vario.owl
type: Ontology
version IRI: vario.owl
auto-generated-by: OBO-Edit 2.3.1
date: 08:11:2018 10:07
default-namespace: variation_ontology
has_obo_format_version: 1.2
saved-by: med-mnv
comment: A Variation Ontology

definition
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

adjacent_to
type: ObjectProperty
definition: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.
has_obo_namespace: variation_ontology
id: adjacent_to

Axiom
annotated source: adjacent_to
annotated property: definition
annotated target: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.
database_cross_reference: SO:ke

associated_with
type: ObjectProperty
has_obo_namespace: variation_ontology
id: associated_with
comment: This relationship is vague and up for discussion.

complete_evidence_for_feature
type: ObjectProperty
type: TransitiveProperty
definition: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
has_obo_namespace: variation_ontology
id: complete_evidence_for_feature
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

Axiom
annotated source: complete_evidence_for_feature
annotated property: definition
annotated target: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
database_cross_reference: SO:ke

contains
type: ObjectProperty
type: TransitiveProperty
definition: 'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
has_obo_namespace: variation_ontology
id: contains
comment: The inverse relationship to "part of".

Axiom
annotated source: contains
annotated property: definition
annotated target: 'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
database_cross_reference: PSI-MOD:ref

derives_from
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: variation_ontology
id: derives_from

evidence_for_feature
type: ObjectProperty
type: TransitiveProperty
definition: B is evidence_for_feature A, if an instance of B supports the existence of A.
has_obo_namespace: variation_ontology
id: evidence_for_feature
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

Axiom
annotated source: evidence_for_feature
annotated property: definition
annotated target: B is evidence_for_feature A, if an instance of B supports the existence of A.
database_cross_reference: SO:ke

genome_of
type: ObjectProperty
has_obo_namespace: variation_ontology
id: genome_of

has functional parent
type: ObjectProperty
type: TransitiveProperty
definition: 'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification.
has_obo_namespace: variation_ontology
id: has_functional_parent
comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.

Axiom
annotated source: has functional parent
annotated property: definition
annotated target: 'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification.
database_cross_reference: PSI-MOD:ref

has_origin
type: ObjectProperty
has_obo_namespace: variation_ontology
id: has_origin

has_part
type: ObjectProperty
has_obo_namespace: variation_ontology
id: has_part

has_quality
type: ObjectProperty
has_obo_namespace: variation_ontology
id: has_quality
comment: The relationship between a feature and an attribute.

member_of
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: variation_ontology
id: member_of
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.

negatively_regulates
type: ObjectProperty
has_obo_namespace: variation_ontology
id: negatively_regulates

non_functional_homolog_of
type: ObjectProperty
definition: A relationship between a pseudogenic feature and its functional ancestor.
has_obo_namespace: variation_ontology
id: non_functional_homolog_of

Axiom
annotated source: non_functional_homolog_of
annotated property: definition
annotated target: A relationship between a pseudogenic feature and its functional ancestor.
database_cross_reference: SO:ke

part_of
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: variation_ontology
id: part_of

partial_evidence_for_feature
type: ObjectProperty
definition: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
has_obo_namespace: variation_ontology
id: partial_evidence_for_feature

Axiom
annotated source: partial_evidence_for_feature
annotated property: definition
annotated target: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
database_cross_reference: SO:ke

position_of
type: ObjectProperty
has_obo_namespace: variation_ontology
id: position_of

positively_regulates
type: ObjectProperty
has_obo_namespace: variation_ontology
id: positively_regulates

regulates
type: ObjectProperty
property chain axiom: part_of
has_obo_namespace: variation_ontology
id: regulates

sequence_of
type: ObjectProperty
has_obo_namespace: variation_ontology
id: sequence_of

variant_of
type: ObjectProperty
definition: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
has_obo_namespace: variation_ontology
id: variant_of
comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.

Axiom
annotated source: variant_of
annotated property: definition
annotated target: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
database_cross_reference: SO:immuno_workshop

variation
type: Class
definition: Alteration in DNA, RNA or protein.
has_obo_namespace: variation_ontology
id: VariO:0001

Axiom
annotated source: variation
annotated property: definition
annotated target: Alteration in DNA, RNA or protein.
database_cross_reference: VariO:mv

variation affecting protein
type: Class
subclass of: variation
definition: Effects of a variation on protein level.
has_obo_namespace: variation_ontology
id: VariO:0002

Axiom
annotated source: variation affecting protein
annotated property: definition
annotated target: Effects of a variation on protein level.
database_cross_reference: VariO:mv

variation affecting protein function
type: Class
subclass of: variation affecting protein
definition: Effect of variation on protein function.
has_obo_namespace: variation_ontology
id: VariO:0003

Axiom
annotated source: variation affecting protein function
annotated property: definition
annotated target: Effect of variation on protein function.
database_cross_reference: VariO:mv

effect on protein movement
type: Class
subclass of: variation affecting protein function
definition: Effect of variation on the movement of a protein along filament of a polymeric molecule.
has_obo_namespace: variation_ontology
id: VariO:0004

Axiom
annotated source: effect on protein movement
annotated property: definition
annotated target: Effect of variation on the movement of a protein along filament of a polymeric molecule.
database_cross_reference: VariO:mv

effect on protein storage
type: Class
subclass of: variation affecting protein function
definition: Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions.
has_obo_namespace: variation_ontology
id: VariO:0005

Axiom
annotated source: effect on protein storage
annotated property: definition
annotated target: Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions.
database_cross_reference: VariO:mv

effect on structural protein
type: Class
subclass of: variation affecting protein function
definition: Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems.
has_obo_namespace: variation_ontology
id: VariO:0006

Axiom
annotated source: effect on structural protein
annotated property: definition
annotated target: Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems.
database_cross_reference: VariO:mv

effect on protein recognition
type: Class
subclass of: variation affecting protein function
definition: Effect of variation on selective non-covalent interaction of protein.
has_obo_namespace: variation_ontology
id: VariO:0007

Axiom
annotated source: effect on protein recognition
annotated property: definition
annotated target: Effect of variation on selective non-covalent interaction of protein.
database_cross_reference: VariO:mv

effect on catalytic protein function
type: Class
subclass of: variation affecting protein function
definition: Effect of variation on catalytic function of protein.
has_obo_namespace: variation_ontology
id: VariO:0008

Axiom
annotated source: effect on catalytic protein function
annotated property: definition
annotated target: Effect of variation on catalytic function of protein.
database_cross_reference: VariO:mv

effect on transport function of protein
type: Class
subclass of: variation affecting protein function
definition: Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane.
has_obo_namespace: variation_ontology
id: VariO:0009

Axiom
annotated source: effect on transport function of protein
annotated property: definition
annotated target: Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane.
database_cross_reference: VariO:mv

effect on RNA abundance
type: Class
subclass of: variation affecting RNA property
definition: Variation affecting abundance of produced RNA molecules.
has_obo_namespace: variation_ontology
id: VariO:0010

Axiom
annotated source: effect on RNA abundance
annotated property: definition
annotated target: Variation affecting abundance of produced RNA molecules.
database_cross_reference: VariO:mv

effect on protein information transfer
type: Class
subclass of: variation affecting protein function
definition: Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs.
has_obo_namespace: variation_ontology
id: VariO:0011

Axiom
annotated source: effect on protein information transfer
annotated property: definition
annotated target: Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs.
database_cross_reference: VariO:mv

protein variation type
type: Class
subclass of: variation affecting protein
definition: Type of protein variation. Describes origin and classification of a variant.
has_obo_namespace: variation_ontology
id: VariO:0012

Axiom
annotated source: protein variation type
annotated property: definition
annotated target: Type of protein variation. Describes origin and classification of a variant.
database_cross_reference: VariO:mv

protein variation of genetic origin
type: Class
subclass of: protein variation origin
definition: Protein variation that has genetic origin.
has_obo_namespace: variation_ontology
id: VariO:0013

Axiom
annotated source: protein variation of genetic origin
annotated property: definition
annotated target: Protein variation that has genetic origin.
database_cross_reference: VariO:mv

amino acid deletion
type: Class
subclass of: protein variation classification
definition: Removal of one or more continuous amino acids from protein.
has_obo_namespace: variation_ontology
id: VariO:0014

Axiom
annotated source: amino acid deletion
annotated property: definition
annotated target: Removal of one or more continuous amino acids from protein.
database_cross_reference: VariO:mv

protein truncation
type: Class
subclass of: amino acid deletion
definition: Shortening of protein sequence from terminus.
has_obo_namespace: variation_ontology
id: VariO:0015

Axiom
annotated source: protein truncation
annotated property: definition
annotated target: Shortening of protein sequence from terminus.
database_cross_reference: VariO:mv

sequence retaining amino acid deletion
type: Class
subclass of: amino acid deletion
definition: Deletion of one or more amino acids from a protein, without affecting the sequence after deletion.
has_obo_namespace: variation_ontology
id: VariO:0016

Axiom
annotated source: sequence retaining amino acid deletion
annotated property: definition
annotated target: Deletion of one or more amino acids from a protein, without affecting the sequence after deletion.
database_cross_reference: VariO:mv

nonsynonymous variation
type: Class
subclass of: variation attribute
definition: mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid.
created by: med-mnv
creation date: 2015-06-04T13:23:24Z
has_obo_namespace: variation_ontology
id: VariO:0017

Axiom
annotated source: nonsynonymous variation
annotated property: definition
annotated target: mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid.
database_cross_reference: Vario:mv

amino acid insertion
type: Class
subclass of: protein variation classification
definition: Addition of one or more amino acids to protein sequence.
has_obo_namespace: variation_ontology
id: VariO:0018

Axiom
annotated source: amino acid insertion
annotated property: definition
annotated target: Addition of one or more amino acids to protein sequence.
database_cross_reference: VariO:mv

amphigoric amino acid insertion
type: Class
subclass of: amino acid insertion
definition: Insertion of one or more amino acids to protein with sequence completely changed after the insertion position. Caused by insertion of number of RNA nucleotides not divisible by three leading to frame shift of mRNA reading frame.
has_obo_namespace: variation_ontology
id: VariO:0019

Axiom
annotated source: amphigoric amino acid insertion
annotated property: definition
annotated target: Insertion of one or more amino acids to protein with sequence completely changed after the insertion position. Caused by insertion of number of RNA nucleotides not divisible by three leading to frame shift of mRNA reading frame.
database_cross_reference: VariO:mv

sequence retaining amino acid insertion
type: Class
subclass of: amino acid insertion
definition: Insertion of one or more amino acids to the protein without affecting the sequence after insertion.
has_obo_namespace: variation_ontology
id: VariO:0020

Axiom
annotated source: sequence retaining amino acid insertion
annotated property: definition
annotated target: Insertion of one or more amino acids to the protein without affecting the sequence after insertion.
database_cross_reference: VariO:mv

amino acid substitution
type: Class
subclass of: protein variation classification
definition: Substitution of an amino acid in protein.
database_cross_reference: SO:0001606
has_obo_namespace: variation_ontology
id: VariO:0021

Axiom
annotated source: amino acid substitution
annotated property: definition
annotated target: Substitution of an amino acid in protein.
database_cross_reference: VariO:mv

amino acid indel
type: Class
subclass of: protein variation classification
definition: A complex protein variation consisting of both amino acid insertion(s) and deletion(s).
has_obo_namespace: variation_ontology
id: VariO:0022

Axiom
annotated source: amino acid indel
annotated property: definition
annotated target: A complex protein variation consisting of both amino acid insertion(s) and deletion(s).
database_cross_reference: VariO:mv

amphigoric amino acid indel
type: Class
subclass of: amino acid indel
definition: Amino acid indel with sequence completely changed after the indel position. Caused by indel of number of RNA nucleotides not divisible by three leading to frameshift of reading frame.
created by: Mauno Vihnen
creation date: 2013-03-06T10:59:41Z
has_obo_namespace: variation_ontology
id: VariO:0023

Axiom
annotated source: amphigoric amino acid indel
annotated property: definition
annotated target: Amino acid indel with sequence completely changed after the indel position. Caused by indel of number of RNA nucleotides not divisible by three leading to frameshift of reading frame.
database_cross_reference: VariO:mv

variation emerging at protein level
type: Class
subclass of: protein variation origin
definition: Protein variation that does not have genetic origin being modified at protein level.
has_obo_namespace: variation_ontology
id: VariO:0024

Axiom
annotated source: variation emerging at protein level
annotated property: definition
annotated target: Protein variation that does not have genetic origin being modified at protein level.
database_cross_reference: VariO:mv

epigenetic protein variation
type: Class
subclass of: variation emerging at protein level
definition: Heritable protein variation of non-genetic origin.
has_obo_namespace: variation_ontology
id: VariO:0025

Axiom
annotated source: epigenetic protein variation
annotated property: definition
annotated target: Heritable protein variation of non-genetic origin.
database_cross_reference: VariO:mv

protein structural inheritance
type: Class
subclass of: epigenetic protein variation
definition: Inheritance of protein or protein complex structure without involvement of genetic information.
has_obo_namespace: variation_ontology
id: VariO:0026

Axiom
annotated source: protein structural inheritance
annotated property: definition
annotated target: Inheritance of protein or protein complex structure without involvement of genetic information.
database_cross_reference: VariO:mv

proteinaceous infection
type: Class
subclass of: epigenetic protein variation
definition: Protein conformation change induced by structurally modified protein.
has_obo_namespace: variation_ontology
id: VariO:0027

Axiom
annotated source: proteinaceous infection
annotated property: definition
annotated target: Protein conformation change induced by structurally modified protein.
database_cross_reference: VariO:mv

post translational modification
type: Class
subclass of: variation emerging at protein level
definition: Protein molecule chemically modified after translation.
has_obo_namespace: variation_ontology
id: VariO:0028

Axiom
annotated source: post translational modification
annotated property: definition
annotated target: Protein molecule chemically modified after translation.
database_cross_reference: VariO:mv

sequence retaining amino acid indel
type: Class
subclass of: amino acid indel
definition: Amino acid indel without affecting the sequence after the indel position.
created by: Mauno Vihnen
creation date: 2013-03-06T11:04:21Z
has_obo_namespace: variation_ontology
id: VariO:0029

Axiom
annotated source: sequence retaining amino acid indel
annotated property: definition
annotated target: Amino acid indel without affecting the sequence after the indel position.
database_cross_reference: VariO:mv

in-frame indel
type: Class
subclass of: RNA indel
definition: RNA indel not affecting reading frame after indel position.
created by: Mauno Vihnen
creation date: 2013-06-14T10:03:57Z
has_obo_namespace: variation_ontology
id: VariO:0030

Axiom
annotated source: in-frame indel
annotated property: definition
annotated target: RNA indel not affecting reading frame after indel position.
database_cross_reference: VariO:mv

out-of-frame indel
type: Class
subclass of: RNA indel
definition: RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame.
created by: Mauno Vihnen
creation date: 2013-06-14T10:03:57Z
has_obo_namespace: variation_ontology
id: VariO:0031

Axiom
annotated source: out-of-frame indel
annotated property: definition
annotated target: RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame.
database_cross_reference: VariO:mv

variation affecting protein property
type: Class
subclass of: variation affecting protein
definition: Variation affecting characteristic property of protein.
has_obo_namespace: variation_ontology
id: VariO:0032

Axiom
annotated source: variation affecting protein property
annotated property: definition
annotated target: Variation affecting characteristic property of protein.
database_cross_reference: VariO:mv

effect on protein subcellular localization
type: Class
subclass of: variation affecting protein property
definition: Effect of variation on the targeting of a protein within a cell or cellular compartment.
has_obo_namespace: variation_ontology
id: VariO:0033

Axiom
annotated source: effect on protein subcellular localization
annotated property: definition
annotated target: Effect of variation on the targeting of a protein within a cell or cellular compartment.
database_cross_reference: VariO:mv

effect on protein stability
type: Class
subclass of: variation affecting protein property
definition: Effect of variation on stability of protein.
has_obo_namespace: variation_ontology
id: VariO:0034

Axiom
annotated source: effect on protein stability
annotated property: definition
annotated target: Effect of variation on stability of protein.
database_cross_reference: VariO:mv

effect on protein solubility
type: Class
subclass of: variation affecting protein property
definition: Effect of variation on the potential of protein to dissolve in a liquid.
has_obo_namespace: variation_ontology
id: VariO:0035

Axiom
annotated source: effect on protein solubility
annotated property: definition
annotated target: Effect of variation on the potential of protein to dissolve in a liquid.
database_cross_reference: VariO:mv

effect on protein inclusion body formation
type: Class
subclass of: effect on protein solubility
definition: Variation affecting the formation of particles of aggregated proteins.
database_cross_reference: GO:0016234
has_obo_namespace: variation_ontology
id: VariO:0036

Axiom
annotated source: effect on protein inclusion body formation
annotated property: definition
annotated target: Variation affecting the formation of particles of aggregated proteins.
database_cross_reference: VariO:mv

covariant position
type: Class
subclass of: conservation
definition: Variation at a covarying sequence position.
created by: Mauno Vihnen
creation date: 2014-01-16T14:03:51Z
has_obo_namespace: variation_ontology
id: VariO:0037

Axiom
annotated source: covariant position
annotated property: definition
annotated target: Variation at a covarying sequence position.
database_cross_reference: VariO:mv

effect on protein aggregation
type: Class
subclass of: effect on protein solubility
definition: Variation affecting protein aggregation tendency.
has_obo_namespace: variation_ontology
id: VariO:0038

Axiom
annotated source: effect on protein aggregation
annotated property: definition
annotated target: Variation affecting protein aggregation tendency.
database_cross_reference: VariO:mv

protein function change
type: Class
subclass of: variation affecting protein property
definition: Type of protein function affecting variation.
has_obo_namespace: variation_ontology
id: VariO:0039

Axiom
annotated source: protein function change
annotated property: definition
annotated target: Type of protein function affecting variation.
database_cross_reference: VariO:mv

protein gain of function
type: Class
subclass of: protein function change
definition: Effect of variation causing new or enhanced protein activity.
has_obo_namespace: variation_ontology
id: VariO:0040

Axiom
annotated source: protein gain of function
annotated property: definition
annotated target: Effect of variation causing new or enhanced protein activity.
database_cross_reference: VariO:mv

neomorphic protein variation
type: Class
subclass of: protein gain of function
definition: Variation generates new protein function.
has_obo_namespace: variation_ontology
id: VariO:0041

Axiom
annotated source: neomorphic protein variation
annotated property: definition
annotated target: Variation generates new protein function.
database_cross_reference: VariO:mv

antimorphic protein variation
type: Class
subclass of: protein gain of function
definition: Dominant variation that acts to opposite direction than the normal protein.
has_exact_synonym: dominant negative protein variation
has_obo_namespace: variation_ontology
id: VariO:0042

Axiom
annotated source: antimorphic protein variation
annotated property: definition
annotated target: Dominant variation that acts to opposite direction than the normal protein.
database_cross_reference: VariO:mv

protein loss of function
type: Class
subclass of: protein function change
definition: Effect of variation reducing or abolishing protein activity.
has_obo_namespace: variation_ontology
id: VariO:0043

Axiom
annotated source: protein loss of function
annotated property: definition
annotated target: Effect of variation reducing or abolishing protein activity.
database_cross_reference: VariO:mv

effect on protein accessibility
type: Class
subclass of: variation affecting protein property
definition: Effect of variation to the accessibility of protein region to solvent.
has_obo_namespace: variation_ontology
id: VariO:0044

Axiom
annotated source: effect on protein accessibility
annotated property: definition
annotated target: Effect of variation to the accessibility of protein region to solvent.
database_cross_reference: VariO:mv

variation exposing buried region
type: Class
subclass of: effect on protein accessibility
definition: Variation exposing buried region.
has_obo_namespace: variation_ontology
id: VariO:0045

Axiom
annotated source: variation exposing buried region
annotated property: definition
annotated target: Variation exposing buried region.
database_cross_reference: VariO:mv

variation burying exposed region
type: Class
subclass of: effect on protein accessibility
definition: Variation leading to burying of exposed region.
has_obo_namespace: variation_ontology
id: VariO:0046

Axiom
annotated source: variation burying exposed region
annotated property: definition
annotated target: Variation leading to burying of exposed region.
database_cross_reference: VariO:mv

association of protein variation to pathogenicity
type: Class
subclass of: variation affecting protein property
definition: Implication of a protein variant to pathogenicity.
has_obo_namespace: variation_ontology
id: VariO:0047

Axiom
annotated source: association of protein variation to pathogenicity
annotated property: definition
annotated target: Implication of a protein variant to pathogenicity.
database_cross_reference: VariO:mv

effect on protein charge
type: Class
subclass of: variation affecting protein property
definition: Effect of variation on charge in protein.
has_obo_namespace: variation_ontology
id: VariO:0048

Axiom
annotated source: effect on protein charge
annotated property: definition
annotated target: Effect of variation on charge in protein.
database_cross_reference: VariO:mv

effect on protein electrostatics
type: Class
subclass of: effect on protein charge
definition: Variation affecting electrostatics of the protein surface.
has_obo_namespace: variation_ontology
id: VariO:0049

Axiom
annotated source: effect on protein electrostatics
annotated property: definition
annotated target: Variation affecting electrostatics of the protein surface.
database_cross_reference: VariO:mv

effect on protein isoelectric point
type: Class
subclass of: effect on protein charge
definition: Variation changing protein isoelectric point.
has_obo_namespace: variation_ontology
id: VariO:0050

Axiom
annotated source: effect on protein isoelectric point
annotated property: definition
annotated target: Variation changing protein isoelectric point.
database_cross_reference: VariO:mv

effect on protein degradation
type: Class
subclass of: variation affecting protein property
definition: Effect of variation on degradation of protein.
has_obo_namespace: variation_ontology
id: VariO:0051

