en
Adam Goldstein
Alan Ruttenberg
Albert Goldfain
Barry Smith
Bjoern Peters
Carlo Torniai
Chris Mungall
Chris Stoeckert
Christian A. Boelling
Darren Natale
David Osumi-Sutherland
Gwen Frishkoff
Holger Stenzhorn
James A. Overton
James Malone
Jennifer Fostel
Jie Zheng
Jonathan Rees
Larisa Soldatova
Lawrence Hunter
Mathias Brochhausen
Matt Brush
Melanie Courtot
Michel Dumontier
Paolo Ciccarese
Pat Hayes
Philippe Rocca-Serra
Randy Dipert
Ron Rudnicki
Satya Sahoo
Sivaram Arabandi
Werner Ceusters
William Duncan
William Hogan
Yongqun (Oliver) He
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
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred term
example
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
GROUP:OBI
OBI_0000277
in branch
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
editor note
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
is denotator type
relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
expand expression to
ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand expression to
expand assertion to
ObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
expand assertion to
first order logic expression
PERSON:Alan Ruttenberg
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
Alan Ruttenberg
antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID digit count
Datatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
Person:Alan Ruttenberg
has ID range allocated to
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Person:Alan Ruttenberg
has ID policy for
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
Person:Alan Ruttenberg
has ID prefix
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
is allocated id range
Add as annotation triples in the granting ontology
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
PERSON:Alan Ruttenberg
is allocated id range
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
#40
VFB
2018-09-21T16:43:39Z
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
may be identical to
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
https://github.com/geneontology/go-ontology/issues/15532
https://github.com/information-artifact-ontology/ontology-metadata/issues/32
GO ontology
scheduled for obsoletion on or after
has axiom id
Person:Alan Ruttenberg
Person:Alan Ruttenberg
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Add as annotation triples in the granting ontology
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
term replaced by
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
has_Standard_Datum
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 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
has_Descendants
reconciliation_of
belongs_to_Amino_Acid_Character
This property associates a character-state instance with a state value on a continuous numeric scale.
has_Continuous_State
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
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
This property associates a compound character-state instance with its compound state value.
has_Compound_State
This property relates a character-state datum to its TU.
belongs_to_TU
belongs_to_Network
part_of
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
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
belongs_to_Tree_as_Root
has_Hereditary_Change
belongs_to_Character
has_Molecular_Datum
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
BFO:0000031
CDAO:0000002
DesoxiRibonucleotideResidueStateDatum
CDAO:0000003
CoordinatePoint
CDAO:0000004
Lineage
CDAO:0000005
Phylo4Tree
CDAO:0000006
Network
CDAO:0000007
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
CDAO:0000008
StandardStateDatum
CDAO:0000009
ContinuousCharacterLengthType
CDAO:0000010
ContinuousCharBayesianLengthType
CDAO:0000011
NEXUSTreeBlock
1
CDAO:0000012
RootedTree
CDAO:0000013
Kimura2Parameters
CDAO:0000014
TreeProcedure
CDAO:0000015
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
CDAO:0000016
UnrootedSubtree
CDAO:0000017
UnresolvedTree
CDAO:0000018
BifurcatingTree
CDAO:0000019
ContinuousStateDatum
CDAO:0000020
SubstitutionModel
CDAO:0000021
JukesKantor
1
CDAO:0000022
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
CDAO:0000023
UnresolvedRootedTree
CDAO:0000024
'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
CDAO:0000025
Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.
