of: EdgeLengthType

EdgeLengthType
type: Class
subclass of: Thing

ContinuousCharBayesianLengthType
type: Class
subclass of: ContinuousCharacterLengthType

NEXUSTreeBlock
type: Class
subclass of: TreeFormat

cdao resource:arc086eb57
type: Restriction
on property: has_Root
on class: Node
qualified cardinality: 1

UnrootedTree
type: Class
subclass of: Tree

Kimura2Parameters
type: Class
subclass of: SubstitutionModel

SubstitutionModel
type: Class
subclass of: ModelDescription

TreeProcedure
type: Class
subclass of: TreeAnnotation

TreeAnnotation
type: Class
subclass of: cdao resource:arc086eb75

unknown
type: Thing
type: Generic_State
type: NamedIndividual

absent
type: Thing
type: Generic_State
type: NamedIndividual

gap
type: Thing
type: Generic_State
type: NamedIndividual

Categorical
type: Class
subclass of: CharacterStateDomain

UnrootedSubtree
type: Class
subclass of: Subtree

UnresolvedTree
type: Class
subclass of: Tree

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

FullyResolvedTree
type: Class
subclass of: Tree

JukesKantor
type: Class
subclass of: SubstitutionModel

cdao resource:arc086eb62
type: Restriction
on property: has_Coordinate_System
on class: CoordinateSystem
qualified cardinality: 1

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: cdao resource:arc086eb63
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: cdao resource:arc086eb67
subclass of: cdao resource:arc086eb68

cdao resource:arc086eb68
type: Restriction
on property: part_of
on class: RootedTree
min qualified cardinality: 1

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

UncertainStateDomain
type: Class
subclass of: CharacterStateDomain
subclass of: cdao resource:arc086eb69

cdao resource:arc086eb70
type: Restriction
on property: reconciliation_of
on class: Tree
min qualified cardinality: 2

cdao resource:arc086eb71
type: Restriction
on property: has_Value
cardinality: 1

AlignmentProcedure
type: Class
subclass of: CharacterStateDataMatrixAnnotation

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

Bifurcation
type: Class
subclass of: AncestralNode
subclass of: cdao resource:arc086eb143

Polytomy
type: Class
equivalent class: cdao resource:arc086eb73
subclass of: AncestralNode
disjoint with: Bifurcation

Molecular
type: Class
subclass of: Categorical

ContinuousCharParsimonyLengthType
type: Class
subclass of: ContinuousCharacterLengthType

originationEvent
type: Class
subclass of: cdao resource:arc086eb72

cdao resource:arc086eb73
type: Restriction
on property: belongs_to_Edge_as_Parent
min cardinality: 3

PolymorphicStateDomain
type: Class
subclass of: CharacterStateDomain
subclass of: cdao resource:arc086eb74

cdao resource:arc086eb74
type: Restriction
on property: has_Uncertainty_Factor
has value: 1.0

Standard
type: Class
subclass of: Categorical

EdgeLength
type: Class
subclass of: EdgeAnnotation
subclass of: cdao resource:arc086eb79
subclass of: cdao resource:arc086eb80
comment: Its possible that this should not be classed as an 'annotation' since it contains data rather than meta-data.
description: The length of an edge (branch) of a Tree or Network, typically in units of evolutionary changes in character-state per character.

EdgeAnnotation
type: Class
subclass of: cdao resource:arc086eb120

RibonucleotideResidue
type: Class
subclass of: Molecular

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

HolophyleticGroup
type: Class
subclass of: MonophyleticGroup

DiscreteCharParsimonyLengthType
type: Class
subclass of: DiscreteCharacterLengthType

DiscreteCharacterLengthType
type: Class
subclass of: EdgeLengthType

PolyphyleticGroup
type: Class
subclass of: Network
subclass of: cdao resource:arc086eb81
disjoint with: MonophyleticGroup

MonophyleticGroup
type: Class
subclass of: Network

NexusDataBlock
type: Class
subclass of: DataMatrixFormat

DataMatrixFormat
type: Class
subclass of: CharacterStateDataMatrixAnnotation

BranchingNode
type: Class
equivalent class: cdao resource:arc086eb82
subclass of: AncestralNode

cdao resource:arc086eb82
type: Restriction
on property: belongs_to_Edge_as_Parent
min cardinality: 2

RibonucleotideResidueStateDatum
type: Class
subclass of: MolecularStateDatum

TimeCalibratedLengthType
type: Class
subclass of: EdgeLengthType

MRCANode
type: Class
subclass of: CommonAncestralNode
subclass of: cdao resource:arc086eb90

cdao resource:arc086eb90
type: Restriction
on property: nca_node_of
on class: SetOfThings
min qualified cardinality: 1

