hom.owl
type: Ontology
version IRI: hom.owl
namespace-id-rule: * HOM:$sequence(7,0,9999999)$
date: 02:12:2009 15:16
default-namespace: homology_and_related_concepts_in_biology
has_obo_format_version: 1.2

definition
type: AnnotationProperty

namespace-id-rule
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

similarity
type: Class
definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
database_cross_reference: ECO:0000041
database_cross_reference: SO:similar_to
has_exact_synonym: sameness
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: correspondence
has_related_synonym: resemblance
id: HOM:0000000

Axiom
annotated source: similarity
annotated property: definition
annotated target: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
database_cross_reference: BGEE:curator

inferred from similarity
type: Axiom
annotated source: similarity
annotated property: database_cross_reference
annotated target: ECO:0000041

Axiom
annotated source: similarity
annotated property: has_related_synonym
annotated target: correspondence
database_cross_reference: DOI:10.1007/BF02814479

homology
type: Class
subclass of: similarity
disjoint with: homoplasy
definition: Similarity that results from common evolutionary origin.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000001
comment: This broad definition encompasses all the working definitions proposed so far in the literature.

Axiom
annotated source: homology
annotated property: definition
annotated target: Similarity that results from common evolutionary origin.
database_cross_reference: DOI:10.1002/bies.950180611
database_cross_reference: DOI:10.1002/jmor.1051730307
database_cross_reference: DOI:10.1007/BF02814480

homoplasy
type: Class
subclass of: similarity
definition: Similarity that results from independent evolution.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: analogy
id: HOM:0000002

Axiom
annotated source: homoplasy
annotated property: definition
annotated target: Similarity that results from independent evolution.
database_cross_reference: DOI:10.1016/j.jhevol.2006.11.010

homocracy
type: Class
subclass of: similarity
definition: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
database_cross_reference: ECO:0000075
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000003
comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.

Axiom
annotated source: homocracy
annotated property: definition
annotated target: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
database_cross_reference: DOI:10.1007/BF02814484
database_cross_reference: DOI:10.1007/s00427-003-0301-4
database_cross_reference: DOI:10.1186/1742-9994-2-15

inferred from gene expression similarity
type: Axiom
annotated source: homocracy
annotated property: database_cross_reference
annotated target: ECO:0000075

convergence
type: Class
subclass of: homoplasy
definition: Homoplasy that involves different underlying mechanisms or structures.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: analogy
id: HOM:0000004
comment: Convergence usually implies a notion of adaptation.

Axiom
annotated source: convergence
annotated property: definition
annotated target: Homoplasy that involves different underlying mechanisms or structures.
database_cross_reference: DOI:10.1016/j.jhevol.2006.11.010

parallelism
type: Class
subclass of: homoplasy
definition: Homoplasy that involves homologous underlying mechanisms or structures.
has_exact_synonym: parallel evolution
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000005
comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.

Axiom
annotated source: parallelism
annotated property: definition
annotated target: Homoplasy that involves homologous underlying mechanisms or structures.
database_cross_reference: DOI:10.1016/j.jhevol.2006.11.010

structural homology
type: Class
subclass of: homology
definition: Homology that is defined by similarity with regard to selected structural parameters.
database_cross_reference: ECO:0000071
database_cross_reference: MI:2163
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: idealistic homology
id: HOM:0000006

Axiom
annotated source: structural homology
annotated property: definition
annotated target: Homology that is defined by similarity with regard to selected structural parameters.
database_cross_reference: DOI:10.1016/j.jhevol.2006.11.014
database_cross_reference: DOI:10.1146/annurev.es.20.110189.000411
database_cross_reference: ISBN:0123195837

inferred from morphological similarity
type: Axiom
annotated source: structural homology
annotated property: database_cross_reference
annotated target: ECO:0000071

by homology
type: Axiom
annotated source: structural homology
annotated property: database_cross_reference
annotated target: MI:2163

historical homology
type: Class
subclass of: homology
definition: Homology that is defined by common descent.
has_broad_synonym: homology
database_cross_reference: ECO:0000080
database_cross_reference: RO_proposed_relation:homologous_to
database_cross_reference: SO:0000330
database_cross_reference: SO:0000853
database_cross_reference: SO:0000857
database_cross_reference: SO:homologous_to
database_cross_reference: TAO:homologous_to
has_exact_synonym: cladistic homology
has_exact_synonym: phylogenetic homology
has_exact_synonym: taxic homology
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: true homology
id: HOM:0000007

