GENO ontology

IRI:
http://purl.obolibrary.org/obo/geno.owl
Version IRI:
http://purl.obolibrary.org/obo/geno/releases/2023-02-21/geno.owl
Current version :
2023-02-21
Other visualisation :
Ontology source - WebVowl

Table of Content

  1. Introduction
  2. Classes
  3. Object Properties
  4. Data Properties
  5. Named Individuals
  6. Annotation Properties
  7. Namespace Declarations

Introduction

GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013

Classes

A_to_C_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000024

has super-classes
purine_to_pyrimidine_transversionc

A_to_G_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000015

has super-classes
purine_transitionc

A_to_T_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000025

has super-classes
purine_to_pyrimidine_transversionc

abnormal(ly) absent adaxial cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ZP_0005692

has super-classes
zebrafish phenotypec

abnormal(ly) absent dorso-rostral clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ZP_0000386

has super-classes
zebrafish phenotypec

abnormal(ly) disrupted diencephalon developmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ZP_0000755

has super-classes
zebrafish phenotypec

abnormal(ly) disrupted neutrophil aggregationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ZP_0005531

has super-classes
zebrafish phenotypec

abnormal(ly) malformed endocardium cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ZP_0000199

has super-classes
zebrafish phenotypec

allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000512

An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).
is equivalent to
genomic featurec and (varies_withop some genomic featurec)
has super-classes
genomic featurec
varies_withop some genomic featurec
has sub-classes
gene allelec, polymorphic allelec, reference allelec, sequence_alterationc, variant allelec, wild-type allelec

allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000877

has super-classes
sequence feature attributec
has sub-classes
de novo allele originc, inherited allele originc, somatic allele originc, unknown allele originc

allele setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000954

'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'.
has super-classes
genomic feature setc

allelic cellular distributionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000926

has super-classes
sequence feature attributec
has sub-classes
clonalc, constitutionalc

allelic genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000823

An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background.
is equivalent to
intrinsic genotypec and (denotesop some single locus complementc)
has super-classes
intrinsic genotypec
genomic entityc
denotesop some single locus complementc
has sub-classes
diplotypec

allelic phasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000886

has super-classes
sequence feature attributec
has sub-classes
in cisc, in transc

allelic statec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000875

has super-classes
sequence feature attributec
has sub-classes
organellar plasmyc, zygosityc

allosomal inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000935

has super-classes
monogenic inheritancec
has sub-classes
W-linked inheritancec, X-linked inheritancec, Y-linked inheritancec, Z-linked inheritancec

amino acid residuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000782

has super-classes
biological sequence unitc

amino acid sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000722

is equivalent to
biological sequencec and (has_sequence_unitop some amino acid residuec) and (has_sequence_unitop only amino acid residuec)
has super-classes
biological sequencec
has_sequence_unitop some amino acid residuec

analysis subset ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000008

has super-classes
subset ontology modulec

anatomical entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001062

has super-classes
organismal entityc
derives fromop some organismc
has sub-classes
cellc

ancestral polymorphic allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000500

has super-classes
polymorphic allelec

aneusomicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000513

has super-classes
variation attributec

aneusomic chromosomal partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000343

Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome."
has super-classes
chromosome partc
sequence_alterationc
has_sequence_attributeop some aneusomicc
has sub-classes
gained aneusomic chromosomal segmentc, lost aneusomic chromosomal segmentc

aneusomic chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000346

Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication.
has super-classes
chromosomec
sequence_alterationc
has_sequence_attributeop some aneusomicc
has sub-classes
gained aneusomic chromosomec, lost aneusomic chromosomec

aneusomic zygosityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000392

has super-classes
zygosityc
has sub-classes
trisomic heterozygousc, trisomic homozygousc

associationc back to ToC or Class ToC

IRI: http://purl.org/oban/association

has super-classes
information content entityc
has sub-classes
genotype-phenotype associationc

autosomal dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000147

has super-classes
autosomal inheritancec
has sub-classes
co-dominant autosomal inheritancec, complete autosomal dominant inheritancec, incomplete autosomal dominant inheritancec, sex-limited autosomal dominant inheritancec

autosomal inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000934

has super-classes
monogenic inheritancec
has sub-classes
autosomal dominant inheritancec, autosomal recessive inheritancec

autosomal recessive inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000148

has super-classes
autosomal inheritancec
has sub-classes
sex-limited autosomal recessive inheritancec

background genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000010

has super-classes
reference genomec

base ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000001

has super-classes
ontology modulec

biological processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000351

has super-classes
processc
has sub-classes
developmental processc, human life cycle stagec, life cycle stagec, phenotypic inheritance processc

biological sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000702

'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.
has super-classes
biological sequence or setc
has_stringdp some string
has sub-classes
DNA sequencec, RNA sequencec, amino acid sequencec, biological sequence unitc, genomic sequencec, reference sequencec
is in domain of
has_stringdp, is_sequence_ofop
is in range of
has_defining_sequenceop, has_sequenceop
is disjoint with
sequence feature locationc, sequence_featurec

biological sequence or setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000921

has super-classes
generically dependent continuantc
has sub-classes
biological sequencec, biological sequence setc

biological sequence setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000922

'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. A set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence.
has super-classes
biological sequence or setc
has sub-classes
genomic sequence setc

biological sequence unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000779

is equivalent to
biological sequencec and (has_extentdp value 1)
has super-classes
biological sequencec
has sub-classes
DNA residuec, RNA residuec, amino acid residuec

biparental allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/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.
has super-classes
inherited allele originc

Both strandsc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#BothStrandsPosition

has super-classes
Stranded positionc

bridge ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000004

has super-classes
ontology modulec
has sub-classes
taxonomic bridge ontology modulec

C_to_A_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000019

has super-classes
pyrimidine_to_purine_transversionc

C_to_G_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000020

has super-classes
pyrimidine_to_purine_transversionc

C_to_T_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000011

has super-classes
pyrimidine_transitionc
has sub-classes
C_to_T_transition_at_pCpG_sitec

C_to_T_transition_at_pCpG_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000012

has super-classes
C_to_T_transitionc

cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000000

Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies.
has super-classes
anatomical entityc

cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000031

has super-classes
organismal entityc
derives fromop some organismc

centromerec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000577

has super-classes
chromosome partc

chromosomal band intensityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000618

has super-classes
sequence feature attributec
has sub-classes
gnegc, gposc, gvarc

chromosomal deletion inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000970

has super-classes
chromosomal inheritancec

chromosomal duplication inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000971

has super-classes
chromosomal inheritancec

chromosomal inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000969

has super-classes
inheritance patternc
has sub-classes
chromosomal deletion inheritancec, chromosomal duplication inheritancec, chromosomal rearrangement inheritancec

chromosomal rearrangement inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000972

has super-classes
chromosomal inheritancec

chromosomal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000614

has super-classes
chromosome partc
is part ofop some chromosome armc

chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000340

A complete chromosome sequence.
has super-classes
genomic featurec
has sub-classes
aneusomic chromosomec

chromosome armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000105

has super-classes
chromosome partc
is part ofop some chromosome partc
has sub-classes
long chromosome armc, short chromosome armc

chromosome bandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000341

"Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.
has super-classes
chromosome partc
is part ofop some chromosomal regionc
has_sequence_attributeop some chromosomal band intensityc

chromosome partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000830

is equivalent to
genomic featurec and (is_proper_part_ofop some chromosomec)
has super-classes
genomic featurec
is_proper_part_ofop some chromosomec
has sub-classes
aneusomic chromosomal partc, centromerec, chromosomal regionc, chromosome armc, chromosome bandc, chromosome sub-bandc

chromosome sub-bandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000616

has super-classes
chromosome partc
is part ofop some chromosome bandc
has_sequence_attributeop some chromosomal band intensityc

clonalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000928

has super-classes
allelic cellular distributionc
has sub-classes
mosaicc

co-dominant autosomal inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000143

has super-classes
autosomal dominant inheritancec

co-dominant X-linked inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000939

has super-classes
X-linked dominant inheritancec

co-dominant Z-linked inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000946

has super-classes
Z-linked dominant inheritancec

collection of organismsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PCO_0000000

