format-version: 1.2
data-version: 2015-04-22
date: 20:04:2015 10:53
saved-by: med-mnv
auto-generated-by: OBO-Edit 2.3.1
default-namespace: variation_ontology
remark: A Variation Ontology
ontology: vario

[Term]
id: VariO:0001
name: variation
def: "Alteration in DNA, RNA or protein." [VariO:mv]

[Term]
id: VariO:0002
name: variation affecting protein
def: "Effects of a variation on protein level." [VariO:mv]
is_a: VariO:0001 ! variation

[Term]
id: VariO:0003
name: variation affecting protein function
def: "Effect of variation on protein function." [VariO:mv]
is_a: VariO:0002 ! variation affecting protein

[Term]
id: VariO:0004
name: effect on protein movement
def: "Effect of variation on the movement of a protein along filament of a polymeric molecule." [VariO:mv]
is_a: VariO:0003 ! variation affecting protein function

[Term]
id: VariO:0005
name: effect on protein storage
def: "Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions." [VariO:mv]
is_a: VariO:0003 ! variation affecting protein function

[Term]
id: VariO:0006
name: effect on structural protein
def: "Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems." [VariO:mv]
is_a: VariO:0003 ! variation affecting protein function

[Term]
id: VariO:0007
name: effect on protein recognition
def: "Effect of variation on selective non-covalent interaction of protein." [VariO:mv]
is_a: VariO:0003 ! variation affecting protein function

[Term]
id: VariO:0008
name: effect on catalytic protein function
def: "Effect of variation on catalytic function of protein." [VariO:mv]
is_a: VariO:0003 ! variation affecting protein function

[Term]
id: VariO:0009
name: effect on transport function of protein
def: "Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane." [VariO:mv]
is_a: VariO:0003 ! variation affecting protein function

[Term]
id: VariO:0010
name: effect on RNA abundance
def: "Variation affecting abundance of produced RNA molecules." [VariO:mv]
is_a: VariO:0298 ! variation affecting RNA property

[Term]
id: VariO:0011
name: effect on protein information transfer
def: "Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs." [VariO:mv]
is_a: VariO:0003 ! variation affecting protein function

[Term]
id: VariO:0012
name: protein variation type
def: "Type of protein variation. Describes origin and classification of a variant." [VariO:mv]
is_a: VariO:0002 ! variation affecting protein

[Term]
id: VariO:0013
name: protein variation of genetic origin
def: "Protein variation that has genetic origin." [VariO:mv]
is_a: VariO:0323 ! protein variation origin

[Term]
id: VariO:0014
name: amino acid deletion
def: "Removal of one or more continuous amino acids from protein." [VariO:mv]
is_a: VariO:0325 ! protein variation classification

[Term]
id: VariO:0015
name: protein truncation
def: "Shortening of protein sequence from terminus." [VariO:mv]
is_a: VariO:0014 ! amino acid deletion

[Term]
id: VariO:0016
name: sequence retaining amino acid deletion
def: "Deletion of one or more amino acids from a protein, without affecting the sequence after deletion." [VariO:mv]
is_a: VariO:0014 ! amino acid deletion

[Term]
id: VariO:0018
name: amino acid insertion
def: "Addition of one or more amino acids to protein sequence." [VariO:mv]
is_a: VariO:0325 ! protein variation classification

[Term]
id: VariO:0019
name: amphigoric amino acid insertion
def: "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." [VariO:mv]
is_a: VariO:0018 ! amino acid insertion

[Term]
id: VariO:0020
name: sequence retaining amino acid insertion
def: "Insertion of one or more amino acids to the protein without affecting the sequence after insertion." [VariO:mv]
is_a: VariO:0018 ! amino acid insertion

[Term]
id: VariO:0021
name: amino acid substitution
def: "Substitution of an amino acid in protein." [VariO:mv]
xref: SO:0001606
is_a: VariO:0325 ! protein variation classification

[Term]
id: VariO:0022
name: amino acid indel
def: "A complex protein variation consisting of both amino acid insertion(s) and deletion(s)." [VariO:mv]
is_a: VariO:0325 ! protein variation classification

[Term]
id: VariO:0023
name: amphigoric amino acid indel
def: "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." [VariO:mv]
is_a: VariO:0022 ! amino acid indel
created_by: Mauno Vihnen
creation_date: 2013-03-06T10:59:41Z

[Term]
id: VariO:0024
name: variation emerging at protein level
def: "Protein variation that does not have genetic origin being modified at protein level." [VariO:mv]
is_a: VariO:0323 ! protein variation origin

[Term]
id: VariO:0025
name: epigenetic protein variation
def: "Heritable protein variation of non-genetic origin." [VariO:mv]
is_a: VariO:0024 ! variation emerging at protein level

