similarity
type: Class
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: sameness
has related synonym: resemblance
has db xref: ECO:0000041
  type: DbXref
  has URI: http://purl.org/obo/owl/ECO#ECO_0000041
has db xref: SO:similar_to
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_similar_to
has related synonym: correspondence
  type: Synonym
  has db xref: DOI:10.1007/BF02814479_"Richter_S_(2005)_Homologies_in_phylogenetic_analyseso?=concept_and_tests._Theory_in_Biosciences_124
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI
  has db xref: 2:_105-120"
    type: DbXref
    has URI: http://purl.org/obo/owl/2#2__105-120"
has definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
  type: Definition
  has db xref: BGEE:curator
    type: DbXref
    has URI: http://purl.org/obo/owl/BGEE#BGEE_curator

homology
type: Class
subclass of: similarity
disjoint with: homoplasy
comment: This broad definition encompasses all the working definitions proposed so far in the literature.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Similarity that results from common evolutionary origin.
  type: Definition
  has db xref: DOI:10.1002/bies.950180611_"Bolker_JA_and_Rudolf_AR_(1996)_Developmental_genetics_and_traditional_homology._BioEssays_18
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1002/bies.950180611_"Bolker_JA_and_Rudolf_AR_(1996)_Developmental_genetics_and_traditional_homology._BioEssays_18
  has db xref: DOI:10.1002/jmor.1051730307_"van_Valen_LM_(1982)_Homology_and_causes._Journal_of_Morphology_173
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1002/jmor.1051730307_"van_Valen_LM_(1982)_Homology_and_causes._Journal_of_Morphology_173
  has db xref: 6:_489-494"
    type: DbXref
    has URI: http://purl.org/obo/owl/6#6__489-494"
  has db xref: DOI:10.1007/BF02814480_"Scholtz_G_(2005)_Homology_and_ontogeny:_pattern_and_process_in_comparative_developmental_biology._Theory_in_Biosciences_124
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814480_"Scholtz_G_(2005)_Homology_and_ontogeny:_pattern_and_process_in_comparative_developmental_biology._Theory_in_Biosciences_124
  has db xref: 3:_305-312"
    type: DbXref
    has URI: http://purl.org/obo/owl/3#3__305-312"
  has db xref: 2:_121-143"
    type: DbXref
    has URI: http://purl.org/obo/owl/2#2__121-143"

homoplasy
type: Class
subclass of: similarity
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Similarity that results from independent evolution.
  type: Definition
  has db xref: DOI:10.1016/j.jhevol.2006.11.010
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/j.jhevol.2006.11.010
has related synonym: analogy

homocracy
type: Class
subclass of: similarity
comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
has OBO namespace: homology_and_related_concepts_in_biology
has db xref: ECO:0000075
  type: DbXref
  has URI: http://purl.org/obo/owl/ECO#ECO_0000075
has definition: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
  type: Definition
  has db xref: DOI:10.1007/BF02814484_"Theissen_G_(2005)_Birth
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814484_"Theissen_G_(2005)_Birth
  has db xref: DOI:10.1186/1742-9994-2-15
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1186/1742-9994-2-15
  has db xref: life_and_death_of_developmental_control_genes:_New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
    type: DbXref
    has URI: http://purl.org/obo/owl/life_and_death_of_developmental_control_genes#life_and_death_of_developmental_control_genes__New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
  has db xref: DOI:10.1007/s00427-003-0301-4
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/s00427-003-0301-4

convergence
type: Class
subclass of: homoplasy
comment: Convergence usually implies a notion of adaptation.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Homoplasy that involves different underlying mechanisms or structures.
  type: Definition
  has db xref: DOI:10.1016/j.jhevol.2006.11.010
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/j.jhevol.2006.11.010
has related synonym: analogy

parallelism
type: Class
subclass of: homoplasy
comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Homoplasy that involves homologous underlying mechanisms or structures.
  type: Definition
  has db xref: DOI:10.1016/j.jhevol.2006.11.010
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/j.jhevol.2006.11.010
has exact synonym: parallel evolution

structural homology
type: Class
subclass of: homology
has OBO namespace: homology_and_related_concepts_in_biology
has db xref: ECO:0000071
  type: DbXref
  has URI: http://purl.org/obo/owl/ECO#ECO_0000071
has db xref: MI:2163
  type: DbXref
  has URI: http://purl.org/obo/owl/MI#MI_2163
has related synonym: idealistic homology
has definition: Homology that is defined by similarity with regard to selected structural parameters.
  type: Definition
  has db xref: DOI:10.1016/j.jhevol.2006.11.014_"Rendall_D_and_Di_Fiore_A_(2007)_Homoplasy
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/j.jhevol.2006.11.014_"Rendall_D_and_Di_Fiore_A_(2007)_Homoplasy
  has db xref: homology:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/homology#homology_NULL
  has db xref: and_the_perceived_special_status_of_behavior_in_evolution._Journal_of_Human_Evolution_52:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/and_the_perceived_special_status_of_behavior_in_evolution._Journal_of_Human_Evolution_52#and_the_perceived_special_status_of_behavior_in_evolution._Journal_of_Human_Evolution_5…
  has db xref: 5:_504-521"
    type: DbXref
    has URI: http://purl.org/obo/owl/5#5__504-521"
  has db xref: DOI:10.1146/annurev.es.20.110189.000411
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.es.20.110189.000411
  has db xref: ISBN:0123195837_"Lauder_GV_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_0123195837_"Lauder_GV_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
  has db xref: p._153":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/p._153"#p._153"_NULL