A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role).
has super-classes
organismal entityc
has memberop some organismc
has sub-classes
familyc, taxonomic groupc

complete autosomal dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000144

has super-classes
autosomal dominant inheritancec

complete X-linked dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000937

has super-classes
X-linked dominant inheritancec

complete Z-linked dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000944

has super-classes
Z-linked dominant inheritancec

complex_structural_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001784

has super-classes
structural_alterationc

complex_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000005

has super-classes
substitutionc

compound heterozygousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000402

has super-classes
heterozygousc

constitutionalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000927

has super-classes
allelic cellular distributionc

continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000002

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
entityc
has sub-classes
generically dependent continuantc, independent continuantc, specifically dependent continuantc
is disjoint with
occurrentc

copy number complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000961

The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.
has super-classes
genomic sequence setc
has sub-classes
variant copy number complementc

copy_number_gainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001742

has super-classes
copy_number_variationc

copy_number_lossc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001743

has super-classes
copy_number_variationc

copy_number_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001019

has super-classes
sequence_alterationc
has sub-classes
copy_number_gainc, copy_number_lossc

curation status specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000078

is equivalent to
{ example to be eventually removed , metadata complete , organizational term , ready for release , metadata incomplete , uncurated , pending final vetting , to be replaced with external ontology term , requires discussion }
has super-classes
data about an ontology partc
has members
example to be eventually removedni, metadata completeni, metadata incompleteni, organizational termni, pending final vettingni, ready for releaseni, requires discussionni, to be replaced with external ontology termni, uncuratedni

curation subset ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000007

has super-classes
subset ontology modulec

Danio rerioc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_7955

has super-classes
organismc

danio rerio cdkn1ca genec back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/399483

has super-classes
danio rerio genec

danio rerio genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000047

is equivalent to
genec and (in taxonop some Danio rerioc)
has super-classes
genec
in taxonop some Danio rerioc
has sub-classes
danio rerio cdkn1ca genec, danio rerio shha genec

danio rerio shha genec back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/30269

has super-classes
danio rerio genec

danio rerio strainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000119

has super-classes
strain or breedc
has memberop some Danio rerioc
has memberop only Danio rerioc

data about an ontology partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000102

has super-classes
data itemc
has sub-classes
curation status specificationc, denotator typec, obsolescence reason specificationc, ontology modulec
has members
exemplar termni, exploratory termni

data itemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000027

has super-classes
information content entityc
has sub-classes
data about an ontology partc

de novo allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/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.
has super-classes
allele originc

deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000159

has super-classes
sequence_alterationc
has_extentdp value 0

denotator typec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000409

is equivalent to
{ universal , defined class , named class expression }
has super-classes
data about an ontology partc
has members
defined classni, named class expressionni, universalni

developmental processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032502

has super-classes
biological processc

digenic inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000930

has super-classes
multifactorial inheritancec

diplotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000885

"Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes." From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/
is equivalent to
allelic genotypec and (denotesop some single locus complementc and (has memberop exactly 2 allelec))
has super-classes
allelic genotypec
denotesop some single locus complementc and (has memberop exactly 2 allelec)

direct_tandem_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000039

has super-classes
tandem_duplicationc

disomic zygosityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000391

has super-classes
zygosityc
has sub-classes
hemizygousc, heterozygousc, homozygousc

dispositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000016

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
realizable entityc
has sub-classes
heritabililtyc, inheritance patternc
is disjoint with
rolec

DNA residuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000780

has super-classes
biological sequence unitc

DNA sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000720

is equivalent to
biological sequencec and (has_sequence_unitop some DNA residuec) and (has_sequence_unitop only DNA residuec)
has super-classes
biological sequencec
has_sequence_unitop some DNA residuec

duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000035

has super-classes
insertionc
has sub-classes
tandem_duplicationc

editors ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000002

has super-classes
ontology modulec

effective genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000525

An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment.
has super-classes
genotypec
has partop some extrinsic genotypec
has partop some intrinsic genotypec

EL++ ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000020

has super-classes
ontology module subsetted by OWL profilec

engineeredc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000783

has super-classes
sequence feature attributec

engineered genetic constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000856

Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors.
has super-classes
engineered_regionc
has sub-classes
P-element constructc, enhancer_trap_constructc, expression constructc, gene_trap_constructc, promoter_trap_constructc

engineered_foreign_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000281

has super-classes
genec
engineered_regionc

engineered_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000804

is equivalent to
sequence_featurec and (has_sequence_attributeop some engineeredc)
has super-classes
sequence_featurec
has_sequence_attributeop some engineeredc
has sub-classes
engineered genetic constructc, engineered_foreign_genec, gene knockdown reagentc, reporter transgenec, selectable marker transgenec

enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000165

has super-classes
regulatory_regionc

enhancer_trap_constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001479

has super-classes
engineered genetic constructc

entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000001

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has sub-classes
continuantc, occurrentc

environmental systemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01000254

In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
has super-classes
material entityc

Exact positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ExactPosition

has super-classes
Positionc

exclusion subset ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000010

has super-classes
subset ontology modulec

expressed transgene regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000638

has super-classes
transgene partc
has sub-classes
reporter regionc, selectable marker regionc

expression constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000495

has super-classes
engineered genetic constructc

expression-qualified sequence featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000737

has super-classes
qualified genomic featurec
has sub-classes
expression-variant genec, reagent-targeted gene subregionc

expression-variant genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000529

Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system.
has super-classes
expression-qualified sequence featurec
is_expression_variant_ofop some genec
has sub-classes
reagent targeted genec, transiently-expressed transgenec

external import ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000011

has super-classes
import ontology modulec

extra-chromosomal transgenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000861

has super-classes
transgenec

extrachromosomal repliconc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000494

is equivalent to
genomic featurec and (not (is_proper_part_ofop some chromosomec)) and (has_sequence_attributeop some heritablec)
has super-classes
genomic featurec
has_sequence_attributeop some heritablec
has sub-classes
novel extrachromosomal repliconc

extrinsic genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000524

An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations.
has super-classes
genotypec

familyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PCO_0000020

has super-classes
collection of organismsc

femalec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000383

has super-classes
phenotypic sexc

female intrinsic genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000647

has super-classes
genomic genotype (sex-qualified)c

functional copy complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000963

A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. 'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele.
has super-classes
genomic sequence setc

G_to_A_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000016

has super-classes
purine_transitionc

G_to_C_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000026

has super-classes
purine_to_pyrimidine_transversionc

G_to_T_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000027

has super-classes
purine_to_pyrimidine_transversionc

gained aneusomic chromosomal segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000344

Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location.
has super-classes
aneusomic chromosomal partc

gained aneusomic chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000338

This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome.
has super-classes
aneusomic chromosomec
has_sequence_attributeop some novelc

genec back to ToC or Class ToC

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

A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion.
has super-classes
genomic featurec
has sub-classes
danio rerio genec, engineered_foreign_genec, homo sapiens genec, mus musculus genec, transgenec, wild-type genec

gene allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000014

In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene.
has super-classes
allelec
is_allele_ofop some genec
has sub-classes
variant gene allelec

gene knockdown reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000533

has super-classes
engineered_regionc
has sub-classes
RNAi_reagentc, morpholino_oligoc

gene partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000666

is equivalent to
genomic featurec and (is subsequence ofop some gene allelec)
has super-classes
genomic featurec
is subsequence ofop some gene allelec
has sub-classes
regulatory_regionc, transgene partc

gene productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000907

has super-classes
sequence_featurec

gene trap insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000092

has super-classes
insertionc

gene_trap_constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001477

has super-classes
engineered genetic constructc

generated ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000014

has super-classes
ontology modulec
has sub-classes
template generated ontology modulec

generically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000031

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
continuantc
has sub-classes
biological sequence or setc, genomic entityc, information content entityc, qualified sequence feature or collectionc, sequence feature locationc, sequence feature or setc

genetic materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000482

This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material.
has super-classes
nucleic acidc
has sub-classes
genomic materialc

genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001026

A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'.
has super-classes
genomic feature setc
has sub-classes
reference genomec, variant genomec

genomic backgroundc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000611

is equivalent to
genomic genotypec and (sequence roleop some referencec)
has super-classes
genomic genotypec
sequence roleop some referencec
denotesop some background genomec
has sub-classes
unspecified genomic backgroundc

genomic entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000897

is equivalent to
genomic featurec or (has partop some genomic featurec) or (has_sequence_featureop some genomic featurec or genomic feature setc) or (denotesop some genomic featurec or genomic feature setc or qualified genomic feature setc)
has super-classes
generically dependent continuantc
in taxonop some organismc
has sub-classes
allelic genotypec, genomic featurec, genomic feature setc, genomic genotypec, qualified genomic featurec, qualified genomic feature setc

genomic featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000481

1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. 2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). 3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.
is equivalent to
sequence_featurec and (has_locationop some genomic feature locationc)
has super-classes
genomic entityc
sequence_featurec
is part ofop some genomec
has_sequenceop some genomic sequencec
has_locationop some genomic feature locationc
has sub-classes
QTLc, allelec, chromosomec, chromosome partc, extrachromosomal repliconc, genec, gene partc, haplotype blockc, heritable_phenotypic_markerc, microsatellitec
is in domain of
is_allele_ofop

genomic feature locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000902

1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.
has super-classes
sequence feature locationc
has sub-classes
Positionc

genomic feature setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000660

A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.
has super-classes
sequence feature setc
genomic entityc
has memberop some genomic featurec
has sub-classes
allele setc, genomec, genomic variation complementc, haplotypec, single locus complementc

genomic genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000899

1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. 2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.
is equivalent to
intrinsic genotypec and (denotesop some genomec)
has super-classes
intrinsic genotypec
genomic entityc
has_reference_partop some genomic backgroundc
denotesop some genomec
has sub-classes
genomic backgroundc, genomic genotype (sex-agnostic)c, genomic genotype (sex-qualified)c, karyotypec, variant genomic genotypec

genomic genotype (sex-agnostic)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000000

In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances).
has super-classes
genomic genotypec

genomic genotype (sex-qualified)c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000645

We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome.
has super-classes
genomic genotypec
has_sex_agnostic_partop some genomic genotype (sex-agnostic)c
has sub-classes
female intrinsic genotypec, male intrinsic genotypec

genomic materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000106

1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. 2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms.
has super-classes
genetic materialc
has dispositionop some heritablec

genomic sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000960

A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome.
is equivalent to
is_sequence_ofop some genomic featurec
has super-classes
biological sequencec
is_sequence_ofop some genomic featurec

genomic sequence setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000872

A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location.
has super-classes
biological sequence setc
has sub-classes
copy number complementc, functional copy complementc

genomic variation complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000009

A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation. In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)).
is equivalent to
genomic feature setc and (has_variant_partop some variant single locus complementc)
has super-classes
genomic feature setc
has_variant_partop some variant single locus complementc

genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000536

1. Scope of 'Genetic State': 'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. 2. Genotype Subtypes: In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. 3. The Genotype Partonomy: 'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) - Genomic Background: AB (the reference against which the GVC is variant) - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data.
has super-classes
information content entityc
denotesop some genomic feature setc or qualified genomic feature setc
has sub-classes
effective genotypec, extrinsic genotypec, intrinsic genotypec

genotype-phenotype associationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000833

has super-classes
associationc
has_qualifierop some environmental systemc
has_qualifierop some developmental processc and ((starts duringop some life cycle stagec) and (ends duringop some life cycle stagec))
association has objectop some Phenotypec
association has subjectop some genotypec or (is part ofop some genotypec)

germline allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/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.
has super-classes
inherited allele originc
has sub-classes
maternal allele originc, paternal allele originc

gnegc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000620

has super-classes
chromosomal band intensityc

gposc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000619

has super-classes
chromosomal band intensityc
has sub-classes
gpos100c, gpos25c, gpos33c, gpos50c, gpos66c, gpos75c

gpos100c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000622

has super-classes
gposc

gpos25c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000625

has super-classes
gposc

gpos33c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000633

has super-classes
gposc

gpos50c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000624

has super-classes
gposc

gpos66c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000632

has super-classes
gposc

gpos75c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000623

has super-classes
gposc

gvarc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000621

has super-classes
chromosomal band intensityc

haplotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000871

A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': 1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. 2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). 3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.
has super-classes
genomic feature setc
has memberop some allelec

haplotype blockc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000898

A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.
has super-classes
genomic featurec

hemizygousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000134

has super-classes
disomic zygosityc
has sub-classes
hemizygous X-linkedc, hemizygous Y-linkedc, hemizygous insertion-linkedc

hemizygous insertion-linkedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000606

has super-classes
hemizygousc

hemizygous X-linkedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000604

has super-classes
hemizygousc

hemizygous Y-linkedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000605

has super-classes
hemizygousc

heritabililtyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000138

We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms.
has super-classes
dispositionc
has sub-classes
heritablec, non-heritablec

heritablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000139

has super-classes
heritabililtyc

heritable_phenotypic_markerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001500

has super-classes
genomic featurec

heteroplasmicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000603

has super-classes
organellar plasmyc

heteroplasmic mitochondrial inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000892

has super-classes
mitochondrial inheritancec

heterozygousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000135

has super-classes
disomic zygosityc
has sub-classes
compound heterozygousc, simple heterozygousc

Homo sapiensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9606

has super-classes
organismc

homo sapiens genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000054

is equivalent to
genec and (in taxonop some Homo sapiensc)
has super-classes
genec
in taxonop some Homo sapiensc
has sub-classes
homo sapiens SHH genec

homo sapiens SHH genec back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/6469

Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 Codes for: http://www.uniprot.org/uniprot/Q15465
has super-classes
homo sapiens genec

homoplasmicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000602

has super-classes
organellar plasmyc

homoplasmic mitochondrial inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000893

has super-classes
mitochondrial inheritancec

homozygousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000136

has super-classes
disomic zygosityc

human life cycle stagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/HsapDv_0000000

has super-classes
biological processc

human phenotypic abnormalityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/HP_0000118

pulling in HP 'phenotypic abnormality' root here
has super-classes
Phenotypec

human populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000111

has super-classes
populationc

import ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000005

has super-classes
subset ontology modulec
has sub-classes
external import ontology modulec

in cisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000131

has super-classes
allelic phasec

in transc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000132

has super-classes
allelic phasec

incomplete autosomal dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000145

has super-classes
autosomal dominant inheritancec

incomplete X-linked dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000938

has super-classes
X-linked dominant inheritancec

incomplete Z-linked dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000945

has super-classes
Z-linked dominant inheritancec

indelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000032

Indels can have a different number of bases than the corresponding reference sequence.
has super-classes
sequence_alterationc

independent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000004

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
continuantc
has sub-classes
material entityc

information content entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000030

has super-classes
generically dependent continuantc
has sub-classes
associationc, data itemc, genotypec, sequence intervalc

inheritance patternc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000141

An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. These genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y.
has super-classes
dispositionc
has sub-classes
chromosomal inheritancec, mitochondrial inheritancec, monogenic inheritancec, multifactorial inheritancec, undetermined inheritancec
is in range of
obsolete_participates_in_inheritance_processop

inherited allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000974

has super-classes
allele originc
has sub-classes
biparental allele originc, germline allele originc, uniparental allele originc

insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000667

has super-classes
sequence_alterationc
has sub-classes
duplicationc, gene trap insertionc, transgenic_insertionc

integrated transgenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000093

An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome.
has super-classes
transgenec
is part ofop some transgenic_insertionc

intrinsic genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000719

1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. 2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.
has super-classes
genotypec
denotesop some single locus complementc or genomec
has sub-classes
allelic genotypec, genomic genotypec

inversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000036

has super-classes
sequence_alterationc

inverted_tandem_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000040

has super-classes
tandem_duplicationc

junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000699

A junction is a boundary between regions. A boundary has an extent of zero.
has super-classes
sequence_featurec

karyotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000644

Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation).
has super-classes
genomic genotypec

knockdown reagent targeted gene complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000839

has super-classes
reagent-targeted gene complementc
has_variant_partop some reagent targeted genec

life cycle stagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000105

has super-classes
biological processc
has sub-classes
unspecified life cycle stagec

location-qualified sequence featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000736

As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell).
has super-classes
qualified genomic featurec

long chromosome armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000629

has super-classes
chromosome armc

lost aneusomic chromosomal segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000345

This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus.
has super-classes
aneusomic chromosomal partc
has_extentdp value 0

lost aneusomic chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000339

has super-classes
aneusomic chromosomec
has_extentdp value 0

main release ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000003

has super-classes
ontology modulec

major polymorphic allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000498

has super-classes
polymorphic allelec

malec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000384

has super-classes
phenotypic sexc

male intrinsic genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000646

has super-classes
genomic genotype (sex-qualified)c

mammalian phenotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MP_0000001

where to place this depends on if we take the organismal view or the quality centric view.
has super-classes
Phenotypec

material entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
independent continuantc
has sub-classes
environmental systemc, material genomec, molecular entityc, organismal entityc

material genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000108

A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome.
has super-classes
material entityc

maternal allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000878

has super-classes
germline allele originc

maternal_uniparental_disomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001745

has super-classes
UPDc

microsatellitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000289

A defined feature that includes any type of VNTR or SSLP locus.
has super-classes
genomic featurec

microsatellite alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000873

has super-classes
repeat region alterationc

minor polymorphic allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000499

has super-classes
polymorphic allelec

mitochondrial inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000949

Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy).
has super-classes
inheritance patternc
has sub-classes
heteroplasmic mitochondrial inheritancec, homoplasmic mitochondrial inheritancec

MNPc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001013

has super-classes
substitutionc

modification-qualified sequence featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000818

has super-classes
qualified genomic featurec

molecular entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_23367

has super-classes
material entityc
has sub-classes
nucleic acidc

monogenic inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000933

has super-classes
inheritance patternc
has sub-classes
allosomal inheritancec, autosomal inheritancec

morpholino_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000034

has super-classes
gene knockdown reagentc

mosaicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000964

A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type.
has super-classes
clonalc

multifactorial inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000929

Diseases inherited in this manner are termed 'complex diseases'.
has super-classes
inheritance patternc
has sub-classes
digenic inheritancec, oligogenic inheritancec, polygenic inheritancec

Mus musculusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10090

has super-classes
organismc

mus musculus genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000057

is equivalent to
genec and (in taxonop some Mus musculusc)
has super-classes
genec
in taxonop some Mus musculusc
has sub-classes
mus musculus shh genec

mus musculus shh genec back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/20423

Equivalent to: http://www.informatics.jax.org/marker/MGI:98297
has super-classes
mus musculus genec

mus musculus strainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000118

has super-classes
strain or breedc

mutantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000480

has super-classes
variation attributec

mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000492

has super-classes
sequence_alterationc
varies_withop some wild-type allelec

Negative strandc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ReverseStrandPosition

has super-classes
Stranded positionc

non-heritablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000140

has super-classes
heritabililtyc

novelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000685

has super-classes
variation attributec

novel extrachromosomal repliconc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000681

Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'.
has super-classes
extrachromosomal repliconc
novel repliconc
not (is_proper_part_ofop some chromosomec)

novel repliconc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000684

Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles.
has super-classes
sequence_alterationc
has_sequence_attributeop some novelc
has sub-classes
novel extrachromosomal repliconc

nucleic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33696

has super-classes
molecular entityc
has sub-classes
genetic materialc

obo basic subset ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000018

has super-classes
ontology module subsetted by expressivityc

obsolescence reason specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000225

is equivalent to
{ failed exploratory term , placeholder removed , terms merged , term imported , term split , out of scope }
has super-classes
data about an ontology partc
has members
failed exploratory termni, out of scopeni, placeholder removedni, term importedni, term splitni, terms mergedni

obsolete allele cellular contextc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000901

Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others.

obsolete assembly_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000143

obsolete autosomal recessive inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000150

obsolete biological sequence collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000725

obsolete biological sequence or collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000724

obsolete canonical allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000890

As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)

obsolete chromosome complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000324

obsolete coding sequence alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000848

obsolete color brightnessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000016

obsolete contextual allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000891

The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene.

obsolete contigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000149

obsolete copy number complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000956

1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. 2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. 3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members.

obsolete dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000142

obsolete engineered_plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000637

obsolete enhancer trapping techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000171

obsolete experimental insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000091

obsolete experimental_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001410

obsolete extrinsic sequence feature attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000925

obsolete functional copy number complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000923

As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage).

obsolete gameticc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000883

obsolete gene trapping techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000172

obsolete genetic dosagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000876

Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found.

obsolete genetic insertion techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000164

obsolete genomic feature collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000022

Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection.

obsolete genomic positionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000768

obsolete haplotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000915

1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). 2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. 3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.

obsolete haplotype blockc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000916

A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. ----------------------- * One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces.

obsolete intrinsic sequence feature attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000924

obsolete mutagen treatment techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000165

obsolete mutant allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000491

'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line.
is in domain of
is_mutant_allele_ofop

obsolete null featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000680

obsolete promoter trapping techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000173

obsolete random genetic insertion techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000169

obsolete random transgene insertion techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000175

obsolete reagent sequence featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000415

obsolete reference gene allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000060

Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared.

obsolete reference junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000042

In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation.

obsolete reference single locus complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000029

obsolete sequence feature collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000019

1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions.

obsolete sequence feature collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000870

obsolete sequence feature collection attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000125

obsolete sequence information entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000778

obsolete targeted gene mutation techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000166

obsolete targeted genetic insertion techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000170

obsolete targeted knock-in techniquec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000174

obsolete unspecifiedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000772

obsolete unspecified featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000037

An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele).

obsolete variant copy number complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000955

In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class.

occurrentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000003

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
entityc
has sub-classes
processc
is disjoint with
continuantc

oligogenic inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000931

It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform.
has super-classes
multifactorial inheritancec

ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000000

has super-classes
data about an ontology partc
has sub-classes
base ontology modulec, bridge ontology modulec, editors ontology modulec, generated ontology modulec, main release ontology modulec, reasoned ontology modulec, subset ontology modulec

ontology module subsetted by expressivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000017

has super-classes
subset ontology modulec
has sub-classes
obo basic subset ontology modulec, ontology module subsetted by OWL profilec

ontology module subsetted by OWL profilec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000019

has super-classes
ontology module subsetted by expressivityc
has sub-classes
EL++ ontology modulec

organellar plasmyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000918

Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene.
has super-classes
allelic statec
has sub-classes
heteroplasmicc, homoplasmicc

organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100026

has super-classes
organismal entityc
has sub-classes
Danio rerioc, Homo sapiensc, Mus musculusc, Oryzias latipesc, Virusesc

organismal entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000904

is equivalent to
organismc or (derives fromop some organismc) or (has memberop some organismc)
has super-classes
material entityc
has sub-classes
anatomical entityc, cell linec, collection of organismsc, organismc

Oryzias latipesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_8090

has super-classes
organismc

oryzias latipes strainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000887

has super-classes
strain or breedc
has memberop some Oryzias latipesc
has memberop only Oryzias latipesc

P-element constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000850

has super-classes
engineered genetic constructc

paternal allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000879

has super-classes
germline allele originc

paternal_uniparental_disomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001746

has super-classes
UPDc

Phenotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UPHENO_0001001

1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) 2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment
has super-classes
specifically dependent continuantc
has sub-classes
human phenotypic abnormalityc, mammalian phenotypec, worm phenotypec, zebrafish phenotypec
is in domain of
phenotype ofop
is in range of
has phenotypeop

phenotypic inheritance processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000770

has super-classes
biological processc

phenotypic sexc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001894

has super-classes
qualityc
has sub-classes
femalec, malec

planned processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000011

has super-classes
processc

point_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000008

has super-classes
SNVc

polygenic inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000932

Typically used for traits/conditions governed by more than three gene loci.
has super-classes
multifactorial inheritancec

polymorphicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000477

has super-classes
variation attributec

polymorphic allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000497

Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%).
has super-classes
allelec
has sub-classes
ancestral polymorphic allelec, major polymorphic allelec, minor polymorphic allelec
is in domain of
is_polymorphic_allele_ofop

populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000181

has super-classes
taxonomic groupc
has sub-classes
human populationc

Positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#Position

has super-classes
genomic feature locationc
has sub-classes
Exact positionc, Stranded positionc

Positive strandc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ForwardStrandPosition

has super-classes
Stranded positionc

processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000015

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
occurrentc
has sub-classes
biological processc, planned processc

promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000167

has super-classes
regulatory_regionc

promoter_trap_constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001478

has super-classes
engineered genetic constructc

purine_to_pyrimidine_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000023

has super-classes
transversionc
has sub-classes
A_to_C_transversionc, A_to_T_transversionc, G_to_C_transversionc, G_to_T_transversionc

purine_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000014

has super-classes
transitionc
has sub-classes
A_to_G_transitionc, G_to_A_transitionc

pyrimidine_to_purine_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000018

has super-classes
transversionc
has sub-classes
C_to_A_transversionc, C_to_G_transversionc, T_to_A_transversionc, T_to_G_transversionc

pyrimidine_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000010

has super-classes
transitionc
has sub-classes
C_to_T_transitionc, T_to_C_transitionc

QTLc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000771

has super-classes
genomic featurec

qualified genomic featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000714

has super-classes
genomic entityc
qualified sequence featurec
has_qualifierop some thingc
has_sequence_featureop some genomic featurec
has sub-classes
expression-qualified sequence featurec, location-qualified sequence featurec, modification-qualified sequence featurec

qualified genomic feature setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000715

A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome.
has super-classes
genomic entityc
qualified sequence feature setc
has_sequence_featureop some genomic feature setc
has memberop some qualified genomic featurec
has sub-classes
reagent-targeted gene complementc, transiently-expressed transgene complementc

qualified sequence featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000919

GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).
has super-classes
qualified sequence feature or collectionc
has sub-classes
qualified genomic featurec

qualified sequence feature or collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000713

has super-classes
generically dependent continuantc
has sub-classes
qualified sequence featurec, qualified sequence feature setc

qualified sequence feature setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000920

'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'.
has super-classes
qualified sequence feature or collectionc
has partop some qualified sequence featurec
has_sequence_featureop some sequence feature setc
has sub-classes
qualified genomic feature setc

qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000019

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
specifically dependent continuantc
has sub-classes
phenotypic sexc
is disjoint with
realizable entityc

reagent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000086

has super-classes
rolec

reagent targeted genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000504

The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position.
has super-classes
expression-variant genec
has_proper_partop some reagent-targeted gene subregionc
is_gene_target_ofop some gene knockdown reagentc

reagent-targeted gene complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000527

A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment.
has super-classes
qualified genomic feature setc
has memberop some reagent targeted genec
has sub-classes
knockdown reagent targeted gene complementc

reagent-targeted gene subregionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000534

has super-classes
expression-qualified sequence featurec

realizable entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000017

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
specifically dependent continuantc
has sub-classes
dispositionc, rolec
is disjoint with
qualityc

reasoned ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000013

has super-classes
ontology modulec

referencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000152

Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another.
has super-classes
variation attributec

reference allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000036

Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared.
is equivalent to
allelec and (sequence roleop some referencec)
has super-classes
allelec
sequence roleop some referencec
is in domain of
is_reference_allele_ofop

reference genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000914

has super-classes
genomec
has_sequenceop some reference genome sequencec
has sub-classes
background genomec

reference genome sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001505

has super-classes
reference sequencec

reference sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000017

A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence.
is equivalent to
biological sequencec and (sequence roleop some referencec)
has super-classes
biological sequencec
sequence roleop some referencec
has sub-classes
reference genome sequencec

Regionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#Region

has super-classes
sequence_featurec
(beginop exactly 1 Positionc) and (endop exactly 1 Positionc)

regulatory transgene regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000637

has super-classes
transgene partc
regulatory_regionc

regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005836

has super-classes
gene partc
has sub-classes
enhancerc, promoterc, regulatory transgene regionc

repeat region alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000874

has super-classes
sequence_alterationc
has sub-classes
microsatellite alterationc

reporterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000910

has super-classes
sequence feature attributec

reporter regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000640

has super-classes
expressed transgene regionc

reporter transgenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000667

is equivalent to
transgenec and (has_sequence_attributeop some reporterc)
has super-classes
engineered_regionc
transgenec
has partop some reporter regionc
has_sequence_attributeop some reporterc

RNA residuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000781

has super-classes
biological sequence unitc

RNA sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000721

is equivalent to
biological sequencec and (has_sequence_unitop some RNA residuec) and (has_sequence_unitop only RNA residuec)
has super-classes
biological sequencec
has_sequence_unitop some RNA residuec

RNAi_reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000337

has super-classes
gene knockdown reagentc

rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000023

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
realizable entityc
has sub-classes
reagent rolec
is disjoint with
dispositionc

selectable markerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000911

has super-classes
sequence feature attributec

selectable marker regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000912

has super-classes
expressed transgene regionc

selectable marker transgenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000642

is equivalent to
transgenec and (has_sequence_attributeop some selectable markerc)
has super-classes
engineered_regionc
transgenec
has_sequence_attributeop some selectable markerc

sequence feature attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000788

Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity.
has super-classes
specifically dependent continuantc
has sub-classes
allele originc, allelic cellular distributionc, allelic phasec, allelic statec, chromosomal band intensityc, engineeredc, reporterc, selectable markerc, variation attributec

sequence feature locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000815

1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.
has super-classes
generically dependent continuantc
has sub-classes
genomic feature locationc
is in domain of
has_intervalop
is in range of
has_defining_locationop, has_locationop
is disjoint with
biological sequencec, sequence_featurec

sequence feature or setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000701

GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.
is equivalent to
sequence feature or setc or sequence_featurec
has super-classes
generically dependent continuantc
has sub-classes
sequence feature setc, sequence_featurec

sequence feature setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000659

'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. [1] https://www.snpedia.com/index.php/APOE-%CE%B54 [2] https://www.snpedia.com/index.php/APOE-%CE%B52 [3] https://www.snpedia.com/index.php/Gs270
has super-classes
sequence feature or setc
has memberop some sequence_featurec
has_member_countdp some int
has sub-classes
genomic feature setc

sequence intervalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000965

has super-classes
information content entityc

sequence_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001059

1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. 2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. 3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism.
is equivalent to
allelec and (completely_varies_withop some genomic featurec)
has super-classes
allelec
completely_varies_withop some genomic featurec
has sub-classes
UPDc, aneusomic chromosomal partc, aneusomic chromosomec, copy_number_variationc, deletionc, indelc, insertionc, inversionc, mutationc, novel repliconc, repeat region alterationc, structural_alterationc, substitutionc, translocationc

sequence_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000110

A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.
has super-classes
sequence feature or setc
has_sequenceop some biological sequencec
has_locationop some sequence feature locationc
has sub-classes
Regionc, engineered_regionc, gene productc, genomic featurec, junctionc, terminusc
is in domain of
has_locationop, has_sequence_stringdp
is in range of
has_defining_featureop, has_sequence_featureop
is disjoint with
biological sequencec, sequence feature locationc

sequence_length_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000248

has super-classes
substitutionc
has sub-classes
simple_sequence_length_variationc

sex-limited autosomal dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000952

has super-classes
autosomal dominant inheritancec

sex-limited autosomal recessive inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000953

has super-classes
autosomal recessive inheritancec

short chromosome armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000628

has super-classes
chromosome armc

simple heterozygousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000458

a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>)
has super-classes
heterozygousc

simple_sequence_length_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000207

has super-classes
sequence_length_variationc

single layer subset ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000009

has super-classes
subset ontology modulec

single locus complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000516

A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.
has super-classes
genomic feature setc
has sub-classes
variant single locus complementc
is in domain of
has_zygosityop

SNPc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000694

has super-classes
SNVc

SNVc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001483

has super-classes
substitutionc
has sub-classes
SNPc, point_mutationc, transitionc, transversionc

somatic allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000882

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. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations.
has super-classes
allele originc

species subset ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000012

has super-classes
subset ontology modulec

specifically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000020

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
continuantc
has sub-classes
Phenotypec, qualityc, realizable entityc, sequence feature attributec

strain or breedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000112

Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)
has super-classes
taxonomic groupc
in taxonop some organismc
has sub-classes
danio rerio strainc, mus musculus strainc, oryzias latipes strainc

Stranded positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#StrandedPosition

Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'.
has super-classes
Positionc
has sub-classes
Both strandsc, Negative strandc, Positive strandc

structural_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001785

has super-classes
sequence_alterationc
has sub-classes
complex_structural_alterationc

subset ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000006

has super-classes
ontology modulec
has sub-classes
analysis subset ontology modulec, curation subset ontology modulec, exclusion subset ontology modulec, import ontology modulec, ontology module subsetted by expressivityc, single layer subset ontology modulec, species subset ontology modulec

substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000002

has super-classes
sequence_alterationc
has sub-classes
MNPc, SNVc, complex_substitutionc, sequence_length_variationc

T_to_A_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000021

has super-classes
pyrimidine_to_purine_transversionc

T_to_C_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000013

has super-classes
pyrimidine_transitionc

T_to_G_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000022

has super-classes
pyrimidine_to_purine_transversionc

tandem_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000173

has super-classes
duplicationc
has sub-classes
direct_tandem_duplicationc, inverted_tandem_duplicationc

taxonomic bridge ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000016

has super-classes
bridge ontology modulec

taxonomic groupc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000113

has super-classes
collection of organismsc
has sub-classes
populationc, strain or breedc

template generated ontology modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000015

has super-classes
generated ontology modulec

terminusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000688

has super-classes
sequence_featurec

transgenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000902

On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach.
has super-classes
genec
has sub-classes
extra-chromosomal transgenec, integrated transgenec, reporter transgenec, selectable marker transgenec

transgene partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000460

is equivalent to
gene partc and (is subsequence ofop some transgenec)
has super-classes
gene partc
is subsequence ofop some transgenec
has sub-classes
expressed transgene regionc, regulatory transgene regionc

transgenic_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001218

has super-classes
insertionc
has partop some integrated transgenec

transiently-expressed transgenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000506

has super-classes
expression-variant genec

transiently-expressed transgene complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000528

has super-classes
qualified genomic feature setc
has_variant_partop some transiently-expressed transgenec

transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000009

has super-classes
SNVc
has sub-classes
purine_transitionc, pyrimidine_transitionc

translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000199

has super-classes
sequence_alterationc

transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000017

has super-classes
SNVc
has sub-classes
purine_to_pyrimidine_transversionc, pyrimidine_to_purine_transversionc

trisomic heterozygousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000394

has super-classes
aneusomic zygosityc

trisomic homozygousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000393

has super-classes
aneusomic zygosityc

undetermined inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000889

has super-classes
inheritance patternc

uniparental allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/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
has super-classes
inherited allele originc

unknown allele originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000881

has super-classes
allele originc

unspecified genomic backgroundc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000649

has super-classes
genomic backgroundc

unspecified life cycle stagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000160

has super-classes
life cycle stagec

unspecified zygosityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000137

has super-classes
zygosityc

UPDc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001744

has super-classes
sequence_alterationc
has sub-classes
maternal_uniparental_disomyc, paternal_uniparental_disomyc

variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000476

has super-classes
variation attributec

variant allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000002

Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence.
is equivalent to
allelec and (varies_withop some reference allelec)
has super-classes
allelec
sequence_alterationc or (has subsequenceop some sequence_alterationc)
varies_withop some reference allelec
has sub-classes
variant gene allelec
is in domain of
is_variant_allele_ofop

variant copy number complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000962

'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome.
has super-classes
copy number complementc

variant gene allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000515

A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset.
is equivalent to
gene allelec and (varies_withop some reference allelec)
has super-classes
variant allelec
gene allelec
has_variant_partop some sequence_alterationc
is_variant_allele_ofop some genec

variant genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000033

is equivalent to
genomec and (varies_withop some reference genomec)
has super-classes
genomec
has_variant_partop some sequence_alterationc
varies_withop some reference genomec

variant genomic genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000777

is equivalent to
genomic genotypec and (denotesop some variant genomec)
has super-classes
genomic genotypec
denotesop some variant genomec

variant single locus complementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000030

Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant.
is equivalent to
single locus complementc and (has_variant_partop some variant allelec)
has super-classes
single locus complementc
has_variant_partop some variant allelec

variation attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000773

has super-classes
sequence feature attributec
has sub-classes
aneusomicc, mutantc, novelc, polymorphicc, referencec, variantc, wild-typec

Virusesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10239

Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies.
has super-classes
organismc

W-linked inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000948

has super-classes
allosomal inheritancec

wild-typec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000511

has super-classes
variation attributec

wild-type allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000501

'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis.
has super-classes
allelec
has sub-classes
wild-type genec
is in domain of
is_wild_type_allele_ofop

wild-type genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000502

A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation.
has super-classes
wild-type allelec
genec

worm phenotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/WBPhenotype_0000886

has super-classes
Phenotypec

X-linked dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000146

has super-classes
X-linked inheritancec
has sub-classes
co-dominant X-linked inheritancec, complete X-linked dominant inheritancec, incomplete X-linked dominant inheritancec

X-linked inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000936

has super-classes
allosomal inheritancec
has sub-classes
X-linked dominant inheritancec, X-linked recessive inheritancec

X-linked recessive inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000149

has super-classes
X-linked inheritancec

Y-linked inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000941

has super-classes
allosomal inheritancec

Z-linked dominant inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000943

has super-classes
Z-linked inheritancec
has sub-classes
co-dominant Z-linked inheritancec, complete Z-linked dominant inheritancec, incomplete Z-linked dominant inheritancec

Z-linked inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000942

has super-classes
allosomal inheritancec
has sub-classes
Z-linked dominant inheritancec, Z-linked reccessive inheritancec

Z-linked reccessive inheritancec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000947

has super-classes
Z-linked inheritancec

zebrafish phenotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000575

ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes.
has super-classes
Phenotypec
has sub-classes
abnormal(ly) absent adaxial cellc, abnormal(ly) absent dorso-rostral clusterc, abnormal(ly) disrupted diencephalon developmentc, abnormal(ly) disrupted neutrophil aggregationc, abnormal(ly) malformed endocardium cellc

zygosityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000133

has super-classes
allelic statec
inheres_inop some single locus complementc
has sub-classes
aneusomic zygosityc, disomic zygosityc, unspecified zygosityc
is in range of
has_zygosityop

Object Properties

association has objectop back to ToC or Object Property ToC

IRI: http://purl.org/oban/association_has_object

association has predicateop back to ToC or Object Property ToC

IRI: http://purl.org/oban/association_has_predicate

association has subjectop back to ToC or Object Property ToC

IRI: http://purl.org/oban/association_has_subject

bearer ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000053

has sub-properties
has dispositionop, has qualityop, has roleop, sequence roleop

bears_concretization_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000211

Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence.
has sub-property chains
bearer ofop o concretizesop

beginop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#begin

has super-properties
faldo propertiesop

benign_for_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000843

has super-properties
non-causal_for_conditionop

bounds sequence ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002522

has super-properties
has_sequence_partop

causes conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003303

has super-properties
causes or contributes to conditionop
has sub-properties
likely_pathogenic_for_conditionop, pathogenic_for_conditionop

causes or contributes to conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003302

Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
has super-properties
related_conditionop
has sub-properties
causes conditionop, contributes to conditionop

completely_varies_withop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000784

has characteristics : symmetric

has super-properties
varies_withop

concretizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000059

contributes to conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003304

has super-properties
causes or contributes to conditionop
has sub-properties
contributes to frequency of conditionop, contributes to severity of conditionop

contributes to frequency of conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003306

has super-properties
contributes to conditionop

contributes to severity of conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003305

has super-properties
contributes to conditionop

correlated with conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003308

has super-properties
related_conditionop

denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000219

has super-properties
is aboutop

derives fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001000

endop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#end

has super-properties
faldo propertiesop

ends duringop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002093

has super-properties
temporally related toop

faldo propertiesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000708

organizational property to hold imports from faldo.
has sub-properties
beginop, endop, locationop, reference (faldo)op

has dispositionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000091

has super-properties
bearer ofop

has inputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002233

has super-properties
has participantop
has sub-properties
has_specified_inputop

has memberop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002351

has super-properties
has partop
is inverse of
is member ofop

has outputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002234

has super-properties
has participantop
has sub-properties
has_specified_outputop
is inverse of
output ofop

has partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000051

has characteristics : transitive

has super-properties
overlapsop
has sub-properties
has memberop, has_proper_partop, has_sequence_partop
is inverse of
is part ofop

has participantop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000057

has sub-properties
has inputop, has outputop
is inverse of
participates inop

has phenotypeop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002200

has sub-properties
has_asserted_phenotypeop, has_inferred_phenotypeop
has range
Phenotypec
is inverse of
phenotype ofop

has qualityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000086

has super-properties
bearer ofop

has roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000087

has super-properties
bearer ofop

has subsequenceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002524

has super-properties
has_sequence_partop
is inverse of
is subsequence ofop

has_affected_featureop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000418

This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset.
has sub-properties
is_allele_ofop, is_expression_variant_ofop, targets_geneop
is inverse of
is_feature_affected_byop
has sub-property chains
has_variant_partop o has_affected_featureop
is_variant_part_ofop o has_affected_featureop

has_alleleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000413

has super-properties
is_feature_affected_byop
is inverse of
is_allele_ofop

has_asserted_phenotypeop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000743

has super-properties
has phenotypeop

has_defining_featureop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000959

Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.
has domain
copy number complementc or functional copy complementc
has range
sequence_featurec

has_defining_locationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000957

Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.
has domain
copy number complementc or functional copy complementc
has range
sequence feature locationc

has_defining_sequenceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000958

Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement.
has domain
copy number complementc or functional copy complementc
has range
biological sequencec

has_expression_variantop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000449

has super-properties
is_feature_affected_byop
is inverse of
is_expression_variant_ofop

has_genotypeop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000222

The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations.
has domain
genotypec or (is part ofop some genotypec)
is inverse of
is_genotype_ofop

has_inferred_phenotypeop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000740

has super-properties
has phenotypeop
has sub-property chains
has_variant_partop o has_asserted_phenotypeop
is_variant_part_ofop o is_sex_agnostic_part_ofop o has_asserted_phenotypeop
is_variant_part_ofop o has_asserted_phenotypeop
has_alleleop o is_variant_part_ofop o has_asserted_phenotypeop
has_alleleop o has_asserted_phenotypeop
has_expression_variantop o is_variant_part_ofop o has_asserted_phenotypeop
has_expression_variantop o has_asserted_phenotypeop
is_sex_agnostic_part_ofop o has_asserted_phenotypeop

has_intervalop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000966

Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects.
has domain
sequence feature locationc

has_locationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000903

has domain
sequence_featurec
has range
sequence feature locationc

has_proper_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000231

has characteristics : transitive

has super-properties
has partop
is inverse of
is_proper_part_ofop

has_qualifierop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000580

has sub-properties
has_qualifying_environmentop, has_qualifying_processop

has_qualifying_environmentop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000847

has super-properties
has_qualifierop

has_qualifying_processop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000846

has super-properties
has_qualifierop

has_reference_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000385

has characteristics : transitive

has super-properties
has_sequence_partop
is inverse of
is_reference_part_ofop

has_reference_sequenceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000967

has_sequenceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000239

'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.
has range
biological sequencec
is inverse of
is_sequence_ofop

has_sequence_attributeop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000207

has super-properties
top object property
has sub-properties
has_staining_intensityop, has_zygosityop
has domain
sequence feature or setc or biological sequencec or qualified sequence feature or collectionc

has_sequence_featureop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000726

In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism.
has domain
qualified sequence featurec or qualified sequence feature setc
has range
sequence_featurec

has_sequence_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000654

has super-properties
has partop
has sub-properties
bounds sequence ofop, has subsequenceop, has_reference_partop, has_sequence_unitop, has_sex_agnostic_partop, has_variant_partop
is inverse of
is_sequence_part_ofop

has_sequence_unitop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000783

has super-properties
has_sequence_partop

has_sex_agnostic_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000650

has super-properties
has_sequence_partop
is inverse of
is_sex_agnostic_part_ofop

has_specified_inputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000293

has super-properties
has inputop

has_specified_outputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000299

has super-properties
has outputop

has_staining_intensityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000626

Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized.
has super-properties
has_sequence_attributeop

has_uncertain_significance_for_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000845

has super-properties
related_conditionop

has_variant_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000382

has characteristics : transitive

has super-properties
has_sequence_partop
is inverse of
is_variant_part_ofop

has_zygosityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000608

has super-properties
has_sequence_attributeop
has domain
single locus complementc
has range
zygosityc

in taxonop back to ToC or Object Property ToC

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

inferred_to_cause_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000791

has super-properties
related_conditionop
has sub-property chains
has_variant_partop o is_sex_agnostic_part_ofop o causes conditionop
has_variant_partop o causes conditionop
is_variant_part_ofop o is_sex_agnostic_part_ofop o is_variant_part_ofop o causes conditionop
is_variant_part_ofop o is_sex_agnostic_part_ofop o causes conditionop
is_variant_part_ofop o causes conditionop
has_alleleop o is_variant_part_ofop o is_sex_agnostic_part_ofop o is_variant_part_ofop o causes conditionop
has_alleleop o is_variant_part_ofop o is_sex_agnostic_part_ofop o causes conditionop
is_feature_affected_byop o has_variant_partop o causes conditionop
is_feature_affected_byop o is_variant_part_ofop o causes conditionop
is_feature_affected_byop o causes conditionop
is_sex_agnostic_part_ofop o is_variant_part_ofop o causes conditionop
is_sex_agnostic_part_ofop o causes conditionop

inferred_to_contribute_to_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000793

has super-properties
related_conditionop

inferred_to_correlate_with_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000794

has super-properties
related_conditionop

inheres_inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000052

input ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002352

has super-properties
participates inop

is aboutop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000136

has sub-properties
denotesop
is inverse of
is_subject_ofop

is downstream of sequence ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002529

is member ofop back to ToC or Object Property ToC

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

has super-properties
is part ofop
is inverse of
has memberop

is model ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003301

The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.

is part ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000050

has characteristics : transitive

has super-properties
overlapsop
has sub-properties
is member ofop, is_proper_part_ofop, is_sequence_part_ofop
is inverse of
has partop

is preventative for conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003307

Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
has super-properties
related_conditionop

is subsequence ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002525

has super-properties
is_sequence_part_ofop
is inverse of
has subsequenceop

is upstream of sequence ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002528

is_allele_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000408

To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\GAL4 gene. At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'.
has super-properties
has_affected_featureop
has sub-properties
is_reference_allele_ofop, is_variant_allele_ofop, is_wild_type_allele_ofop
has domain
genomic featurec
is inverse of
has_alleleop

is_candidate_variant_forop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000849

has super-properties
related_conditionop

is_expression_variant_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000443

This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class.
has super-properties
has_affected_featureop
is inverse of
has_expression_variantop

is_feature_affected_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000445

This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)
has sub-properties
has_alleleop, has_expression_variantop, is_gene_target_ofop
is inverse of
has_affected_featureop

is_gene_target_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000447

Domain = punned gene class Range = gene knockdown reagent
has super-properties
is_feature_affected_byop
is inverse of
targets_geneop

is_genotype_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000220

is inverse of
has_genotypeop

is_mutant_allele_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000651

A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of.
has super-properties
is_variant_allele_ofop
has domain
obsolete mutant allelec

is_polymorphic_allele_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000652

has super-properties
is_variant_allele_ofop
has domain
polymorphic allelec

is_proper_part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000248

has super-properties
is part ofop
is inverse of
has_proper_partop

is_reference_allele_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000610

has super-properties
is_allele_ofop
has domain
reference allelec

is_reference_part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000387

has super-properties
is_sequence_part_ofop
is inverse of
has_reference_partop

is_regulatory_part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000761

has super-properties
is_sequence_part_ofop

is_sequence_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000251

has domain
biological sequencec
is inverse of
has_sequenceop

is_sequence_part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000655

has super-properties
is part ofop
has sub-properties
is subsequence ofop, is_reference_part_ofop, is_regulatory_part_ofop, is_sex_agnostic_part_ofop, is_variant_part_ofop
is inverse of
has_sequence_partop

is_sex_agnostic_part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000661

has super-properties
is_sequence_part_ofop
is inverse of
has_sex_agnostic_partop

is_subject_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000252

is inverse of
is aboutop

is_targeted_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000634

is_variant_allele_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000641

has super-properties
is_allele_ofop
has sub-properties
is_mutant_allele_ofop, is_polymorphic_allele_ofop
has domain
variant allelec

is_variant_part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000383

has characteristics : transitive

has super-properties
is_sequence_part_ofop
is inverse of
has_variant_partop

is_wild_type_allele_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000653

has super-properties
is_allele_ofop
has domain
wild-type allelec

likely_benign_for_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000844

has super-properties
non-causal_for_conditionop

likely_pathogenic_for_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000841

has super-properties
causes conditionop

locationop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#location

has super-properties
faldo propertiesop

molecularly controlsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_000244

non-causal_for_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000842

has super-properties
related_conditionop
has sub-properties
benign_for_conditionop, likely_benign_for_conditionop

obsolete_approximates_sequenceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000243

has super-properties
obsolete propertyop

obsolete_formed as result ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002354

has super-properties
obsolete propertyop

obsolete_has_genetic_variantop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000411