Axiom
annotated source: effect on protein degradation
annotated property: definition
annotated target: Effect of variation on degradation of protein.
database_cross_reference: VariO:mv

effect on protein abundance
type: Class
subclass of: variation affecting protein property
definition: Variation affecting abundance of produced protein molecules.
has_obo_namespace: variation_ontology
id: VariO:0052

Axiom
annotated source: effect on protein abundance
annotated property: definition
annotated target: Variation affecting abundance of produced protein molecules.
database_cross_reference: VariO:mv

effect on protein activity
type: Class
subclass of: variation affecting protein property
definition: Effect of variation on activity of protein.
has_obo_namespace: variation_ontology
id: VariO:0053

Axiom
annotated source: effect on protein activity
annotated property: definition
annotated target: Effect of variation on activity of protein.
database_cross_reference: VariO:mv

effect on protein affinity
type: Class
subclass of: effect on protein activity
definition: Effect of variation on protein affinity to binding molecule(s).
has_obo_namespace: variation_ontology
id: VariO:0054

Axiom
annotated source: effect on protein affinity
annotated property: definition
annotated target: Effect of variation on protein affinity to binding molecule(s).
database_cross_reference: VariO:mv

effect on protein specificity
type: Class
subclass of: effect on protein activity
definition: Effect of variation on substrate binding specificity of protein.
has_obo_namespace: variation_ontology
id: VariO:0055

Axiom
annotated source: effect on protein specificity
annotated property: definition
annotated target: Effect of variation on substrate binding specificity of protein.
database_cross_reference: VariO:mv

effect on enzyme reaction kinetics
type: Class
subclass of: effect on protein reaction kinetics
definition: Effect of variation to enzyme reaction kinetics.
has_obo_namespace: variation_ontology
id: VariO:0056

Axiom
annotated source: effect on enzyme reaction kinetics
annotated property: definition
annotated target: Effect of variation to enzyme reaction kinetics.
database_cross_reference: VariO:mv

conservation of protein variation site
type: Class
subclass of: variation affecting protein property
definition: Conservation of the variant site in related protein sequences.
has_obo_namespace: variation_ontology
id: VariO:0057

Axiom
annotated source: conservation of protein variation site
annotated property: definition
annotated target: Conservation of the variant site in related protein sequences.
database_cross_reference: VariO:mv

effect on protein interaction
type: Class
subclass of: variation affecting protein property
definition: Effect of variation on the interaction of protein with its partner.
has_obo_namespace: variation_ontology
id: VariO:0058

Axiom
annotated source: effect on protein interaction
annotated property: definition
annotated target: Effect of variation on the interaction of protein with its partner.
database_cross_reference: VariO:mv

effect on protein contact energy
type: Class
subclass of: effect on protein interaction
definition: Effect of variation on contact energy between interacting molecules.
has_obo_namespace: variation_ontology
id: VariO:0059

Axiom
annotated source: effect on protein contact energy
annotated property: definition
annotated target: Effect of variation on contact energy between interacting molecules.
database_cross_reference: VariO:mv

variation affecting protein structure
type: Class
subclass of: variation affecting protein
definition: Variation affecting structure of protein.
has_obo_namespace: variation_ontology
id: VariO:0060

Axiom
annotated source: variation affecting protein structure
annotated property: definition
annotated target: Variation affecting structure of protein.
database_cross_reference: VariO:mv

epigenetic protein modification
type: Class
subclass of: variation affecting protein structure
definition: Hereditary protein structure modification of non-genetic origin.
has_obo_namespace: variation_ontology
id: VariO:0061

Axiom
annotated source: epigenetic protein modification
annotated property: definition
annotated target: Hereditary protein structure modification of non-genetic origin.
database_cross_reference: VariO:mv

prion formation
type: Class
subclass of: epigenetic protein modification
definition: Variation affecting the formation of infectious protein having misfolded structure.
has_obo_namespace: variation_ontology
id: VariO:0062

Axiom
annotated source: prion formation
annotated property: definition
annotated target: Variation affecting the formation of infectious protein having misfolded structure.
database_cross_reference: VariO:mv

epigenetic protein complex structure
type: Class
subclass of: epigenetic protein modification
definition: Variation affecting heritable protein complex structure.
has_obo_namespace: variation_ontology
id: VariO:0063

Axiom
annotated source: epigenetic protein complex structure
annotated property: definition
annotated target: Variation affecting heritable protein complex structure.
database_cross_reference: VariO:mv

effect on protein 3D structure
type: Class
subclass of: variation affecting protein structure
definition: Variation affecting protein three dimensional structure.
has_obo_namespace: variation_ontology
id: VariO:0064

Axiom
annotated source: effect on protein 3D structure
annotated property: definition
annotated target: Variation affecting protein three dimensional structure.
database_cross_reference: VariO:mv

effect on protein dynamics
type: Class
subclass of: effect on protein 3D structure
definition: Variation affecting dynamics in protein structure.
has_obo_namespace: variation_ontology
id: VariO:0065

Axiom
annotated source: effect on protein dynamics
annotated property: definition
annotated target: Variation affecting dynamics in protein structure.
database_cross_reference: VariO:mv

effect on structural flexibility
type: Class
subclass of: effect on protein dynamics
definition: Variation affecting protein structural flexibility.
has_obo_namespace: variation_ontology
id: VariO:0066

Axiom
annotated source: effect on structural flexibility
annotated property: definition
annotated target: Variation affecting protein structural flexibility.
database_cross_reference: VariO:mv

effect on induced fit
type: Class
subclass of: effect on protein dynamics
definition: Variation affecting induced fit of protein binding to its partner.
has_obo_namespace: variation_ontology
id: VariO:0067

Axiom
annotated source: effect on induced fit
annotated property: definition
annotated target: Variation affecting induced fit of protein binding to its partner.
database_cross_reference: VariO:mv

effect on structural disorder
type: Class
subclass of: effect on protein dynamics
definition: Variation affecting protein structural disorder.
has_obo_namespace: variation_ontology
id: VariO:0068

Axiom
annotated source: effect on structural disorder
annotated property: definition
annotated target: Variation affecting protein structural disorder.
database_cross_reference: VariO:mv

effect on allosteric site
type: Class
subclass of: effect on protein dynamics
definition: Variation in affecting protein allosteric site.
has_obo_namespace: variation_ontology
id: VariO:0069

Axiom
annotated source: effect on allosteric site
annotated property: definition
annotated target: Variation in affecting protein allosteric site.
database_cross_reference: VariO:mv

effect on protein tertiary structure
type: Class
subclass of: effect on protein 3D structure
definition: Variation affecting protein three dimensional structure.
has_obo_namespace: variation_ontology
id: VariO:0070

Axiom
annotated source: effect on protein tertiary structure
annotated property: definition
annotated target: Variation affecting protein three dimensional structure.
database_cross_reference: VariO:mv

effect on protein folding rate
type: Class
subclass of: effect on protein tertiary structure
definition: Variation affecting rate of protein folding.
has_obo_namespace: variation_ontology
id: VariO:0071

Axiom
annotated source: effect on protein folding rate
annotated property: definition
annotated target: Variation affecting rate of protein folding.
database_cross_reference: VariO:mv

extrachromosomal DNA affected
type: Class
subclass of: affected DNA level
definition: Variation effect on nonchromosomal DNA.
created by: Mauno Vihinen
creation date: 2012-11-09T14:16:30Z
has_obo_namespace: variation_ontology
id: VariO:0072

Axiom
annotated source: extrachromosomal DNA affected
annotated property: definition
annotated target: Variation effect on nonchromosomal DNA.
database_cross_reference: VariO:mv

effect to protein fold
type: Class
subclass of: effect on protein tertiary structure
definition: Variation affecting protein tertiary structure.
has_obo_namespace: variation_ontology
id: VariO:0073

Axiom
annotated source: effect to protein fold
annotated property: definition
annotated target: Variation affecting protein tertiary structure.
database_cross_reference: VariO:mv

protein conformational change
type: Class
subclass of: effect to protein fold
definition: Variation changing protein conformation.
has_obo_namespace: variation_ontology
id: VariO:0074

Axiom
annotated source: protein conformational change
annotated property: definition
annotated target: Variation changing protein conformation.
database_cross_reference: VariO:mv

global protein conformation change
type: Class
subclass of: protein conformational change
definition: Variation causing large overall protein conformational change.
has_obo_namespace: variation_ontology
id: VariO:0075

Axiom
annotated source: global protein conformation change
annotated property: definition
annotated target: Variation causing large overall protein conformational change.
database_cross_reference: VariO:mv

local protein conformation change
type: Class
subclass of: protein conformational change
definition: Variation causing local and minor conformational change.
has_obo_namespace: variation_ontology
id: VariO:0076

Axiom
annotated source: local protein conformation change
annotated property: definition
annotated target: Variation causing local and minor conformational change.
database_cross_reference: VariO:mv

changed domain orientation
type: Class
subclass of: effect to protein fold
definition: Variation affecting protein structure due to alteration to domain orientation.
has_obo_namespace: variation_ontology
id: VariO:0077

Axiom
annotated source: changed domain orientation
annotated property: definition
annotated target: Variation affecting protein structure due to alteration to domain orientation.
database_cross_reference: VariO:mv

effect on protein disulphide formation
type: Class
subclass of: effect to protein fold
definition: Variation affecting formation of intramolecular disulphide bonds.
has_obo_namespace: variation_ontology
id: VariO:0078

Axiom
annotated source: effect on protein disulphide formation
annotated property: definition
annotated target: Variation affecting formation of intramolecular disulphide bonds.
database_cross_reference: VariO:mv

effect on protein secondary structural element
type: Class
subclass of: effect on protein tertiary structure
definition: Variation affecting protein secondary structural element of local ordered structure.
has_obo_namespace: variation_ontology
id: VariO:0079

Axiom
annotated source: effect on protein secondary structural element
annotated property: definition
annotated target: Variation affecting protein secondary structural element of local ordered structure.
database_cross_reference: VariO:mv

effect on protein helix
type: Class
subclass of: effect on protein secondary structural element
definition: Variation affecting secondary structure conformation where the peptide backbone forms a coil.
has_obo_namespace: variation_ontology
id: VariO:0080

Axiom
annotated source: effect on protein helix
annotated property: definition
annotated target: Variation affecting secondary structure conformation where the peptide backbone forms a coil.
database_cross_reference: VariO:mv

effect on left handed protein helix
type: Class
subclass of: effect on protein helix
definition: Variation affecting protein left handed helix turning anticlockwise.
has_obo_namespace: variation_ontology
id: VariO:0081

Axiom
annotated source: effect on left handed protein helix
annotated property: definition
annotated target: Variation affecting protein left handed helix turning anticlockwise.
database_cross_reference: VariO:mv

effect on right handed protein helix
type: Class
subclass of: effect on protein helix
definition: Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw.
has_obo_namespace: variation_ontology
id: VariO:0082

Axiom
annotated source: effect on right handed protein helix
annotated property: definition
annotated target: Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw.
database_cross_reference: VariO:mv

effect on pi helix
type: Class
subclass of: effect on right handed protein helix
definition: Variation affecting protein helix having 4.1 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
has_obo_namespace: variation_ontology
id: VariO:0083

Axiom
annotated source: effect on pi helix
annotated property: definition
annotated target: Variation affecting protein helix having 4.1 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
database_cross_reference: VariO:mv

effect on three ten helix
type: Class
subclass of: effect on right handed protein helix
definition: Variation affecting protein helix having 3 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
has_obo_namespace: variation_ontology
id: VariO:0084

Axiom
annotated source: effect on three ten helix
annotated property: definition
annotated target: Variation affecting protein helix having 3 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
database_cross_reference: VariO:mv

effect on alpha helix
type: Class
subclass of: effect on right handed protein helix
definition: Variation affecting protein helix having 3.6 residues per turn. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
has_obo_namespace: variation_ontology
id: VariO:0085

Axiom
annotated source: effect on alpha helix
annotated property: definition
annotated target: Variation affecting protein helix having 3.6 residues per turn. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
database_cross_reference: VariO:mv

effect on protein beta strand
type: Class
subclass of: effect on protein secondary structural element
definition: Variation affecting extended protein backbone structure.
has_obo_namespace: variation_ontology
id: VariO:0086

Axiom
annotated source: effect on protein beta strand
annotated property: definition
annotated target: Variation affecting extended protein backbone structure.
database_cross_reference: VariO:mv

effect on protein antiparallel beta strand
type: Class
subclass of: effect on protein beta strand
definition: Variation affecting beta strand forming part of antiparallel beta sheet. Hydrogen bonds are formed with another region of protein running in the opposite direction. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees).
has_obo_namespace: variation_ontology
id: VariO:0087
comment: Range.

Axiom
annotated source: effect on protein antiparallel beta strand
annotated property: definition
annotated target: Variation affecting beta strand forming part of antiparallel beta sheet. Hydrogen bonds are formed with another region of protein running in the opposite direction. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees).
database_cross_reference: VariO:mv

effect on protein parallel beta strand
type: Class
subclass of: effect on protein beta strand
definition: Variation affecting beta strand forming part of parallel beta sheet. Hydrogen bonds are formed with another region of protein running in the same direction. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees).
has_obo_namespace: variation_ontology
id: VariO:0088
comment: Range.

Axiom
annotated source: effect on protein parallel beta strand
annotated property: definition
annotated target: Variation affecting beta strand forming part of parallel beta sheet. Hydrogen bonds are formed with another region of protein running in the same direction. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees).
database_cross_reference: VariO:mv

effect on protein turn motif
type: Class
subclass of: effect on protein secondary structural element
definition: Variation affecting protein backbone turn motif.
has_obo_namespace: variation_ontology
id: VariO:0089

Axiom
annotated source: effect on protein turn motif
annotated property: definition
annotated target: Variation affecting protein backbone turn motif.
database_cross_reference: VariO:mv

effect on protein alpha beta motif
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.
has_obo_namespace: variation_ontology
id: VariO:0090

Axiom
annotated source: effect on protein alpha beta motif
annotated property: definition
annotated target: Variation affecting protein motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.
database_cross_reference: VariO:mv

effect on protein beta turn
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which is used to sub-categorize the turns.
has_obo_namespace: variation_ontology
id: VariO:0091

Axiom
annotated source: effect on protein beta turn
annotated property: definition
annotated target: Variation affecting protein motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which is used to sub-categorize the turns.
database_cross_reference: VariO:mv

effect on protein st motif
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of five consecutive residues and two H-bonds, where residue(i) is either serine or threonine. Side chain O of residue(i) is H-bonded to the main chain NH of residue(i+2) or (i+3), and main chain CO or residue(i) is H-bonded to the main chain NH or residue(i+3) or (i+4).
has_obo_namespace: variation_ontology
id: VariO:0092

Axiom
annotated source: effect on protein st motif
annotated property: definition
annotated target: Variation affecting protein motif of five consecutive residues and two H-bonds, where residue(i) is either serine or threonine. Side chain O of residue(i) is H-bonded to the main chain NH of residue(i+2) or (i+3), and main chain CO or residue(i) is H-bonded to the main chain NH or residue(i+3) or (i+4).
database_cross_reference: VariO:mv

effect on protein st staple
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of four or five consecutive residues and one H-bond in which residue(i) is serine or threonine, the side chain OH of residue(i) is H-bonded to the main chain CO or residue(i-3) or (i-4), and phi angles of residues(i-1), (i-2) and (i-3) are negative.
has_obo_namespace: variation_ontology
id: VariO:0093

Axiom
annotated source: effect on protein st staple
annotated property: definition
annotated target: Variation affecting protein motif of four or five consecutive residues and one H-bond in which residue(i) is serine or threonine, the side chain OH of residue(i) is H-bonded to the main chain CO or residue(i-3) or (i-4), and phi angles of residues(i-1), (i-2) and (i-3) are negative.
database_cross_reference: VariO:mv

effect on protein gamma turn
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein turn defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
has_obo_namespace: variation_ontology
id: VariO:0094

Axiom
annotated source: effect on protein gamma turn
annotated property: definition
annotated target: Variation affecting protein turn defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
database_cross_reference: VariO:mv

effect on protein st turn
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is serine or threonine, the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
has_obo_namespace: variation_ontology
id: VariO:0095

Axiom
annotated source: effect on protein st turn
annotated property: definition
annotated target: Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is serine or threonine, the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
database_cross_reference: VariO:mv

effect on protein schellman loop
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds.
has_obo_namespace: variation_ontology
id: VariO:0096

Axiom
annotated source: effect on protein schellman loop
annotated property: definition
annotated target: Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds.
database_cross_reference: VariO:mv

effect on protein nest motif
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline.
has_obo_namespace: variation_ontology
id: VariO:0097

Axiom
annotated source: effect on protein nest motif
annotated property: definition
annotated target: Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline.
database_cross_reference: VariO:mv

effect on protein niche motif
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs.
has_obo_namespace: variation_ontology
id: VariO:0098

Axiom
annotated source: effect on protein niche motif
annotated property: definition
annotated target: Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs.
database_cross_reference: VariO:mv

effect on protein asx motif
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of five consecutive residues and two H-bonds in which: Residue(i) is aspartate or asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
has_obo_namespace: variation_ontology
id: VariO:0099

Axiom
annotated source: effect on protein asx motif
annotated property: definition
annotated target: Variation affecting protein motif of five consecutive residues and two H-bonds in which: Residue(i) is aspartate or asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
database_cross_reference: VariO:mv

effect on protein beta bulge
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
has_obo_namespace: variation_ontology
id: VariO:0100

Axiom
annotated source: effect on protein beta bulge
annotated property: definition
annotated target: Variation affecting protein motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
database_cross_reference: VariO:mv

effect on protein asx turn
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is aspartate or asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
has_obo_namespace: variation_ontology
id: VariO:0101

Axiom
annotated source: effect on protein asx turn
annotated property: definition
annotated target: Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is aspartate or asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
database_cross_reference: VariO:mv

effect on protein beta bulge loop
type: Class
subclass of: effect on protein turn motif
definition: Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds.
has_obo_namespace: variation_ontology
id: VariO:0102

Axiom
annotated source: effect on protein beta bulge loop
annotated property: definition
annotated target: Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds.
database_cross_reference: VariO:mv

effect on protein coil
type: Class
subclass of: effect on protein secondary structural element
definition: Variation affecting irregular, unstructured region of protein.
has_obo_namespace: variation_ontology
id: VariO:0103

Axiom
annotated source: effect on protein coil
annotated property: definition
annotated target: Variation affecting irregular, unstructured region of protein.
database_cross_reference: VariO:mv

effect on transmembrane polypeptide
type: Class
subclass of: effect on protein tertiary structure
definition: Variation altering membrane spanning protein.
has_obo_namespace: variation_ontology
id: VariO:0104

Axiom
annotated source: effect on transmembrane polypeptide
annotated property: definition
annotated target: Variation altering membrane spanning protein.
database_cross_reference: VariO:mv

effect on membrane protein extramembrane region
type: Class
subclass of: effect on transmembrane polypeptide
definition: Variation affecting region not traversing the lipid bilayer in a membrane protein.
has_obo_namespace: variation_ontology
id: VariO:0105

Axiom
annotated source: effect on membrane protein extramembrane region
annotated property: definition
annotated target: Variation affecting region not traversing the lipid bilayer in a membrane protein.
database_cross_reference: VariO:mv

effect on membrane protein intramembrane region
type: Class
subclass of: effect on transmembrane polypeptide
definition: Variation affecting region present in the lipid bilayer in a membrane protein.
has_obo_namespace: variation_ontology
id: VariO:0106

Axiom
annotated source: effect on membrane protein intramembrane region
annotated property: definition
annotated target: Variation affecting region present in the lipid bilayer in a membrane protein.
database_cross_reference: VariO:mv

effect on protein post translational modification
type: Class
subclass of: effect on protein tertiary structure
definition: Variation affecting the covalent alteration of protein amino acid by post translational process.
has_obo_namespace: variation_ontology
id: VariO:0107

Axiom
annotated source: effect on protein post translational modification
annotated property: definition
annotated target: Variation affecting the covalent alteration of protein amino acid by post translational process.
database_cross_reference: VariO:mv

deletion of a post translational modification site
type: Class
subclass of: effect on protein post translational modification
definition: Variation causing deletion of a post translational modification site.
has_obo_namespace: variation_ontology
id: VariO:0108

Axiom
annotated source: deletion of a post translational modification site
annotated property: definition
annotated target: Variation causing deletion of a post translational modification site.
database_cross_reference: VariO:mv

effect on protein processing
type: Class
subclass of: effect on protein post translational modification
definition: Variation affecting site of protein maturation by cleavage of peptide bond(s).
has_obo_namespace: variation_ontology
id: VariO:0109

Axiom
annotated source: effect on protein processing
annotated property: definition
annotated target: Variation affecting site of protein maturation by cleavage of peptide bond(s).
database_cross_reference: VariO:mv

effect on protein splicing
type: Class
subclass of: effect on protein processing
definition: Variation affecting post-translational removal of peptide sequences from within a protein sequence.
has_obo_namespace: variation_ontology
id: VariO:0110

Axiom
annotated source: effect on protein splicing
annotated property: definition
annotated target: Variation affecting post-translational removal of peptide sequences from within a protein sequence.
database_cross_reference: VariO:mv

variation generating a novel protein processing site
type: Class
subclass of: effect on protein processing
definition: Variation that generates a novel protein processing site.
has_obo_namespace: variation_ontology
id: VariO:0111

Axiom
annotated source: variation generating a novel protein processing site
annotated property: definition
annotated target: Variation that generates a novel protein processing site.
database_cross_reference: VariO:mv

variation preventing polypeptide processing
type: Class
subclass of: effect on protein processing
definition: Variation causing prevention of polypeptide processing.
has_obo_namespace: variation_ontology
id: VariO:0112