Axiom
annotated source: historical homology
annotated property: definition
annotated target: Homology that is defined by common descent.
database_cross_reference: DOI:10.1016/S0169-5347(97)01125-7
database_cross_reference: ISBN:0123195837

inferred from phylogeny
type: Axiom
annotated source: historical homology
annotated property: database_cross_reference
annotated target: ECO:0000080

conserved_region
type: Axiom
annotated source: historical homology
annotated property: database_cross_reference
annotated target: SO:0000330

homologous_region
type: Axiom
annotated source: historical homology
annotated property: database_cross_reference
annotated target: SO:0000853

homologous
type: Axiom
annotated source: historical homology
annotated property: database_cross_reference
annotated target: SO:0000857

biological homology
type: Class
subclass of: homology
definition: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
database_cross_reference: ECO:0000067
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: transformational homology
id: HOM:0000008
comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.

Axiom
annotated source: biological homology
annotated property: definition
annotated target: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
database_cross_reference: DOI:10.1016/S0169-5347(97)01125-7
database_cross_reference: DOI:10.1146/annurev.es.20.110189.000411

inferred from developmental similarity
type: Axiom
annotated source: biological homology
annotated property: database_cross_reference
annotated target: ECO:0000067

reversal
type: Class
subclass of: homoplasy
definition: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
has_exact_synonym: atavism
has_exact_synonym: rudiment
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: reversion
id: HOM:0000009

Axiom
annotated source: reversal
annotated property: definition
annotated target: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
database_cross_reference: DOI:10.1016/j.jhevol.2006.11.010

syntenic homology
type: Class
subclass of: structural homology
definition: Structural homology that is detected by similarity in content and organization between chromosomes.
database_cross_reference: MeSH:Synteny
database_cross_reference: SO:0000860
database_cross_reference: SO:0005858
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: synteny
id: HOM:0000010

Axiom
annotated source: syntenic homology
annotated property: definition
annotated target: Structural homology that is detected by similarity in content and organization between chromosomes.
database_cross_reference: MeSH:Synteny

syntenic
type: Axiom
annotated source: syntenic homology
annotated property: database_cross_reference
annotated target: SO:0000860

syntenic_region
type: Axiom
annotated source: syntenic homology
annotated property: database_cross_reference
annotated target: SO:0005858

paralogy
type: Class
subclass of: historical homology
disjoint with: orthology
definition: Historical homology that involves genes that diverged after a duplication event.
database_cross_reference: SO:0000854
database_cross_reference: SO:0000859
database_cross_reference: SO:paralogous_to
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000011

Axiom
annotated source: paralogy
annotated property: definition
annotated target: Historical homology that involves genes that diverged after a duplication event.
database_cross_reference: DOI:10.1016/S0168-9525(00)02005-9
database_cross_reference: DOI:10.1146/annurev.genet.39.073003.114725
database_cross_reference: PMID:5449325

paralogous_region
type: Axiom
annotated source: paralogy
annotated property: database_cross_reference
annotated target: SO:0000854

paralogous
type: Axiom
annotated source: paralogy
annotated property: database_cross_reference
annotated target: SO:0000859

syntenic paralogy
type: Class
subclass of: syntenic homology
subclass of: paralogy
definition: Paralogy that involves sets of syntenic blocks.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: duplicon
has_related_synonym: paralogon
id: HOM:0000012

