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.
CDAO Team
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.
comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics
Comparative Data Analysis Ontology
This property associates a character data matrix with a character (a column) represented in the matrix.
has_Character
The property links a Node to the Edge it belongs to in the child position.
belongs_to_Edge_as_Child
The property links a node to any of the other nodes that are its ancestors in a rooted tree.
has_Ancestor
This property associates a nucleotide character-state instance with a state value from the domain of nucleotide states.
has_Nucleotide_State
The property links a Node to one of the edges that are incident on such node.
belongs_to_Edge
belongs_to_Character_State_Data_Matrix
The property links a rooted tree to the specific node that represents the unique root of the tree.
has_Root
The property links a node to a node that is an immediate descendant in the tree.
has_Child
The property that relates a coordinate list to the first item in the list.
has_First_Coordinate_Item
has_Coordinate
belongs_to_Continuous_Character
This property relates a character to a state datum for the character.
has_Datum
has_Standard_Datum
This property links two networks where the latter is a substructure of the former
subtree_of
This property associates a amino acid character-state instance with a state value from the domain of amino acid states.
has_Amino_Acid_State
is_annotation_of
has_RNA_Datum
This property relates a transformation to a 'left' state (the state associated with the 'left' node).
has_Left_State
precedes
exclude
Property that associates to each Edge the Nodes it connects.
has_Node
nca_node_of
Associates a TU to some external taxonomy reference.
has_External_Reference
This property links a coordinate to the coordinate system it references.
has_Coordinate_System
belongs_to_Nucleotide_Character
connects_to
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).
has_Amino_Acid_Datum
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.
hereditary_change_of
This property relates a compound character (a character with some states that are subdividable) to a state datum for the character.
has_Compound_Datum
has_Descendants
reconciliation_of
belongs_to_Amino_Acid_Character
A property that links a node to any of its descendants in a rooted tree.
has_Descendant
This property associates a character-state instance with a state value on a continuous numeric scale.
has_Continuous_State
has_Type
The property links a Node to one of the Edges where the node appears in the parent position (i.e., closer to the root).
belongs_to_Edge_as_Parent
Generic 'has' property.
has
The property that links a node to its unique parent in a rooted tree.
has_Parent
belongs_to_Compound_Character
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).
homologous_to
This property relates a transformation to the components that compose it.
has_Change_Component
has_Categorical_Datum
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_State
This property relates a transformation to a 'left' node (the node that has the 'left' state).
has_Left_Node
This property relates a transformation to a 'right' state (the state associated with the 'right' node).
has_Right_State
This property relates a TU or taxonomic unit (typically associated with character data) to a phylogenetic history (Tree).
represents_TU
exclude_Node
This property associates a compound character-state instance with its compound state value.
has_Compound_State
Generic property that links a concept to another concept it is a constituent of. The property is a synonym of part_of.
belongs_to
This property relates a character-state datum to its TU.
belongs_to_TU
belongs_to_Network
has_Annotation
obsolete part_of
true
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).
has_Nucleotide_Datum
This property relates a TU to a node that represents it in a network.
represented_by_Node
The property that relates a coordinate list to the item in the list beyond the first item.
has_Remaining_Coordinate_List
has_Element
exclude_Subtree
belongs_to_Tree
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_Parent_Node
has_Lineage_node
belongs_to_Tree_as_Root
has_Hereditary_Change
belongs_to_Character
has_Molecular_Datum
This property relates a continuous character to a state datum for the character.
has_Continuous_Datum
This property associates a character data matrix with a TU (a row) represented in the matrix.
has_TU
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_Child_Node
This property relates a transformation to a 'right' node (the node that has the 'right' state).
has_Right_Node
has_Precision
has_Point_Coordinate_Value
has_Int_Value
has_Support_Value
has_Value
has_Uncertainty_Factor
has_Range_End_Value
has_Float_Value
has_Range_Start_Value
DesoxiRibonucleotideResidueStateDatum
CoordinatePoint
Lineage
Phylo4Tree
Network
Description of a model of transformations.
