IRI:
http://purl.org/net/orth
Version IRI:
http://purl.org/net/orth/2.0
Current version:
This ontology is the second version of the orthology ontology first published in 2015 and available at http://purl.bioontology.org/ontology/ORTH . @authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov, C. Dessimoz and F. Villiers.
Other visualisation:
Ontology source

Table of Content

  1. Classes
  2. Object Properties
  3. Data Properties
  4. Annotation Properties
  5. Namespace Declarations

Classes

cladogeneticChangec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000064

Evolutionary event
has sub-classes
geneDuplicationc, speciationc
is in range of
has evolutionary eventop

Cluster of homologous sequencesc back to ToC or Class ToC

IRI: http://purl.org/net/orth#HomologsCluster

Set of homologous sequences
has super-classes
gene_groupc
Gene tree nodec
has homologous memberop only Gene tree nodec
has evolutionary eventop only cladogeneticChangec
has taxonomic levelop only Taxonomic levelc
in datasetop some Orthology datasourcec
has sub-classes
Cluster of orthologsc, Cluster of paralogsc

Cluster of orthologsc back to ToC or Class ToC

IRI: http://purl.org/net/orth#OrthologsCluster

Set of homologous sequences derived from a speciation event.
has super-classes
Cluster of homologous sequencesc
has evolutionary eventop only speciationc
is disjoint with
Cluster of paralogsc

Cluster of paralogsc back to ToC or Class ToC

IRI: http://purl.org/net/orth#ParalogsCluster

Set of homologous sequences derived from a duplication event
has super-classes
Cluster of homologous sequencesc
has evolutionary eventop only geneDuplicationc
is disjoint with
Cluster of orthologsc

co-orthology relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#CoOrthologyRelation

Co-orthology is a relation defined over three genes, where two of them are inparalogs with respect to the speciation event associated to the third gene. The two inparalogous genes are said to be co-orthologous to the third (out-group) gene.
has super-classes
homology relationc
(has co-orthologous memberop exactly 1 Sequence unitc) and (has inparalogous memberop exactly 1 inparalogy relationc)
is in domain of
has co-orthologous memberop, has inparalogous memberop

databasec back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000750

A database is a data store such as relational, hierarchical and graph databases.

genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000704

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
is equivalent to
Genec

Genec back to ToC or Class ToC

IRI: http://purl.org/net/orth#Gene

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
has super-classes
Sequence unitc
in organismop some Organismc
contained inop only databasec
is disjoint with
Proteinc

gene regionc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Subgene

A region of the sequence of the gene.
has super-classes
Sequence unitc
part_ofop some Genec

Gene tree nodec back to ToC or Class ToC

IRI: http://purl.org/net/orth#GeneTreeNode

A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs
has super-classes
Nodec
has sub-classes
Cluster of homologous sequencesc, Sequence unitc

gene_groupc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005855

A collection of related genes.
has sub-classes
Cluster of homologous sequencesc

gene_member_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000831

A manufactured term used to allow the parts of a gene to have an is_a path to the root.
is equivalent to
gene regionc

geneDuplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000077

Evolutionary event that consists on the duplication of a gene
has super-classes
cladogeneticChangec

Hierarchical clustering treec back to ToC or Class ToC

IRI: http://purl.org/net/orth#HierarchicalClusteringTree

A tree whose content is the result of the application of hierarchical clustering to a dataset
has super-classes
RootedTreec
has sub-classes
Hierarchical gene tree c

Hierarchical gene tree c back to ToC or Class ToC

IRI: http://purl.org/net/orth#HierarchicalGeneTree

A tree whose leaf nodes correspond to sequence units (e.g.: genes).
has super-classes
Hierarchical clustering treec
hasop only Gene tree nodec
hasop some Gene tree nodec

homology relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#HomologyRelation

This class represents homology relations among sequence units (e.g genes, proteins or gene regions).
has super-classes
in datasetop only Orthology datasourcec
has homologous memberop only Sequence unitc
has sub-classes
co-orthology relationc, orthology relationc, paralogy relationc, xenology relationc

inparalogy relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#InparalogyRelation

Inparalogy is a relation defined over a triplet. It involves a pair of genes and a speciation event of reference. A gene pair is an inparalog if they are paralogs and duplicated after the speciation event of reference.
has super-classes
paralogy relationc
has ancestral evolutionary eventop only speciationc
is in range of
has inparalogous memberop

least diverged orthology relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#LeastDivergedOrthologyRelation