CharacterStateDataMatrixAnnotation
1
CDAO:0000026
AncestralNode
CDAO:0000027
UnresolvedUnrootedTree
CDAO:0000029
UncertainStateDomain
2
CDAO:0000030
ReconcileTree
1
CDAO:0000031
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
CDAO:0000032
AlignmentProcedure
CDAO:0000033
Dichotomy
CDAO:0000034
Molecular
CDAO:0000035
ContinuousCharParsimonyLengthType
CDAO:0000039
Categorical
CDAO:0000040
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
CDAO:0000041
originationEvent
3
CDAO:0000042
Polytomy
1.0
CDAO:0000043
PolymorphicStateDomain
CDAO:0000044
TreeAnnotation
CDAO:0000045
Standard
CDAO:0000046
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
CDAO:0000047
RibonucleotideResidue
CDAO:0000048
Clade
CDAO:0000049
DiscreteCharParsimonyLengthType
CDAO:0000050
MolecularStateDatum
CDAO:0000051
PolyphyleticGroup
CDAO:0000052
NexusDataBlock
2
CDAO:0000053
BranchingNode
CDAO:0000055
Compound
CDAO:0000056
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
CDAO:0000057
RibonucleotideResidueStateDatum
CDAO:0000058
TimeCalibratedLengthType
CDAO:0000059
SetOfNodes
1
CDAO:0000060
MRCANode
CDAO:0000061
FASTADataMatrix
1
1
1
CDAO:0000062
evolutionaryTransition
CDAO:0000063
EdgeLengthType
CDAO:0000064
cladogeneticChange
CDAO:0000065
anageneticChange
CDAO:0000066
TUAnnotation
CDAO:0000067
PhyloTree
CDAO:0000068
ContinuousCharacter
CDAO:0000069
PHYLIPTree
CDAO:0000070
Subtree
CDAO:0000071
Traits shown to be relevant for phylogenetic classification
Character
CDAO:0000072
GalledTree
CDAO:0000073
SpeciesTree
CDAO:0000074
TreeFormat
CDAO:0000075
StandardCharacter
CDAO:0000076
This class will be declared equivalent ot the amino acid class description imported
AminoAcidResidue
CDAO:0000077
geneDuplication
CDAO:0000078
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
CDAO:0000079
SIMMAPTree
CDAO:0000080
CommonAncestralNode
CDAO:0000081
NewickTree
CDAO:0000082
TimeProportionalLengthType
CDAO:0000083
DiscreteCharDistanceLengthType
CDAO:0000084
StarTree
CDAO:0000085
FullyResolvedUnrootedTree
CDAO:0000086
ParaphyleticGroup
CDAO:0000087
geneticEvent
CDAO:0000088
UnrootedTree
CDAO:0000089
CategoricalStateDatum
CDAO:0000090
DiscreteCharLikelihoodLengthType
CDAO:0000091
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
CDAO:0000092
CoordinateList
CDAO:0000093
GammaDistribution
CDAO:0000094
DesoxiRibonucleotideResidueCharacter
CDAO:0000095
CoordinateRange
CDAO:0000096
ReticulateEvolution
1
1
1
CDAO:0000097
hereditaryChange
1
1
CDAO:0000098
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
CDAO:0000099
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
CDAO:0000100
DiscreteCharacterLengthType
CDAO:0000101
EdgeAnnotation
CDAO:0000102
FullyResolvedRootedTree
CDAO:0000103
GrafenLengthType
CDAO:0000104
A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.
CoordinateSystem
CDAO:0000105
GenBankDataMatrix
CDAO:0000107
DataMatrixFormat
CDAO:0000108
TerminalNode
CDAO:0000109
RibonucleotideResidueCharacter
CDAO:0000110
Tree
CDAO:0000111
CategoricalCharacter
CDAO:0000112
AminoAcidResidueStateDatum
CDAO:0000113
PHYLIPDataMatrix
CDAO:0000114
ContinuousCharLikelihoodLengthType
CDAO:0000115
MolecularCharacter
CDAO:0000116
hereditaryPersistance
CDAO:0000117
SetOfCharacters
CDAO:0000118
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
CDAO:0000120
A set of ordered states, typically the residues in a macromolecular sequence.
Sequence
CDAO:0000121
speciation
CDAO:0000122
cladogenesis
2
CDAO:0000124
Bifurcation
CDAO:0000125
DiscreteCharBayesianLengthType
CDAO:0000126
Link to an externally defined taxonomic hierarchy.