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.
ModelDescription
StandardStateDatum
ContinuousCharacterLengthType
ContinuousCharBayesianLengthType
NEXUSTreeBlock
1
RootedTree
Kimura2Parameters
TreeProcedure
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.
This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing.
Generic_State
UnrootedSubtree
UnresolvedTree
BifurcatingTree
ContinuousStateDatum
SubstitutionModel
JukesCantor
1
A positional coordinate giving the source of a character state, used for molecular sequences.
drawing from seqloc categories from NCBI at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML#_Seq-loc:_Locations_on
DatumCoordinate
UnresolvedRootedTree
'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.
Branch
Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.
CharacterStateDataMatrixAnnotation
AncestralNode
UnresolvedUnrootedTree
UncertainStateDomain
2
ReconcileTree
1
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).
Continuous
AlignmentProcedure
Dichotomy
Molecular
ContinuousCharParsimonyLengthType
Categorical
The base class of annotations in CDAO.
Its possible that this base class should be discarded and that annotations should inherit from an imported base class if one exists.
CDAOAnnotation
originationEvent
3
Polytomy
1.0
PolymorphicStateDomain
TreeAnnotation
Standard
The length of an edge (branch) of a Tree or Network, typically in units of evolutionary changes in character-state per character.
Its possible that this should not be classed as an 'annotation' since it contains data rather than meta-data.
EdgeLength
RibonucleotideResidue
Clade
DiscreteCharParsimonyLengthType
MolecularStateDatum
PolyphyleticGroup
NexusDataBlock
2
BranchingNode
Compound
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
CharacterStateDataMatrix
RibonucleotideResidueStateDatum
TimeCalibratedLengthType
SetOfNodes
1
MRCANode
FASTADataMatrix
1
1
1
evolutionaryTransition
EdgeLengthType
cladogeneticChange
anageneticChange
TUAnnotation
PhyloTree
ContinuousCharacter
PHYLIPTree
Subtree
Traits shown to be relevant for phylogenetic classification
Character
GalledTree
SpeciesTree
TreeFormat
StandardCharacter
This class will be declared equivalent ot the amino acid class description imported
AminoAcidResidue
geneDuplication
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.
CompoundCharacter
SIMMAPTree
CommonAncestralNode
NewickTree
TimeProportionalLengthType
DiscreteCharDistanceLengthType
StarTree
FullyResolvedUnrootedTree
ParaphyleticGroup
geneticEvent
UnrootedTree
CategoricalStateDatum
DiscreteCharLikelihoodLengthType
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.
CharacterStateDomain
CoordinateList
GammaDistribution
DesoxiRibonucleotideResidueCharacter
CoordinateRange
ReticulateEvolution
1
1
1
hereditaryChange
1
1
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.
CharacterStateDatum
2
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.
Edge
DiscreteCharacterLengthType
EdgeAnnotation
FullyResolvedRootedTree
GrafenLengthType
A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.
CoordinateSystem
GenBankDataMatrix
DataMatrixFormat
TerminalNode
RibonucleotideResidueCharacter
Tree
CategoricalCharacter
AminoAcidResidueStateDatum
PHYLIPDataMatrix
ContinuousCharLikelihoodLengthType
MolecularCharacter
hereditaryPersistance
SetOfCharacters
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.
SetOfThings
1
A set of ordered states, typically the residues in a macromolecular sequence.
Sequence
speciation
cladogenesis
2
Bifurcation
DiscreteCharBayesianLengthType
Link to an externally defined taxonomic hierarchy.
TaxonomicLink
MonophyleticGroup
molecularRecombination
HolophyleticGroup
FullyResolvedTree
AminoAcidResidueCharacter
recombination
DesoxiRibonucleotideResidue
RootedSubtree
CompoundStateDatum
GapCost
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'.
TU
1
1
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.
DirectedEdge
1
Node
ContinuousCharDistanceLengthType
dA
absent
unknown
gap
dG
rU
dC
dT