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
Least diverged orthologs (LDOs) are the genes in two different organisms that have diverged the least since their common ancestor and are most likely to retain the greatest functional similarities. This is a symmetric relation.
is equivalent to
is least diverged orthologdp value true
has super-classes
orthology relationc

Nodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000140

Basic unit of graphs and trees. This class was modified from its original definition (with class restrictions) to avoid multiple statements that relates a Node to a Network (e.g.: RootedTree). In its orignal definition, for each created instance of a Node, an additional statement must be defined to declare that a given node belongs to a Network what is quite verbose. However, we know that sub-nodes of a root node must belong to the same given Rooted Tree (e.g.: HOGs). Therefore, no needs to state sub-nodes to be part of a RootedTree.
has sub-classes
Gene tree nodec
is in range of
has_Rootop

Organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C14250

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
A living thing, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. EXAMPLE(S): animal, human being.
is equivalent to
Organismc
is disjoint with
Taxonc

Organismc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Organism

A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim is associated to a taxon such as "Homo Sapiens", NCBI taxonomy identifier: 9606.
has super-classes
in taxonop some Taxonc
is in range of
in organismop

Orthology datasourcec back to ToC or Class ToC

IRI: http://purl.org/net/orth#OrthologyDataset

Dataset that provides orthology relations including clusters of orthologs, pairwise orthology relations, and so on. Examples would be the content of resources such as OMA, InParanoid, TreeFam, PhylomeDB and so on. Each release of the resources is different dataset.
has super-classes
Versiondp some string
is in domain of
has homology dataop, in database
is in range of
in datasetop

orthology relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#OrthologyRelation

homology pairwise relation that involves sequences that diverged after a speciation event.
has super-classes
homology relationc
has evolutionary eventop only speciationc
(has taxonomic levelop only Taxonomic levelc) and (has homologous memberop exactly 2 Sequence unitc)
has sub-classes
least diverged orthology relationc
is in domain of
is least diverged orthologdp
is disjoint with
paralogy relationc

outparalogy relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#OutparalogyRelation

Outparalogy is also a relation defined over a pair of genes and a speciation event of reference. This pair are outparalogs if the duplication event through which they are related to each other predates the speciation event of reference.
has super-classes
paralogy relationc
has descendant evolutionary eventop only speciationc

paralogy relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#ParalogyRelation

Homology relation that involves sequences that diverged after a duplication event.
has super-classes
homology relationc
has evolutionary eventop only geneDuplicationc
(has taxonomic levelop only Taxonomic levelc) and (has homologous memberop exactly 2 Sequence unitc)
has sub-classes
inparalogy relationc, outparalogy relationc
is disjoint with
orthology relationc

polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000104

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
is equivalent to
Proteinc

Proteinc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Protein

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
has super-classes
Sequence unitc
in organismop some Organismc
contained inop only databasec
is disjoint with
Genec

RootedTreec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000012

Tree with a root node, which is the common ancestor to all the nodes in the tree
has super-classes
has_Rootop exactly 1 Nodec
has sub-classes
Hierarchical clustering treec
is in domain of
has_Rootop

Sequence unitc back to ToC or Class ToC

IRI: http://purl.org/net/orth#SequenceUnit

protein or DNA sequence as a unit of comparison
has super-classes
Gene tree nodec
has sub-classes
Genec, Proteinc, gene regionc
is in domain of
has homologop, has least diverged orthologop, in organismop
is in range of
has co-orthologous memberop, has homologop, has least diverged orthologop

speciationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000121

Evolutionary event related with the evolution of a gene in different species
has super-classes
cladogeneticChangec

Taxonc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Taxon

An element of a taxonomy for classifying life forms.
has super-classes
replacesop only Taxonc
Mnemonicdp max 1
is in domain of
replacesop
is in range of
replacesop
is disjoint with
Organismc

Taxonomic levelc back to ToC or Class ToC

IRI: http://purl.org/net/orth#TaxonomicRange

The taxonomic level represents the taxon at which a group of sequences are considered members of the same cluster of orthologs/paralogs
is in domain of
taxonomic leveldp
is in range of
has taxonomic levelop

xenology relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#XenologyRelation

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
Gene pairs whose history, since their divergence, includes a horizontal transfer.
has super-classes
homology relationc