Axiom
annotated source: variation preventing polypeptide processing
annotated property: definition
annotated target: Variation causing prevention of polypeptide processing.
database_cross_reference: VariO:mv

generation of a novel post translational modification site
type: Class
subclass of: effect on protein post translational modification
definition: Variation generating a novel post translational modification site.
has_obo_namespace: variation_ontology
id: VariO:0113

Axiom
annotated source: generation of a novel post translational modification site
annotated property: definition
annotated target: Variation generating a novel post translational modification site.
database_cross_reference: VariO:mv

effect on amino acid size
type: Class
subclass of: effect on protein tertiary structure
definition: Variation affecting amino acid side chain size.
has_obo_namespace: variation_ontology
id: VariO:0114

Axiom
annotated source: effect on amino acid size
annotated property: definition
annotated target: Variation affecting amino acid side chain size.
database_cross_reference: VariO:mv

effect on protein packing
type: Class
subclass of: effect on amino acid size
definition: Variation affecting amino acid packing in folded protein.
has_obo_namespace: variation_ontology
id: VariO:0115

Axiom
annotated source: effect on protein packing
annotated property: definition
annotated target: Variation affecting amino acid packing in folded protein.
database_cross_reference: VariO:mv

protein cavity formation
type: Class
subclass of: effect on protein packing
definition: Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one.
has_obo_namespace: variation_ontology
id: VariO:0116

Axiom
annotated source: protein cavity formation
annotated property: definition
annotated target: Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one.
database_cross_reference: VariO:mv

protein overpacking
type: Class
subclass of: effect on protein packing
definition: Variation causing over packing of amino acids due to replacement by larger amino acid side chain.
has_obo_namespace: variation_ontology
id: VariO:0117

Axiom
annotated source: protein overpacking
annotated property: definition
annotated target: Variation causing over packing of amino acids due to replacement by larger amino acid side chain.
database_cross_reference: VariO:mv

effect on protein interaction site
type: Class
subclass of: effect on protein tertiary structure
definition: Variation affecting ligand binding amino acid(s) in protein.
has_obo_namespace: variation_ontology
id: VariO:0118

Axiom
annotated source: effect on protein interaction site
annotated property: definition
annotated target: Variation affecting ligand binding amino acid(s) in protein.
database_cross_reference: VariO:mv

effect on protein binding site
type: Class
subclass of: effect on protein interaction site
definition: Variation affecting region on the surface of a protein that interacts with another molecule.
has_obo_namespace: variation_ontology
id: VariO:0119

Axiom
annotated source: effect on protein binding site
annotated property: definition
annotated target: Variation affecting region on the surface of a protein that interacts with another molecule.
database_cross_reference: VariO:mv

effect on protein catalytic site
type: Class
subclass of: effect on protein interaction site
definition: Variation affecting amino acid(s) in protein catalytic site.
has_obo_namespace: variation_ontology
id: VariO:0120

Axiom
annotated source: effect on protein catalytic site
annotated property: definition
annotated target: Variation affecting amino acid(s) in protein catalytic site.
database_cross_reference: VariO:mv

effect on protein quaternary structure
type: Class
subclass of: effect on protein 3D structure
definition: Variation affecting three dimensional structure of a protein complex.
has_obo_namespace: variation_ontology
id: VariO:0121

Axiom
annotated source: effect on protein quaternary structure
annotated property: definition
annotated target: Variation affecting three dimensional structure of a protein complex.
database_cross_reference: VariO:mv

effect on protein quaternary structure forming interaction
type: Class
subclass of: effect on protein quaternary structure
definition: Variation affecting interaction between protein subunits in quaternary structure.
has_obo_namespace: variation_ontology
id: VariO:0122

Axiom
annotated source: effect on protein quaternary structure forming interaction
annotated property: definition
annotated target: Variation affecting interaction between protein subunits in quaternary structure.
database_cross_reference: VariO:mv

complex 3D structural change
type: Class
subclass of: effect on protein 3D structure
definition: Complex change of protein three dimensional structure.
has_obo_namespace: variation_ontology
id: VariO:0123

Axiom
annotated source: complex 3D structural change
annotated property: definition
annotated target: Complex change of protein three dimensional structure.
database_cross_reference: VariO:mv

protein elongation
type: Class
subclass of: effect on protein tertiary structure
definition: Variation prolonging protein chain at an end.
has_obo_namespace: variation_ontology
id: VariO:0124

Axiom
annotated source: protein elongation
annotated property: definition
annotated target: Variation prolonging protein chain at an end.
database_cross_reference: VariO:mv

C-terminal protein elongation
type: Class
subclass of: protein elongation
definition: Addition of one or more amino acids to protein C-terminus.
has_obo_namespace: variation_ontology
id: VariO:0125

Axiom
annotated source: C-terminal protein elongation
annotated property: definition
annotated target: Addition of one or more amino acids to protein C-terminus.
database_cross_reference: VariO:mv

N-terminal protein elongation
type: Class
subclass of: protein elongation
definition: Addition of one or more amino acids to protein N-terminus.
has_obo_namespace: variation_ontology
id: VariO:0126

Axiom
annotated source: N-terminal protein elongation
annotated property: definition
annotated target: Addition of one or more amino acids to protein N-terminus.
database_cross_reference: VariO:mv

DNA variation origin
type: Class
subclass of: DNA variation type
definition: Origin of DNA variation.
created by: Mauno Vihnen
creation date: 2013-10-11T08:46:32Z
has_obo_namespace: variation_ontology
id: VariO:0127

Axiom
annotated source: DNA variation origin
annotated property: definition
annotated target: Origin of DNA variation.
database_cross_reference: VariO:mv

variation affecting DNA
type: Class
subclass of: variation
definition: Effects of a variation on DNA level.
has_obo_namespace: variation_ontology
id: VariO:0128

Axiom
annotated source: variation affecting DNA
annotated property: definition
annotated target: Effects of a variation on DNA level.
database_cross_reference: VariO:mv

DNA variation type
type: Class
subclass of: variation affecting DNA
definition: Type of DNA variation. Describes origin and classification of a variant.
has_obo_namespace: variation_ontology
id: VariO:0129

Axiom
annotated source: DNA variation type
annotated property: definition
annotated target: Type of DNA variation. Describes origin and classification of a variant.
database_cross_reference: VariO:mv

DNA variation of genetic origin
type: Class
subclass of: DNA variation origin
definition: DNA variation that has genetic origin.
has_obo_namespace: variation_ontology
id: VariO:0130

Axiom
annotated source: DNA variation of genetic origin
annotated property: definition
annotated target: DNA variation that has genetic origin.
database_cross_reference: VariO:mv

genomic variation
type: Class
subclass of: DNA variation classification
definition: Variation of genomic level.
has_obo_namespace: variation_ontology
id: VariO:0131

Axiom
annotated source: genomic variation
annotated property: definition
annotated target: Variation of genomic level.
database_cross_reference: VariO:mv

chromosomal variation
type: Class
subclass of: DNA variation classification
definition: Variation at chromosomal level.
has_obo_namespace: variation_ontology
id: VariO:0132

Axiom
annotated source: chromosomal variation
annotated property: definition
annotated target: Variation at chromosomal level.
database_cross_reference: VariO:mv

variation of chromosome number
type: Class
subclass of: chromosomal variation
definition: Variation affecting chromosome number.
has_obo_namespace: variation_ontology
has_related_synonym: aneuploidy
id: VariO:0133

Axiom
annotated source: variation of chromosome number
annotated property: definition
annotated target: Variation affecting chromosome number.
database_cross_reference: VariO:mv

variation of chromosome structure
type: Class
subclass of: chromosomal variation
definition: Variation affecting structure of chromosome.
has_obo_namespace: variation_ontology
id: VariO:0134

Axiom
annotated source: variation of chromosome structure
annotated property: definition
annotated target: Variation affecting structure of chromosome.
database_cross_reference: VariO:mv

DNA chain variation
type: Class
subclass of: DNA variation classification
definition: Variation at DNA chain.
has_obo_namespace: variation_ontology
id: VariO:0135

Axiom
annotated source: DNA chain variation
annotated property: definition
annotated target: Variation at DNA chain.
database_cross_reference: VariO:mv

DNA substitution
type: Class
subclass of: DNA chain variation
definition: Substitution of a DNA nucleotide.
has_obo_namespace: variation_ontology
id: VariO:0136

Axiom
annotated source: DNA substitution
annotated property: definition
annotated target: Substitution of a DNA nucleotide.
database_cross_reference: VariO:mv

effect on RNA tertiary structure
type: Class
subclass of: variation affecting RNA structure
definition: Variation affecting RNA tertiary structure.
created by: med-mnv
creation date: 2018-04-26T12:45:52Z
has_obo_namespace: variation_ontology
id: VariO:0137

Axiom
annotated source: effect on RNA tertiary structure
annotated property: definition
annotated target: Variation affecting RNA tertiary structure.
database_cross_reference: VariO:mv

variant
type: Class
subclass of: variation attribute
definition: A genetic character, organism or individual with a difference to reference state.
created by: Mauno Vihinen
creation date: 2012-11-11T19:43:00Z
has_obo_namespace: variation_ontology
id: VariO:0138

Axiom
annotated source: variant
annotated property: definition
annotated target: A genetic character, organism or individual with a difference to reference state.
database_cross_reference: VariO:mv

mutation
type: Class
subclass of: variation attribute
definition: Any process generating variation.
created by: Mauno Vihinen
creation date: 2012-11-11T19:43:39Z
has_obo_namespace: variation_ontology
id: VariO:0139

Axiom
annotated source: mutation
annotated property: definition
annotated target: Any process generating variation.
database_cross_reference: VariO:mv

not changed
type: Class
subclass of: quantity change
definition: The observed feature is not changed in relation to the wild type form.
created by: Mauno Vihinen
creation date: 2012-11-11T19:46:40Z
has_obo_namespace: variation_ontology
id: VariO:0140

Axiom
annotated source: not changed
annotated property: definition
annotated target: The observed feature is not changed in relation to the wild type form.
database_cross_reference: VariO:mv

DNA deletion
type: Class
subclass of: DNA chain variation
definition: Removal of one or more continuous nucleotides from DNA sequence.
has_exact_synonym: nucleotide deletion
has_obo_namespace: variation_ontology
id: VariO:0141

Axiom
annotated source: DNA deletion
annotated property: definition
annotated target: Removal of one or more continuous nucleotides from DNA sequence.
database_cross_reference: VariO:mv

DNA insertion
type: Class
subclass of: DNA chain variation
definition: Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence.
has_exact_synonym: nucleotide insertion
has_obo_namespace: variation_ontology
id: VariO:0142

Axiom
annotated source: DNA insertion
annotated property: definition
annotated target: Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence.
database_cross_reference: VariO:mv

DNA indel
type: Class
subclass of: DNA chain variation
definition: A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s).
has_obo_namespace: variation_ontology
id: VariO:0143

Axiom
annotated source: DNA indel
annotated property: definition
annotated target: A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s).
database_cross_reference: VariO:mv

DNA translocation
type: Class
subclass of: DNA chain variation
definition: A continuous stretch of DNA sequence moved to a new position within a chromosome.
database_cross_reference: MI:0593
database_cross_reference: SO:0000199
has_obo_namespace: variation_ontology
id: VariO:0144

Axiom
annotated source: DNA translocation
annotated property: definition
annotated target: A continuous stretch of DNA sequence moved to a new position within a chromosome.
database_cross_reference: VariO:mv

DNA inversion
type: Class
subclass of: DNA translocation
definition: A continuous stretch of DNA sequence inserted to the same position in reverse orientation.
database_cross_reference: SO:1000036
has_obo_namespace: variation_ontology
id: VariO:0145

Axiom
annotated source: DNA inversion
annotated property: definition
annotated target: A continuous stretch of DNA sequence inserted to the same position in reverse orientation.
database_cross_reference: VariO:mv

DNA variation of non-genetic origin
type: Class
subclass of: DNA variation origin
definition: DNA variation that does not have genetic origin.
has_obo_namespace: variation_ontology
id: VariO:0146

Axiom
annotated source: DNA variation of non-genetic origin
annotated property: definition
annotated target: DNA variation that does not have genetic origin.
database_cross_reference: VariO:mv

epigenetic DNA variation
type: Class
subclass of: DNA variation of non-genetic origin
definition: Heritable DNA variation of non-genetic origin.
has_obo_namespace: variation_ontology
id: VariO:0147

Axiom
annotated source: epigenetic DNA variation
annotated property: definition
annotated target: Heritable DNA variation of non-genetic origin.
database_cross_reference: VariO:mv

variation affecting DNA function
type: Class
subclass of: variation affecting DNA
definition: Variation having effect on DNA function and usage.
has_obo_namespace: variation_ontology
id: VariO:0148

Axiom
annotated source: variation affecting DNA function
annotated property: definition
annotated target: Variation having effect on DNA function and usage.
database_cross_reference: VariO:mv

effect on transcription
type: Class
subclass of: variation affecting DNA function
definition: Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA.
has_obo_namespace: variation_ontology
id: VariO:0149

Axiom
annotated source: effect on transcription
annotated property: definition
annotated target: Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA.
database_cross_reference: VariO:mv

effect on DNA information transfer
type: Class
subclass of: variation affecting DNA function
definition: Variation affecting information transfer of DNA.
has_obo_namespace: variation_ontology
id: VariO:0150

Axiom
annotated source: effect on DNA information transfer
annotated property: definition
annotated target: Variation affecting information transfer of DNA.
database_cross_reference: VariO:mv

effect on DNA repair
type: Class
subclass of: variation affecting DNA function
definition: Variation affecting the process of restoring DNA after damage.
database_cross_reference: GO:0006281
database_cross_reference: Wikipedia:DNA_repair
has_obo_namespace: variation_ontology
id: VariO:0151

Axiom
annotated source: effect on DNA repair
annotated property: definition
annotated target: Variation affecting the process of restoring DNA after damage.
database_cross_reference: VariO:mv

effect on regulatory function of DNA
type: Class
subclass of: variation affecting DNA function
definition: Variation affecting regulatory function of DNA.
has_obo_namespace: variation_ontology
id: VariO:0152

Axiom
annotated source: effect on regulatory function of DNA
annotated property: definition
annotated target: Variation affecting regulatory function of DNA.
database_cross_reference: VariO:mv

chromatin variation
type: Class
subclass of: DNA variation classification
definition: Variation affecting chromatin.
created by: med-mnv
creation date: 2018-03-05T16:05:29Z
has_obo_namespace: variation_ontology
id: VariO:0153

Axiom
annotated source: chromatin variation
annotated property: definition
annotated target: Variation affecting chromatin.
database_cross_reference: VariO:mv

effect on DNA replication
type: Class
subclass of: variation affecting DNA function
definition: Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule.
has_obo_namespace: variation_ontology
id: VariO:0154

Axiom
annotated source: effect on DNA replication
annotated property: definition
annotated target: Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule.
database_cross_reference: VariO:mv

variation affecting DNA structure
type: Class
subclass of: variation affecting DNA
definition: Variation affecting structure of DNA.
has_obo_namespace: variation_ontology
id: VariO:0155

Axiom
annotated source: variation affecting DNA structure
annotated property: definition
annotated target: Variation affecting structure of DNA.
database_cross_reference: VariO:mv

epigenetic DNA modification
type: Class
subclass of: variation affecting DNA structure
definition: Hereditary variation of DNA not affecting primary sequence.
has_obo_namespace: variation_ontology
id: VariO:0156

Axiom
annotated source: epigenetic DNA modification
annotated property: definition
annotated target: Hereditary variation of DNA not affecting primary sequence.
database_cross_reference: VariO:mv

epigenetic DNA methylation
type: Class
subclass of: epigenetic DNA modification
definition: Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression.
has_obo_namespace: variation_ontology
id: VariO:0157

Axiom
annotated source: epigenetic DNA methylation
annotated property: definition
annotated target: Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression.
database_cross_reference: VariO:mv

nucleosome positioning
type: Class
subclass of: Restriction
  on property: part_of
  some values from: epigenetic DNA modification
subclass of: Restriction
  on property: part_of
  some values from: chromatin structure variation
definition: Positioning of nucleosomes to DNA strand.
has_exact_synonym: chromatin modeling
has_exact_synonym: chromatin remodelling
has_obo_namespace: variation_ontology
id: VariO:0158

Axiom
annotated source: nucleosome positioning
annotated property: definition
annotated target: Positioning of nucleosomes to DNA strand.
database_cross_reference: VariO:mv

Axiom
annotated source: nucleosome positioning
annotated property: has_exact_synonym
annotated target: chromatin modeling
database_cross_reference: GO:0006338

Axiom
annotated source: nucleosome positioning
annotated property: has_exact_synonym
annotated target: chromatin remodelling
database_cross_reference: GO:0006338

affected DNA level
type: Class
subclass of: variation affecting DNA structure
definition: Affected level of DNA.
has_obo_namespace: variation_ontology
id: VariO:0159

Axiom
annotated source: affected DNA level
annotated property: definition
annotated target: Affected level of DNA.
database_cross_reference: VariO:mv

DNA chain affected
type: Class
subclass of: affected DNA level
definition: Variation effect on DNA level.
has_obo_namespace: variation_ontology
id: VariO:0160

Axiom
annotated source: DNA chain affected
annotated property: definition
annotated target: Variation effect on DNA level.
database_cross_reference: VariO:mv

variation in intron
type: Class
subclass of: DNA chain affected
definition: Variation located in intron.
database_cross_reference: SO:0001627
has_obo_namespace: variation_ontology
id: VariO:0161

Axiom
annotated source: variation in intron
annotated property: definition
annotated target: Variation located in intron.
database_cross_reference: VariO:mv

variation in exon
type: Class
subclass of: DNA chain affected
definition: Variation located in exon.
has_obo_namespace: variation_ontology
id: VariO:0162

Axiom
annotated source: variation in exon
annotated property: definition
annotated target: Variation located in exon.
database_cross_reference: VariO:mv

variation at intergenic DNA
type: Class
subclass of: DNA chain affected
definition: Variation located in intergenic DNA.
database_cross_reference: SO:0001628
has_obo_namespace: variation_ontology
id: VariO:0163

Axiom
annotated source: variation at intergenic DNA
annotated property: definition
annotated target: Variation located in intergenic DNA.
database_cross_reference: VariO:mv

chromosome affected
type: Class
subclass of: affected DNA level
definition: Variation effect on chromosome level.
has_obo_namespace: variation_ontology
id: VariO:0164

Axiom
annotated source: chromosome affected
annotated property: definition
annotated target: Variation effect on chromosome level.
database_cross_reference: VariO:mv

genome affected
type: Class
subclass of: affected DNA level
definition: Variation effect on genome level.
has_obo_namespace: variation_ontology
id: VariO:0165

Axiom
annotated source: genome affected
annotated property: definition
annotated target: Variation effect on genome level.
database_cross_reference: VariO:mv

immunological receptor gene rearrangement
type: Class
subclass of: immunological recognition molecule diversification
definition: Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes.
created by: med-mnv
creation date: 2015-09-22T19:10:52Z
has_obo_namespace: variation_ontology
id: VariO:0166

Axiom
annotated source: immunological receptor gene rearrangement
annotated property: definition
annotated target: Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes.
database_cross_reference: VariO:mv

effect on DNA form
type: Class
subclass of: effect on DNA tertiary structure
definition: Variation affecting DNA structural form.
created by: med-mnv
creation date: 2017-01-16T12:52:26Z
has_obo_namespace: variation_ontology
id: VariO:0167

Axiom
annotated source: effect on DNA form
annotated property: definition
annotated target: Variation affecting DNA structural form.
database_cross_reference: VariO:mv

somatic hypermutation
type: Class
subclass of: immunological recognition molecule diversification
definition: Immunoglobulin diversification mechanism by producing variations to antigen variable regions.
created by: med-mnv
creation date: 2015-09-22T19:12:51Z
has_obo_namespace: variation_ontology
id: VariO:0168

Axiom
annotated source: somatic hypermutation
annotated property: definition
annotated target: Immunoglobulin diversification mechanism by producing variations to antigen variable regions.
database_cross_reference: VariO:mv

class switch recombination
type: Class
subclass of: immunological recognition molecule diversification
definition: Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain.
created by: med-mnv
creation date: 2015-09-22T19:12:51Z
has_obo_namespace: variation_ontology
id: VariO:0169

Axiom
annotated source: class switch recombination
annotated property: definition
annotated target: Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain.
database_cross_reference: VariO:mv

immunological receptor gene conversion
type: Class
subclass of: immunological recognition molecule diversification
definition: Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence.
created by: med-mnv
creation date: 2015-09-22T19:12:51Z
has_obo_namespace: variation_ontology
id: VariO:0170

Axiom
annotated source: immunological receptor gene conversion
annotated property: definition
annotated target: Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence.
database_cross_reference: VariO:mv

effect on DNA tertiary structure
type: Class
subclass of: variation affecting DNA structure
definition: Variation affecting DNA tertiary structure.
has_obo_namespace: variation_ontology
id: VariO:0171

Axiom
annotated source: effect on DNA tertiary structure
annotated property: definition
annotated target: Variation affecting DNA tertiary structure.
database_cross_reference: VariO:mv

artificial DNA variation
type: Class
subclass of: DNA variation of non-genetic origin
definition: Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA.
created by: Mauno Vihnen
creation date: 2012-11-16T08:44:55Z
has_obo_namespace: variation_ontology
id: VariO:0172

Axiom
annotated source: artificial DNA variation
annotated property: definition
annotated target: Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA.
database_cross_reference: VariO:mv

effect on nucleic acid G-quadruplex
type: Class
subclass of: Restriction
  on property: part_of
  some values from: effect on four-stranded DNA
subclass of: Restriction
  on property: part_of
  some values from: effect on four-stranded RNA
definition: Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular.
has_obo_namespace: variation_ontology
id: VariO:0173

