Hilmar Lapp
The Phyloreferencing Ontology is an application ontology for defining, computing with, and resolving phylogenetic clade definitions in the form of logic expressions.
Phyloreferencing Ontology
Generated by ROBOT version 1.8.1 from phyloref.ofn
The expression of a phylogenetic tree or network topology (and possibly the limited set of metadata supported by the format) in the Newick format.
Relates a phyloreference to an apormorphy it uses for defining a clade.
An apomorphy here is generally understood as an instance of SIO:phenotype (http://semanticscience.org/resource/SIO_010056), though this is not currently asserted.
This property is related to, but not strictly a subproperty of RO:has_phenotype (http://purl.obolibrary.org/obo/RO_0002200) because the RO property is defined as holding _between a biological entity and a phenotype_. A phyloreference is an information content entity.
uses apomorphy
part of
has part
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
A relation between a process and a continuant, in which the continuant is somehow involved in the process.
has participant
A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and
the a supports either the existence of b, or the truth value of b.
is evidence for
inverse of is evidence for
x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
has evidence
An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
In the Gene Ontology association model, this corresponds to the With/From field
is evidence with support from
related via evidence or inference to
The Node to which a Phyloreference is expected to resolve, i.e., which is expected to be an instance of it.
An evidence type that is based on a phylogenetic reconstruction.
phylogenetic evidence
A phylogenetic evidence that consists of a phylogeny, such as a phylogenetic tree or network.
phylogeny evidence
Phyloreference that uses an apomorphy-based clade definition. An apomorphy-based clade definition designates the clade arising from the first node exhibiting a trait synapomorphic with a specified descendent (a.k.a. internal specifier).
Phyloreference using apomorphy
Phyloreference that uses a maximum clade definition, such as a branch-based clade definition with excluded specifiers.
Phyloreference using maximum clade
Phyloreferences that uses a minimum clade definition, such as a last common ancestor definition or node-based definition.
Phyloreference using minimum clade
A phyloreference that has a reference tree provided as evidence.
A phylogeny evidence that is based on a reference phylogeny. If multiple phylogenies act as evidence for the same entity, then a reference phylogeny evidence will outweigh non-reference phylogenies in case of conflict.
reference phylogeny evidence
A type of information that is used to support an assertion.
evidence
A process by which an event or an entity is described before it actually happens or is being discovered and identified.
prediction
A phenotype is an observable characteristic of an individual.
phenotype