Object Properties

contained inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001018

This property was simplified. Original range and domain were removed due to be highly abstracted because it is well-know the domain of discourse: orthology databases. The rage restriction of this property is defined as a class restriction in (e.g.: orth:Gene).

encodesop back to ToC or Object Property ToC

IRI: http://semanticscience.org/resource/SIO_010078

is defined by
http://semanticscience.org/ontology/sio.owl
A relation between two objects, in which the first object contains information that is used to produce the second object.
is inverse of
is encoded byop

hasop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000178

Generic 'has' property.
has sub-properties
has homologop, has homology dataop, has taxonomic levelop, has_Rootop
is inverse of
part_ofop

has ancestral evolutionary eventop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasAncestralEvolutionaryEvent

A property of a homology relation (e.g.: "inparalogy relation") to state an ancestral evolutionary event. An ancestral evolutionary event is an event that precedes another evolutionary event. For example, a speciation event before a duplication event.
has super-properties
has evolutionary eventop

has co-orthologous memberop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasCoOrthologousMember

A property to define the membership of a sequence unit into a co-orthology relation.
has super-properties
has partop
has domain
co-orthology relationc
has range
Sequence unitc

has descendant evolutionary eventop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasDescendantEvolutionaryEvent

A property of a homology relation (e.g.: "outparalogy relation") to state a descendant evolutionary event. A descendant evolutionary event is an event that occurs after another evolutionary event. For example, a speciation event after a duplication event.
has super-properties
has evolutionary eventop

has evolutionary eventop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasEvolutionaryEvent

A property of a homology relation (e.g.: "paralogy relation") to state an evolutionary event such as a duplication or a speciation event.
has sub-properties
has ancestral evolutionary eventop, has descendant evolutionary eventop
has domain
Cluster of homologous sequencesc or orthology relationc or paralogy relationc
has range
cladogeneticChangec

has homologop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasHomolog

Homologous pairwise relation between sequence units (e.g.: genes, proteins or gene regions). For example, A Gene(A) hasHomolog Gene(B). This property can be materialized or inferred by applying a logical rule.

has characteristics: symmetric

has super-properties
hasop
has sub-properties
has orthologop, has paralogop, has xenologop
has domain
Sequence unitc
has range
Sequence unitc

has homologous memberop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasHomologousMember

Property that permits to define the membership of a cluster of homologs or a sequence unit to a clusters of homologs.
has super-properties
has partop
has domain
Cluster of homologous sequencesc or homology relationc
has range
Cluster of homologous sequencesc or Sequence unitc
is inverse of
is homologous memberop

has homology dataop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasHomologyData

Inverse property of inDataset. It permits to retrieve the clusters or homology relations included in a particular dataset.
has super-properties
hasop
has domain
Orthology datasourcec
has range
Cluster of homologous sequencesc or homology relationc
is inverse of
in datasetop

has inparalogous memberop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasInparalogousMember

A property to define the membership of a in-paralogy relation into co-orthology relation.
has super-properties
has partop
has domain
co-orthology relationc
has range
inparalogy relationc

has least diverged orthologop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasLeastDivergedOrtholog

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
Least diverged orthologs (LDOs) are the genes in two different organisms that have diverged the least since their common ancestor and are most likely to retain the greatest functional similarities.

has characteristics: symmetric

has super-properties
has orthologop
has domain
Sequence unitc
has range
Sequence unitc

has orthologop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasOrtholog

Orthologous pairwise relation between genes/proteins. For example, A Gene(A) hasOrtholog Gene(B). This property can be materialized or inferred by applying a logical rule.

has characteristics: symmetric

has super-properties
has homologop
has sub-properties
has least diverged orthologop

has paralogop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasParalog

Paralogous pairwise relation between genes/proteins. For example, a Gene(A) hasParalog Gene(B). This property can be materialized or inferred by applying a logical rule.

has characteristics: symmetric

has super-properties
has homologop

has partop back to ToC or Object Property ToC

IRI: http://semanticscience.org/resource/SIO_000028

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part.

has characteristics: reflexive, transitive

has sub-properties
has co-orthologous memberop, has homologous memberop, has inparalogous memberop

has taxonomic levelop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasTaxonomicRange

Property that associates a cluster of homologs with the taxonomic range at which it has been calculated
has super-properties
hasop
has domain
Cluster of homologous sequencesc or orthology relationc or paralogy relationc
has range
Taxonomic levelc

has xenologop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasXenolog

Xenologous pairwise relation between genes/proteins. For example, a Gene(A) hasXenolog Gene(B).