Axiom
annotated source: effect on nucleic acid G-quadruplex
annotated property: definition
annotated target: Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular.
database_cross_reference: VariO:mv

effect on i motif
type: Class
subclass of: effect on four-stranded DNA
definition: Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly.
has_obo_namespace: variation_ontology
id: VariO:0174

Axiom
annotated source: effect on i motif
annotated property: definition
annotated target: Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly.
database_cross_reference: VariO:mv

effect on DNA triple helix
type: Class
subclass of: effect on DNA tertiary structure
definition: Variation affecting DNA helix formed of three strands.
has_obo_namespace: variation_ontology
id: VariO:0175

Axiom
annotated source: effect on DNA triple helix
annotated property: definition
annotated target: Variation affecting DNA helix formed of three strands.
database_cross_reference: VariO:mv

chromosome variation
type: Class
subclass of: variation affecting DNA structure
definition: Variation affecting chromosome.
database_cross_reference: SO:0000240
has_obo_namespace: variation_ontology
id: VariO:0176

Axiom
annotated source: chromosome variation
annotated property: definition
annotated target: Variation affecting chromosome.
database_cross_reference: VariO:mv

telomere length change
type: Class
subclass of: chromosome structure variation
definition: Variation affecting length of telomere sequence.
has_obo_namespace: variation_ontology
id: VariO:0177

Axiom
annotated source: telomere length change
annotated property: definition
annotated target: Variation affecting length of telomere sequence.
database_cross_reference: VariO:mv

telomere shortening
type: Class
subclass of: telomere length change
definition: Variation shortening length of telomere sequence.
has_obo_namespace: variation_ontology
id: VariO:0178

Axiom
annotated source: telomere shortening
annotated property: definition
annotated target: Variation shortening length of telomere sequence.
database_cross_reference: VariO:mv

telomere extension
type: Class
subclass of: telomere length change
definition: Variation extending length of telomere sequence.
has_obo_namespace: variation_ontology
id: VariO:0179

Axiom
annotated source: telomere extension
annotated property: definition
annotated target: Variation extending length of telomere sequence.
database_cross_reference: VariO:mv

chromosome structure variation
type: Class
subclass of: chromosome variation
definition: Variation affecting structure of chromosome.
database_cross_reference: SO:1000183
has_obo_namespace: variation_ontology
id: VariO:0180

Axiom
annotated source: chromosome structure variation
annotated property: definition
annotated target: Variation affecting structure of chromosome.
database_cross_reference: VariO:mv

isochromosome
type: Class
subclass of: chromosome structure variation
definition: Chromosome lacking one arm with duplication of the other arm.
has_obo_namespace: variation_ontology
id: VariO:0181

Axiom
annotated source: isochromosome
annotated property: definition
annotated target: Chromosome lacking one arm with duplication of the other arm.
database_cross_reference: VariO:mv

ring chromosome
type: Class
subclass of: chromosome structure variation
definition: Circular chromosome with ends joined.
database_cross_reference: SO:1000045
has_obo_namespace: variation_ontology
id: VariO:0182

Axiom
annotated source: ring chromosome
annotated property: definition
annotated target: Circular chromosome with ends joined.
database_cross_reference: VariO:mv

chromosomal amplification
type: Class
subclass of: chromosome structure variation
definition: Increase in the frequency of a chromosomal region.
has_obo_namespace: variation_ontology
id: VariO:0183

Axiom
annotated source: chromosomal amplification
annotated property: definition
annotated target: Increase in the frequency of a chromosomal region.
database_cross_reference: VariO:mv

interspersed repeat
type: Class
subclass of: type of chromosomal amplification
definition: Copies of a chromosomal region of length greater than one scattered to genome sequence.
database_cross_reference: SO:0000658
has_obo_namespace: variation_ontology
id: VariO:0184

Axiom
annotated source: interspersed repeat
annotated property: definition
annotated target: Copies of a chromosomal region of length greater than one scattered to genome sequence.
database_cross_reference: VariO:mv

tandem repeat
type: Class
subclass of: type of chromosomal amplification
definition: Adjacent copies of a chromosomal region of length greater than 1.
database_cross_reference: SO:0000705
has_obo_namespace: variation_ontology
id: VariO:0185

Axiom
annotated source: tandem repeat
annotated property: definition
annotated target: Adjacent copies of a chromosomal region of length greater than 1.
database_cross_reference: VariO:mv

minisatellite
type: Class
subclass of: nucleotide expansion
definition: Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs.
has_obo_namespace: variation_ontology
id: VariO:0186

Axiom
annotated source: minisatellite
annotated property: definition
annotated target: Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs.
database_cross_reference: VariO:mv

copy number variation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: chromosomal amplification
subclass of: Restriction
  on property: part_of
  some values from: chromosomal deletion
definition: Increase or decrease of the number of copies of a chromosomal region. Sizes of copy number variations range from about 1 kilobase to several megabases.
database_cross_reference: SO:0001019
has_obo_namespace: variation_ontology
id: VariO:0187

Axiom
annotated source: copy number variation
annotated property: definition
annotated target: Increase or decrease of the number of copies of a chromosomal region. Sizes of copy number variations range from about 1 kilobase to several megabases.
database_cross_reference: VariO:mv

microsatellite
type: Class
subclass of: nucleotide expansion
definition: Tandem repetitive sequence consisting of units of two to six base pair.
has_obo_namespace: variation_ontology
id: VariO:0188

Axiom
annotated source: microsatellite
annotated property: definition
annotated target: Tandem repetitive sequence consisting of units of two to six base pair.
database_cross_reference: VariO:mv

trinucleotide expansion
type: Class
subclass of: microsatellite
definition: Tandem repetitive sequence consisting of three nucleotide units.
has_obo_namespace: variation_ontology
id: VariO:0189

Axiom
annotated source: trinucleotide expansion
annotated property: definition
annotated target: Tandem repetitive sequence consisting of three nucleotide units.
database_cross_reference: VariO:mv

mononucleotide expansion
type: Class
subclass of: microsatellite
definition: Tandem repetitive sequence consisting of one nucleotide type.
has_obo_namespace: variation_ontology
id: VariO:0190

Axiom
annotated source: mononucleotide expansion
annotated property: definition
annotated target: Tandem repetitive sequence consisting of one nucleotide type.
database_cross_reference: VariO:mv

tetranucleotide expansion
type: Class
subclass of: microsatellite
definition: Tandem repetitive sequence consisting of four nucleotide units.
has_obo_namespace: variation_ontology
id: VariO:0191

Axiom
annotated source: tetranucleotide expansion
annotated property: definition
annotated target: Tandem repetitive sequence consisting of four nucleotide units.
database_cross_reference: VariO:mv

DNA mobile genetic element insertion
type: Class
subclass of: chromosomal amplification
definition: Mobile genetic element incorporated into chromosome.
has_obo_namespace: variation_ontology
id: VariO:0192

Axiom
annotated source: DNA mobile genetic element insertion
annotated property: definition
annotated target: Mobile genetic element incorporated into chromosome.
database_cross_reference: VariO:mv

chromosomal deletion
type: Class
subclass of: chromosome structure variation
definition: Deletion of chromosomal region.
has_obo_namespace: variation_ontology
id: VariO:0193

Axiom
annotated source: chromosomal deletion
annotated property: definition
annotated target: Deletion of chromosomal region.
database_cross_reference: VariO:mv

interstitial deletion
type: Class
subclass of: chromosomal deletion
definition: Deletion of chromosomal region not including terminus.
has_obo_namespace: variation_ontology
id: VariO:0194

Axiom
annotated source: interstitial deletion
annotated property: definition
annotated target: Deletion of chromosomal region not including terminus.
database_cross_reference: VariO:mv

terminal deletion
type: Class
subclass of: chromosomal deletion
definition: Deletion of chromosomal region from the end of chromosome arm.
has_obo_namespace: variation_ontology
id: VariO:0195

Axiom
annotated source: terminal deletion
annotated property: definition
annotated target: Deletion of chromosomal region from the end of chromosome arm.
database_cross_reference: VariO:mv

complex chromosomal variation
type: Class
subclass of: chromosome structure variation
definition: Chromosome structure variation with four or more breakpoints.
database_cross_reference: SO:1000146
has_obo_namespace: variation_ontology
id: VariO:0196

Axiom
annotated source: complex chromosomal variation
annotated property: definition
annotated target: Chromosome structure variation with four or more breakpoints.
database_cross_reference: SO:ke
database_cross_reference: VariO:mv

chromosomal translocation
type: Class
subclass of: chromosome structure variation
definition: Translocation of chromosomal region.
database_cross_reference: SO:0000199
has_obo_namespace: variation_ontology
id: VariO:0197

Axiom
annotated source: chromosomal translocation
annotated property: definition
annotated target: Translocation of chromosomal region.
database_cross_reference: VariO:mv

intrachromosomal translocation
type: Class
subclass of: chromosomal translocation
definition: Translocation of chromosomal region within a chromosome.
has_obo_namespace: variation_ontology
id: VariO:0198

Axiom
annotated source: intrachromosomal translocation
annotated property: definition
annotated target: Translocation of chromosomal region within a chromosome.
database_cross_reference: VariO:mv

chromosomal inversion
type: Class
subclass of: intrachromosomal translocation
definition: Intrachromosomal variation where a chromosomal region is inserted in reverse direction.
has_obo_namespace: variation_ontology
id: VariO:0199

Axiom
annotated source: chromosomal inversion
annotated property: definition
annotated target: Intrachromosomal variation where a chromosomal region is inserted in reverse direction.
database_cross_reference: VariO:mv

paracentric inversion
type: Class
subclass of: chromosomal inversion
definition: Chromosomal inversion within a chromosome arm.
database_cross_reference: SO:1000047
has_obo_namespace: variation_ontology
id: VariO:0200

Axiom
annotated source: paracentric inversion
annotated property: definition
annotated target: Chromosomal inversion within a chromosome arm.
database_cross_reference: VariO:mv

pericentric inversion
type: Class
subclass of: chromosomal inversion
definition: Chromosomal inversion including centromere.
database_cross_reference: SO:1000046
has_obo_namespace: variation_ontology
id: VariO:0201

Axiom
annotated source: pericentric inversion
annotated property: definition
annotated target: Chromosomal inversion including centromere.
database_cross_reference: VariO:mv

interchromosomal translocation
type: Class
subclass of: chromosomal translocation
definition: Translocation of chromosomal region to another chromosome.
has_obo_namespace: variation_ontology
id: VariO:0202

Axiom
annotated source: interchromosomal translocation
annotated property: definition
annotated target: Translocation of chromosomal region to another chromosome.
database_cross_reference: VariO:mv

reciprocal chromosomal translocation
type: Class
subclass of: interchromosomal translocation
definition: Switching of chromosomal regions between nonhomologous chromosomes.
database_cross_reference: SO:1000048
has_obo_namespace: variation_ontology
id: VariO:0203

Axiom
annotated source: reciprocal chromosomal translocation
annotated property: definition
annotated target: Switching of chromosomal regions between nonhomologous chromosomes.
database_cross_reference: VariO:mv

Robertsonian translocation
type: Class
subclass of: interchromosomal translocation
definition: Fusion of long arms of two acrocentric chromosomes having very short p arms.
database_cross_reference: SO:1000043
has_obo_namespace: variation_ontology
id: VariO:0204

Axiom
annotated source: Robertsonian translocation
annotated property: definition
annotated target: Fusion of long arms of two acrocentric chromosomes having very short p arms.
database_cross_reference: VariO:mv

dinucleotide expansion
type: Class
subclass of: microsatellite
definition: Tandem repetitive sequence consisting of two nucleotide units.
created by: med-mnv
creation date: 2015-09-17T10:53:06Z
has_obo_namespace: variation_ontology
id: VariO:0205

Axiom
annotated source: dinucleotide expansion
annotated property: definition
annotated target: Tandem repetitive sequence consisting of two nucleotide units.
database_cross_reference: VariO:mv

chromosome number variation
type: Class
subclass of: chromosome variation
definition: Variation affecting the number of chromosomes.
has_exact_synonym: aneuploidy
has_obo_namespace: variation_ontology
id: VariO:0206

Axiom
annotated source: chromosome number variation
annotated property: definition
annotated target: Variation affecting the number of chromosomes.
database_cross_reference: VariO:mv

trisomy
type: Class
subclass of: chromosome number variation
definition: Three copies of a chromosome in a cell or organism.
has_obo_namespace: variation_ontology
id: VariO:0207

Axiom
annotated source: trisomy
annotated property: definition
annotated target: Three copies of a chromosome in a cell or organism.
database_cross_reference: VariO:mv

disomy
type: Class
subclass of: chromosome number variation
definition: Two copies of a chromosome in a cell or organism .
has_obo_namespace: variation_ontology
id: VariO:0208

Axiom
annotated source: disomy
annotated property: definition
annotated target: Two copies of a chromosome in a cell or organism .
database_cross_reference: VariO:mv

uniparental disomy
type: Class
subclass of: disomy
definition: Both copies of a chromosome or a part of it in diploid cell or organism are from one parent.
has_obo_namespace: variation_ontology
id: VariO:0209

Axiom
annotated source: uniparental disomy
annotated property: definition
annotated target: Both copies of a chromosome or a part of it in diploid cell or organism are from one parent.
database_cross_reference: VariO:mv

isodisomy
type: Class
subclass of: disomy
definition: Uniparental disomy with duplication of a single chromosome from one parent.
has_obo_namespace: variation_ontology
id: VariO:0210

Axiom
annotated source: isodisomy
annotated property: definition
annotated target: Uniparental disomy with duplication of a single chromosome from one parent.
database_cross_reference: VariO:mv

heterodisomy
type: Class
subclass of: disomy
definition: Uniparental disomy with both homologous chromosomes from one parent.
has_obo_namespace: variation_ontology
id: VariO:0211

Axiom
annotated source: heterodisomy
annotated property: definition
annotated target: Uniparental disomy with both homologous chromosomes from one parent.
database_cross_reference: VariO:mv

nullisomy
type: Class
subclass of: chromosome number variation
definition: No copies of a chromosome in a cell or organism.
has_obo_namespace: variation_ontology
id: VariO:0212

Axiom
annotated source: nullisomy
annotated property: definition
annotated target: No copies of a chromosome in a cell or organism.
database_cross_reference: VariO:mv

tetrasomy
type: Class
subclass of: chromosome number variation
definition: Four copies of a chromosome in a cell or organism.
has_obo_namespace: variation_ontology
id: VariO:0213

Axiom
annotated source: tetrasomy
annotated property: definition
annotated target: Four copies of a chromosome in a cell or organism.
database_cross_reference: VariO:mv

monosomy
type: Class
subclass of: chromosome number variation
definition: One copy of a chromosome in a cell or organism.
has_obo_namespace: variation_ontology
id: VariO:0214

Axiom
annotated source: monosomy
annotated property: definition
annotated target: One copy of a chromosome in a cell or organism.
database_cross_reference: VariO:mv

chromosome set number variation
type: Class
subclass of: genome variation
definition: Variation affecting number of entire chromosome sets.
has_exact_synonym: euploidy
has_obo_namespace: variation_ontology
id: VariO:0215

Axiom
annotated source: chromosome set number variation
annotated property: definition
annotated target: Variation affecting number of entire chromosome sets.
database_cross_reference: VariO:mv

diploidy
type: Class
subclass of: chromosome set number variation
definition: Variation with two sets of chromosomes.
has_obo_namespace: variation_ontology
id: VariO:0216

Axiom
annotated source: diploidy
annotated property: definition
annotated target: Variation with two sets of chromosomes.
database_cross_reference: VariO:mv

tetraploidy
type: Class
subclass of: chromosome set number variation
definition: Variation with four sets of chromosomes.
created by: Mauno
creation date: 2011-03-04T12:19:35Z
has_obo_namespace: variation_ontology
id: VariO:0217

Axiom
annotated source: tetraploidy
annotated property: definition
annotated target: Variation with four sets of chromosomes.
database_cross_reference: VariO:mv

polyploidy
type: Class
subclass of: chromosome set number variation
definition: Variation with several sets of chromosomes.
has_obo_namespace: variation_ontology
id: VariO:0218

Axiom
annotated source: polyploidy
annotated property: definition
annotated target: Variation with several sets of chromosomes.
database_cross_reference: VariO:mv

autopolyploidy
type: Class
subclass of: polyploidy
definition: Variation with several sets of chromosomes originating from the same organism.
has_obo_namespace: variation_ontology
id: VariO:0219

Axiom
annotated source: autopolyploidy
annotated property: definition
annotated target: Variation with several sets of chromosomes originating from the same organism.
database_cross_reference: VariO:mv

allopolyploidy
type: Class
subclass of: polyploidy
definition: Variation with several sets of chromosomes originating from a different organism.
has_obo_namespace: variation_ontology
id: VariO:0220

Axiom
annotated source: allopolyploidy
annotated property: definition
annotated target: Variation with several sets of chromosomes originating from a different organism.
database_cross_reference: VariO:mv

nulliploidy
type: Class
subclass of: chromosome set number variation
definition: Variation without chromosomes.
has_obo_namespace: variation_ontology
id: VariO:0221

Axiom
annotated source: nulliploidy
annotated property: definition
annotated target: Variation without chromosomes.
database_cross_reference: VariO:mv

triploidy
type: Class
subclass of: chromosome set number variation
definition: Variation with three sets of chromosomes.
has_obo_namespace: variation_ontology
id: VariO:0222

Axiom
annotated source: triploidy
annotated property: definition
annotated target: Variation with three sets of chromosomes.
database_cross_reference: VariO:mv

pentaploidy
type: Class
subclass of: chromosome set number variation
definition: Variation with five sets of chromosomes.
has_obo_namespace: variation_ontology
id: VariO:0223

Axiom
annotated source: pentaploidy
annotated property: definition
annotated target: Variation with five sets of chromosomes.
database_cross_reference: VariO:mv

hexaploidy
type: Class
subclass of: chromosome set number variation
definition: Variation with six sets of chromosomes.
has_obo_namespace: variation_ontology
id: VariO:0224

Axiom
annotated source: hexaploidy
annotated property: definition
annotated target: Variation with six sets of chromosomes.
database_cross_reference: VariO:mv

monoploidy
type: Class
subclass of: chromosome set number variation
definition: Variation with a single set of chromosomes.
has_exact_synonym: haploidy
has_obo_namespace: variation_ontology
id: VariO:0225

Axiom
annotated source: monoploidy
annotated property: definition
annotated target: Variation with a single set of chromosomes.
database_cross_reference: VariO:mv

chromatin structure variation
type: Class
subclass of: variation affecting DNA structure
definition: Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins.
has_obo_namespace: variation_ontology
id: VariO:0226

Axiom
annotated source: chromatin structure variation
annotated property: definition
annotated target: Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins.
database_cross_reference: VariO:mv

variation affecting DNA property
type: Class
subclass of: variation affecting DNA
definition: Variation affecting characteristic property of DNA.
has_obo_namespace: variation_ontology
id: VariO:0227

Axiom
annotated source: variation affecting DNA property
annotated property: definition
annotated target: Variation affecting characteristic property of DNA.
database_cross_reference: VariO:mv

protein fusion
type: Class
subclass of: protein elongation
definition: Fusion of two protein chains. Produced from fusion gene of two joined genes.
created by: Mauno Vihnen
creation date: 2012-12-11T08:59:44Z
has_obo_namespace: variation_ontology
id: VariO:0228

Axiom
annotated source: protein fusion
annotated property: definition
annotated target: Fusion of two protein chains. Produced from fusion gene of two joined genes.
database_cross_reference: VariO:mv

association of DNA variation to pathogenicity
type: Class
subclass of: variation affecting DNA property
definition: Implication of a DNA variant to pathogenicity.
has_obo_namespace: variation_ontology
id: VariO:0229

Axiom
annotated source: association of DNA variation to pathogenicity
annotated property: definition
annotated target: Implication of a DNA variant to pathogenicity.
database_cross_reference: VariO:mv

effect on DNA interaction
type: Class
subclass of: variation affecting DNA property
definition: Variation affecting interaction of DNA with its partner.
has_obo_namespace: variation_ontology
id: VariO:0230

Axiom
annotated source: effect on DNA interaction
annotated property: definition
annotated target: Variation affecting interaction of DNA with its partner.
database_cross_reference: VariO:mv

conservation of DNA variation site
type: Class
subclass of: variation affecting DNA property
definition: Conservation of the variation site in related DNA sequences.
has_obo_namespace: variation_ontology
id: VariO:0231

Axiom
annotated source: conservation of DNA variation site
annotated property: definition
annotated target: Conservation of the variation site in related DNA sequences.
database_cross_reference: VariO:mv

variation attribute
type: Class
subclass of: variation
definition: Attributes define and modulate terms at other levels.
has_obo_namespace: variation_ontology
id: VariO:0232

Axiom
annotated source: variation attribute
annotated property: definition
annotated target: Attributes define and modulate terms at other levels.
database_cross_reference: VariO:mv

conservation
type: Class
subclass of: variation attribute
definition: Sequence conservation attribute.
has_obo_namespace: variation_ontology
id: VariO:0233

Axiom
annotated source: conservation
annotated property: definition
annotated target: Sequence conservation attribute.
database_cross_reference: VariO:mv

conserved region
type: Class
subclass of: conservation
definition: Variation at a region of sequence similarity in multiple sequence alignment of related sequences.
has_obo_namespace: variation_ontology
id: VariO:0234

Axiom
annotated source: conserved region
annotated property: definition
annotated target: Variation at a region of sequence similarity in multiple sequence alignment of related sequences.
database_cross_reference: VariO:mv

invariant region
type: Class
subclass of: conservation
definition: Variation at invariant sequence region in multiple sequence alignment of related sequences.
has_obo_namespace: variation_ontology
id: VariO:0235