Axiom
annotated source: syntenic paralogy
annotated property: definition
annotated target: Paralogy that involves sets of syntenic blocks.
database_cross_reference: DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
database_cross_reference: DOI:10.1186/1471-213X-7-100

syntenic orthology
type: Class
subclass of: syntenic homology
definition: Syntenic homology that involves chromosomes of different species.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000013

Axiom
annotated source: syntenic orthology
annotated property: definition
annotated target: Syntenic homology that involves chromosomes of different species.
database_cross_reference: DOI:10.1101/gr.6380007

partial homology
type: Class
subclass of: structural homology
definition: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
has_exact_synonym: fractional homology
has_exact_synonym: segmental homology
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: mixed homology
has_related_synonym: modular homology
has_related_synonym: partial correspondence
has_related_synonym: percent homology
id: HOM:0000014

Axiom
annotated source: partial homology
annotated property: definition
annotated target: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
database_cross_reference: ISBN:0123195837
database_cross_reference: ISBN:978-0471984931

protein structural homology
type: Class
subclass of: structural homology
definition: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
database_cross_reference: MeSH:Structural Homology, Protein
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000015

Axiom
annotated source: protein structural homology
annotated property: definition
annotated target: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
database_cross_reference: DOI:10.1016/0022-2836(76)90195-9

non functional homology
type: Class
subclass of: structural homology
disjoint with: equivalogy
definition: Structural homology that involves a pseudogenic feature and its functional ancestor.
has_broad_synonym: pseudogene
database_cross_reference: SO:non_functional_homolog_of
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000016

Axiom
annotated source: non functional homology
annotated property: definition
annotated target: Structural homology that involves a pseudogenic feature and its functional ancestor.
database_cross_reference: SO:non_functional_homolog_of

orthology
type: Class
subclass of: historical homology
definition: Historical homology that involves genes that diverged after a speciation event.
database_cross_reference: ECO:00000060
database_cross_reference: SO:0000855
database_cross_reference: SO:0000858
database_cross_reference: SO:orthologous_to
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000017
comment: The term is sometimes also used for anatomical structures.

Axiom
annotated source: orthology
annotated property: definition
annotated target: Historical homology that involves genes that diverged after a speciation event.
database_cross_reference: DOI:10.1007/BF02814484
database_cross_reference: DOI:10.1016/S0168-9525(00)02005-9
database_cross_reference: DOI:10.1146/annurev.genet.39.073003.114725
database_cross_reference: PMID:5449325

inferred from sequence orthology
type: Axiom
annotated source: orthology
annotated property: database_cross_reference
annotated target: ECO:00000060

orthologous_region
type: Axiom
annotated source: orthology
annotated property: database_cross_reference
annotated target: SO:0000855

orthologous
type: Axiom
annotated source: orthology
annotated property: database_cross_reference
annotated target: SO:0000858

xenology
type: Class
subclass of: historical homology
definition: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000018
comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).

Axiom
annotated source: xenology
annotated property: definition
annotated target: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
database_cross_reference: DOI:10.1016/S0168-9525(00)02005-9
database_cross_reference: DOI:10.1146/annurev.genet.39.073003.114725

1 to 1 homology
type: Class
subclass of: historical homology
definition: Historical homology that involves two members sharing no other homologs in the lineages considered.
has_exact_synonym: 1:1 homology
has_exact_synonym: one-to-one homology
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000019

Axiom
annotated source: 1 to 1 homology
annotated property: definition
annotated target: Historical homology that involves two members sharing no other homologs in the lineages considered.
database_cross_reference: BGEE:curator

1 to 1 orthology
type: Class
subclass of: orthology
subclass of: 1 to 1 homology
definition: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
has_exact_synonym: 1:1 orthology
has_exact_synonym: one-to-one orthology
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000020

Axiom
annotated source: 1 to 1 orthology
annotated property: definition
annotated target: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
database_cross_reference: DOI:10.1007/BF02814484
database_cross_reference: http://www.ensembl.org/info/docs/compara/homology_method.html

allogeny
type: Class
definition: Relationship between recognizably corresponding characters that occurs in two or more taxa and have different generative bases.
has_exact_synonym: generative homoplasy
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000021
deprecated: true