[Term]
id: VariO:0026
name: protein structural inheritance
def: "Inheritance of protein or protein complex structure without involvement of genetic information." [VariO:mv]
is_a: VariO:0025 ! epigenetic protein variation

[Term]
id: VariO:0027
name: proteinaceous infection
def: "Protein conformation change induced by structurally modified protein." [VariO:mv]
is_a: VariO:0025 ! epigenetic protein variation

[Term]
id: VariO:0028
name: post translational modification
def: "Protein molecule chemically modified after translation." [VariO:mv]
is_a: VariO:0024 ! variation emerging at protein level

[Term]
id: VariO:0029
name: sequence retaining amino acid indel
def: "Amino acid indel without affecting the sequence after the indel position." [VariO:mv]
is_a: VariO:0022 ! amino acid indel
created_by: Mauno Vihnen
creation_date: 2013-03-06T11:04:21Z

[Term]
id: VariO:0030
name: in-frame indel
def: "RNA indel not affecting reading frame after indel position." [VariO:mv]
is_a: VariO:0311 ! RNA indel
created_by: Mauno Vihnen
creation_date: 2013-06-14T10:03:57Z

[Term]
id: VariO:0031
name: out-of-frame indel
def: "RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame." [VariO:mv]
is_a: VariO:0311 ! RNA indel
created_by: Mauno Vihnen
creation_date: 2013-06-14T10:03:57Z

[Term]
id: VariO:0032
name: variation affecting protein property
def: "Variation affecting characteristic property of protein." [VariO:mv]
is_a: VariO:0002 ! variation affecting protein

[Term]
id: VariO:0033
name: effect on protein subcellular localization
def: "Effect of variation on the targeting of a protein within a cell or cellular compartment." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0034
name: effect on protein stability
def: "Effect of variation on stability of protein." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0035
name: effect on protein solubility
def: "Effect of variation on the potential of protein to dissolve in a liquid." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0036
name: effect on protein inclusion body formation
def: "Variation affecting the formation of particles of aggregated proteins." [VariO:mv]
xref: GO:0016234
is_a: VariO:0035 ! effect on protein solubility

[Term]
id: VariO:0037
name: covariant position
def: "Variation at a covarying sequence position." [VariO:mv]
is_a: VariO:0233 ! conservation
created_by: Mauno Vihnen
creation_date: 2014-01-16T14:03:51Z

[Term]
id: VariO:0038
name: effect on protein aggregation
def: "Variation affecting protein aggregation tendency." [VariO:mv]
is_a: VariO:0035 ! effect on protein solubility

[Term]
id: VariO:0039
name: protein function change
def: "Type of protein function affecting variation." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0040
name: protein gain of function
def: "Effect of variation causing new or enhanced protein activity." [VariO:mv]
is_a: VariO:0039 ! protein function change

[Term]
id: VariO:0041
name: neomorphic protein variation
def: "Variation generates new protein function." [VariO:mv]
is_a: VariO:0040 ! protein gain of function

[Term]
id: VariO:0042
name: antimorphic protein variation
def: "Dominant variation that acts to opposite direction than the normal protein." [VariO:mv]
synonym: "dominant negative protein variation" EXACT []
is_a: VariO:0040 ! protein gain of function

[Term]
id: VariO:0043
name: protein loss of function
def: "Effect of variation reducing or abolishing protein activity." [VariO:mv]
is_a: VariO:0039 ! protein function change

[Term]
id: VariO:0044
name: effect on protein accessibility
def: "Effect of variation to the accessibility of protein region to solvent." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0045
name: variation exposing buried region
def: "Variation exposing buried region." [VariO:mv]
is_a: VariO:0044 ! effect on protein accessibility

[Term]
id: VariO:0046
name: variation burying exposed region
def: "Variation leading to burying of exposed region." [VariO:mv]
is_a: VariO:0044 ! effect on protein accessibility

[Term]
id: VariO:0047
name: association of protein variation to pathogenicity
def: "Implication of a protein variant to pathogenicity." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0048
name: effect on protein charge
def: "Effect of variation on charge in protein." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0049
name: effect on protein electrostatics
def: "Variation affecting electrostatics of the protein surface." [VariO:mv]
is_a: VariO:0048 ! effect on protein charge

[Term]
id: VariO:0050
name: effect on protein isoelectric point
def: "Variation changing protein isoelectric point." [VariO:mv]
is_a: VariO:0048 ! effect on protein charge