FASTADataMatrix
type: Class
subclass of: DataMatrixFormat

evolutionaryTransition
type: Class
equivalent class: anageneticChange
subclass of: hereditaryChange
subclass of: cdao resource:arc086eb91
subclass of: cdao resource:arc086eb92
subclass of: cdao resource:arc086eb93

anageneticChange
type: Class
subclass of: hereditaryChange

cdao resource:arc086eb91
type: Restriction
on property: has_Left_State
on class: CharacterStateDomain
qualified cardinality: 1

cdao resource:arc086eb92
type: Restriction
on property: has_Right_State
on class: CharacterStateDomain
qualified cardinality: 1

cdao resource:arc086eb93
type: Restriction
on property: hereditary_change_of
on class: Character
qualified cardinality: 1

cladogeneticChange
type: Class
subclass of: hereditaryChange

TUAnnotation
type: Class
subclass of: cdao resource:arc086eb94

PhyloTree
type: Class
subclass of: TreeFormat

PHYLIPTree
type: Class
subclass of: TreeFormat

GalledTree
type: Class
subclass of: Network

SpeciesTree
type: Class
subclass of: Tree

CategoricalCharacter
type: Class
subclass of: Character

geneDuplication
type: Class
subclass of: cladogeneticChange

SIMMAPTree
type: Class
subclass of: TreeFormat

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: cdao resource:arc086eb109

TerminalNode
type: Class
equivalent class: cdao resource:arc086eb129
subclass of: Node

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

ParaphyleticGroup
type: Class
subclass of: MonophyleticGroup
subclass of: cdao resource:arc086eb110
disjoint with: HolophyleticGroup

geneticEvent
type: Class
subclass of: originationEvent

DiscreteCharLikelihoodLengthType
type: Class
subclass of: DiscreteCharacterLengthType

GammaDistribution
type: Class
subclass of: SubstitutionModel

ReticulateEvolution
type: Class
subclass of: Network

cdao resource:arc086eb113
type: Restriction
on property: has_Right_State
on class: CharacterStateDomain
qualified cardinality: 1

cdao resource:arc086eb114
type: Restriction
on property: has_Left_State
on class: CharacterStateDomain
qualified cardinality: 1

cdao resource:arc086eb115
type: Restriction
on property: hereditary_change_of
on class: Character
qualified cardinality: 1

cdao resource:arc086eb116
type: Restriction
on property: belongs_to_Character
on class: Character
qualified cardinality: 1

cdao resource:arc086eb117
type: Restriction
on property: belongs_to_TU
on class: TU
qualified cardinality: 1

cdao resource:arc086eb118
type: Restriction
on property: has_Node
on class: Node
qualified cardinality: 2

FullyResolvedRootedTree
type: Class
subclass of: RootedTree
subclass of: BifurcatingTree
subclass of: cdao resource:arc086eb124

GrafenLengthType
type: Class
subclass of: EdgeLengthType

GenBankDataMatrix
type: Class
subclass of: DataMatrixFormat

RibonucleotideResidueCharacter
type: Class
subclass of: MolecularCharacter
subclass of: cdao resource:arc086eb134

PHYLIPDataMatrix
type: Class
subclass of: DataMatrixFormat

ContinuousCharLikelihoodLengthType
type: Class
subclass of: ContinuousCharacterLengthType

hereditaryPersistance
type: Class
subclass of: cdao resource:arc086eb135

SetOfCharacters
type: Class
subclass of: cdao resource:arc086eb136

Sequence
type: Class
subclass of: Thing
subclass of: cdao resource:arc086eb140
subclass of: cdao resource:arc086eb141
description: A set of ordered states, typically the residues in a macromolecular sequence.

cdao resource:arc086eb142
type: Restriction
on property: has_Coordinate
on class: DatumCoordinate
min qualified cardinality: 1

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

cladogenesis
type: Class
subclass of: cladogeneticChange

cdao resource:arc086eb143
type: 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.

molecularRecombination
type: Class
subclass of: recombination

recombination
type: Class
subclass of: geneticEvent

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

GapCost
type: Class
subclass of: ModelDescription

cdao resource:arc086eb148
type: Restriction
on property: has_Parent_Node
on class: Node
qualified cardinality: 1

cdao resource:arc086eb150
type: Restriction
on property: has_Child_Node
on class: Node
qualified cardinality: 1

cdao resource:arc086eb152
type: Restriction
on property: part_of
on class: Network
min qualified cardinality: 1

cdao resource:arc086eb153
type: Restriction
on property: belongs_to_Edge_as_Child
on class: DirectedEdge
max qualified cardinality: 1

ContinuousCharDistanceLengthType
type: Class
subclass of: ContinuousCharacterLengthType

dA
type: Thing
type: DesoxiRibonucleotideResidue
type: NamedIndividual

dG
type: Thing
type: DesoxiRibonucleotideResidue
type: NamedIndividual

rU
type: Thing
type: RibonucleotideResidueStateDatum
type: NamedIndividual

dC
type: Thing
type: DesoxiRibonucleotideResidue
type: NamedIndividual

dT
type: Thing
type: DesoxiRibonucleotideResidue
type: NamedIndividual