Axiom
annotated source: allogeny
annotated property: definition
annotated target: Relationship between recognizably corresponding characters that occurs in two or more taxa and have different generative bases.
database_cross_reference: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R

ohnology
type: Class
subclass of: paralogy
definition: Paralogy that results from a whole genome duplication event.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: homoeology
id: HOM:0000022

Axiom
annotated source: ohnology
annotated property: definition
annotated target: Paralogy that results from a whole genome duplication event.
database_cross_reference: DOI:10.1038/75560

in-paralogy
type: Class
subclass of: paralogy
disjoint with: out-paralogy
definition: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
has_exact_synonym: inparalogy
has_exact_synonym: symparalogy
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000023

Axiom
annotated source: in-paralogy
annotated property: definition
annotated target: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
database_cross_reference: DOI:10.1146/annurev.genet.39.073003.114725

out-paralogy
type: Class
subclass of: paralogy
definition: Paralogy that results from a duplication preceding a given speciation event.
has_exact_synonym: alloparalogy
has_exact_synonym: outparalogy
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000024

Axiom
annotated source: out-paralogy
annotated property: definition
annotated target: Paralogy that results from a duplication preceding a given speciation event.
database_cross_reference: DOI:10.1146/annurev.genet.39.073003.114725

pro-orthology
type: Class
subclass of: 1 to many orthology
definition: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000025

Axiom
annotated source: pro-orthology
annotated property: definition
annotated target: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
database_cross_reference: DOI:10.1006/scdb.1999.0338
database_cross_reference: DOI:10.1038/nrg2099

semi-orthology
type: Class
subclass of: 1 to many orthology
definition: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000026
comment: The converse of pro-orthologous.

Axiom
annotated source: semi-orthology
annotated property: definition
annotated target: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
database_cross_reference: DOI:10.1006/scdb.1999.0338
database_cross_reference: DOI:10.1038/nrg2099

serial homology
type: Class
subclass of: iterative homology
definition: Iterative homology that involves structures arranged along the main body axis.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: homonomy
id: HOM:0000027

Axiom
annotated source: serial homology
annotated property: definition
annotated target: Iterative homology that involves structures arranged along the main body axis.
database_cross_reference: DOI:10.1146/annurev.es.20.110189.000411

heterochronous homology
type: Class
subclass of: biological homology
definition: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
has_exact_synonym: heterochrony
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000028

Axiom
annotated source: heterochronous homology
annotated property: definition
annotated target: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
database_cross_reference: ISBN:978-0674639416

paedomorphorsis
type: Class
subclass of: heterochronous homology
disjoint with: peramorphosis
definition: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
has_exact_synonym: juvenification
has_exact_synonym: pedomorphosis
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000029

Axiom
annotated source: paedomorphorsis
annotated property: definition
annotated target: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
database_cross_reference: ISBN:978-0674639416
database_cross_reference: http://en.wikipedia.org/wiki/Pedomorphosis

peramorphosis
type: Class
subclass of: heterochronous homology
definition: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000030

Axiom
annotated source: peramorphosis
annotated property: definition
annotated target: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
database_cross_reference: http://en.wikipedia.org/wiki/Peramorphosis

progenesis
type: Class
subclass of: paedomorphorsis
definition: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000031

Axiom
annotated source: progenesis
annotated property: definition
annotated target: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
database_cross_reference: ISBN:978-0674639416
database_cross_reference: http://en.wikipedia.org/wiki/Progenesis

neoteny
type: Class
subclass of: paedomorphorsis
definition: Paedomorphosis that is produced by a retardation of somatic development.
has_exact_synonym: juvenilization
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000032

Axiom
annotated source: neoteny
annotated property: definition
annotated target: Paedomorphosis that is produced by a retardation of somatic development.
database_cross_reference: ISBN:978-0674639416
database_cross_reference: http://en.wikipedia.org/wiki/Neoteny

mimicry
type: Class
subclass of: convergence
definition: Convergence that results from co-evolution usually involving an evolutionary arms race.
created by: admin
creation date: 2009-07-30T11:28:41Z
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000033