historical homology
type: Class
subclass of: homology
has OBO namespace: homology_and_related_concepts_in_biology
has db xref: TAO:homologous_to
  type: DbXref
  has URI: http://purl.org/obo/owl/TAO#TAO_homologous_to
has related synonym: true homology
has db xref: RO_proposed_relation:homologous_to
  type: DbXref
  has URI: http://purl.org/obo/owl/RO_proposed_relation#RO_proposed_relation_homologous_to
has exact synonym: cladistic homology
has db xref: SO:0000330
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000330
has db xref: SO:0000853
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000853
has db xref: SO:0000857
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000857
has broad synonym: homology
has db xref: ECO:0000080
  type: DbXref
  has URI: http://purl.org/obo/owl/ECO#ECO_0000080
has exact synonym: taxic homology
has db xref: SO:homologous_to
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_homologous_to
has definition: Homology that is defined by common descent.
  type: Definition
  has db xref: Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
    type: DbXref
    has URI: http://purl.org/obo/owl/Homology#Homology__The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
  has db xref: p._65":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/p._65"#p._65"_NULL
  has db xref: DOI:10.1016/S0169-5347(97)01125-7_"Abouheif_E_(1997)_Developmental_genetics_and_homology:_a_hierarchical_approach._Trends_in_Ecology_&_Evolution
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0169-5347(97)01125-7_"Abouheif_E_(1997)_Developmental_genetics_and_homology:_a_hierarchical_approach._Trends_in_Ecology_&_Evolution
  has db xref: 12_405-408.":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/12_405-408."#12_405-408."_NULL
  has db xref: ISBN:0123195837_"Rieppel_O_(1994)_in_Hall_BK_(Ed.)
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_0123195837_"Rieppel_O_(1994)_in_Hall_BK_(Ed.)
has exact synonym: phylogenetic homology

biological homology
type: Class
subclass of: homology
comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
has OBO namespace: homology_and_related_concepts_in_biology
has db xref: ECO:0000067
  type: DbXref
  has URI: http://purl.org/obo/owl/ECO#ECO_0000067
has 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.
  type: Definition
  has db xref: DOI:10.1146/annurev.es.20.110189.000411
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.es.20.110189.000411
  has db xref: 12_405-408.":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/12_405-408."#12_405-408."_NULL
  has db xref: DOI:10.1016/S0169-5347(97)01125-7_"Abouheif_E_(1997)_Developmental_genetics_and_homology:_a_hierarchical_approach._Trends_in_Ecology_&_Evolution
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0169-5347(97)01125-7_"Abouheif_E_(1997)_Developmental_genetics_and_homology:_a_hierarchical_approach._Trends_in_Ecology_&_Evolution
has related synonym: transformational homology

reversal
type: Class
subclass of: homoplasy
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: atavism
has exact synonym: rudiment
has definition: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
  type: Definition
  has db xref: DOI:10.1016/j.jhevol.2006.11.010
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/j.jhevol.2006.11.010
has related synonym: reversion

syntenic homology
type: Class
subclass of: structural homology
has OBO namespace: homology_and_related_concepts_in_biology
has db xref: SO:0005858
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0005858
has definition: Structural homology that is detected by similarity in content and organization between chromosomes.
  type: Definition
  has db xref: MeSH:Synteny
    type: DbXref
    has URI: http://purl.org/obo/owl/MeSH#MeSH_Synteny
has db xref: SO:0000860
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000860
has db xref: MeSH:Synteny
  type: DbXref
  has URI: http://purl.org/obo/owl/MeSH#MeSH_Synteny
has related synonym: synteny

paralogy
type: Class
subclass of: historical homology
disjoint with: orthology
has OBO namespace: homology_and_related_concepts_in_biology
has db xref: SO:0000854
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000854
has db xref: SO:0000859
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000859
has definition: Historical homology that involves genes that diverged after a duplication event.
  type: Definition
  has db xref: DOI:10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
  has db xref: AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics#AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics_NULL
  has db xref: PARALOGS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PARALOGS#PARALOGS_NULL
  has db xref: PMID:5449325
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_5449325
  has db xref: 39:_309-338"
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39__309-338"
  has db xref: DOI:10.1016/S0168-9525(00)02005-9
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0168-9525(00)02005-9
has db xref: SO:paralogous_to
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_paralogous_to

syntenic paralogy
type: Class
subclass of: syntenic homology
subclass of: paralogy
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paralogy that involves sets of syntenic blocks.
  type: Definition
  has db xref: DOI:10.1186/1471-213X-7-100
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1186/1471-213X-7-100
  has db xref: DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
has related synonym: duplicon
has related synonym: paralogon

syntenic orthology
type: Class
subclass of: syntenic homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Syntenic homology that involves chromosomes of different species.
  type: Definition
  has db xref: DOI:10.1101/gr.6380007_"Pontius_JU_et_al._(2007)_Initial_sequence_and_comparative_analysis_of_the_cat_genome._Genome_Research
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1101/gr.6380007_"Pontius_JU_et_al._(2007)_Initial_sequence_and_comparative_analysis_of_the_cat_genome._Genome_Research
  has db xref: 17:_1675-1689_."
    type: DbXref
    has URI: http://purl.org/obo/owl/17#17__1675-1689_."