Axiom
annotated source: invariant region
annotated property: definition
annotated target: Variation at invariant sequence region in multiple sequence alignment of related sequences.
database_cross_reference: VariO:mv

interaction
type: Class
subclass of: variation attribute
definition: Mutual or reciprocal action or influence that happens at a given place and time between participating molecules.
has_obo_namespace: variation_ontology
id: VariO:0236

Axiom
annotated source: interaction
annotated property: definition
annotated target: Mutual or reciprocal action or influence that happens at a given place and time between participating molecules.
database_cross_reference: VariO:mv
database_cross_reference: src_code:NR

genetic interaction
type: Class
subclass of: interaction
definition: Two genes A and B "genetically interact" when the phenotype generated as the result of variations in both genes (double variant ab) is unexpectedly not just a combination of the phenotypes of the two single variants a and b.
database_cross_reference: MI:0208
has_obo_namespace: variation_ontology
id: VariO:0237

Axiom
annotated source: genetic interaction
annotated property: definition
annotated target: Two genes A and B "genetically interact" when the phenotype generated as the result of variations in both genes (double variant ab) is unexpectedly not just a combination of the phenotypes of the two single variants a and b.
database_cross_reference: PMID:16527956
database_cross_reference: VariO:mv

genetic interaction defined by inequality
type: Class
subclass of: genetic interaction
definition: Two genes A and B present a genetic interaction defined by inequality if the phenotypes of the two single variants a and b, the double variant ab and the wild-type can be measured quantitatively and described relative to each other by an inequality relationship.
database_cross_reference: MI:0931
has_exact_synonym: genetic inequality
has_obo_namespace: variation_ontology
id: VariO:0238

Axiom
annotated source: genetic interaction defined by inequality
annotated property: definition
annotated target: Two genes A and B present a genetic interaction defined by inequality if the phenotypes of the two single variants a and b, the double variant ab and the wild-type can be measured quantitatively and described relative to each other by an inequality relationship.
database_cross_reference: PMID:14755292
database_cross_reference: VariO:mv

Axiom
annotated source: genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: genetic inequality
database_cross_reference: MI:0931

single nonmonotonic genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
definition: The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g. WT > a > ab > b.
database_cross_reference: MI:0800
has_exact_synonym: single nonmonotonic
has_exact_synonym: single nonmonotonic genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0239

Axiom
annotated source: single nonmonotonic genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g. WT > a > ab > b.
database_cross_reference: PMID:15833125

Axiom
annotated source: single nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: single nonmonotonic
database_cross_reference: MI:0800

Axiom
annotated source: single nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: single nonmonotonic genetic interaction (sensu inequality)
database_cross_reference: MI:0800

missing protein
type: Class
subclass of: protein variation classification
definition: Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism.
created by: Mauno Vihnen
creation date: 2012-12-11T13:07:02Z
has_obo_namespace: variation_ontology
id: VariO:0240

Axiom
annotated source: missing protein
annotated property: definition
annotated target: Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism.
database_cross_reference: VariO:mv

RNA translocation
type: Class
subclass of: RNA variation classification
definition: A continuous stretch of RNA sequence moved to a new position.
created by: Mauno Vihnen
creation date: 2012-12-18T16:17:33Z
has_obo_namespace: variation_ontology
id: VariO:0241

Axiom
annotated source: RNA translocation
annotated property: definition
annotated target: A continuous stretch of RNA sequence moved to a new position.
database_cross_reference: VariO:mv

conditional genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
definition: The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b variant has an effect only in the a background. A has an effect only in the b background, or the b variant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
database_cross_reference: MI:0798
has_exact_synonym: conditional
has_exact_synonym: conditional genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0242

Axiom
annotated source: conditional genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b variant has an effect only in the a background. A has an effect only in the b background, or the b variant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
database_cross_reference: PMID:15833125
database_cross_reference: VariO:mv

Axiom
annotated source: conditional genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: conditional
database_cross_reference: MI:0798

Axiom
annotated source: conditional genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: conditional genetic interaction (sensu inequality)
database_cross_reference: MI:0798

additive genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
definition: Single-variant phenotype effects combine to give a double-variant effect different from the wild type and different from single variant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
database_cross_reference: MI:0799
has_exact_synonym: additive
has_exact_synonym: additive genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0243

Axiom
annotated source: additive genetic interaction defined by inequality
annotated property: definition
annotated target: Single-variant phenotype effects combine to give a double-variant effect different from the wild type and different from single variant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
database_cross_reference: PMID:15833125
database_cross_reference: VariO:mv

Axiom
annotated source: additive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: additive
database_cross_reference: MI:0799

Axiom
annotated source: additive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: additive genetic interaction (sensu inequality)
database_cross_reference: MI:0799

RNA inversion
type: Class
subclass of: RNA translocation
definition: A continuous stretch of RNA sequence inserted to the same position in reverse orientation.
created by: Mauno Vihnen
creation date: 2012-12-18T16:17:33Z
has_obo_namespace: variation_ontology
id: VariO:0244

Axiom
annotated source: RNA inversion
annotated property: definition
annotated target: A continuous stretch of RNA sequence inserted to the same position in reverse orientation.
database_cross_reference: VriO:mv

missing RNA
type: Class
subclass of: RNA variation classification
definition: Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site.
created by: Mauno Vihnen
creation date: 2013-01-04T09:23:09Z
has_obo_namespace: variation_ontology
id: VariO:0245

Axiom
annotated source: missing RNA
annotated property: definition
annotated target: Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site.
database_cross_reference: VariO:mv

artificial protein variation
type: Class
subclass of: variation emerging at protein level
definition: Protein variation generated on purpose.
created by: gerard
creation date: 2013-02-01T11:24:30Z
has_obo_namespace: variation_ontology
id: VariO:0246

Axiom
annotated source: artificial protein variation
annotated property: definition
annotated target: Protein variation generated on purpose.
database_cross_reference: VariO:mv

artificial RNA variation
type: Class
subclass of: RNA variation of non-genetic origin
definition: RNA variation generated on purpose.
created by: gerard
creation date: 2013-02-01T11:27:07Z
has_obo_namespace: variation_ontology
id: VariO:0247

Axiom
annotated source: artificial RNA variation
annotated property: definition
annotated target: RNA variation generated on purpose.
database_cross_reference: VariO:mv

positive genetic interaction
type: Class
subclass of: genetic interaction
definition: The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b.
database_cross_reference: MI:0935
has_exact_synonym: positive gent int
has_obo_namespace: variation_ontology
id: VariO:0248

Axiom
annotated source: positive genetic interaction
annotated property: definition
annotated target: The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b.
database_cross_reference: PMID:14755292
database_cross_reference: VariO:mv

Axiom
annotated source: positive genetic interaction
annotated property: has_exact_synonym
annotated target: positive gent int
database_cross_reference: MI:0935

double nonmonotonic genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
subclass of: positive genetic interaction
definition: The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other variant gene. E.g. WT >= ab > a >= b.
database_cross_reference: MI:0801
has_exact_synonym: double nonmonotonic
has_exact_synonym: double nonmonotonic genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0249

Axiom
annotated source: double nonmonotonic genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other variant gene. E.g. WT >= ab > a >= b.
database_cross_reference: PMID:15833125
database_cross_reference: VariO:mv

Axiom
annotated source: double nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: double nonmonotonic
database_cross_reference: MI:0801

Axiom
annotated source: double nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: double nonmonotonic genetic interaction (sensu inequality)
database_cross_reference: MI:0801

epistatic genetic interaction
type: Class
subclass of: positive genetic interaction
definition: The genetic interaction between a group of genes, in which the effects of an allele of one member gene of the group hide the effects of alleles of other genes in the group.
database_cross_reference: MI:0930
has_exact_synonym: epistatis
has_obo_namespace: variation_ontology
id: VariO:0250

Axiom
annotated source: epistatic genetic interaction
annotated property: definition
annotated target: The genetic interaction between a group of genes, in which the effects of an allele of one member gene of the group hide the effects of alleles of other genes in the group.
database_cross_reference: PMID:11988766

Axiom
annotated source: epistatic genetic interaction
annotated property: has_exact_synonym
annotated target: epistatis
database_cross_reference: MI:0930

epistatic genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
subclass of: epistatic genetic interaction
definition: The phenotype resulting from genetic perturbation of A and B have different effects (in terms of direction or magnitude) on the wild-type background and the double variant has the same phenotype as either A or B (for example, A < WT < B = AB).
database_cross_reference: MI:0797
has_exact_synonym: epistatic
has_exact_synonym: epistatic genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0251

Axiom
annotated source: epistatic genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of A and B have different effects (in terms of direction or magnitude) on the wild-type background and the double variant has the same phenotype as either A or B (for example, A < WT < B = AB).
database_cross_reference: PMID:15833125
database_cross_reference: VariO:mv

Axiom
annotated source: epistatic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: epistatic
database_cross_reference: MI:0797

Axiom
annotated source: epistatic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: epistatic genetic interaction (sensu inequality)
database_cross_reference: MI:0797

asynthetic genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
subclass of: epistatic genetic interaction
definition: The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. E. g., WT > a = b = ab.
database_cross_reference: MI:0795
has_exact_synonym: asynthetic
has_exact_synonym: asynthetic genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0252

Axiom
annotated source: asynthetic genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. E. g., WT > a = b = ab.
database_cross_reference: PMID:15833125

Axiom
annotated source: asynthetic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: asynthetic
database_cross_reference: MI:0795

Axiom
annotated source: asynthetic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: asynthetic genetic interaction (sensu inequality)
database_cross_reference: MI:0795

suppressive genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
subclass of: epistatic genetic interaction
definition: The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor b, which itself shows no single-variant effect. E. g., WT = b = ab > a.
database_cross_reference: MI:0796
has_exact_synonym: suppression
has_exact_synonym: suppressive genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0253

Axiom
annotated source: suppressive genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor b, which itself shows no single-variant effect. E. g., WT = b = ab > a.
database_cross_reference: PMID:15833125
database_cross_reference: VariO:mv

Axiom
annotated source: suppressive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: suppression
database_cross_reference: MI:0796

Axiom
annotated source: suppressive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: suppressive genetic interaction (sensu inequality)
database_cross_reference: MI:0796

neutral genetic interaction
type: Class
subclass of: genetic interaction
definition: The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b.
database_cross_reference: MI:0934
has_exact_synonym: neutral gent int
has_obo_namespace: variation_ontology
id: VariO:0254

Axiom
annotated source: neutral genetic interaction
annotated property: definition
annotated target: The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b.
database_cross_reference: PMID:14755292
database_cross_reference: VariO:mv

Axiom
annotated source: neutral genetic interaction
annotated property: has_exact_synonym
annotated target: neutral gent int
database_cross_reference: MI:0934

noninteractive genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
subclass of: neutral genetic interaction
definition: Variation that has no effect in the WT and b backgrounds, or b has no effect in the a and WT backgrounds, or both hold true. E. g., WT = a > b = ab.
database_cross_reference: MI:0932
has_exact_synonym: noninteractive
has_exact_synonym: noninteractive genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0255

Axiom
annotated source: noninteractive genetic interaction defined by inequality
annotated property: definition
annotated target: Variation that has no effect in the WT and b backgrounds, or b has no effect in the a and WT backgrounds, or both hold true. E. g., WT = a > b = ab.
database_cross_reference: PMID:15833125
database_cross_reference: VariO:mv

Axiom
annotated source: noninteractive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: noninteractive
database_cross_reference: MI:0932

Axiom
annotated source: noninteractive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: noninteractive genetic interaction (sensu inequality)
database_cross_reference: MI:0932

negative genetic interaction
type: Class
subclass of: genetic interaction
definition: The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b.
database_cross_reference: MI:0933
has_exact_synonym: negative gen int
has_obo_namespace: variation_ontology
id: VariO:0256

Axiom
annotated source: negative genetic interaction
annotated property: definition
annotated target: The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b.
database_cross_reference: PMID:14755292
database_cross_reference: VariO:mv

Axiom
annotated source: negative genetic interaction
annotated property: has_exact_synonym
annotated target: negative gen int
database_cross_reference: MI:0933

synthetic genetic interaction defined by inequality
type: Class
subclass of: genetic interaction defined by inequality
subclass of: negative genetic interaction
definition: The phenotype resulting from genetic perturbation a and the phenotype resulting from genetic perturbation b have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. E. g., WT = a = b > ab.
database_cross_reference: MI:0794
has_exact_synonym: synthetic
has_exact_synonym: synthetic genetic interaction (sensu inequality)
has_obo_namespace: variation_ontology
id: VariO:0257

Axiom
annotated source: synthetic genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation a and the phenotype resulting from genetic perturbation b have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. E. g., WT = a = b > ab.
database_cross_reference: PMID:15833125

Axiom
annotated source: synthetic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: synthetic
database_cross_reference: MI:0794

Axiom
annotated source: synthetic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: synthetic genetic interaction (sensu inequality)
database_cross_reference: MI:0794

structural level of interaction
type: Class
subclass of: interaction
definition: Molecular structural level of interaction.
has_obo_namespace: variation_ontology
id: VariO:0258

Axiom
annotated source: structural level of interaction
annotated property: definition
annotated target: Molecular structural level of interaction.
database_cross_reference: VariO:mv

intermolecular interaction
type: Class
subclass of: structural level of interaction
definition: Interaction between molecules.
has_obo_namespace: variation_ontology
id: VariO:0259

Axiom
annotated source: intermolecular interaction
annotated property: definition
annotated target: Interaction between molecules.
database_cross_reference: VariO:mv

intramolecular interaction
type: Class
subclass of: structural level of interaction
definition: Interaction within a molecule.
has_obo_namespace: variation_ontology
id: VariO:0260

Axiom
annotated source: intramolecular interaction
annotated property: definition
annotated target: Interaction within a molecule.
database_cross_reference: VariO:mv

colocalization
type: Class
subclass of: interaction
definition: Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
database_cross_reference: MI:0403
has_obo_namespace: variation_ontology
id: VariO:0261

Axiom
annotated source: colocalization
annotated property: definition
annotated target: Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
database_cross_reference: PMID:14755292

interactor
type: Class
subclass of: interaction
definition: Entity participating in a physical or functional interaction.
database_cross_reference: SBO:0000336
has_obo_namespace: variation_ontology
id: VariO:0262

Axiom
annotated source: interactor
annotated property: definition
annotated target: Entity participating in a physical or functional interaction.
database_cross_reference: SBO:0000336

small molecule
type: Class
subclass of: interactor
definition: Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
database_cross_reference: MI:0328
has_obo_namespace: variation_ontology
id: VariO:0263

Axiom
annotated source: small molecule
annotated property: definition
annotated target: Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
database_cross_reference: PMID:14755292

metal
type: Class
subclass of: small molecule
definition: Metal atom.
database_cross_reference: CHEBI:33521
has_obo_namespace: variation_ontology
id: VariO:0264

Axiom
annotated source: metal
annotated property: definition
annotated target: Metal atom.
database_cross_reference: CHEBI:33521

solvent
type: Class
subclass of: small molecule
definition: A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
database_cross_reference: CHEBI:46787
has_obo_namespace: variation_ontology
id: VariO:0265

Axiom
annotated source: solvent
annotated property: definition
annotated target: A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
database_cross_reference: CHEBI:46787

water
type: Class
subclass of: solvent
definition: An inorganic hydroxy compound that has formula H2O.
database_cross_reference: CHEBI:15377
has_obo_namespace: variation_ontology
id: VariO:0266

Axiom
annotated source: water
annotated property: definition
annotated target: An inorganic hydroxy compound that has formula H2O.
database_cross_reference: CHEBI:15377

complex
type: Class
subclass of: interactor
definition: Set of interacting molecules that can be copurified.
database_cross_reference: MI:0314
has_obo_namespace: variation_ontology
id: VariO:0267

Axiom
annotated source: complex
annotated property: definition
annotated target: Set of interacting molecules that can be copurified.
database_cross_reference: PMID:14755292

ribonucleoprotein complex
type: Class
subclass of: complex
definition: A macromolecular complex containing both protein and RNA molecules.
database_cross_reference: MI:0316
has_exact_synonym: ribonucleoprot compl
has_obo_namespace: variation_ontology
id: VariO:0268

Axiom
annotated source: ribonucleoprotein complex
annotated property: definition
annotated target: A macromolecular complex containing both protein and RNA molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: ribonucleoprotein complex
annotated property: has_exact_synonym
annotated target: ribonucleoprot compl
database_cross_reference: MI:0316

protein complex
type: Class
subclass of: complex
definition: A stable set of interacting proteins that can be copurified and operate as a functional unit.
database_cross_reference: GO:0043234
database_cross_reference: MI:0315
has_exact_synonym: protein-protein complex
has_obo_namespace: variation_ontology
id: VariO:0269

Axiom
annotated source: protein complex
annotated property: definition
annotated target: A stable set of interacting proteins that can be copurified and operate as a functional unit.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein complex
annotated property: has_exact_synonym
annotated target: protein-protein complex
database_cross_reference: GO:0043234

protein dna complex
type: Class
subclass of: complex
definition: A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
database_cross_reference: MI:0233
has_obo_namespace: variation_ontology
id: VariO:0270

Axiom
annotated source: protein dna complex
annotated property: definition
annotated target: A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
database_cross_reference: PMID:14755292

unknown participant
type: Class
subclass of: interactor
definition: Any type of molecule, including complexes, that may be observed but not identified.
database_cross_reference: MI:0329
has_obo_namespace: variation_ontology
id: VariO:0271

Axiom
annotated source: unknown participant
annotated property: definition
annotated target: Any type of molecule, including complexes, that may be observed but not identified.
database_cross_reference: PMID:14755292

gene
type: Class
subclass of: interactor
definition: Interactor of genetic interaction.
database_cross_reference: MI:0250
has_obo_namespace: variation_ontology
id: VariO:0272

Axiom
annotated source: gene
annotated property: definition
annotated target: Interactor of genetic interaction.
database_cross_reference: MI:0000704

biopolymer
type: Class
subclass of: interactor
definition: Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
database_cross_reference: MI:0383
has_obo_namespace: variation_ontology
id: VariO:0273

Axiom
annotated source: biopolymer
annotated property: definition
annotated target: Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
database_cross_reference: PMID:14577292

nucleic acid
type: Class
subclass of: biopolymer
definition: Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages.
database_cross_reference: GO:0005561
database_cross_reference: MI:0318
has_obo_namespace: variation_ontology
id: VariO:0274

Axiom
annotated source: nucleic acid
annotated property: definition
annotated target: Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages.
database_cross_reference: PMID:14755292

peptide
type: Class
subclass of: biopolymer
definition: Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
database_cross_reference: MI:0327
has_exact_synonym: oligopeptide
has_exact_synonym: polypeptide
has_obo_namespace: variation_ontology
id: VariO:0275

Axiom
annotated source: peptide
annotated property: definition
annotated target: Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
database_cross_reference: PMID:14755292

Axiom
annotated source: peptide
annotated property: has_exact_synonym
annotated target: oligopeptide
database_cross_reference: MI:0327

Axiom
annotated source: peptide
annotated property: has_exact_synonym
annotated target: polypeptide
database_cross_reference: MI:0327

polysaccharide
type: Class
subclass of: biopolymer
definition: A polysaccharide is a complex polymer of carbohydrate monomers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
database_cross_reference: MI:0904
has_obo_namespace: variation_ontology
id: VariO:0276

Axiom
annotated source: polysaccharide
annotated property: definition
annotated target: A polysaccharide is a complex polymer of carbohydrate monomers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
database_cross_reference: PMID:14755292

protein
type: Class
subclass of: biopolymer
definition: A linear polymer of amino acids joined by peptide bonds in a specific sequence.
database_cross_reference: GO:0003675
database_cross_reference: MI:0326
has_obo_namespace: variation_ontology
id: VariO:0277

Axiom
annotated source: protein
annotated property: definition
annotated target: A linear polymer of amino acids joined by peptide bonds in a specific sequence.
database_cross_reference: PMID:14755292

association
type: Class
subclass of: interaction
definition: Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule.
database_cross_reference: MI:0914
has_obo_namespace: variation_ontology
id: VariO:0278

Axiom
annotated source: association
annotated property: definition
annotated target: Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule.
database_cross_reference: PMID:14755292

interaction physical force
type: Class
subclass of: interaction
definition: Interaction physical force.
has_obo_namespace: variation_ontology
id: VariO:0279

Axiom
annotated source: interaction physical force
annotated property: definition
annotated target: Interaction physical force.
database_cross_reference: VariO:mv

covalent bond
type: Class
subclass of: interaction physical force
definition: A chemical link between two atoms in which electrons are shared between them.
has_obo_namespace: variation_ontology
id: VariO:0280

Axiom
annotated source: covalent bond
annotated property: definition
annotated target: A chemical link between two atoms in which electrons are shared between them.
database_cross_reference: http://chemistry.about.com/od/chemistryglossary/a/covalentbonddef.htm

disulphide bridge
type: Class
subclass of: covalent bond
definition: The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain.
database_cross_reference: SO:0001088
has_obo_namespace: variation_ontology
id: VariO:0281

Axiom
annotated source: disulphide bridge
annotated property: definition
annotated target: The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual
database_cross_reference: VariO:mv

non covalent bond
type: Class
subclass of: interaction physical force
definition: Interaction between biochemical entities that results in the formation of a non-covalent bond.
database_cross_reference: SBO:0000177
has_obo_namespace: variation_ontology
id: VariO:0282

Axiom
annotated source: non covalent bond
annotated property: definition
annotated target: Interaction between biochemical entities that results in the formation of a non-covalent bond.
database_cross_reference: VariO:mv

hydrogen bond
type: Class
subclass of: non covalent bond
definition: Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom.
database_cross_reference: FIX:0000503
database_cross_reference: http://chemistry.about.com/od/chemistryglossary/g/hbond.htm
has_obo_namespace: variation_ontology
has_related_synonym: H-bond
id: VariO:0283