TaxonomicLink
CDAO:0000127
MonophyleticGroup
CDAO:0000128
molecularRecombination
CDAO:0000129
HolophyleticGroup
CDAO:0000130
FullyResolvedTree
CDAO:0000131
AminoAcidResidueCharacter
CDAO:0000132
recombination
CDAO:0000133
DesoxiRibonucleotideResidue
CDAO:0000134
RootedSubtree
CDAO:0000136
CompoundStateDatum
CDAO:0000137
GapCost
CDAO:0000138
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
CDAO:0000139
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
1
CDAO:0000140
Node
CDAO:0000141
ContinuousCharDistanceLengthType
IAO:0000027
data item
IAO:0000030
information content entity
IAO:0000078
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
IAO:0000102
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
IAO:0000225
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
IAO:0000409
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
IAO:8000000
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
cjm
2018-05-20T20:55:03Z
ontology module
IAO:8000001
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
cjm
2018-05-20T20:55:30Z
base ontology module
IAO:8000002
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
cjm
2018-05-20T20:55:47Z
editors ontology module
IAO:8000003
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
cjm
2018-05-20T20:56:13Z
main release ontology module
IAO:8000004
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
cjm
2018-05-20T20:56:23Z
bridge ontology module
IAO:8000005
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
cjm
2018-05-20T20:56:47Z
import ontology module
IAO:8000006
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
cjm
2018-05-20T20:58:11Z
subset ontology module
IAO:8000007
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
cjm
2018-05-20T20:58:38Z
curation subset ontology module
IAO:8000008
An ontology module that is intended for usage in analysis or discovery applications.
cjm
2018-05-20T20:58:49Z
analysis subset ontology module
IAO:8000009
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
cjm
2018-05-20T20:59:19Z
single layer subset ontology module
IAO:8000010
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
cjm
2018-05-20T20:59:57Z
exclusion subset ontology module
IAO:8000011
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
cjm
2018-05-20T21:00:14Z
external import ontology module
IAO:8000012
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
cjm
2018-05-20T21:14:16Z
species subset ontology module
IAO:8000013
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
cjm
2018-05-20T21:20:33Z
reasoned ontology module
IAO:8000014
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
cjm
2018-05-20T21:21:12Z
generated ontology module
IAO:8000015
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
cjm
2018-05-20T21:21:21Z
template generated ontology module
IAO:8000016
cjm
2018-05-20T21:28:15Z
taxonomic bridge ontology module
IAO:8000017
cjm
2018-05-22T04:15:54Z
ontology module subsetted by expressivity
IAO:8000018
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.
Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).
An ontology is OBO Basic if and only if it has the following characteristics:
DAG
Unidirectional
No Dangling Clauses
Fully Asserted
Fully Labeled
No equivalence axioms
Singly labeled edges
No qualifier lists
No disjointness axioms
No owl-axioms header
No imports
cjm
2018-05-22T04:16:10Z
obo basic subset ontology module
IAO:8000019
cjm
2018-05-22T04:16:28Z
ontology module subsetted by OWL profile
IAO:8000020
cjm
2018-05-22T04:16:48Z
EL++ ontology module
oboInOwl:DbXref
oboInOwl:Definition
oboInOwl:Subset
oboInOwl:Synonym
oboInOwl:SynonymType
owl:Thing
dA
absent
unknown
gap
dG
rU
dC
dT
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
core
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
This property associates a character data matrix with a character (a column) represented in the matrix.
has_Character
This property relates a character to a state datum for the character.
has_Datum
This property links two networks where the latter is a substructure of the former
subtree_of
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 compound character (a character with some states that are subdividable) to a state datum for the character.
has_Compound_Datum
A property that links a node to any of its descendants in a rooted tree.
has_Descendant
has_Type
Generic 'has' property.
has
exclude_Node
Generic property that links a concept to another concept it is a constituent of. The property is a synonym of part_of.
belongs_to
has_Annotation
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
exclude_Subtree
has_Lineage_node
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
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
en
Adam Goldstein
Alan Ruttenberg
Albert Goldfain
Barry Smith
Bjoern Peters
Carlo Torniai
Chris Mungall
Chris Stoeckert
Christian A. Boelling
Darren Natale
David Osumi-Sutherland
Gwen Frishkoff
Holger Stenzhorn
James A. Overton
James Malone
Jennifer Fostel
Jie Zheng
Jonathan Rees
Larisa Soldatova
Lawrence Hunter
Mathias Brochhausen
Matt Brush
Melanie Courtot
Michel Dumontier
Paolo Ciccarese
Pat Hayes
Philippe Rocca-Serra
Randy Dipert
Ron Rudnicki
Satya Sahoo
Sivaram Arabandi
Werner Ceusters
William Duncan
William Hogan
Yongqun (Oliver) He