partial homology
type: Class
subclass of: structural homology
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: fractional homology
has related synonym: mixed homology
has related synonym: modular homology
has related synonym: partial correspondence
has related synonym: percent homology
has definition: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
  type: Definition
  has db xref: ISBN:0123195837_"Hillis_DM_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_0123195837_"Hillis_DM_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
  has db xref: p._348":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/p._348"#p._348"_NULL
  has db xref: ISBN:0123195837_"Sattler_R_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_0123195837_"Sattler_R_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
  has db xref: p._425":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/p._425"#p._425"_NULL
  has db xref: ISBN:978-0471984931
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0471984931
has exact synonym: segmental homology

protein structural homology
type: Class
subclass of: structural homology
has OBO namespace: homology_and_related_concepts_in_biology
has 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.
  type: Definition
  has db xref: 1:75-95"
    type: DbXref
    has URI: http://purl.org/obo/owl/1#1_75-95"
  has db xref: DOI:10.1016/0022-2836(76)90195-9_"Rossmann_MG_and_Argos_P_(1976)_Exploring_structural_homology_of_proteins._Journal_of_Molecular_Biology_105
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/0022-2836(76)90195-9_"Rossmann_MG_and_Argos_P_(1976)_Exploring_structural_homology_of_proteins._Journal_of_Molecular_Biology_105
has db xref: MeSH:Structural_Homology,_Protein
  type: DbXref
  has URI: http://purl.org/obo/owl/MeSH#MeSH_Structural_Homology,_Protein

non functional homology
type: Class
subclass of: structural homology
disjoint with: equivalogy
has OBO namespace: homology_and_related_concepts_in_biology
has broad synonym: pseudogene
has db xref: SO:non_functional_homolog_of
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_non_functional_homolog_of
has definition: Structural homology that involves a pseudogenic feature and its functional ancestor.
  type: Definition
  has db xref: SO:non_functional_homolog_of
    type: DbXref
    has URI: http://purl.org/obo/owl/SO#SO_non_functional_homolog_of

orthology
type: Class
subclass of: historical homology
comment: The term is sometimes also used for anatomical structures.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that involves genes that diverged after a speciation event.
  type: Definition
  has db xref: DOI:10.1016/S0168-9525(00)02005-9
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0168-9525(00)02005-9
  has db xref: life_and_death_of_developmental_control_genes:_New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
    type: DbXref
    has URI: http://purl.org/obo/owl/life_and_death_of_developmental_control_genes#life_and_death_of_developmental_control_genes__New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
  has db xref: DOI:10.1007/BF02814484_"Theissen_G_(2005)_Birth
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814484_"Theissen_G_(2005)_Birth
  has db xref: 39:_309-338"
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39__309-338"
  has db xref: PMID:5449325
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_5449325
  has db xref: PARALOGS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PARALOGS#PARALOGS_NULL
  has db xref: AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics#AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics_NULL
  has db xref: DOI:10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
has db xref: SO:orthologous_to
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_orthologous_to
has db xref: SO:0000858
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000858
has db xref: SO:0000855
  type: DbXref
  has URI: http://purl.org/obo/owl/SO#SO_0000855
has db xref: ECO:00000060
  type: DbXref
  has URI: http://purl.org/obo/owl/ECO#ECO_00000060

xenology
type: Class
subclass of: historical homology
comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
  type: Definition
  has db xref: PARALOGS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PARALOGS#PARALOGS_NULL
  has db xref: AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics#AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics_NULL
  has db xref: DOI:10.1016/S0168-9525(00)02005-9
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0168-9525(00)02005-9
  has db xref: DOI:10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
  has db xref: 39:_309-338"
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39__309-338"

1 to 1 homology
type: Class
subclass of: historical homology
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: one-to-one homology
has definition: Historical homology that involves two members sharing no other homologs in the lineages considered.
  type: Definition
  has db xref: BGEE:curator
    type: DbXref
    has URI: http://purl.org/obo/owl/BGEE#BGEE_curator
has exact synonym: 1:1 homology