Axiom
annotated source: mimicry
annotated property: definition
annotated target: Convergence that results from co-evolution usually involving an evolutionary arms race.
database_cross_reference: http:://en.wikipedia.org/wiki/Mimicry

1 to many orthology
type: Class
subclass of: orthology
subclass of: 1 to many homology
definition: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
has_exact_synonym: 1:many orthology
has_exact_synonym: one-to-many orthology
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: co-orthology
has_related_synonym: many to 1 orthology
id: HOM:0000034

Axiom
annotated source: 1 to many orthology
annotated property: definition
annotated target: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
database_cross_reference: DOI:10.1038/415741a
database_cross_reference: http://www.ensembl.org/info/docs/compara/homology_method.html

many to many homology
type: Class
subclass of: historical homology
definition: Historical homology that involves two members of a larger set of homologs.
has_exact_synonym: many-to-many homology
has_exact_synonym: many:many homology
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000036

Axiom
annotated source: many to many homology
annotated property: definition
annotated target: Historical homology that involves two members of a larger set of homologs.
database_cross_reference: DOI:10.1093/molbev/msp002

1 to many homology
type: Class
subclass of: historical homology
definition: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
has_exact_synonym: one-to-many homology
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: 1:many homology
id: HOM:0000037

Axiom
annotated source: 1 to many homology
annotated property: definition
annotated target: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
database_cross_reference: BGEE:curator

apomorphy
type: Class
subclass of: historical homology
disjoint with: plesiomorphy
definition: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: synapomorphy
id: HOM:0000042

Axiom
annotated source: apomorphy
annotated property: definition
annotated target: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
database_cross_reference: ISBN:978-0252068140

plesiomorphy
type: Class
subclass of: historical homology
definition: Historical homology that is based on distant shared ancestry.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: symplesiomorphy
id: HOM:0000043
comment: This term is usually contrasted to apomorphy.

Axiom
annotated source: plesiomorphy
annotated property: definition
annotated target: Historical homology that is based on distant shared ancestry.
database_cross_reference: ISBN:978-0252068140

deep homology
type: Class
subclass of: homocracy
subclass of: parallelism
definition: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
has_exact_synonym: deep genetic homology
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: generative homology
has_related_synonym: homoiology
id: HOM:0000044
comment: Used for structures in distantly related taxa.

Axiom
annotated source: deep homology
annotated property: definition
annotated target: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
database_cross_reference: DOI:10.1007/BF02814485
database_cross_reference: DOI:10.1038/nature07891

hemiplasy
type: Class
subclass of: historical homology
definition: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000045

Axiom
annotated source: hemiplasy
annotated property: definition
annotated target: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
database_cross_reference: DOI:10.1073/pnas.0807433105

gametology
type: Class
subclass of: chromosomal homology
definition: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000046

Axiom
annotated source: gametology
annotated property: definition
annotated target: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
database_cross_reference: PMID:11110898

chromosomal homology
type: Class
subclass of: historical homology
definition: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
database_cross_reference: MeSH:Chromosome Pairing
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000047

Axiom
annotated source: chromosomal homology
annotated property: definition
annotated target: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
database_cross_reference: ISBN:0195307615

many to many orthology
type: Class
subclass of: orthology
subclass of: many to many homology
definition: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
has_exact_synonym: many-to-many orthology
has_exact_synonym: many:many orthology
has_exact_synonym: trans-orthology
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: co-orthology
has_related_synonym: trans-homology
id: HOM:0000048

Axiom
annotated source: many to many orthology
annotated property: definition
annotated target: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
database_cross_reference: DOI:10.1038/415741a
database_cross_reference: http://www.ensembl.org/info/docs/compara/homology_method.html

within-species paralogy
type: Class
subclass of: paralogy
disjoint with: between-species paralogy
definition: Paralogy that involves genes from the same species.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000049

Axiom
annotated source: within-species paralogy
annotated property: definition
annotated target: Paralogy that involves genes from the same species.
database_cross_reference: http://www.ensembl.org/info/docs/compara/homology_method.html

between-species paralogy
type: Class
subclass of: paralogy
definition: Paralogy that involves genes from different species.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000050
comment: The genes have diverged before a speciation event.