[Term]
id: VariO:0051
name: effect on protein degradation
def: "Effect of variation on degradation of protein." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0052
name: effect on protein abundance
def: "Variation affecting abundance of produced protein molecules." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0053
name: effect on protein activity
def: "Effect of variation on activity of protein." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0054
name: effect on protein affinity
def: "Effect of variation on protein affinity to binding molecule(s)." [VariO:mv]
is_a: VariO:0053 ! effect on protein activity

[Term]
id: VariO:0055
name: effect on protein specificity
def: "Effect of variation on substrate binding specificity." [VariO:mv]
is_a: VariO:0053 ! effect on protein activity

[Term]
id: VariO:0056
name: effect on enzyme reaction kinetics
def: "Effect of variation to enzyme reaction kinetics." [VariO:mv]
is_a: VariO:0053 ! effect on protein activity

[Term]
id: VariO:0057
name: conservation of protein variation site
def: "Conservation of the variant site in related protein sequences." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0058
name: effect on protein interaction
def: "Effect of variation on the interaction of protein with its partner." [VariO:mv]
is_a: VariO:0032 ! variation affecting protein property

[Term]
id: VariO:0059
name: effect on protein contact energy
def: "Effect of variation on contact energy between interacting molecules." [VariO:mv]
is_a: VariO:0058 ! effect on protein interaction

[Term]
id: VariO:0060
name: variation affecting protein structure
def: "Variation affecting structure of protein." [VariO:mv]
is_a: VariO:0002 ! variation affecting protein

[Term]
id: VariO:0061
name: epigenetic protein modification
def: "Hereditary protein structure modification of non-genetic origin." [VariO:mv]
is_a: VariO:0060 ! variation affecting protein structure

[Term]
id: VariO:0062
name: prion formation
def: "Variation affecting the formation of infectious protein having misfolded structure." [VariO:mv]
is_a: VariO:0061 ! epigenetic protein modification

[Term]
id: VariO:0063
name: epigenetic protein complex structure
def: "Variation affecting heritable protein complex structure." [VariO:mv]
is_a: VariO:0061 ! epigenetic protein modification

[Term]
id: VariO:0064
name: effect on protein 3D structure
def: "Variation affecting protein three dimensional structure." [VariO:mv]
is_a: VariO:0060 ! variation affecting protein structure

[Term]
id: VariO:0065
name: effect on protein dynamics
def: "Variation affecting dynamics in protein structure." [VariO:mv]
is_a: VariO:0064 ! effect on protein 3D structure

[Term]
id: VariO:0066
name: effect on structural flexibility
def: "Variation affecting protein structural flexibility." [VariO:mv]
is_a: VariO:0065 ! effect on protein dynamics

[Term]
id: VariO:0067
name: effect on induced fit
def: "Variation affecting induced fit of protein binding to its partner." [VariO:mv]
is_a: VariO:0065 ! effect on protein dynamics

[Term]
id: VariO:0068
name: effect on structural disorder
def: "Variation affecting protein structural disorder." [VariO:mv]
is_a: VariO:0065 ! effect on protein dynamics

[Term]
id: VariO:0069
name: effect on allosteric site
def: "Variation in affecting protein allosteric site." [VariO:mv]
is_a: VariO:0065 ! effect on protein dynamics

[Term]
id: VariO:0070
name: effect on protein tertiary structure
def: "Variation affecting protein three dimensional structure." [VariO:mv]
is_a: VariO:0064 ! effect on protein 3D structure

[Term]
id: VariO:0071
name: effect on protein folding rate
def: "Variation affecting rate of protein folding." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0072
name: extrachromosomal DNA affected
def: "Variation effect on nonchromosomal DNA." [VariO:mv]
is_a: VariO:0159 ! affected DNA level
created_by: Mauno Vihinen
creation_date: 2012-11-09T14:16:30Z

[Term]
id: VariO:0073
name: effect to protein fold
def: "Variation affecting protein tertiary structure." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0074
name: protein conformational change
def: "Variation changing protein conformation." [VariO:mv]
is_a: VariO:0073 ! effect to protein fold

[Term]
id: VariO:0075
name: global protein conformation change
def: "Variation causing large overall protein conformational change." [VariO:mv]
is_a: VariO:0074 ! protein conformational change

[Term]
id: VariO:0076
name: local protein conformation change
def: "Variation causing local and minor conformational change." [VariO:mv]
is_a: VariO:0074 ! protein conformational change

[Term]
id: VariO:0077
name: changed domain orientation
def: "Variation affecting protein structure due to alteration to domain orientation." [VariO:mv]
is_a: VariO:0073 ! effect to protein fold

[Term]
id: VariO:0078
name: effect on protein disulphide formation
def: "Variation affecting formation of intramolecular disuphide bonds." [VariO:mv]
is_a: VariO:0073 ! effect to protein fold