1 to 1 orthology
type: Class
subclass of: orthology
subclass of: 1 to 1 homology
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: 1:1 orthology
has exact synonym: one-to-one orthology
has definition: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
  type: Definition
  has db xref: URL:http://www.ensembl.org/info/docs/compara/homology_method.html
    type: DbXref
    has URI: http://www.ensembl.org/info/docs/compara/homology_method.html
  has db xref: DOI:10.1007/BF02814484_"Theissen_G_(2005)_Birth
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814484_"Theissen_G_(2005)_Birth
  has db xref: life_and_death_of_developmental_control_genes:_New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
    type: DbXref
    has URI: http://purl.org/obo/owl/life_and_death_of_developmental_control_genes#life_and_death_of_developmental_control_genes__New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"

allogeny
type: Class
subclass of: ObsoleteClass
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Relationship between recognizably corresponding characters that occurs in two or more taxa and have different generative bases.
  type: Definition
  has db xref: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R_"Butler_AB_and_Saidel_WM_(2000)_Defining_sameness:_historical
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R_"Butler_AB_and_Saidel_WM_(2000)_Defining_sameness:_historical
  has db xref: and_generative_homology._Bioessays_22:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/and_generative_homology._Bioessays_22#and_generative_homology._Bioessays_22_NULL
  has db xref: biological:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/biological#biological_NULL
  has db xref: 9:_846-53"
    type: DbXref
    has URI: http://purl.org/obo/owl/9#9__846-53"
has exact synonym: generative homoplasy

ohnology
type: Class
subclass of: paralogy
has OBO namespace: homology_and_related_concepts_in_biology
has related synonym: homoeology
has definition: Paralogy that results from a whole genome duplication event.
  type: Definition
  has db xref: DOI:10.1038/75560_"Wolfe_K_(2000)_Robustness-it's_not_where_you_think_it_is._Nature_Genetics_25
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1038/75560_"Wolfe_K_(2000)_Robustness-it's_not_where_you_think_it_is._Nature_Genetics_25
  has db xref: 3-4":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/3-4"#3-4"_NULL

in-paralogy
type: Class
subclass of: paralogy
disjoint with: out-paralogy
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: inparalogy
has exact synonym: symparalogy
has definition: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
  type: Definition
  has db xref: 39:_309-338"
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39__309-338"
  has db xref: PARALOGS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PARALOGS#PARALOGS_NULL
  has db xref: AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics#AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics_NULL
  has db xref: DOI:10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS

out-paralogy
type: Class
subclass of: paralogy
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: outparalogy
has exact synonym: alloparalogy
has definition: Paralogy that results from a duplication preceding a given speciation event.
  type: Definition
  has db xref: 39:_309-338"
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39__309-338"
  has db xref: AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics#AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics_NULL
  has db xref: PARALOGS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PARALOGS#PARALOGS_NULL
  has db xref: DOI:10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS

pro-orthology
type: Class
subclass of: 1 to many orthology
has OBO namespace: homology_and_related_concepts_in_biology
has 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.
  type: Definition
  has db xref: 6:_473-9"
    type: DbXref
    has URI: http://purl.org/obo/owl/6#6__473-9"
  has db xref: 5:_561-563"
    type: DbXref
    has URI: http://purl.org/obo/owl/5#5__561-563"
  has db xref: DOI:10.1038/nrg2099_"Wagner_GP_(2007)_The_developmental_genetics_of_homology._Nature_Reviews_Genetics._8
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1038/nrg2099_"Wagner_GP_(2007)_The_developmental_genetics_of_homology._Nature_Reviews_Genetics._8
  has db xref: DOI:10.1006/scdb.1999.0338_"Sharman_AC_(1999)_Some_new_terms_for_duplicated_genes._Seminars_in_Cell_and_Developmental_Biology
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1006/scdb.1999.0338_"Sharman_AC_(1999)_Some_new_terms_for_duplicated_genes._Seminars_in_Cell_and_Developmental_Biology
  has db xref: 10:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/10#10_NULL

semi-orthology
type: Class
subclass of: 1 to many orthology
comment: The converse of pro-orthologous.
has OBO namespace: homology_and_related_concepts_in_biology
has 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.
  type: Definition
  has db xref: 10:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/10#10_NULL
  has db xref: 5:_561-563"
    type: DbXref
    has URI: http://purl.org/obo/owl/5#5__561-563"
  has db xref: DOI:10.1006/scdb.1999.0338_"Sharman_AC_(1999)_Some_new_terms_for_duplicated_genes._Seminars_in_Cell_and_Developmental_Biology
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1006/scdb.1999.0338_"Sharman_AC_(1999)_Some_new_terms_for_duplicated_genes._Seminars_in_Cell_and_Developmental_Biology
  has db xref: 6:_473-9"
    type: DbXref
    has URI: http://purl.org/obo/owl/6#6__473-9"
  has db xref: DOI:10.1038/nrg2099_"Wagner_GP_(2007)_The_developmental_genetics_of_homology._Nature_Reviews_Genetics._8
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1038/nrg2099_"Wagner_GP_(2007)_The_developmental_genetics_of_homology._Nature_Reviews_Genetics._8

serial homology
type: Class
subclass of: iterative homology
has OBO namespace: homology_and_related_concepts_in_biology
has related synonym: homonomy
has definition: Iterative homology that involves structures arranged along the main body axis.
  type: Definition
  has db xref: DOI:10.1146/annurev.es.20.110189.000411
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.es.20.110189.000411

heterochronous homology
type: Class
subclass of: biological homology
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: heterochrony
has definition: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
  type: Definition
  has db xref: ISBN:978-0674639416
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0674639416

paedomorphorsis
type: Class
subclass of: heterochronous homology
disjoint with: peramorphosis
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
  type: Definition
  has db xref: URL:http://en.wikipedia.org/wiki/Pedomorphosis
    type: DbXref
    has URI: http://en.wikipedia.org/wiki/Pedomorphosis
  has db xref: ISBN:978-0674639416
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0674639416
has exact synonym: juvenification
has exact synonym: pedomorphosis

peramorphosis
type: Class
subclass of: heterochronous homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
  type: Definition
  has db xref: URL:http://en.wikipedia.org/wiki/Peramorphosis
    type: DbXref
    has URI: http://en.wikipedia.org/wiki/Peramorphosis

progenesis
type: Class
subclass of: paedomorphorsis
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
  type: Definition
  has db xref: URL:http://en.wikipedia.org/wiki/Progenesis
    type: DbXref
    has URI: http://en.wikipedia.org/wiki/Progenesis
  has db xref: ISBN:978-0674639416
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0674639416

neoteny
type: Class
subclass of: paedomorphorsis
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paedomorphosis that is produced by a retardation of somatic development.
  type: Definition
  has db xref: ISBN:978-0674639416
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0674639416
  has db xref: URL:http://en.wikipedia.org/wiki/Neoteny
    type: DbXref
    has URI: http://en.wikipedia.org/wiki/Neoteny
has exact synonym: juvenilization

mimicry
type: Class
subclass of: convergence
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Convergence that results from co-evolution usually involving an evolutionary arms race.
  type: Definition
  has db xref: http:://en.wikipedia.org/wiki/Mimicry
    type: DbXref
    has URI: http://purl.org/obo/owl/http#http_://en.wikipedia.org/wiki/Mimicry

1 to many orthology
type: Class
subclass of: orthology
subclass of: 1 to many homology
has OBO namespace: homology_and_related_concepts_in_biology
has related synonym: co-orthology
has exact synonym: one-to-many orthology
has related synonym: many to 1 orthology
has definition: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
  type: Definition
  has db xref: URL:http://www.ensembl.org/info/docs/compara/homology_method.html
    type: DbXref
    has URI: http://www.ensembl.org/info/docs/compara/homology_method.html
  has db xref: DOI:10.1038/415741a
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1038/415741a
has exact synonym: 1:many orthology

many to many homology
type: Class
subclass of: historical homology
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: many-to-many homology
has exact synonym: many:many homology
has definition: Historical homology that involves two members of a larger set of homologs.
  type: Definition
  has db xref: DOI:10.1093/molbev/msp002
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1093/molbev/msp002

1 to many homology
type: Class
subclass of: historical homology
has OBO namespace: homology_and_related_concepts_in_biology
has 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.
  type: Definition
  has db xref: BGEE:curator
    type: DbXref
    has URI: http://purl.org/obo/owl/BGEE#BGEE_curator
has related synonym: 1:many homology
has exact synonym: one-to-many homology

apomorphy
type: Class
subclass of: historical homology
disjoint with: plesiomorphy
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
  type: Definition
  has db xref: Urbana.":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/Urbana."#Urbana."_NULL
  has db xref: ISBN:978-0252068140_"Hennig_W_(1966)_Phylogenetic_systematics._University_of_Illinois_Press
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0252068140_"Hennig_W_(1966)_Phylogenetic_systematics._University_of_Illinois_Press
has related synonym: synapomorphy

plesiomorphy
type: Class
subclass of: historical homology
comment: This term is usually contrasted to apomorphy.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that is based on distant shared ancestry.
  type: Definition
  has db xref: Urbana.":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/Urbana."#Urbana."_NULL
  has db xref: ISBN:978-0252068140_"Hennig_W_(1966)_Phylogenetic_systematics._University_of_Illinois_Press
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0252068140_"Hennig_W_(1966)_Phylogenetic_systematics._University_of_Illinois_Press
has related synonym: symplesiomorphy

deep homology
type: Class
subclass of: homocracy
subclass of: parallelism
comment: Used for structures in distantly related taxa.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
  type: Definition
  has db xref: Nature:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/Nature#Nature_NULL
  has db xref: 457:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/457#457_NULL
  has db xref: 818-823":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/818-823"#818-823"_NULL
  has db xref: DOI:10.1007/BF02814485
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814485
  has db xref: Tabin_C_and_Carroll_S_(2009)_Deep_homology_and_the_origins_of_evolutionary_novelty:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/Tabin_C_and_Carroll_S_(2009)_Deep_homology_and_the_origins_of_evolutionary_novelty#Tabin_C_and_Carroll_S_(2009)_Deep_homology_and_the_origins_of_evolutionary_novelty_NULL
  has db xref: DOI:10.1038/nature07891_"Shubin_N
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1038/nature07891_"Shubin_N
has related synonym: generative homology
has related synonym: homoiology
has exact synonym: deep genetic homology

hemiplasy
type: Class
subclass of: historical homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Definition
  label: 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 db xref: 38:_14477-14481"
    type: DbXref
    has URI: http://purl.org/obo/owl/38#38__14477-14481"
  has db xref: DOI:10.1073/pnas.0807433105_"Robinson_TJ_et_al.(2008)_Hemiplasy_and_homoplasy_in_the_karyotypic_phylogenies_of_mammals
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1073/pnas.0807433105_"Robinson_TJ_et_al.(2008)_Hemiplasy_and_homoplasy_in_the_karyotypic_phylogenies_of_mammals
  has db xref: PNAS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PNAS#PNAS_NULL
  has db xref: 105:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/105#105_NULL

gametology
type: Class
subclass of: chromosomal homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
  type: Definition
  has db xref: PMID:11110898_"Garcia-Moreno_J_and_Mindell_DP_(2000)_Rooting_a_Phylogeny_with_Homologous_Genes_on_Opposite_Sex_Chromosomes_(Gametologs):_A_Case_Study_Using_Avian_CHD
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_11110898_"Garcia-Moreno_J_and_Mindell_DP_(2000)_Rooting_a_Phylogeny_with_Homologous_Genes_on_Opposite_Sex_Chromosomes_(Gametologs):_A_Case_Study_Using_Avian_CHD
  has db xref: Mol_Biol_Evol:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/Mol_Biol_Evol#Mol_Biol_Evol_NULL
  has db xref: 17:_1826-1832"
    type: DbXref
    has URI: http://purl.org/obo/owl/17#17__1826-1832"

chromosomal homology
type: Class
subclass of: historical homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
  type: Definition
  has db xref: ISBN:0195307615
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_0195307615
has db xref: MeSH:Chromosome_Pairing
  type: DbXref
  has URI: http://purl.org/obo/owl/MeSH#MeSH_Chromosome_Pairing

many to many orthology
type: Class
subclass of: orthology
subclass of: many to many homology
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: trans-orthology
has exact synonym: many-to-many orthology
has exact synonym: many:many orthology
has related synonym: trans-homology
has definition: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
  type: Definition
  has db xref: URL:http://www.ensembl.org/info/docs/compara/homology_method.html
    type: DbXref
    has URI: http://www.ensembl.org/info/docs/compara/homology_method.html
  has db xref: DOI:10.1038/415741a
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1038/415741a
has related synonym: co-orthology

within-species paralogy
type: Class
subclass of: paralogy
disjoint with: between-species paralogy
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paralogy that involves genes from the same species.
  type: Definition
  has db xref: URL:http://www.ensembl.org/info/docs/compara/homology_method.html
    type: DbXref
    has URI: http://www.ensembl.org/info/docs/compara/homology_method.html

between-species paralogy
type: Class
subclass of: paralogy
comment: The genes have diverged before a speciation event.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paralogy that involves genes from different species.
  type: Definition
  has db xref: URL:http://www.ensembl.org/info/docs/compara/homology_method.html
    type: DbXref
    has URI: http://www.ensembl.org/info/docs/compara/homology_method.html

postdisplacement
type: Class
subclass of: paedomorphorsis
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
  type: Definition
  has db xref: URL:http://en.wikipedia.org/wiki/Pedomorphosis
    type: DbXref
    has URI: http://en.wikipedia.org/wiki/Pedomorphosis
has exact synonym: post-displacement

hypermorphosis
type: Class
subclass of: peramorphosis
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Peramorphosis that is produced by a delay in the offset of development.
  type: Definition
  has db xref: ISBN:978-0674639416
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0674639416
  has db xref: URL:http://en.wikipedia.org/wiki/Peramorphosis
    type: DbXref
    has URI: http://en.wikipedia.org/wiki/Peramorphosis

synology
type: Class
subclass of: xenology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
  type: Definition
  has db xref: DOI:10.1007/BF00173425_"Gogarten_JP_(1994)_Which_is_the_most_conserved_group_of_proteins?_Homology-orthology
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF00173425_"Gogarten_JP_(1994)_Which_is_the_most_conserved_group_of_proteins?_Homology-orthology
  has db xref: xenology:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/xenology#xenology_NULL
  has db xref: paralogy:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/paralogy#paralogy_NULL
  has db xref: and_the_fusion_of_independent_lineages._J_Mol_Evol:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/and_the_fusion_of_independent_lineages._J_Mol_Evol#and_the_fusion_of_independent_lineages._J_Mol_Evol_NULL
  has db xref: DOI:10.1016/S0168-9525(00)02005-9
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0168-9525(00)02005-9
  has db xref: 541-543":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/541-543"#541-543"_NULL
  has db xref: 39:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39_NULL

isoorthology
type: Class
subclass of: orthology
subclass of: equivalogy
has OBO namespace: homology_and_related_concepts_in_biology
has db xref: ECO:0000080
  type: DbXref
  has URI: http://purl.org/obo/owl/ECO#ECO_0000080
has definition: Orthology that involves functional equivalent genes with retention of the ancestral function.
  type: Definition
  has db xref: DOI:10.1016/S0168-9525(00)02005-9
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0168-9525(00)02005-9

tandem paralogy
type: Class
subclass of: paralogy
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
  type: Definition
  has db xref: MA)":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/MA)"#MA)"_NULL
  has db xref: Sunderland:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/Sunderland#Sunderland_NULL
  has db xref: ISBN:978-0878932665_"Graur_D_and_Li_WH_(2000)_Molecular_evolution._(Sinauer_Associates
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_978-0878932665_"Graur_D_and_Li_WH_(2000)_Molecular_evolution._(Sinauer_Associates
  has db xref: DOI:10.1016/S0168-9525(00)02005-9
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/S0168-9525(00)02005-9
has related synonym: iterative paralogy
has related synonym: serial paralogy

latent homology
type: Class
subclass of: parallelism
subclass of: syngeny
comment: Used for structures in closely related taxa.
has OBO namespace: homology_and_related_concepts_in_biology
has related synonym: homoplastic tendency
has related synonym: re-awakening
has related synonym: homoiology
has exact synonym: underlying synapomorphy
has definition: Definition
  label: 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 db xref: ISBN:0199141118_"de_Beer_G_(1971)._Homology
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_0199141118_"de_Beer_G_(1971)._Homology
  has db xref: DOI:10.1186/1742-9994-2-15
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1186/1742-9994-2-15
  has db xref: 473-479":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/473-479"#473-479"_NULL
  has db xref: DOI:10.1016/j.jhevol.2006.11.010_"Hall_BK_(2007)_Homoplasy_and_homology:_Dichotomy_or_continuum?_Journal_of_Human_Evolution._52:5
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/j.jhevol.2006.11.010_"Hall_BK_(2007)_Homoplasy_and_homology:_Dichotomy_or_continuum?_Journal_of_Human_Evolution._52:5
  has db xref: DOI:10.1007/BF02814485
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814485
  has db xref: an_unsolved_problem._London:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/an_unsolved_problem._London#an_unsolved_problem._London_NULL
  has db xref: Oxford_University_Press.":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/Oxford_University_Press."#Oxford_University_Press."_NULL
has exact synonym: cryptic homology
has exact synonym: apomorphic tendency

syngeny
type: Class
subclass of: homocracy
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.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
  type: Definition
  has db xref: DOI:10.1186/1742-9994-2-15
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1186/1742-9994-2-15
  has db xref: 9:_846-53"
    type: DbXref
    has URI: http://purl.org/obo/owl/9#9__846-53"
  has db xref: and_generative_homology._Bioessays_22:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/and_generative_homology._Bioessays_22#and_generative_homology._Bioessays_22_NULL
  has db xref: biological:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/biological#biological_NULL
  has db xref: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R_"Butler_AB_and_Saidel_WM_(2000)_Defining_sameness:_historical
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R_"Butler_AB_and_Saidel_WM_(2000)_Defining_sameness:_historical
has exact synonym: generative homology

apparent orthology
type: Class
subclass of: 1 to 1 homology
subclass of: between-species paralogy
comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: 1:1 paralogy
has exact synonym: apparent 1:1 orthology
has exact synonym: pseudoorthology
has definition: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
  type: Definition
  has db xref: DOI:10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
  has db xref: URL:http://www.ensembl.org/info/docs/compara/homology_method.html
    type: DbXref
    has URI: http://www.ensembl.org/info/docs/compara/homology_method.html
  has db xref: 39:_309-338"
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39__309-338"
  has db xref: PARALOGS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PARALOGS#PARALOGS_NULL
  has db xref: AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics#AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics_NULL

pseudoparalogy
type: Class
subclass of: xenology
comment: These genes may come out as paralogs in a single-genome analysis.
has OBO namespace: homology_and_related_concepts_in_biology
has 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.
  type: Definition
  has db xref: DOI:10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.genet.39.073003.114725_"Koonin_EV_(2005)_ORTHOLOGS
  has db xref: 39:_309-338"
    type: DbXref
    has URI: http://purl.org/obo/owl/39#39__309-338"
  has db xref: AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics#AND_EVOLUTIONARY_GENOMICS._Annual_Review_of_Genetics_NULL
  has db xref: PARALOGS:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/PARALOGS#PARALOGS_NULL

equivalogy
type: Class
subclass of: historical homology
subclass of: functional equivalence
comment: This may include examples of orthology, paralogy and xenology.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that involves functional equivalent genes with retention of the ancestral function.
  type: Definition
  has db xref: 35:_D260-D264"
    type: DbXref
    has URI: http://purl.org/obo/owl/35#35__D260-D264"
  has db xref: DOI:10.1093/nar/gkl1043_"Selengut_JD_et_al._(2007)_TIGRFAMs_and_Genome_Properties:_tools_for_the_assignment_of_molecular_function_and_biological_process_in_prokaryotic_genomes._Nucleic_Acid_Research
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1093/nar/gkl1043_"Selengut_JD_et_al._(2007)_TIGRFAMs_and_Genome_Properties:_tools_for_the_assignment_of_molecular_function_and_biological_process_in_prokaryotic_geno…

interology
type: Class
subclass of: historical homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
  type: Definition
  has db xref: DOI:10.1101/gr.1774904
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1101/gr.1774904
  has db xref: DOI:10.1126/science.287.5450.116
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1126/science.287.5450.116

functional equivalence
type: Class
subclass of: similarity
has OBO namespace: homology_and_related_concepts_in_biology
has related synonym: functional similarity
has definition: Similarity that is characterized by interchangeability in function.
  type: Definition
  has db xref: life_and_death_of_developmental_control_genes:_New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
    type: DbXref
    has URI: http://purl.org/obo/owl/life_and_death_of_developmental_control_genes#life_and_death_of_developmental_control_genes__New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
  has db xref: DOI:10.1038/415741a
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1038/415741a
  has db xref: DOI:10.1007/BF02814484_"Theissen_G_(2005)_Birth
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814484_"Theissen_G_(2005)_Birth

iterative homology
type: Class
subclass of: biological homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Biological homology that involves parts of the same organism.
  type: Definition
  has db xref: DOI:10.1146/annurev.es.20.110189.000411
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1146/annurev.es.20.110189.000411

paraxenology
type: Class
subclass of: xenology
has OBO namespace: homology_and_related_concepts_in_biology
has exact synonym: multiple xenology
has 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.
  type: Definition
  has db xref: PMID:3065587
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_3065587
has exact synonym: duplicate xenology

plerology
type: Class
subclass of: paralogy
comment: This phenomenon is usually due to gene conversion process.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
  type: Definition
  has db xref: PMID:3065587
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_3065587

homotopy
type: Class
subclass of: structural homology
disjoint with: homeosis
comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Structural homology that involves structures with the same or similar relative positions.
  type: Definition
  has db xref: DOI:10.1007/BF02814485
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814485
  has db xref: ISBN:0123195837_"Sattler_R_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
    type: DbXref
    has URI: http://purl.org/obo/owl/ISBN#ISBN_0123195837_"Sattler_R_(1994)_in_Hall_BK_(Ed.)_Homology:_The_Hierarchical_Basis_of_Comparative_Biology._Academic_Press
  has db xref: life_and_death_of_developmental_control_genes:_New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
    type: DbXref
    has URI: http://purl.org/obo/owl/life_and_death_of_developmental_control_genes#life_and_death_of_developmental_control_genes__New_challenges_for_the_homology_concept._Theory_in_Biosciences_124:199-212"
  has db xref: DOI:10.1007/BF02814484_"Theissen_G_(2005)_Birth
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814484_"Theissen_G_(2005)_Birth
  has db xref: p._429":NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/p._429"#p._429"_NULL

homeosis
type: Class
subclass of: biological homology
has OBO namespace: homology_and_related_concepts_in_biology
has related synonym: heterotopy
has definition: Biological homology that involves an ectopic structure and the normally positioned structure.
  type: Definition
  has db xref: DOI:10.1007/BF02814485
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/BF02814485
  has db xref: DOI:10.1016/j.cell.2008.06.030_"Carroll_SB_(2008)_Evo-Devo_and_an_Expanding_Evolutionary_Synthesis:_A_Genetic_Theory_of_Morphological_Evolution._Cell_134
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1016/j.cell.2008.06.030_"Carroll_SB_(2008)_Evo-Devo_and_an_Expanding_Evolutionary_Synthesis:_A_Genetic_Theory_of_Morphological_Evolution._Cell_134
  has db xref: 1:_25-36"
    type: DbXref
    has URI: http://purl.org/obo/owl/1#1__25-36"

homoeology
type: Class
subclass of: ohnology
subclass of: synology
comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Synology that results from allopolyploidy.
  type: Definition
  has db xref: 45:_16490-16495"
    type: DbXref
    has URI: http://purl.org/obo/owl/45#45__16490-16495"
  has db xref: DOI:10.1073/pnas.0505156102_"Nomura_T_et_al._(2005)_Three_genomes_differentially_contribute_to_the_biosynthesis_of_benzoxazinones_in_hexaploid_wheat._Proc._Natl._Acad._Sci._102
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1073/pnas.0505156102_"Nomura_T_et_al._(2005)_Three_genomes_differentially_contribute_to_the_biosynthesis_of_benzoxazinones_in_hexaploid_wheat._Proc._Natl._Acad._Sci.…

paramorphism
type: Class
subclass of: homocracy
subclass of: iterative homology
has OBO namespace: homology_and_related_concepts_in_biology
has 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.
  type: Definition
  has db xref: DOI:10.1046/j.1525-142x.2000.00054.x_"Minelli_A_(2000)_Limbs_and_tail_as_evolutionarily_diverging_duplicates_of_the_main_body_axis._Evolution_and_Development
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1046/j.1525-142x.2000.00054.x_"Minelli_A_(2000)_Limbs_and_tail_as_evolutionarily_diverging_duplicates_of_the_main_body_axis._Evolution_and_Development
  has db xref: 4:_317-340"
    type: DbXref
    has URI: http://purl.org/obo/owl/4#4__317-340"
  has db xref: 3:157-165"
    type: DbXref
    has URI: http://purl.org/obo/owl/3#3_157-165"
  has db xref: 2:NULL
    type: DbXref
    has URI: http://purl.org/obo/owl/2#2_NULL
  has db xref: DOI:10.1007/s10441-007-9023-8_"Kleisner_K_(2007)_The_Formation_of_the_Theory_of_Homology_in_Biological_Sciences._Acta_Biotheoretica_55
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1007/s10441-007-9023-8_"Kleisner_K_(2007)_The_Formation_of_the_Theory_of_Homology_in_Biological_Sciences._Acta_Biotheoretica_55
has related synonym: axis paramorphism

regulogy
type: Class
subclass of: historical homology
has OBO namespace: homology_and_related_concepts_in_biology
has definition: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
  type: Definition
  has db xref: DOI:10.1101/gr.1774904
    type: DbXref
    has URI: http://purl.org/obo/owl/DOI#DOI_10.1101/gr.1774904