Axiom
annotated source: between-species paralogy
annotated property: definition
annotated target: Paralogy that involves genes from different species.
database_cross_reference: http://www.ensembl.org/info/docs/compara/homology_method.html

postdisplacement
type: Class
subclass of: paedomorphorsis
definition: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
has_exact_synonym: post-displacement
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000051

Axiom
annotated source: postdisplacement
annotated property: definition
annotated target: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
database_cross_reference: http://en.wikipedia.org/wiki/Pedomorphosis

hypermorphosis
type: Class
subclass of: peramorphosis
definition: Peramorphosis that is produced by a delay in the offset of development.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000052

Axiom
annotated source: hypermorphosis
annotated property: definition
annotated target: Peramorphosis that is produced by a delay in the offset of development.
database_cross_reference: ISBN:978-0674639416
database_cross_reference: http://en.wikipedia.org/wiki/Peramorphosis

synology
type: Class
subclass of: xenology
definition: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000053

Axiom
annotated source: synology
annotated property: definition
annotated target: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
database_cross_reference: DOI:10.1007/BF00173425
database_cross_reference: DOI:10.1016/S0168-9525(00)02005-9

isoorthology
type: Class
subclass of: orthology
subclass of: equivalogy
definition: Orthology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: ECO:0000080
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000054

Axiom
annotated source: isoorthology
annotated property: definition
annotated target: Orthology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: DOI:10.1016/S0168-9525(00)02005-9

inferred from phylogeny
type: Axiom
annotated source: isoorthology
annotated property: database_cross_reference
annotated target: ECO:0000080

tandem paralogy
type: Class
subclass of: paralogy
definition: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: iterative paralogy
has_related_synonym: serial paralogy
id: HOM:0000055

Axiom
annotated source: tandem paralogy
annotated property: definition
annotated target: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
database_cross_reference: DOI:10.1016/S0168-9525(00)02005-9
database_cross_reference: ISBN:978-0878932665

latent homology
type: Class
subclass of: parallelism
subclass of: syngeny
definition: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
has_exact_synonym: apomorphic tendency
has_exact_synonym: cryptic homology
has_exact_synonym: underlying synapomorphy
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: homoiology
has_related_synonym: homoplastic tendency
has_related_synonym: re-awakening
id: HOM:0000057
comment: Used for structures in closely related taxa.

Axiom
annotated source: latent homology
annotated property: definition
annotated target: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
database_cross_reference: DOI:10.1007/BF02814485
database_cross_reference: DOI:10.1016/j.jhevol.2006.11.010
database_cross_reference: DOI:10.1186/1742-9994-2-15
database_cross_reference: ISBN:0199141118

syngeny
type: Class
subclass of: homocracy
definition: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
has_exact_synonym: generative homology
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000058
comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.

Axiom
annotated source: syngeny
annotated property: definition
annotated target: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
database_cross_reference: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R
database_cross_reference: DOI:10.1186/1742-9994-2-15

apparent orthology
type: Class
subclass of: 1 to 1 homology
subclass of: between-species paralogy
definition: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
has_exact_synonym: 1:1 paralogy
has_exact_synonym: apparent 1:1 orthology
has_exact_synonym: pseudoorthology
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000060
comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.

Axiom
annotated source: apparent orthology
annotated property: definition
annotated target: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
database_cross_reference: DOI:10.1146/annurev.genet.39.073003.114725
database_cross_reference: http://www.ensembl.org/info/docs/compara/homology_method.html

pseudoparalogy
type: Class
subclass of: xenology
definition: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000061
comment: These genes may come out as paralogs in a single-genome analysis.