Axiom
annotated source: hydrogen bond
annotated property: definition
annotated target: Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom.
database_cross_reference: VariO:mv

Axiom
annotated source: hydrogen bond
annotated property: has_related_synonym
annotated target: H-bond
database_cross_reference: FIX:0000503

hydrogen bond network
type: Class
subclass of: hydrogen bond
definition: Network of interactions formed by several hydrogen bonds.
has_obo_namespace: variation_ontology
id: VariO:0284

Axiom
annotated source: hydrogen bond network
annotated property: definition
annotated target: Network of interactions formed by several hydrogen bonds.
database_cross_reference: VariO:mv

hydrophobic interaction
type: Class
subclass of: non covalent bond
definition: Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction.
has_obo_namespace: variation_ontology
id: VariO:0285

Axiom
annotated source: hydrophobic interaction
annotated property: definition
annotated target: Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction.
database_cross_reference: http://medical-dictionary.thefreedictionary.com/Hydrophobic+Interaction

salt bridge
type: Class
subclass of: non covalent bond
definition: Interaction between charged groups.
has_obo_namespace: variation_ontology
id: VariO:0286

Axiom
annotated source: salt bridge
annotated property: definition
annotated target: Interaction between charged groups.
database_cross_reference: VariO:mv

van der Waals interaction
type: Class
subclass of: non covalent bond
definition: Weak attractive electrical force between neutral groups or molecules.
database_cross_reference: FIX:0000506
has_obo_namespace: variation_ontology
id: VariO:0287

Axiom
annotated source: van der Waals interaction
annotated property: definition
annotated target: Weak attractive electrical force between neutral groups or molecules.
database_cross_reference: VariO:mv

electrostatic interaction
type: Class
subclass of: non covalent bond
definition: Attraction between two electrically charged groups or molecules.
has_obo_namespace: variation_ontology
id: VariO:0288

Axiom
annotated source: electrostatic interaction
annotated property: definition
annotated target: Attraction between two electrically charged groups or molecules.
database_cross_reference: VariO:mv

quantity change
type: Class
subclass of: variation attribute
definition: Quantity attribute.
has_obo_namespace: variation_ontology
id: VariO:0289

Axiom
annotated source: quantity change
annotated property: definition
annotated target: Quantity attribute.
database_cross_reference: VariO:mv

decreased
type: Class
subclass of: quantity change
definition: The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.).
database_cross_reference: APO:0000003
has_obo_namespace: variation_ontology
id: VariO:0290

Axiom
annotated source: decreased
annotated property: definition
annotated target: The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.).
database_cross_reference: SGD:curators

increased
type: Class
subclass of: quantity change
definition: The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.).
database_cross_reference: APO:0000004
has_obo_namespace: variation_ontology
id: VariO:0291

Axiom
annotated source: increased
annotated property: definition
annotated target: The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.).
database_cross_reference: SGD:curators

missing
type: Class
subclass of: quantity change
definition: The observed feature is missing compared to that in the wild type.
has_obo_namespace: variation_ontology
id: VariO:0292

Axiom
annotated source: missing
annotated property: definition
annotated target: The observed feature is missing compared to that in the wild type.
database_cross_reference: VariO:mv

pathogenicity association
type: Class
subclass of: variation attribute
definition: Pathogenicity attribute.
has_obo_namespace: variation_ontology
id: VariO:0293

Axiom
annotated source: pathogenicity association
annotated property: definition
annotated target: Pathogenicity attribute.
database_cross_reference: VariO:mv

disease causing
type: Class
subclass of: pathogenicity association
definition: Variation is causative of disease.
has_obo_namespace: variation_ontology
id: VariO:0294

Axiom
annotated source: disease causing
annotated property: definition
annotated target: Variation is causative of disease.
database_cross_reference: VariO:mv

not related to clinical phenotype
type: Class
subclass of: pathogenicity association
definition: Variation is not related to clinical phenotype.
has_obo_namespace: variation_ontology
id: VariO:0295

Axiom
annotated source: not related to clinical phenotype
annotated property: definition
annotated target: Variation is not related to clinical phenotype.
database_cross_reference: VariO:mv

disease associated
type: Class
subclass of: pathogenicity association
definition: Variation is disease related.
has_obo_namespace: variation_ontology
id: VariO:0296

Axiom
annotated source: disease associated
annotated property: definition
annotated target: Variation is disease related.
database_cross_reference: VariO:mv

variation affecting RNA
type: Class
subclass of: variation
definition: Effects of a variation on RNA level.
has_obo_namespace: variation_ontology
id: VariO:0297

Axiom
annotated source: variation affecting RNA
annotated property: definition
annotated target: Effects of a variation on RNA level.
database_cross_reference: VariO:mv

variation affecting RNA property
type: Class
subclass of: variation affecting RNA
definition: Variation affecting characteristic property of RNA.
has_obo_namespace: variation_ontology
id: VariO:0298

Axiom
annotated source: variation affecting RNA property
annotated property: definition
annotated target: Variation affecting characteristic property of RNA.
database_cross_reference: VariO:mv

effect on RNA degradation
type: Class
subclass of: variation affecting RNA property
definition: Variation affecting degradation of RNA.
has_obo_namespace: variation_ontology
id: VariO:0299

Axiom
annotated source: effect on RNA degradation
annotated property: definition
annotated target: Variation affecting degradation of RNA.
database_cross_reference: VariO:mv

effect on RNA folding
type: Class
subclass of: variation affecting RNA property
definition: Variation affecting folding of RNA.
has_obo_namespace: variation_ontology
id: VariO:0300

Axiom
annotated source: effect on RNA folding
annotated property: definition
annotated target: Variation affecting folding of RNA.
database_cross_reference: VariO:mv

effect on RNA stability
type: Class
subclass of: variation affecting RNA property
definition: Variation affecting stability of transcript.
database_cross_reference: SO:0001546
has_obo_namespace: variation_ontology
id: VariO:0301

Axiom
annotated source: effect on RNA stability
annotated property: definition
annotated target: Variation affecting stability of transcript.
database_cross_reference: VariO:mv

conservation of RNA variation site
type: Class
subclass of: variation affecting RNA property
definition: Conservation of the variation site in related RNA sequences.
has_obo_namespace: variation_ontology
id: VariO:0302

Axiom
annotated source: conservation of RNA variation site
annotated property: definition
annotated target: Conservation of the variation site in related RNA sequences.
database_cross_reference: VariO:mv

polysomy
type: Class
subclass of: chromosome number variation
definition: An excess of a particular chromosome in a cell or organism.
created by: gerard
creation date: 2013-02-01T11:30:39Z
has_obo_namespace: variation_ontology
id: VariO:0303

Axiom
annotated source: polysomy
annotated property: definition
annotated target: An excess of a particular chromosome in a cell or organism.
database_cross_reference: VariO:mv

association of RNA variation to pathogenicity
type: Class
subclass of: variation affecting RNA property
definition: Implication of an RNA variant to pathogenicity.
has_obo_namespace: variation_ontology
id: VariO:0304

Axiom
annotated source: association of RNA variation to pathogenicity
annotated property: definition
annotated target: Implication of an RNA variant to pathogenicity.
database_cross_reference: VariO:mv

effect on RNA interaction
type: Class
subclass of: variation affecting RNA property
definition: Variation affecting interaction of RNA with its partner.
has_obo_namespace: variation_ontology
id: VariO:0305

Axiom
annotated source: effect on RNA interaction
annotated property: definition
annotated target: Variation affecting interaction of RNA with its partner.
database_cross_reference: VariO:mv

RNA variation type
type: Class
subclass of: variation affecting RNA
definition: Type of RNA variation. Describes origin and classification of a variant.
has_obo_namespace: variation_ontology
id: VariO:0306

Axiom
annotated source: RNA variation type
annotated property: definition
annotated target: Type of RNA variation. Describes origin and classification of a variant.
database_cross_reference: VariO:mv

RNA variation of genetic origin
type: Class
subclass of: RNA variation origin
definition: RNA variation that has genetic origin.
has_obo_namespace: variation_ontology
id: VariO:0307

Axiom
annotated source: RNA variation of genetic origin
annotated property: definition
annotated target: RNA variation that has genetic origin.
database_cross_reference: VariO:mv

missense variation
type: Class
subclass of: RNA substitution
definition: Nucleotide change in the mRNA triplet codon codes for another amino acid.
has_obo_namespace: variation_ontology
id: VariO:0308

Axiom
annotated source: missense variation
annotated property: definition
annotated target: Nucleotide change in the mRNA triplet codon codes for another amino acid.
database_cross_reference: VariO:mv

termination codon change
type: Class
subclass of: RNA variation classification
definition: RNA nucleotide change in termination codon.
database_cross_reference: SO:0001590
has_obo_namespace: variation_ontology
id: VariO:0309

Axiom
annotated source: termination codon change
annotated property: definition
annotated target: RNA nucleotide change in termination codon.
database_cross_reference: VariO:mv

nonsense variation
type: Class
subclass of: RNA substitution
definition: Nucleotide change in the mRNA codon triplet creates a terminator codon.
has_obo_namespace: variation_ontology
id: VariO:0310

Axiom
annotated source: nonsense variation
annotated property: definition
annotated target: Nucleotide change in the mRNA codon triplet creates a terminator codon.
database_cross_reference: VariO:mv

RNA indel
type: Class
subclass of: RNA variation classification
definition: A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s).
has_obo_namespace: variation_ontology
id: VariO:0311

Axiom
annotated source: RNA indel
annotated property: definition
annotated target: A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s).
database_cross_reference: VariO:mv

RNA substitution
type: Class
subclass of: RNA variation classification
definition: Substitution of RNA nucleotide.
has_obo_namespace: variation_ontology
id: VariO:0312

Axiom
annotated source: RNA substitution
annotated property: definition
annotated target: Substitution of RNA nucleotide.
database_cross_reference: VariO:mv

transition
type: Class
subclass of: Restriction
  on property: part_of
  some values from: DNA substitution
subclass of: Restriction
  on property: part_of
  some values from: RNA substitution
definition: Change of a pyrimidine nucleotide, C or T (or U), into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.
has_obo_namespace: variation_ontology
id: VariO:0313

Axiom
annotated source: transition
annotated property: definition
annotated target: Change of a pyrimidine nucleotide, C or T (or U), into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.
database_cross_reference: VariO:mv

pyrimidine transition
type: Class
subclass of: transition
definition: A substitution of a pyrimidine, C or T (or U), for another pyrimidine.
has_obo_namespace: variation_ontology
id: VariO:0314

Axiom
annotated source: pyrimidine transition
annotated property: definition
annotated target: A substitution of a pyrimidine, C or T (or U), for another pyrimidine.
database_cross_reference: VariO:mv

purine transition
type: Class
subclass of: transition
definition: A substitution of a purine, A or G, for another purine.
has_obo_namespace: variation_ontology
id: VariO:0315

Axiom
annotated source: purine transition
annotated property: definition
annotated target: A substitution of a purine, A or G, for another purine.
database_cross_reference: VariO:mv

transversion
type: Class
subclass of: Restriction
  on property: part_of
  some values from: DNA substitution
subclass of: Restriction
  on property: part_of
  some values from: RNA substitution
definition: Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa.
database_cross_reference: http://en.wikipedia.org/wiki/Transversion
has_obo_namespace: variation_ontology
id: VariO:0316

Axiom
annotated source: transversion
annotated property: definition
annotated target: Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa.
database_cross_reference: VariO:mv

wiki
type: Axiom
annotated source: transversion
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Transversion

initiation codon change
type: Class
subclass of: RNA variation classification
definition: RNA nucleotide change in the initiation codon.
database_cross_reference: SO:0001582
has_obo_namespace: variation_ontology
id: VariO:0317

Axiom
annotated source: initiation codon change
annotated property: definition
annotated target: RNA nucleotide change in the initiation codon.
database_cross_reference: VariO:mv

silent variation
type: Class
subclass of: RNA substitution
definition: RNA variation that does not change the encoded amino acid.
has_obo_namespace: variation_ontology
id: VariO:0318

Axiom
annotated source: silent variation
annotated property: definition
annotated target: RNA variation that does not change the encoded amino acid.
database_cross_reference: VariO:mv

RNA deletion
type: Class
subclass of: RNA variation classification
definition: One or more continuous nucleotides are missing from RNA sequence.
has_obo_namespace: variation_ontology
id: VariO:0319

Axiom
annotated source: RNA deletion
annotated property: definition
annotated target: One or more continuous nucleotides are missing from RNA sequence.
database_cross_reference: VariO:mv

in-frame deletion
type: Class
subclass of: RNA deletion
definition: Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained.
has_obo_namespace: variation_ontology
id: VariO:0320

Axiom
annotated source: in-frame deletion
annotated property: definition
annotated target: Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained.
database_cross_reference: VariO:mv

out-of-frame deletion
type: Class
subclass of: RNA deletion
definition: Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame.
has_obo_namespace: variation_ontology
id: VariO:0321

Axiom
annotated source: out-of-frame deletion
annotated property: definition
annotated target: Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame.
database_cross_reference: VariO:mv

DNA variation classification
type: Class
subclass of: DNA variation type
definition: Classification of DNA variation.
created by: Mauno Vihnen
creation date: 2013-10-11T08:46:32Z
has_obo_namespace: variation_ontology
id: VariO:0322

Axiom
annotated source: DNA variation classification
annotated property: definition
annotated target: Classification of DNA variation.
database_cross_reference: VariO:mv

protein variation origin
type: Class
subclass of: protein variation type
definition: Origin of protein variation.
created by: Mauno Vihnen
creation date: 2013-10-11T08:53:23Z
has_obo_namespace: variation_ontology
id: VariO:0323

Axiom
annotated source: protein variation origin
annotated property: definition
annotated target: Origin of protein variation.
database_cross_reference: VariO:mv

RNA variation origin
type: Class
subclass of: RNA variation type
definition: Origin of RNA variation.
created by: Mauno Vihnen
creation date: 2013-10-11T09:04:23Z
has_obo_namespace: variation_ontology
id: VariO:0324

Axiom
annotated source: RNA variation origin
annotated property: definition
annotated target: Origin of RNA variation.
database_cross_reference: VariO:mv

protein variation classification
type: Class
subclass of: protein variation type
definition: Classification of protein variation.
created by: Mauno Vihnen
creation date: 2013-10-11T08:59:04Z
has_obo_namespace: variation_ontology
id: VariO:0325

Axiom
annotated source: protein variation classification
annotated property: definition
annotated target: Classification of protein variation.
database_cross_reference: VariO:mv

RNA insertion
type: Class
subclass of: RNA variation classification
definition: Addition of one or more nucleotides between adjacent nucleotides in RNA sequence.
has_obo_namespace: variation_ontology
id: VariO:0326

Axiom
annotated source: RNA insertion
annotated property: definition
annotated target: Addition of one or more nucleotides between adjacent nucleotides in RNA sequence.
database_cross_reference: VariO:mv

out-of-frame insertion
type: Class
subclass of: RNA insertion
definition: Insertion of nucleotide(s) causing alteration of mRNA reading frame.
has_obo_namespace: variation_ontology
id: VariO:0327

Axiom
annotated source: out-of-frame insertion
annotated property: definition
annotated target: Insertion of nucleotide(s) causing alteration of mRNA reading frame.
database_cross_reference: VariO:mv

RNA variation classification
type: Class
subclass of: RNA variation type
definition: Classification of RNA variation.
created by: Mauno Vihnen
creation date: 2013-10-11T09:05:02Z
has_obo_namespace: variation_ontology
id: VariO:0328

Axiom
annotated source: RNA variation classification
annotated property: definition
annotated target: Classification of RNA variation.
database_cross_reference: VariO:mv

alternative RNA form
type: Class
subclass of: RNA variation of non-genetic origin
definition: RNA variation due to defective fidelity of transcription.
created by: Mauno Vihnen
creation date: 2014-10-23T00:29:53Z
has_obo_namespace: variation_ontology
id: VariO:0329

Axiom
annotated source: alternative RNA form
annotated property: definition
annotated target: RNA variation due to defective fidelity of transcription.
database_cross_reference: VariO:mv

mistranslated protein
type: Class
subclass of: variation emerging at protein level
definition: Protein variation due to defective fidelity of translation.
created by: Mauno Vihnen
creation date: 2014-10-23T00:31:56Z
has_obo_namespace: variation_ontology
id: VariO:0330

Axiom
annotated source: mistranslated protein
annotated property: definition
annotated target: Protein variation due to defective fidelity of translation.
database_cross_reference: VariO:mv

alternative form of RNA
type: Class
subclass of: protein coding RNA
definition: Alternative form of RNA molecule.
created by: med-mnv
creation date: 2018-04-26T14:47:12Z
has_obo_namespace: variation_ontology
id: VariO:0331

Axiom
annotated source: alternative form of RNA
annotated property: definition
annotated target: Alternative form of RNA molecule.
database_cross_reference: VariO:mv

in-frame insertion
type: Class
subclass of: RNA insertion
definition: Insertion of nucleotides in multiples of three so that the reading frame is retained.
has_obo_namespace: variation_ontology
id: VariO:0332

Axiom
annotated source: in-frame insertion
annotated property: definition
annotated target: Insertion of nucleotides in multiples of three so that the reading frame is retained.
database_cross_reference: VariO:mv

RNA variation of non-genetic origin
type: Class
subclass of: RNA variation origin
definition: RNA variation that does not have genetic origin being modified at RNA level.
has_obo_namespace: variation_ontology
id: VariO:0333

Axiom
annotated source: RNA variation of non-genetic origin
annotated property: definition
annotated target: RNA variation that does not have genetic origin being modified at RNA level.
database_cross_reference: VariO:mv

edited RNA
type: Class
subclass of: RNA variation of non-genetic origin
definition: Post transcriptionally chemically modified RNA.
has_obo_namespace: variation_ontology
id: VariO:0334

Axiom
annotated source: edited RNA
annotated property: definition
annotated target: Post transcriptionally chemically modified RNA.
database_cross_reference: VariO:mv

decayed RNA
type: Class
subclass of: RNA variation of non-genetic origin
definition: RNA molecule destroyed due to appearance of a premature termination codon.
has_obo_namespace: variation_ontology
id: VariO:0335

Axiom
annotated source: decayed RNA
annotated property: definition
annotated target: RNA molecule destroyed due to appearance of a premature termination codon.
database_cross_reference: VariO:mv

modified RNA
type: Class
subclass of: RNA variation of non-genetic origin
definition: Post transcriptionally modified RNA.
has_obo_namespace: variation_ontology
id: VariO:0336

Axiom
annotated source: modified RNA
annotated property: definition
annotated target: Post transcriptionally modified RNA.
database_cross_reference: VariO:mv

modified DNA
type: Class
subclass of: DNA variation of non-genetic origin
definition: DNA variation due to biological, chemical, physical or other modification.
created by: Mauno Vihnen
creation date: 2014-10-23T00:42:47Z
has_obo_namespace: variation_ontology
id: VariO:0337

Axiom
annotated source: modified DNA
annotated property: definition
annotated target: DNA variation due to biological, chemical, physical or other modification.
database_cross_reference: VariO:mv

variation affecting RNA structure
type: Class
subclass of: variation affecting RNA
definition: Variation affecting structure of RNA.
has_obo_namespace: variation_ontology
id: VariO:0338

Axiom
annotated source: variation affecting RNA structure
annotated property: definition
annotated target: Variation affecting structure of RNA.
database_cross_reference: VariO:mv

RNA modification by editing
type: Class
subclass of: variation affecting RNA structure
definition: Chemical modification of RNA transcript by RNA editing mechanism.
has_obo_namespace: variation_ontology
id: VariO:0339

Axiom
annotated source: RNA modification by editing
annotated property: definition
annotated target: Chemical modification of RNA transcript by RNA editing mechanism.
database_cross_reference: VariO:mv

RNA substitution editing
type: Class
subclass of: RNA modification by editing
definition: RNA editing process of chemical modification of a nucleotide in RNA.
has_obo_namespace: variation_ontology
id: VariO:0340

Axiom
annotated source: RNA substitution editing
annotated property: definition
annotated target: RNA editing process of chemical modification of a nucleotide in RNA.
database_cross_reference: VariO:mv

RNA insertion editing
type: Class
subclass of: RNA modification by editing
definition: Insertion of one or more nucleotides to RNA by RNA editing process.
has_obo_namespace: variation_ontology
id: VariO:0341

Axiom
annotated source: RNA insertion editing
annotated property: definition
annotated target: Insertion of one or more nucleotides to RNA by RNA editing process.
database_cross_reference: VariO:mv

RNA deletion editing
type: Class
subclass of: RNA modification by editing
definition: Deletion of one or more nucleotides from RNA by RNA editing process.
has_obo_namespace: variation_ontology
id: VariO:0342

Axiom
annotated source: RNA deletion editing
annotated property: definition
annotated target: Deletion of one or more nucleotides from RNA by RNA editing process.
database_cross_reference: VariO:mv

synonymous variation
type: Class
subclass of: variation attribute
definition: mRNA variation not affecting the sequence of the translated protein.
created by: med-mnv
creation date: 2015-06-04T13:23:24Z
has_obo_namespace: variation_ontology
id: VariO:0343

Axiom
annotated source: synonymous variation
annotated property: definition
annotated target: mRNA variation not affecting the sequence of the translated protein.
database_cross_reference: VariO:mv

RNA degradation by decay
type: Class
subclass of: effect on RNA degradation
definition: Variation causing degradation of RNA.
has_obo_namespace: variation_ontology
id: VariO:0344

Axiom
annotated source: RNA degradation by decay
annotated property: definition
annotated target: Variation causing degradation of RNA.
database_cross_reference: VariO:mv

RNA degradation by nonstop decay
type: Class
subclass of: RNA degradation by decay
definition: Variation causing nonstop RNA decay.
has_obo_namespace: variation_ontology
id: VariO:0345

