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: The Character Data Analysis Ontology
domain: The Character Data Analysis Ontology

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

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

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

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

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

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: Class
  union of: AminoAcidResidueCharacter
  union of: TU

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: Class
  union of: AminoAcidResidue
  union of: Generic State

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
sub property of: has
inverse of: has Descendant

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

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

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: belongs to Edge as Parent
property chain axiom: has Child Node

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 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: Class
  union of: CompoundCharacter
  union of: TU

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: Class
  union of: Compound
  union of: Generic State

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: Class
  union of: ContinuousCharacter
  union of: TU

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

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

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

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 External Reference
type: ObjectProperty
comment: Associates a TU to some external taxonomy reference.
domain: TU
range: The Character Data Analysis Ontology

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: Class
  union of: CoordinatePoint
  union of: CoordinateRange

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

has Left State
type: ObjectProperty
description: This property relates a transformation to a 'left' state (the state associated with the 'left' node).
range: CharacterStateDomain
sub property of: has Change Component
domain: hereditaryChange

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

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: Class
  union of: DesoxiRibonucleotideResidueCharacter
  union of: TU

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: Class
  union of: DesoxiRibonucleotideResidue
  union of: Generic State

has Parent
type: ObjectProperty
description: The property that links a node to its unique parent in a rooted tree.
domain: Node
range: Node
sub property of: has Ancestor
property chain axiom: belongs to Edge as Child
property chain axiom: has Parent Node

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

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

has Right State
type: ObjectProperty
description: This property relates a transformation to a 'right' state (the state associated with the 'right' node).
range: CharacterStateDomain
sub property of: has Change Component
domain: hereditaryChange

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.
range: Node
domain: RootedTree
sub property of: has

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.
domain: CharacterStateDatum
range: CharacterStateDomain
sub property of: has

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

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

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

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

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).
domain: Node
range: TU

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

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

AncestralNode
type: Class
subclass of: Node
subclass of: Restriction
  on property: part of
  on class: RootedTree
  min qualified cardinality: 1
subclass of: Restriction
  on property: has Descendant
  on class: Node
  min qualified cardinality: 1

Bifurcation
type: Class
equivalent class: Dichotomy
subclass of: AncestralNode
subclass of: Restriction
  on property: has Child
  on class: Node
  qualified cardinality: 2
disjoint with: Polytomy

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.

CDAOAnnotation
type: Class
subclass of: The Character Data Analysis Ontology
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.

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

CharacterStateDataMatrix
type: Class
subclass of: The Character Data Analysis Ontology
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

CharacterStateDataMatrixAnnotation
type: Class
subclass of: CDAOAnnotation
description: Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.

CharacterStateDatum
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: belongs to TU
  on class: TU
  qualified cardinality: 1
subclass of: Restriction
  on property: belongs to Character
  on class: Character
  qualified cardinality: 1
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.

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.

CommonAncestralNode
type: Class
subclass of: AncestralNode
subclass of: Restriction
  on property: has Descendant
  on class: TerminalNode
  min qualified cardinality: 2

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.

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).

CoordinateSystem
type: Class
subclass of: The Character Data Analysis Ontology
description: A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.

DatumCoordinate
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has Coordinate System
  on class: CoordinateSystem
  qualified cardinality: 1
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

DirectedEdge
type: Class
equivalent class: Class
  intersection of: Edge
  intersection of: Restriction
    on property: has Child Node
    on class: Node
    qualified cardinality: 1
  intersection of: Restriction
    on property: has Parent Node
    on class: Node
    qualified cardinality: 1
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.

Edge
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has Annotation
  some values from: EdgeAnnotation
subclass of: Restriction
  on property: has Node
  on class: Node
  qualified cardinality: 2
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.

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: anySimpleType
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.

Generic State
type: Class
equivalent class: Class
  one of: unknown
  one of: gap
  one of: absent
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.

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

ModelDescription
type: Class
subclass of: CDAOAnnotation
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.
description: Description of a model of transformations.

Node
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: part of
  on class: Network
  min qualified cardinality: 1
subclass of: Restriction
  on property: belongs to Edge as Child
  on class: DirectedEdge
  max qualified cardinality: 1

PolymorphicStateDomain
type: Class
subclass of: CharacterStateDomain
subclass of: Restriction
  on property: has Uncertainty Factor
  has value: 1

Polytomy
type: Class
equivalent class: Class
  intersection of: Node
  intersection of: Restriction
    on property: has Child
    on class: Node
    min qualified cardinality: 3
subclass of: AncestralNode

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

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

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

SetOfThings
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has Element
  all values from: Class
    union of: Character
    union of: SetOfCharacters
description: The class is used to describe either colletions of characters or higher order grouping (e.g., groups of groups of characters). This extends the CharSet block of NEXUS.

TU
type: Class
subclass of: The Character Data Analysis Ontology
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'.

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

TerminalNode
type: Class
equivalent class: Class
  intersection of: Node
  intersection of: Restriction
    on property: has Child
    on class: Node
    qualified cardinality: 0
subclass of: Node

evolutionaryTransition
type: Class
subclass of: hereditaryChange
subclass of: Restriction
  on property: has Left State
  on class: CharacterStateDomain
  qualified cardinality: 1
subclass of: Restriction
  on property: hereditary change of
  on class: Character
  qualified cardinality: 1
subclass of: Restriction
  on property: has Right State
  on class: CharacterStateDomain
  qualified cardinality: 1

hereditaryChange
type: Class
subclass of: Restriction
  on property: hereditary change of
  on class: Character
  qualified cardinality: 1
subclass of: Restriction
  on property: has Left State
  on class: CharacterStateDomain
  qualified cardinality: 1
subclass of: Restriction
  on property: has Right State
  on class: CharacterStateDomain
  qualified cardinality: 1

The Character Data Analysis Ontology
type: Class
date: $Date$
version info: $Id$
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.
rights: GNU General Public License (GPL)
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.
source: http://www.evolutionaryontology.org/CDAO
language: OWL (RDF-XML)
creator: CDAO Team
subject: comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics