Added exploratory terms to allele origin hierarchy (inherited, unipar…

…ental, biparental allele origin)

src/ontology/geno-edit.owl

@@ -309,6 +309,9 @@ Declaration(Class(obo:GENO_0000969))
 Declaration(Class(obo:GENO_0000970))
 Declaration(Class(obo:GENO_0000971))
 Declaration(Class(obo:GENO_0000972))
+Declaration(Class(obo:GENO_0000974))
+Declaration(Class(obo:GENO_0000975))
+Declaration(Class(obo:GENO_0000976))
 Declaration(Class(obo:GO_0032502))
 Declaration(Class(obo:HP_0000118))
 Declaration(Class(obo:HsapDv_0000000))
@@ -3419,9 +3422,9 @@ SubClassOf(obo:GENO_0000879 obo:GENO_0000888)
 
 # Class: obo:GENO_0000880 (de novo allele origin)
 
-AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000880 "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis.")
+AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000880 "Describes an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis.")
 AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000880 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation  and  https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation")
-AnnotationAssertion(rdfs:comment obo:GENO_0000880 "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. 
+AnnotationAssertion(rdfs:comment obo:GENO_0000880 "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed constitutively  in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. 
 
 De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder.")
 AnnotationAssertion(rdfs:label obo:GENO_0000880 "de novo allele origin"@en)
@@ -3478,14 +3481,14 @@ SubClassOf(obo:GENO_0000887 ObjectAllValuesFrom(obo:RO_0002351 obo:NCBITaxon_809
 
 # Class: obo:GENO_0000888 (germline allele origin)
 
-AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000888 "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg).")
+AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000888 "Describes an allele that is inherited from a parent in virtue of the allele being present in the germline of one of the parents.")
 AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000888 "hereditary")
 AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000888 "parental origin")
 AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000888 "parentally inherited")
 AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000888 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant  and  https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation")
-AnnotationAssertion(rdfs:comment obo:GENO_0000888 "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring).  By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell.  De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells.")
+AnnotationAssertion(rdfs:comment obo:GENO_0000888 "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (present constitutively in a parent and passed down to offspring) and *heritable* (passable down to future offspring).  By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell.  Traits caused by de novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells.")
 AnnotationAssertion(rdfs:label obo:GENO_0000888 "germline allele origin"@en)
-SubClassOf(obo:GENO_0000888 obo:GENO_0000877)
+SubClassOf(obo:GENO_0000888 obo:GENO_0000974)
 
 # Class: obo:GENO_0000889 (undetermined inheritance)
 
@@ -4034,6 +4037,30 @@ AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000972 "Alliance of Genomic Resour
 AnnotationAssertion(rdfs:label obo:GENO_0000972 "chromosomal rearrangement inheritance"@en)
 SubClassOf(obo:GENO_0000972 obo:GENO_0000969)
 
+# Class: obo:GENO_0000974 (inherited allele origin)
+
+AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000974 "Describes an allele that is inherited from a parent.")
+AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000974 "Need to consider if/how this is different than 'germline allele origin'.
+
+One scenario that potentially distinguishes them is the case where a de novo mutation occurs in the germ cells of a parent, and is passed to offspring.  This does not qualify as 'germline allele origin', as currently defined.  But it would qualify as 'inherited'")
+AnnotationAssertion(rdfs:label obo:GENO_0000974 "inherited allele origin"@en)
+SubClassOf(obo:GENO_0000974 obo:GENO_0000877)
+
+# Class: obo:GENO_0000975 (uniparental allele origin)
+
+AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000975 "Describes an allele that is part of an allelic complement where both alleles are inherited from the same parent.")
+AnnotationAssertion(rdfs:comment obo:GENO_0000975 "From Wikidedia: Uniparental inheritance is a non-mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father. This phenomenon is most commonly observed in eukaryotic organelles such as mitochondria and chloroplasts. 
+https://en.wikipedia.org/wiki/Uniparental_inheritance")
+AnnotationAssertion(rdfs:label obo:GENO_0000975 "uniparental allele origin"@en)
+SubClassOf(obo:GENO_0000975 obo:GENO_0000974)
+
+# Class: obo:GENO_0000976 (biparental allele origin)
+
+AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000976 "Describes an allele that is part of an allelic complement where one allele is maternally inherited  and other paternally inherited.")
+AnnotationAssertion(rdfs:comment obo:GENO_0000976 "Biparental inheritance of alleles is typical of normal mendelian inheritance, where offspring inherit a maternal and a paternal copies of a given gene.")
+AnnotationAssertion(rdfs:label obo:GENO_0000976 "biparental allele origin"@en)
+SubClassOf(obo:GENO_0000976 obo:GENO_0000974)
+
 # Class: obo:GO_0032502 (developmental process)
 
 AnnotationAssertion(obo:IAO_0000115 obo:GO_0032502 "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]")