Axiom
annotated source: RNA degradation by nonstop decay
annotated property: definition
annotated target: Variation causing nonstop RNA decay.
database_cross_reference: VariO:mv

RNA degradation by no-go decay
type: Class
subclass of: RNA degradation by decay
definition: Variation causing no-go RNA decay.
has_obo_namespace: variation_ontology
id: VariO:0346

Axiom
annotated source: RNA degradation by no-go decay
annotated property: definition
annotated target: Variation causing no-go RNA decay.
database_cross_reference: VariO:mv

RNA degradation by nonsense-mediated decay
type: Class
subclass of: RNA degradation by decay
definition: Variation causing nonsense-mediated decay of RNA due to premature translation termination codon.
has_obo_namespace: variation_ontology
id: VariO:0347

Axiom
annotated source: RNA degradation by nonsense-mediated decay
annotated property: definition
annotated target: Variation causing nonsense-mediated decay of RNA due to premature translation termination codon.
database_cross_reference: VariO:mv

RNA modification by nonsense-associated altered splicing
type: Class
subclass of: variation affecting RNA structure
definition: Nonsense-associated altered RNA splicing.
has_obo_namespace: variation_ontology
id: VariO:0348

Axiom
annotated source: RNA modification by nonsense-associated altered splicing
annotated property: definition
annotated target: Nonsense-associated altered RNA splicing.
database_cross_reference: VariO:mv

affected RNA type
type: Class
subclass of: variation affecting RNA structure
definition: Affected type of RNA.
has_obo_namespace: variation_ontology
id: VariO:0349

Axiom
annotated source: affected RNA type
annotated property: definition
annotated target: Affected type of RNA.
database_cross_reference: VariO:mv

non-protein coding RNA
type: Class
subclass of: affected RNA type
definition: Variation affecting RNA not coding for protein.
has_obo_namespace: variation_ontology
id: VariO:0350

Axiom
annotated source: non-protein coding RNA
annotated property: definition
annotated target: Variation affecting RNA not coding for protein.
database_cross_reference: VariO:mv

protein coding RNA
type: Class
subclass of: affected RNA type
definition: Variation affecting RNA coding for protein.
has_obo_namespace: variation_ontology
id: VariO:0351

Axiom
annotated source: protein coding RNA
annotated property: definition
annotated target: Variation affecting RNA coding for protein.
database_cross_reference: VariO:mv

coding region of mRNA
type: Class
subclass of: protein coding RNA
definition: Variation affecting region coding for protein in protein coding RNA.
has_obo_namespace: variation_ontology
id: VariO:0352

Axiom
annotated source: coding region of mRNA
annotated property: definition
annotated target: Variation affecting region coding for protein in protein coding RNA.
database_cross_reference: VariO:mv

non-coding region of protein coding mRNA
type: Class
subclass of: protein coding RNA
definition: Variation affecting region not coding for protein in protein coding mRNA.
has_obo_namespace: variation_ontology
id: VariO:0353

Axiom
annotated source: non-coding region of protein coding mRNA
annotated property: definition
annotated target: Variation affecting region not coding for protein in protein coding mRNA.
database_cross_reference: VariO:mv

RNA modification by maturation
type: Class
subclass of: variation affecting RNA structure
definition: Maturation of mRNA.
has_obo_namespace: variation_ontology
id: VariO:0354

Axiom
annotated source: RNA modification by maturation
annotated property: definition
annotated target: Maturation of mRNA.
database_cross_reference: VariO:mv

RNA polyadenylation
type: Class
subclass of: RNA modification by maturation
definition: Enzymatic addition of adenylyl residues to the 3' end of RNA molecule.
has_obo_namespace: variation_ontology
id: VariO:0355

Axiom
annotated source: RNA polyadenylation
annotated property: definition
annotated target: Enzymatic addition of adenylyl residues to the 3' end of RNA molecule.
database_cross_reference: VariO:mv

alternatively polyadenylated mRNA
type: Class
subclass of: alternative form of RNA
definition: Polyadenylation of mRNA molecule at alternative site.
has_obo_namespace: variation_ontology
id: VariO:0356

Axiom
annotated source: alternatively polyadenylated mRNA
annotated property: definition
annotated target: Polyadenylation of mRNA molecule at alternative site.
database_cross_reference: VariO:mv

RNA five prime capping
type: Class
subclass of: RNA modification by maturation
definition: Modification of five prime nucleotide in RNA by adding guanine nucleotide with five prime to five prime linkage.
has_obo_namespace: variation_ontology
id: VariO:0357

Axiom
annotated source: RNA five prime capping
annotated property: definition
annotated target: Modification of five prime nucleotide in RNA by adding guanine nucleotide with five prime to five prime linkage.
database_cross_reference: VariO:mv

RNA three prime end processing
type: Class
subclass of: RNA modification by maturation
definition: Three prime end processing of RNA.
has_obo_namespace: variation_ontology
id: VariO:0358

Axiom
annotated source: RNA three prime end processing
annotated property: definition
annotated target: Three prime end processing of RNA.
database_cross_reference: VariO:mv

RNA modification
type: Class
subclass of: RNA modification by maturation
definition: Covalent modification of RNA during maturation.
has_obo_namespace: variation_ontology
id: VariO:0359

Axiom
annotated source: RNA modification
annotated property: definition
annotated target: Covalent modification of RNA during maturation.
database_cross_reference: VariO:mv

RNA base modification
type: Class
subclass of: RNA modification
definition: Post transcriptional modification of RNA base.
has_obo_namespace: variation_ontology
id: VariO:0360

Axiom
annotated source: RNA base modification
annotated property: definition
annotated target: Post transcriptional modification of RNA base.
database_cross_reference: VariO:mv

RNA nucleoside sugar modification
type: Class
subclass of: RNA modification
definition: Post transcriptional modification of RNA nucleoside sugar.
has_obo_namespace: variation_ontology
id: VariO:0361

Axiom
annotated source: RNA nucleoside sugar modification
annotated property: definition
annotated target: Post transcriptional modification of RNA nucleoside sugar.
database_cross_reference: VariO:mv

RNA splicing
type: Class
subclass of: RNA modification by maturation
definition: Process where introns in mRNA are cut away from exons.
database_cross_reference: SO:0001568
has_obo_namespace: variation_ontology
id: VariO:0362

Axiom
annotated source: RNA splicing
annotated property: definition
annotated target: Process where introns in mRNA are cut away from exons.
database_cross_reference: VariO:mv

effect on RNA localization
type: Class
subclass of: variation affecting RNA property
definition: Variation affecting cellular localization of RNA.
created by: med-mnv
creation date: 2018-05-07T11:20:14Z
has_obo_namespace: variation_ontology
id: VariO:0363

Axiom
annotated source: effect on RNA localization
annotated property: definition
annotated target: Variation affecting cellular localization of RNA.
database_cross_reference: VariO:mv

effect on RNA aggregation
type: Class
subclass of: variation affecting RNA property
definition: Variation affecting aggregation tendency of RNA.
created by: med-mnv
creation date: 2018-05-07T11:20:14Z
has_obo_namespace: variation_ontology
id: VariO:0364

Axiom
annotated source: effect on RNA aggregation
annotated property: definition
annotated target: Variation affecting aggregation tendency of RNA.
database_cross_reference: VariO:mv

cis splicing
type: Class
subclass of: RNA splicing
definition: Intronic splicing within a mRNA molecule.
has_obo_namespace: variation_ontology
id: VariO:0365

Axiom
annotated source: cis splicing
annotated property: definition
annotated target: Intronic splicing within a mRNA molecule.
database_cross_reference: VariO:mv

splicing at recursive splice site
type: Class
subclass of: cis splicing
definition: Splicing at recursive splice site which subdivides a large intron.
has_obo_namespace: variation_ontology
id: VariO:0366

Axiom
annotated source: splicing at recursive splice site
annotated property: definition
annotated target: Splicing at recursive splice site which subdivides a large intron.
database_cross_reference: VariO:mv

five prime cis splice site
type: Class
subclass of: cis splicing
definition: Intronic two base pair region bordering exon, at the five prime end of the intron.
has_obo_namespace: variation_ontology
id: VariO:0367

Axiom
annotated source: five prime cis splice site
annotated property: definition
annotated target: Intronic two base pair region bordering exon, at the five prime end of the intron.
database_cross_reference: VariO:mv

canonical five prime splice site
type: Class
subclass of: five prime cis splice site
definition: Canonical prime splice site at five prime end.
has_obo_namespace: variation_ontology
id: VariO:0368

Axiom
annotated source: canonical five prime splice site
annotated property: definition
annotated target: Canonical prime splice site at five prime end.
database_cross_reference: VariO:mv

non canonical five prime splice site
type: Class
subclass of: five prime cis splice site
definition: Non canonical splice site at five prime end.
has_obo_namespace: variation_ontology
id: VariO:0369

Axiom
annotated source: non canonical five prime splice site
annotated property: definition
annotated target: Non canonical splice site at five prime end.
database_cross_reference: VariO:mv

three prime cis splice site
type: Class
subclass of: cis splicing
definition: Intronic two base pair region bordering the exon, at the 3' edge of the intron.
has_obo_namespace: variation_ontology
id: VariO:0370

Axiom
annotated source: three prime cis splice site
annotated property: definition
annotated target: Intronic two base pair region bordering the exon, at the 3' edge of the intron.
database_cross_reference: VariO:mv

non canonical three prime splice site
type: Class
subclass of: three prime cis splice site
definition: Non canonical splice site at three prime end.
has_obo_namespace: variation_ontology
id: VariO:0371

Axiom
annotated source: non canonical three prime splice site
annotated property: definition
annotated target: Non canonical splice site at three prime end.
database_cross_reference: VariO:mv

canonical three prime splice site
type: Class
subclass of: three prime cis splice site
definition: Canonical splice site at three prime end.
has_obo_namespace: variation_ontology
id: VariO:0372

Axiom
annotated source: canonical three prime splice site
annotated property: definition
annotated target: Canonical splice site at three prime end.
database_cross_reference: VariO:mv

cryptic splice site activation
type: Class
subclass of: RNA splicing
definition: Activation of new splice site.
database_cross_reference: SO:0001569
has_obo_namespace: variation_ontology
id: VariO:0373

Axiom
annotated source: cryptic splice site activation
annotated property: definition
annotated target: Activation of new splice site.
database_cross_reference: VariO:mv

cryptic splice donor activation
type: Class
subclass of: cryptic splice site activation
definition: Activation of new splice donor site.
database_cross_reference: SO:0001571
has_obo_namespace: variation_ontology
id: VariO:0374

Axiom
annotated source: cryptic splice donor activation
annotated property: definition
annotated target: Activation of new splice donor site.
database_cross_reference: VariO:mv

cryptic splice acceptor activation
type: Class
subclass of: cryptic splice site activation
definition: Activation of new splice acceptor site.
database_cross_reference: SO:0001570
has_obo_namespace: variation_ontology
id: VariO:0375

Axiom
annotated source: cryptic splice acceptor activation
annotated property: definition
annotated target: Activation of new splice acceptor site.
database_cross_reference: VariO:mv

trans splicing
type: Class
subclass of: RNA splicing
definition: Splicing and ligation of two different mRNA molecules.
has_obo_namespace: variation_ontology
id: VariO:0376

Axiom
annotated source: trans splicing
annotated property: definition
annotated target: Splicing and ligation of two different mRNA molecules.
database_cross_reference: VariO:mv

retrotransposon insertion
type: Class
subclass of: DNA mobile genetic element insertion
definition: Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA.
created by: med-mnv
creation date: 2015-08-26T12:50:29Z
has_obo_namespace: variation_ontology
id: VariO:0377

Axiom
annotated source: retrotransposon insertion
annotated property: definition
annotated target: Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA.
database_cross_reference: VariO:mv

DNA transposon
type: Class
subclass of: DNA mobile genetic element insertion
definition: Insertion of a DNA transposable element into chromosome.
created by: med-mnv
creation date: 2015-08-26T12:50:29Z
has_obo_namespace: variation_ontology
id: VariO:0378

Axiom
annotated source: DNA transposon
annotated property: definition
annotated target: Insertion of a DNA transposable element into chromosome.
database_cross_reference: VariO:mv

LINE
type: Class
subclass of: retrotransposon insertion
definition: Long interspersed nuclear element generated by retrotransposition.
created by: med-mnv
creation date: 2015-08-26T12:51:03Z
has_obo_namespace: variation_ontology
id: VariO:0379

Axiom
annotated source: LINE
annotated property: definition
annotated target: Long interspersed nuclear element generated by retrotransposition.
database_cross_reference: VariO:mv

SINE
type: Class
subclass of: retrotransposon insertion
definition: Short interspersed nuclear element generated by retrotransposition. Length below 500 bp.
created by: med-mnv
creation date: 2015-08-26T12:51:03Z
has_obo_namespace: variation_ontology
id: VariO:0380

Axiom
annotated source: SINE
annotated property: definition
annotated target: Short interspersed nuclear element generated by retrotransposition. Length below 500 bp.
database_cross_reference: VariO:mv

effect on RNA double helix
type: Class
subclass of: effect on RNA tertiary structure
definition: Variation affecting RNA double helix.
created by: med-mnv
creation date: 2018-05-07T11:22:31Z
has_obo_namespace: variation_ontology
id: VariO:0381

Axiom
annotated source: effect on RNA double helix
annotated property: definition
annotated target: Variation affecting RNA double helix.
database_cross_reference: VariO:mv

effect on RNA secondary structure
type: Class
subclass of: variation affecting RNA structure
definition: Variation affecting RNA secondary structure.
has_obo_namespace: variation_ontology
id: VariO:0382

Axiom
annotated source: effect on RNA secondary structure
annotated property: definition
annotated target: Variation affecting RNA secondary structure.
database_cross_reference: VariO:mv

effect on RNA multiloop
type: Class
subclass of: effect on RNA secondary structure
definition: Variation affecting closed RNA structure in which at least two double stranded regions meet.
has_obo_namespace: variation_ontology
id: VariO:0383

Axiom
annotated source: effect on RNA multiloop
annotated property: definition
annotated target: Variation affecting closed RNA structure in which at least two double stranded regions meet.
database_cross_reference: VariO:mv

effect on RNA bulge
type: Class
subclass of: effect on RNA secondary structure
definition: Variation affecting RNA structure in which nucleotides in one strand do not form base pairs.
has_obo_namespace: variation_ontology
id: VariO:0384

Axiom
annotated source: effect on RNA bulge
annotated property: definition
annotated target: Variation affecting RNA structure in which nucleotides in one strand do not form base pairs.
database_cross_reference: VariO:mv

effect on RNA interior loop
type: Class
subclass of: effect on RNA secondary structure
definition: Variation affecting RNA structure in which both the strands do not form base pairs.
has_obo_namespace: variation_ontology
id: VariO:0385

Axiom
annotated source: effect on RNA interior loop
annotated property: definition
annotated target: Variation affecting RNA structure in which both the strands do not form base pairs.
database_cross_reference: VariO:mv

effect on RNA stem
type: Class
subclass of: effect on RNA secondary structure
definition: Variation affecting hydrogen bonding in contiguous nested base pairs in RNA.
has_obo_namespace: variation_ontology
id: VariO:0386

Axiom
annotated source: effect on RNA stem
annotated property: definition
annotated target: Variation affecting hydrogen bonding in contiguous nested base pairs in RNA.
database_cross_reference: VariO:mv

effect on RNA hairpin loop
type: Class
subclass of: effect on RNA secondary structure
definition: Variation affecting loop connecting adjacent regions forming helix in RNA.
has_obo_namespace: variation_ontology
id: VariO:0387

Axiom
annotated source: effect on RNA hairpin loop
annotated property: definition
annotated target: Variation affecting loop connecting adjacent regions forming helix in RNA.
database_cross_reference: VariO:mv

LTR
type: Class
subclass of: retrotransposon insertion
definition: Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb.
created by: med-mnv
creation date: 2015-08-26T12:51:03Z
has_obo_namespace: variation_ontology
id: VariO:0388

Axiom
annotated source: LTR
annotated property: definition
annotated target: Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb.
database_cross_reference: VariO:mv

pentanucleotide expansion
type: Class
subclass of: microsatellite
definition: Tandem repetitive sequence consisting of five nucleotide units.
created by: med-mnv
creation date: 2015-09-17T10:55:04Z
has_obo_namespace: variation_ontology
id: VariO:0389

Axiom
annotated source: pentanucleotide expansion
annotated property: definition
annotated target: Tandem repetitive sequence consisting of five nucleotide units.
database_cross_reference: VariO:mv

effect on DNA double helix
type: Class
subclass of: effect on DNA form
definition: Variation affecting DNA double helical structure.
created by: med-mnv
creation date: 2017-01-16T12:53:57Z
has_obo_namespace: variation_ontology
id: VariO:0390

Axiom
annotated source: effect on DNA double helix
annotated property: definition
annotated target: Variation affecting DNA double helical structure.
database_cross_reference: VariO:mv

plasmid affected
type: Class
subclass of: extrachromosomal DNA affected
definition: Variation effect on independently replicating small DNA molecule.
created by: med-mnv
creation date: 2015-09-18T20:15:22Z
has_obo_namespace: variation_ontology
id: VariO:0391

Axiom
annotated source: plasmid affected
annotated property: definition
annotated target: Variation effect on independently replicating small DNA molecule.
database_cross_reference: VariO:mv

insertion sequence
type: Class
subclass of: DNA mobile genetic element insertion
definition: Simple, relatively short transposable element. IS elements contain only transposition related genes.
created by: med-mnv
creation date: 2015-09-18T20:28:19Z
has_obo_namespace: variation_ontology
id: VariO:0392

Axiom
annotated source: insertion sequence
annotated property: definition
annotated target: Simple, relatively short transposable element. IS elements contain only transposition related genes.
database_cross_reference: VariO:mv

epigenetic RNA variation
type: Class
subclass of: RNA variation of non-genetic origin
definition: RNA variation of epigenetic origin.
created by: med-mnv
creation date: 2018-05-07T11:43:50Z
has_obo_namespace: variation_ontology
id: VariO:0393

Axiom
annotated source: epigenetic RNA variation
annotated property: definition
annotated target: RNA variation of epigenetic origin.
database_cross_reference: VariO:mv

effect on DNA cruciform
type: Class
subclass of: effect on four-stranded DNA
definition: Variation affecting double stranded DNA structure that contains in both strands at corresponding positions a single stranded base pairing forming stem and a connecting loop.
created by: med-mnv
creation date: 2015-09-18T20:44:08Z
has_obo_namespace: variation_ontology
id: VariO:0394

Axiom
annotated source: effect on DNA cruciform
annotated property: definition
annotated target: Variation affecting double stranded DNA structure that contains in both strands at corresponding positions a single stranded base pairing forming stem and a connecting loop.
database_cross_reference: VariO:mv

self-cleavage by ribozyme activity
type: Class
subclass of: variation affecting RNA structure
definition: RNA splicing by inherent ribozyme activity of the mRNA molecule.
created by: med-mnv
creation date: 2015-09-21T08:36:43Z
has_obo_namespace: variation_ontology
id: VariO:0395

Axiom
annotated source: self-cleavage by ribozyme activity
annotated property: definition
annotated target: RNA splicing by inherent ribozyme activity of the mRNA molecule.
database_cross_reference: VariO:mv

variation affecting RNA function
type: Class
subclass of: variation affecting RNA
definition: Variation having effect on RNA function and usage.
has_obo_namespace: variation_ontology
id: VariO:0396

Axiom
annotated source: variation affecting RNA function
annotated property: definition
annotated target: Variation having effect on RNA function and usage.
database_cross_reference: VariO:mv

effect on RNA splicing function
type: Class
subclass of: variation affecting RNA function
definition: Variation affecting splicing function of RNA.
has_obo_namespace: variation_ontology
id: VariO:0397

Axiom
annotated source: effect on RNA splicing function
annotated property: definition
annotated target: Variation affecting splicing function of RNA.
database_cross_reference: VariO:mv

effect on catalytic RNA activity
type: Class
subclass of: variation affecting RNA function
definition: Variation affecting catalytic function of RNA.
has_obo_namespace: variation_ontology
id: VariO:0398

Axiom
annotated source: effect on catalytic RNA activity
annotated property: definition
annotated target: Variation affecting catalytic function of RNA.
database_cross_reference: VariO:mv

effect on translation
type: Class
subclass of: variation affecting RNA function
definition: Variation affecting translation of protein.
has_obo_namespace: variation_ontology
id: VariO:0399

Axiom
annotated source: effect on translation
annotated property: definition
annotated target: Variation affecting translation of protein.
database_cross_reference: VariO:mv

effect on regulatory function of RNA
type: Class
subclass of: variation affecting RNA function
definition: Variation affecting regulatory function of RNA.
has_obo_namespace: variation_ontology
id: VariO:0400

Axiom
annotated source: effect on regulatory function of RNA
annotated property: definition
annotated target: Variation affecting regulatory function of RNA.
database_cross_reference: VariO:mv

effect on amino acid transfer of RNA
type: Class
subclass of: variation affecting RNA function
definition: Variation affecting RNA function in amino acid transfer.
has_obo_namespace: variation_ontology
id: VariO:0401

Axiom
annotated source: effect on amino acid transfer of RNA
annotated property: definition
annotated target: Variation affecting RNA function in amino acid transfer.
database_cross_reference: VariO:mv

effect on RNA information transfer
type: Class
subclass of: variation affecting RNA function
definition: Variation affecting information transfer by RNA.
has_obo_namespace: variation_ontology
id: VariO:0402

Axiom
annotated source: effect on RNA information transfer
annotated property: definition
annotated target: Variation affecting information transfer by RNA.
database_cross_reference: VariO:mv

group I intron
type: Class
subclass of: non-protein coding RNA
definition: Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine.
created by: med-mnv
creation date: 2015-09-21T10:06:37Z
has_obo_namespace: variation_ontology
id: VariO:0403