has characteristics: symmetric

has super-properties
has homologop

has_Rootop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000148

The property links a rooted tree to the specific node that represents the unique root of the tree.
has super-properties
hasop
has domain
RootedTreec
has range
Nodec

in datasetop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#inDataset

Property that provides the dataset associated with a gene tree node
has domain
Cluster of homologous sequencesc or homology relationc
has range
Orthology datasourcec
is inverse of
has homology dataop

in organismop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#organism

A sequence unit (e.g.: gene) comes from an organism.
has domain
Sequence unitc
has range
Organismc

in taxonop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002162

Connects a biological entity to its taxon of origin.

is encoded byop back to ToC or Object Property ToC

IRI: http://semanticscience.org/resource/SIO_010079

is defined by
http://semanticscience.org/ontology/sio.owl
A relation between two objects, in which the first object is produced from the information contained in the second object.
is inverse of
encodesop

is homologous memberop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#isHomologousMember

Inverse of has homologous member. This property permits to find the cluster in which a cluster or sequence unit is included.
has super-properties
member ofop
is inverse of
has homologous memberop

member ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002350

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
Is member of is a mereological relation between a item and a collection.
has sub-properties
is homologous memberop

part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000194

is inverse of
hasop

replacesop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/replaces

A resource that is replaced by this resource.
has domain
Taxonc
has range
Taxonc

Data Properties

identifierdp back to ToC or Data Property ToC

IRI: http://purl.org/dc/terms/identifier

This property is orignally defined in dcterms schema however in the context of the ORTH ontology we define this property as being an OWL datatype property rather than a generic RDF property. This property should be assigned to any individual that have one or more identifiers. For example, uniprot:P01308 dcterms:identifier "P01308".
has range
string

is least diverged orthologdp back to ToC or Data Property ToC

IRI: http://purl.org/net/orth#isLeastDivergedOrtholog

Least diverged orthologs (LDOs) are the genes in two different organisms that have diverged the least since their common ancestor and are most likely to retain the greatest functional similarities. This property assigns a boolean value to state if an orthology relation is a actually LDO relation.
has domain
orthology relationc
has range
boolean

Mnemonicdp back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/mnemonic

A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries.
has range
string

taxonomic leveldp back to ToC or Data Property ToC

IRI: http://purl.org/net/orth#taxRange

Property that stores the name of the taxonomic level at which a given cluster of homologs has been calculated
has domain
Taxonomic levelc
has range
string

taxonomic level identifierdp back to ToC or Data Property ToC

IRI: http://purl.org/net/orth#taxRangeId

This property links a cluster of homologs with its taxonomic level.
has range
integer

Versiondp back to ToC or Data Property ToC

IRI: http://purl.org/pav/version

is defined by
https://qfo.github.io/OrthologyOntology/ontology.ttl
The version number of a resource. This is a freetext string, typical values are "1.5" or "21". The URI identifying the previous version can be provided using prov:previousVersion. This property is normally used in a functional way, although PAV does not formally restrict this.
has range
string

Annotation Properties

alternative labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#altLabel

is defined by
http://www.w3.org/2004/02/skos/core
The range of skos:altLabel is the class of RDF plain literals.
has super-properties
label

definitionap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#definition

is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
noteap

exampleap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#example

is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
noteap

in databaseap back to ToC or Annotation Property ToC

IRI: http://purl.org/net/orth#inDatabase

A property to define the database an orthology dataset belongs to.
has domain
Orthology datasourcec

noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#note

is defined by
http://www.w3.org/2004/02/skos/core
has sub-properties
definitionap, exampleap, scope noteap

preferred labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#prefLabel

is defined by
http://www.w3.org/2004/02/skos/core
A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag.
has super-properties
label

scope noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#scopeNote

is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
noteap

Namespace Declarations back to ToC

default namespace
http://purl.org/net/orth#
core
http://purl.uniprot.org/core/
net
http://purl.org/net/
obo
http://purl.obolibrary.org/obo/
ontology
http://semanticscience.org/ontology/
orth
http://purl.org/net/orth#
owl
http://www.w3.org/2002/07/owl#
pav
http://purl.org/pav/
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
resource
http://semanticscience.org/resource/
skos
http://www.w3.org/2004/02/skos/core#
terms
http://purl.org/dc/terms/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.