Axiom
annotated source: pseudoparalogy
annotated property: definition
annotated target: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
database_cross_reference: DOI:10.1146/annurev.genet.39.073003.114725

equivalogy
type: Class
subclass of: historical homology
subclass of: functional equivalence
definition: Historical homology that involves functional equivalent genes with retention of the ancestral function.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000062
comment: This may include examples of orthology, paralogy and xenology.

Axiom
annotated source: equivalogy
annotated property: definition
annotated target: Historical homology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: DOI:10.1093/nar/gkl1043

interology
type: Class
subclass of: historical homology
definition: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000063

Axiom
annotated source: interology
annotated property: definition
annotated target: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
database_cross_reference: DOI:10.1101/gr.1774904
database_cross_reference: DOI:10.1126/science.287.5450.116

functional equivalence
type: Class
subclass of: similarity
definition: Similarity that is characterized by interchangeability in function.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: functional similarity
id: HOM:0000065

Axiom
annotated source: functional equivalence
annotated property: definition
annotated target: Similarity that is characterized by interchangeability in function.
database_cross_reference: DOI:10.1007/BF02814484
database_cross_reference: DOI:10.1038/415741a

iterative homology
type: Class
subclass of: biological homology
definition: Biological homology that involves parts of the same organism.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000066

Axiom
annotated source: iterative homology
annotated property: definition
annotated target: Biological homology that involves parts of the same organism.
database_cross_reference: DOI:10.1146/annurev.es.20.110189.000411

paraxenology
type: Class
subclass of: xenology
definition: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
has_exact_synonym: duplicate xenology
has_exact_synonym: multiple xenology
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000068

Axiom
annotated source: paraxenology
annotated property: definition
annotated target: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
database_cross_reference: PMID:3065587

plerology
type: Class
subclass of: paralogy
definition: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000069
comment: This phenomenon is usually due to gene conversion process.

Axiom
annotated source: plerology
annotated property: definition
annotated target: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
database_cross_reference: PMID:3065587

homotopy
type: Class
subclass of: structural homology
disjoint with: homeosis
definition: Structural homology that involves structures with the same or similar relative positions.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000071
comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.

Axiom
annotated source: homotopy
annotated property: definition
annotated target: Structural homology that involves structures with the same or similar relative positions.
database_cross_reference: DOI:10.1007/BF02814484
database_cross_reference: DOI:10.1007/BF02814485
database_cross_reference: ISBN:0123195837

homeosis
type: Class
subclass of: biological homology
definition: Biological homology that involves an ectopic structure and the normally positioned structure.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: heterotopy
id: HOM:0000072

Axiom
annotated source: homeosis
annotated property: definition
annotated target: Biological homology that involves an ectopic structure and the normally positioned structure.
database_cross_reference: DOI:10.1007/BF02814485
database_cross_reference: DOI:10.1016/j.cell.2008.06.030

homoeology
type: Class
subclass of: ohnology
subclass of: synology
definition: Synology that results from allopolyploidy.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000073
comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.

Axiom
annotated source: homoeology
annotated property: definition
annotated target: Synology that results from allopolyploidy.
database_cross_reference: DOI:10.1073/pnas.0505156102

paramorphism
type: Class
subclass of: homocracy
subclass of: iterative homology
definition: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
has_obo_namespace: homology_and_related_concepts_in_biology
has_related_synonym: axis paramorphism
id: HOM:0000074

Axiom
annotated source: paramorphism
annotated property: definition
annotated target: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
database_cross_reference: DOI:10.1007/s10441-007-9023-8
database_cross_reference: DOI:10.1046/j.1525-142x.2000.00054.x

regulogy
type: Class
subclass of: historical homology
definition: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
has_obo_namespace: homology_and_related_concepts_in_biology
id: HOM:0000075

Axiom
annotated source: regulogy
annotated property: definition
annotated target: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
database_cross_reference: DOI:10.1101/gr.1774904