Axiom
annotated source: group I intron
annotated property: definition
annotated target: Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine.
database_cross_reference: VariO:mv

group II intron
type: Class
subclass of: non-protein coding RNA
definition: Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP.
created by: med-mnv
creation date: 2015-09-21T10:06:37Z
has_obo_namespace: variation_ontology
id: VariO:0404

Axiom
annotated source: group II intron
annotated property: definition
annotated target: Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP.
database_cross_reference: VariO:mv

dicentric translocation
type: Class
subclass of: interchromosomal translocation
definition: Fusion of two chromosome segments both containing a centromere.
created by: med-mnv
creation date: 2015-09-22T19:15:03Z
has_obo_namespace: variation_ontology
id: VariO:0405

Axiom
annotated source: dicentric translocation
annotated property: definition
annotated target: Fusion of two chromosome segments both containing a centromere.
database_cross_reference: VariO:mv

RNA degradation by Staufen-mediated decay
type: Class
subclass of: RNA degradation by decay
definition: Variation causing Staufen-mediated RNA decay.
created by: med-mnv
creation date: 2018-05-07T13:57:34Z
has_obo_namespace: variation_ontology
id: VariO:0406

Axiom
annotated source: RNA degradation by Staufen-mediated decay
annotated property: definition
annotated target: Variation causing Staufen-mediated RNA decay.
database_cross_reference: VariO:mv

edited DNA
type: Class
subclass of: DNA variation of non-genetic origin
definition: Variation generated by chromosome editing.
created by: med-mnv
creation date: 2015-09-22T19:20:45Z
has_obo_namespace: variation_ontology
id: VariO:0407

Axiom
annotated source: edited DNA
annotated property: definition
annotated target: Variation generated by chromosome editing.
database_cross_reference: VariO:mv

RNA chimera
type: Class
subclass of: RNA variation of non-genetic origin
definition: Fusion transcript of exons from two or more genes.
created by: med-mnv
creation date: 2015-09-24T13:21:02Z
has_obo_namespace: variation_ontology
id: VariO:0408

Axiom
annotated source: RNA chimera
annotated property: definition
annotated target: Fusion transcript of exons from two or more genes.
database_cross_reference: VariO:mv

frameshifted RNA
type: Class
subclass of: RNA variation of non-genetic origin
definition: Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome.
created by: med-mnv
creation date: 2015-09-24T13:21:02Z
has_obo_namespace: variation_ontology
id: VariO:0409

Axiom
annotated source: frameshifted RNA
annotated property: definition
annotated target: Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome.
database_cross_reference: VariO:mv

effect on single stranded DNA structure
type: Class
subclass of: effect on DNA form
definition: Variation affecting single stranded DNA structure.
created by: med-mnv
creation date: 2018-11-08T10:04:23Z
has_obo_namespace: variation_ontology
id: VariO:0410

Axiom
annotated source: effect on single stranded DNA structure
annotated property: definition
annotated target: Variation affecting single stranded DNA structure.
database_cross_reference: VariO:mv

alternatively spliced RNA
type: Class
subclass of: Restriction
  on property: part_of
  some values from: alternative form of RNA
definition: RNA molecule matured by splicing at an alternative site.
created by: med-mnv
creation date: 2015-10-13T19:36:23Z
has_obo_namespace: variation_ontology
id: VariO:0411

Axiom
annotated source: alternatively spliced RNA
annotated property: definition
annotated target: RNA molecule matured by splicing at an alternative site.
database_cross_reference: VariO:mv

effect on catalytic DNA activity
type: Class
subclass of: variation affecting DNA function
definition: Variation affecting catalytic function of DNA.
created by: med-mnv
creation date: 2016-11-29T11:11:11Z
has_obo_namespace: variation_ontology
id: VariO:0412

Axiom
annotated source: effect on catalytic DNA activity
annotated property: definition
annotated target: Variation affecting catalytic function of DNA.
database_cross_reference: VariO:mv

effect on A DNA
type: Class
subclass of: effect on DNA double helix
definition: Variation affecting A form of right-handed DNA.
created by: med-mnv
creation date: 2017-01-16T12:55:40Z
has_obo_namespace: variation_ontology
id: VariO:0413

Axiom
annotated source: effect on A DNA
annotated property: definition
annotated target: Variation affecting A form of right-handed DNA.
database_cross_reference: VariO:mv

effect on B DNA
type: Class
subclass of: effect on DNA double helix
definition: Variation affecting B form of right-handed DNA.
created by: med-mnv
creation date: 2017-01-16T12:55:40Z
has_obo_namespace: variation_ontology
id: VariO:0414

Axiom
annotated source: effect on B DNA
annotated property: definition
annotated target: Variation affecting B form of right-handed DNA.
database_cross_reference: VariO:mv

effect on C DNA
type: Class
subclass of: effect on DNA double helix
definition: Variation affecting C form of right-handed DNA.
created by: med-mnv
creation date: 2017-01-16T12:55:40Z
has_obo_namespace: variation_ontology
id: VariO:0415

Axiom
annotated source: effect on C DNA
annotated property: definition
annotated target: Variation affecting C form of right-handed DNA.
database_cross_reference: VariO:mv

effect on L DNA
type: Class
subclass of: effect on DNA double helix
definition: Variation affecting L form of right-handed DNA.
created by: med-mnv
creation date: 2017-01-16T12:55:40Z
has_obo_namespace: variation_ontology
id: VariO:0416

Axiom
annotated source: effect on L DNA
annotated property: definition
annotated target: Variation affecting L form of right-handed DNA.
database_cross_reference: VariO:mv

effect on S DNA
type: Class
subclass of: effect on DNA double helix
definition: Variation affecting S form of right-handed DNA.
created by: med-mnv
creation date: 2017-01-16T12:55:40Z
has_obo_namespace: variation_ontology
id: VariO:0417

Axiom
annotated source: effect on S DNA
annotated property: definition
annotated target: Variation affecting S form of right-handed DNA.
database_cross_reference: VariO:mv

effect on D DNA
type: Class
subclass of: effect on DNA double helix
definition: Variation affecting D form of right-handed DNA.
created by: med-mnv
creation date: 2017-01-16T13:10:01Z
has_obo_namespace: variation_ontology
id: VariO:0418

Axiom
annotated source: effect on D DNA
annotated property: definition
annotated target: Variation affecting D form of right-handed DNA.
database_cross_reference: VariO:mv

effect on H DNA
type: Class
subclass of: effect on intramolecular DNA triple helix
definition: Variation affecting H form of intramolecular triple helical DNA.
created by: med-mnv
creation date: 2017-01-16T13:14:56Z
has_obo_namespace: variation_ontology
id: VariO:0419

Axiom
annotated source: effect on H DNA
annotated property: definition
annotated target: Variation affecting H form of intramolecular triple helical DNA.
database_cross_reference: VariO:mv

effect on four-stranded DNA
type: Class
subclass of: effect on DNA form
definition: Variation affecting four-stranded DNA.
created by: med-mnv
creation date: 2017-01-16T13:17:51Z
has_obo_namespace: variation_ontology
id: VariO:0420

Axiom
annotated source: effect on four-stranded DNA
annotated property: definition
annotated target: Variation affecting four-stranded DNA.
database_cross_reference: VariO:mv

effect on Z DNA
type: Class
subclass of: effect on DNA double helix
definition: Variation affecting Z form of left-handed DNA.
created by: med-mnv
creation date: 2017-01-16T13:20:36Z
has_obo_namespace: variation_ontology
id: VariO:0421

Axiom
annotated source: effect on Z DNA
annotated property: definition
annotated target: Variation affecting Z form of left-handed DNA.
database_cross_reference: VariO:mv

effect on intramolecular DNA triple helix
type: Class
subclass of: effect on DNA triple helix
definition: Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex.
created by: med-mnv
creation date: 2017-01-16T13:22:35Z
has_obo_namespace: variation_ontology
id: VariO:0422

Axiom
annotated source: effect on intramolecular DNA triple helix
annotated property: definition
annotated target: Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex.
database_cross_reference: VariO:mv

effect on intermolecular DNA triple helix
type: Class
subclass of: effect on DNA triple helix
definition: Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule.
created by: med-mnv
creation date: 2017-01-16T13:24:18Z
has_obo_namespace: variation_ontology
id: VariO:0423

Axiom
annotated source: effect on intermolecular DNA triple helix
annotated property: definition
annotated target: Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule.
database_cross_reference: VariO:mv

effect on DNA-RNA hybrid
type: Class
subclass of: Restriction
  on property: part_of
  some values from: effect on RNA tertiary structure
subclass of: Restriction
  on property: part_of
  some values from: effect on DNA tertiary structure
definition: Variation affecting DNA-RNA hybrid.
created by: med-mnv
creation date: 2017-01-16T13:29:46Z
has_obo_namespace: variation_ontology
id: VariO:0424

Axiom
annotated source: effect on DNA-RNA hybrid
annotated property: definition
annotated target: Variation affecting DNA-RNA hybrid.
database_cross_reference: VariO:mv

effect on RNA triple helix
type: Class
subclass of: effect on RNA tertiary structure
definition: Variation affecting RNA helix formed of three strands.
created by: med-mnv
creation date: 2017-01-16T13:48:49Z
has_obo_namespace: variation_ontology
id: VariO:0425

Axiom
annotated source: effect on RNA triple helix
annotated property: definition
annotated target: Variation affecting RNA helix formed of three strands.
database_cross_reference: VariO:mv

effect on four-stranded RNA
type: Class
subclass of: effect on RNA tertiary structure
definition: Variation affecting four-stranded RNA.
created by: med-mnv
creation date: 2017-01-16T13:48:49Z
has_obo_namespace: variation_ontology
id: VariO:0426

Axiom
annotated source: effect on four-stranded RNA
annotated property: definition
annotated target: Variation affecting four-stranded RNA.
database_cross_reference: VariO:mv

type of chromosomal amplification
type: Class
subclass of: chromosomal amplification
definition: Classification of chromosomal amplification type.
created by: med-mnv
creation date: 2017-01-17T09:34:30Z
has_obo_namespace: variation_ontology
id: VariO:0427

Axiom
annotated source: type of chromosomal amplification
annotated property: definition
annotated target: Classification of chromosomal amplification type.
database_cross_reference: VariO:mv

genome variation
type: Class
subclass of: variation affecting DNA structure
definition: Variation affecting genome.
created by: med-mnv
creation date: 2017-01-23T09:01:36Z
has_obo_namespace: variation_ontology
id: VariO:0428

Axiom
annotated source: genome variation
annotated property: definition
annotated target: Variation affecting genome.
database_cross_reference: VariO:mv

complex genomic variation
type: Class
subclass of: genome variation
definition: Chromosome structure variation due to several breakpoints.
created by: med-mnv
creation date: 2017-01-23T09:03:57Z
has_obo_namespace: variation_ontology
id: VariO:0429

Axiom
annotated source: complex genomic variation
annotated property: definition
annotated target: Chromosome structure variation due to several breakpoints.
database_cross_reference: VariO:mv

nucleotide expansion
type: Class
subclass of: chromosomal amplification
definition: Repetitive sequence consisting of one more nucleotide units.
created by: med-mnv
creation date: 2017-01-23T09:09:22Z
has_obo_namespace: variation_ontology
id: VariO:0430

Axiom
annotated source: nucleotide expansion
annotated property: definition
annotated target: Repetitive sequence consisting of one more nucleotide units.
database_cross_reference: VariO:mv

effect on R loop
type: Class
subclass of: effect on DNA-RNA hybrid
definition: Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA.
created by: med-mnv
creation date: 2017-01-23T09:32:22Z
has_obo_namespace: variation_ontology
id: VariO:0431

Axiom
annotated source: effect on R loop
annotated property: definition
annotated target: Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA.
database_cross_reference: VariO:mv

effect on T loop
type: Class
subclass of: effect on DNA-RNA hybrid
definition: Effect on DNA-RNA T loop structure formed by single-stranded 3' strand looping back to anneal with double-stranded repeats. Appears in telomere end-replication.
created by: med-mnv
creation date: 2017-01-23T09:34:30Z
has_obo_namespace: variation_ontology
id: VariO:0432

Axiom
annotated source: effect on T loop
annotated property: definition
annotated target: Effect on DNA-RNA T loop structure formed by single-stranded 3' strand looping back to anneal with double-stranded repeats. Appears in telomere end-replication.
database_cross_reference: VariO:mv

effect on D loop
type: Class
subclass of: Restriction
  on property: part_of
  some values from: effect on intermolecular DNA triple helix
subclass of: Restriction
  on property: part_of
  some values from: effect on DNA-RNA hybrid
definition: Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA.
created by: med-mnv
creation date: 2017-01-23T09:45:49Z
has_obo_namespace: variation_ontology
id: VariO:0433

Axiom
annotated source: effect on D loop
annotated property: definition
annotated target: Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA.
database_cross_reference: VariO:mv

DNA sugar variation
type: Class
subclass of: variation affecting DNA structure
definition: Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone.
created by: med-mnv
creation date: 2017-03-23T10:54:09Z
has_obo_namespace: variation_ontology
id: VariO:0434

Axiom
annotated source: DNA sugar variation
annotated property: definition
annotated target: Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone.
database_cross_reference: VariO:mv

effect on protein reaction kinetics
type: Class
subclass of: effect on protein activity
definition: Effect of variation to protein reaction kinetics.
created by: med-mnv
creation date: 2017-04-28T14:52:51Z
has_obo_namespace: variation_ontology
id: VariO:0435

Axiom
annotated source: effect on protein reaction kinetics
annotated property: definition
annotated target: Effect of variation to protein reaction kinetics.
database_cross_reference: VariO:mv

matured RNA
type: Class
subclass of: RNA variation of non-genetic origin
definition: RNA molecule that has matured by processing.
created by: med-mnv
creation date: 2017-04-28T14:58:30Z
has_obo_namespace: variation_ontology
id: VariO:0436

Axiom
annotated source: matured RNA
annotated property: definition
annotated target: RNA molecule that has matured by processing.
database_cross_reference: VariO:mv

alternatively initiated mRNA transcript
type: Class
subclass of: alternative form of RNA
definition: RNA variation causing alternative translation initiation.
created by: med-mnv
creation date: 2017-04-28T16:01:26Z
has_obo_namespace: variation_ontology
id: VariO:0437

Axiom
annotated source: alternatively initiated mRNA transcript
annotated property: definition
annotated target: RNA variation causing alternative translation initiation.
database_cross_reference: VariO:mv

epigenetic RNA modification
type: Class
subclass of: variation affecting RNA structure
definition: Epigenetic modification of RNA.
created by: med-mnv
creation date: 2018-05-07T14:40:53Z
has_obo_namespace: variation_ontology
id: VariO:0438

Axiom
annotated source: epigenetic RNA modification
annotated property: definition
annotated target: Epigenetic modification of RNA.
database_cross_reference: VariO:mv

effect on RNA activity
type: Class
subclass of: variation affecting RNA property
definition: Effect of variation on RNA activity.
created by: med-mnv
creation date: 2017-04-28T16:23:47Z
has_obo_namespace: variation_ontology
id: VariO:0439

Axiom
annotated source: effect on RNA activity
annotated property: definition
annotated target: Effect of variation on RNA activity.
database_cross_reference: VariO:mv

effect on RNA reaction kinetics
type: Class
subclass of: effect on RNA activity
definition: Effect of variation on RNA reaction kinetics.
created by: med-mnv
creation date: 2017-04-28T16:26:01Z
has_obo_namespace: variation_ontology
id: VariO:0440

Axiom
annotated source: effect on RNA reaction kinetics
annotated property: definition
annotated target: Effect of variation on RNA reaction kinetics.
database_cross_reference: VariO:mv

effect on RNA affinity
type: Class
subclass of: effect on RNA activity
definition: Effect of variation on RNA affinity to binding molecule(s).
created by: med-mnv
creation date: 2017-04-28T16:26:01Z
has_obo_namespace: variation_ontology
id: VariO:0441

Axiom
annotated source: effect on RNA affinity
annotated property: definition
annotated target: Effect of variation on RNA affinity to binding molecule(s).
database_cross_reference: VariO:mv

effect on RNA specificity
type: Class
subclass of: effect on RNA activity
definition: Effect of variation on substrate binding specificity of RNA.
created by: med-mnv
creation date: 2017-04-28T16:26:01Z
has_obo_namespace: variation_ontology
id: VariO:0442

Axiom
annotated source: effect on RNA specificity
annotated property: definition
annotated target: Effect of variation on substrate binding specificity of RNA.
database_cross_reference: VariO:mv

alternatively initiated protein
type: Class
subclass of: variation emerging at protein level
definition: Protein variant originating from alternative translation initiation.
created by: med-mnv
creation date: 2017-05-03T09:09:05Z
has_obo_namespace: variation_ontology
id: VariO:0443

Axiom
annotated source: alternatively initiated protein
annotated property: definition
annotated target: Protein variant originating from alternative translation initiation.
database_cross_reference: VariO:mv

de novo variation
type: Class
subclass of: DNA variation of genetic origin
definition: Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis.
created by: med-mnv
creation date: 2018-01-08T11:31:50Z
has_obo_namespace: variation_ontology
id: VariO:0444

Axiom
annotated source: de novo variation
annotated property: definition
annotated target: Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis.
database_cross_reference: VariO:mv

germinal variation
type: Class
subclass of: DNA variation of genetic origin
definition: Variation that has been inherited from a germline cell.
created by: med-mnv
creation date: 2017-12-15T09:58:57Z
has_obo_namespace: variation_ontology
has_related_synonym: germline variation
id: VariO:0445

Axiom
annotated source: germinal variation
annotated property: definition
annotated target: Variation that has been inherited from a germline cell.
database_cross_reference: VariO:mv

somatic variation
type: Class
subclass of: DNA variation of genetic origin
definition: Variation that has its origin in a cell in soma.
created by: med-mnv
creation date: 2017-12-15T09:58:57Z
has_obo_namespace: variation_ontology
id: VariO:0446

Axiom
annotated source: somatic variation
annotated property: definition
annotated target: Variation that has its origin in a cell in soma.
database_cross_reference: VariO:mv

immunological recognition molecule diversification
type: Class
subclass of: chromosome structure variation
definition: Processes that recombine and modify genes coding for immunological recognition molecules (antigens, B- and T-cell receptors, MCH type I and II molecules).
created by: med-mnv
creation date: 2017-12-15T10:47:27Z
has_obo_namespace: variation_ontology
id: VariO:0447

Axiom
annotated source: immunological recognition molecule diversification
annotated property: definition
annotated target: Processes that recombine and modify genes coding for immunological recognition molecules (antigens, B- and T-cell receptors, MCH type I and II molecules).
database_cross_reference: VariO:mv

organellar DNA affected
type: Class
subclass of: extrachromosomal DNA affected
definition: Variation effect on DNA within cellular compartment.
created by: med-mnv
creation date: 2018-02-01T12:42:12Z
has_obo_namespace: variation_ontology
id: VariO:0448

Axiom
annotated source: organellar DNA affected
annotated property: definition
annotated target: Variation effect on DNA within cellular compartment.
database_cross_reference: VariO:mv

extrachromosomal circular DNA
type: Class
subclass of: extrachromosomal DNA affected
definition: Circular DNA molecule not part of the chromosomes.
created by: med-mnv
creation date: 2018-02-01T12:47:35Z
has_obo_namespace: variation_ontology
id: VariO:0449

Axiom
annotated source: extrachromosomal circular DNA
annotated property: definition
annotated target: Circular DNA molecule not part of the chromosomes.
database_cross_reference: VariO:mv

mitochondrial DNA affected
type: Class
subclass of: organellar DNA affected
definition: Variation affecting DNA within mitochondria.
created by: med-mnv
creation date: 2018-02-01T12:52:27Z
has_obo_namespace: variation_ontology
id: VariO:0450

Axiom
annotated source: mitochondrial DNA affected
annotated property: definition
annotated target: Variation affecting DNA within mitochondria.
database_cross_reference: VariO:mv

plastid DNA affected
type: Class
subclass of: organellar DNA affected
definition: Variation affecting DNA within plastids e.g. chloroplasts.
created by: med-mnv
creation date: 2018-02-01T12:53:15Z
has_obo_namespace: variation_ontology
id: VariO:0451

Axiom
annotated source: plastid DNA affected
annotated property: definition
annotated target: Variation affecting DNA within plastids e.g. chloroplasts.
database_cross_reference: VariO:mv

heptanucleotide expansion
type: Class
subclass of: microsatellite
definition: Tandem repetitive sequence consisting of six nucleotide units.
created by: med-mnv
creation date: 2018-02-01T14:49:25Z
has_obo_namespace: variation_ontology
id: VariO:0452

Axiom
annotated source: heptanucleotide expansion
annotated property: definition
annotated target: Tandem repetitive sequence consisting of six nucleotide units.
database_cross_reference: VariO:mv

histone modification
type: Class
subclass of: epigenetic DNA modification
definition: Epigenetic modification of histone.
created by: med-mnv
creation date: 2018-02-06T09:08:59Z
has_obo_namespace: variation_ontology
id: VariO:0453

Axiom
annotated source: histone modification
annotated property: definition
annotated target: Epigenetic modification of histone.
database_cross_reference: VariO:mv

variation at topology associating domain
type: Class
subclass of: chromatin structure variation
definition: Variation affecting topology associating domain (TAD).
created by: med-mnv
creation date: 2018-03-05T16:55:07Z
has_obo_namespace: variation_ontology
id: VariO:0454

Axiom
annotated source: variation at topology associating domain
annotated property: definition
annotated target: Variation affecting topology associating domain (TAD).
database_cross_reference: VariO:mv

effect on A motif
type: Class
subclass of: effect on single stranded DNA structure
created by: med-mnv
creation date: 2018-11-08T10:05:56Z
has_obo_namespace: variation_ontology
id: VariO:0455