Domain = punned gene class Range = genomic feature
has super-properties
obsolete propertyop

obsolete_has_position_componentop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000767

has super-properties
obsolete propertyop

obsolete_has_regulatory_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000741

Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes.
has super-properties
obsolete propertyop

obsolete_is_alteration_withinop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000742

has super-properties
obsolete propertyop
has sub-property chains
is_variant_part_ofop o is_allele_ofop

obsolete_is_expression_variant_withop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000488

has super-properties
obsolete propertyop

obsolete_is_genetic_variant_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000410

Domain = genomic feature instance Range = punned gene class IRI
has super-properties
obsolete propertyop

obsolete_is_phenotype_of_genotypeop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000359

Might expand to something like: phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))
has super-properties
obsolete propertyop

obsolete_is_specified_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000253

has super-properties
obsolete propertyop

obsolete_is_variant_withop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000486

This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of.
has super-properties
obsolete propertyop

obsolete_participates_in_inheritance_processop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000368

has super-properties
obsolete propertyop
has range
inheritance patternc

obsolete_resolves_to_sequenceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000244

has super-properties
obsolete propertyop

obsolete_specifiesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000242

has super-properties
obsolete propertyop

on strandop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000906

Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from.

output ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002353

has super-properties
participates inop
is inverse of
has outputop

overlapsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002131

has characteristics : symmetric

has sub-properties
has partop, is part ofop, overlaps sequence ofop

overlaps sequence ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002526

has super-properties
overlapsop

participates inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000056

has sub-properties
input ofop, output ofop
is inverse of
has participantop

pathogenic_for_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000840

has super-properties
causes conditionop

phenotype ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002201

has domain
Phenotypec
is inverse of
has phenotypeop

reference (faldo)op back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#reference

has super-properties
faldo propertiesop

related_conditionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000790

has sub-properties
causes or contributes to conditionop, correlated with conditionop, has_uncertain_significance_for_conditionop, inferred_to_cause_conditionop, inferred_to_contribute_to_conditionop, inferred_to_correlate_with_conditionop, is preventative for conditionop, is_candidate_variant_forop, non-causal_for_conditionop

sequence roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000968

The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants.
has super-properties
bearer ofop

sequence_derives_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000639

has super-properties
top object property
has sub-property chains
has partop o sequence_derives_fromop

starts duringop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002091

has super-properties
temporally related toop

targets_geneop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000414

This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets.
has super-properties
has_affected_featureop
is inverse of
is_gene_target_ofop

temporally related toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002222

has sub-properties
ends duringop, starts duringop

varies_withop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000683

This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)

has characteristics : symmetric

has sub-properties
completely_varies_withop

Data Properties

end_positiondp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000895

has_extentdp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000678

has range
int

has_member_countdp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000917

In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'.

has_quantifierdp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000866

has_sequence_stringdp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000703

has domain
sequence_featurec
has range
string

has_stringdp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000896

has domain
biological sequencec
has range
string

ObsoleteDataPropertydp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000712

positiondp back to ToC or Data Property ToC

IRI: http://biohackathon.org/resource/faldo#position

The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is.

start_positiondp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000894

Named Individuals

defined classni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000420

belongs to
denotator typec

example to be eventually removedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000002

belongs to
curation status specificationc

exemplar termni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000514

belongs to
data about an ontology partc

exploratory termni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000484

belongs to
data about an ontology partc

failed exploratory termni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000103

belongs to
obsolescence reason specificationc

metadata completeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000120

belongs to
curation status specificationc

metadata incompleteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000123

belongs to
curation status specificationc

named class expressionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000421

belongs to
denotator typec

obsolete_coreni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000224

organizational termni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000121

belongs to
curation status specificationc

out of scopeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OMO_0001000

belongs to
obsolescence reason specificationc

pending final vettingni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000125

belongs to
curation status specificationc

placeholder removedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000226

belongs to
obsolescence reason specificationc

ready for releaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000122

belongs to
curation status specificationc

requires discussionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000428

belongs to
curation status specificationc

term importedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000228

belongs to
obsolescence reason specificationc

term splitni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000229

belongs to
obsolescence reason specificationc

terms mergedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000227

belongs to
obsolescence reason specificationc

to be replaced with external ontology termni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000423

belongs to
curation status specificationc

uncuratedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000124

belongs to
curation status specificationc

universalni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000410

belongs to
denotator typec

Annotation Properties

alternative labelap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000118

Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
has sub-properties
has broad synonymap, has exact synonymap, has narrow synonymap, has related synonymap

antisymmetric propertyap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000427

has super-properties
logical characteristic of object propertyap

contributorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/contributor

coverageap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/coverage

created byap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#created_by

creation dateap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#creation_date

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/creator

curator noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000232

dateap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/date

default languageap back to ToC or Annotation Property ToC

IRI: http://protege.stanford.edu/plugins/owl/protege#defaultLanguage

defined by constructap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/OMO_0002000

Contributors :
https://orcid.org/0000-0002-7356-1779
https://orcid.org/0000-0002-8688-6599

definitionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000115

definition sourceap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000119

descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/description

editor noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000116

editor preferred termap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000111

elucidationap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000600

example of usageap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000112

expand assertion toap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000425

expand expression toap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000424

first order logic expressionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000426

formatap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/format

gene symbolap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000909

has associated axiom(fol)ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000602

has associated axiom(nl)ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000601

has axiom labelap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0010000

has broad synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

has super-properties
alternative labelap

has curation statusap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000114

has db xrefap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasDbXref

has exact synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

has super-properties
alternative labelap

has ID digit countap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000596

has ID policy forap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000598

has ID prefixap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000599

has ID range allocated toap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000597

has narrow synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym

has super-properties
alternative labelap

has obsolescence reasonap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000231

has ontology root termap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000700

has related synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym

has super-properties
alternative labelap

i a o alt idap back to ToC or Annotation Property ToC

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

i a o created byap back to ToC or Annotation Property ToC

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

i a o creation dateap back to ToC or Annotation Property ToC

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

i a o idap back to ToC or Annotation Property ToC

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

i a o subsetap back to ToC or Annotation Property ToC

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

i a o xrefap back to ToC or Annotation Property ToC

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

identifierap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/identifier

imported fromap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000412

in branchap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000113

is allocated id rangeap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000603

Add as annotation triples in the granting ontology

is denotator typeap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000411

is_identity_criteriaap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000834

has range
boolean

languageap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/language

licenseap back to ToC or Annotation Property ToC

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

logical characteristic of object propertyap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/OMO_0001001

has sub-properties
antisymmetric propertyap

may be identical toap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0006011

Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

mixinap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000905

Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models.
has range
boolean

OBO foundry unique labelap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000589

ontology term requesterap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000234

The 'term requester' can credit the person, organization or project who request the ontology term.

proabalistic_quantifierap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000867

publisherap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/publisher

relationap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/relation

rightsap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/rights

scheduled for obsoletion on or afterap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0006012

has range
date time

sourceap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/source

sourceap back to ToC or Annotation Property ToC

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

subjectap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/subject

term editorap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000117

term replaced byap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0100001

Add as annotation triples in the granting ontology

term tracker itemap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000233

The 'tracker item' can associate a tracker with a specific ontology term.

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/title

typeap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/type

Namespace Declarations back to ToC

default namespace
http://purl.obolibrary.org/obo/geno.owl#
10-1186
https://doi.org/10.1186/
2023-02-21
http://purl.obolibrary.org/obo/geno/releases/2023-02-21/
dc
http://purl.org/dc/elements/1.1/
faldo
http://biohackathon.org/resource/faldo#
gene
http://www.ncbi.nlm.nih.gov/gene/
issues
https://github.com/ontodev/robot/issues/
oban
http://purl.org/oban/
obo
http://purl.obolibrary.org/obo/
obo-syntax-html
http://owlcollab.github.io/oboformat/doc/obo-syntax.html#
oboInOwl
http://www.geneontology.org/formats/oboInOwl#
orcid-org
http://orcid.org/
owl
http://www.w3.org/2002/07/owl#
page
http://www.geneontology.org/page/
protege
http://protege.stanford.edu/plugins/owl/protege#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
robot-obolibrary-org
http://robot.obolibrary.org/
terms
http://purl.org/dc/terms/
wiki
https://github.com/obophenotype/uberon/wiki/
xsd
http://www.w3.org/2001/XMLSchema#

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