[Term]
id: VariO:0079
name: effect on protein secondary structural element
def: "Variation affecting protein secondary structural element of local ordered structure." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0080
name: effect on protein helix
def: "Variation affecting secondary structure conformation where the peptide backbone forms a coil." [VariO:mv]
is_a: VariO:0079 ! effect on protein secondary structural element

[Term]
id: VariO:0081
name: effect on left handed protein helix
def: "Variation affecting protein left handed helix turning anticlockwise." [VariO:mv]
is_a: VariO:0080 ! effect on protein helix

[Term]
id: VariO:0082
name: effect on right handed protein helix
def: "Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw." [VariO:mv]
is_a: VariO:0080 ! effect on protein helix

[Term]
id: VariO:0083
name: effect on pi helix
def: "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." [VariO:mv]
is_a: VariO:0082 ! effect on right handed protein helix

[Term]
id: VariO:0084
name: effect on three ten helix
def: "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." [VariO:mv]
is_a: VariO:0082 ! effect on right handed protein helix

[Term]
id: VariO:0085
name: effect on alpha helix
def: "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." [VariO:mv]
is_a: VariO:0082 ! effect on right handed protein helix

[Term]
id: VariO:0086
name: effect on protein beta strand
def: "Variation affecting extended protein backbone structure." [VariO:mv]
is_a: VariO:0079 ! effect on protein secondary structural element

[Term]
id: VariO:0087
name: effect on protein antiparallel beta strand
def: "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)." [VariO:mv]
comment: Range.
is_a: VariO:0086 ! effect on protein beta strand

[Term]
id: VariO:0088
name: effect on protein parallel beta strand
def: "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)." [VariO:mv]
comment: Range.
is_a: VariO:0086 ! effect on protein beta strand

[Term]
id: VariO:0089
name: effect on protein turn motif
def: "Variation affecting protein backbone turn motif." [VariO:mv]
is_a: VariO:0079 ! effect on protein secondary structural element

[Term]
id: VariO:0090
name: effect on protein alpha beta motif
def: "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." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0091
name: effect on protein beta turn
def: "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." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0092
name: effect on protein st motif
def: "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)." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0093
name: effect on protein st staple
def: "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." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0094
name: effect on protein gamma turn
def: "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." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0095
name: effect on protein st turn
def: "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)." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0096
name: effect on protein schellman loop
def: "Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0097
name: effect on protein nest motif
def: "Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0098
name: effect on protein niche motif
def: "Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0099
name: effect on protein asx motif
def: "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)." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0100
name: effect on protein beta bulge
def: "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." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0101
name: effect on protein asx turn
def: "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)." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0102
name: effect on protein beta bulge loop
def: "Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds." [VariO:mv]
is_a: VariO:0089 ! effect on protein turn motif

[Term]
id: VariO:0103
name: effect on protein coil
def: "Variation affecting irregular, unstructured region of protein." [VariO:mv]
is_a: VariO:0079 ! effect on protein secondary structural element

[Term]
id: VariO:0104
name: effect on transmembrane polypeptide
def: "Variation altering membrane spanning protein." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0105
name: effect on membrane protein extramembrane region
def: "Variation affecting region not traversing the lipid bilayer in a membrane protein." [VariO:mv]
is_a: VariO:0104 ! effect on transmembrane polypeptide

[Term]
id: VariO:0106
name: effect on membrane protein intramembrane region
def: "Variation affecting region present in the lipid bilayer in a membrane protein." [VariO:mv]
is_a: VariO:0104 ! effect on transmembrane polypeptide

[Term]
id: VariO:0107
name: effect on protein post translational modification
def: "Variation affecting the covalent alteration of protein amino acid by post translational process." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0108
name: deletion of a post translational modification site
def: "Variation causing deletion of a post translational modification site." [VariO:mv]
is_a: VariO:0107 ! effect on protein post translational modification

[Term]
id: VariO:0109
name: effect on protein processing
def: "Variation affecting site of protein maturation by cleavage of peptide bond(s)." [VariO:mv]
is_a: VariO:0107 ! effect on protein post translational modification

[Term]
id: VariO:0110
name: effect on protein splicing
def: "Variation affecting post-translational removal of peptide sequences from within a protein sequence." [VariO:mv]
is_a: VariO:0109 ! effect on protein processing

[Term]
id: VariO:0111
name: variation generating a novel protein processing site
def: "Variation that generates a novel protein processing site." [VariO:mv]
is_a: VariO:0109 ! effect on protein processing

[Term]
id: VariO:0112
name: variation preventing polypeptide processing
def: "Variation causing prevention of polypeptide processing." [VariO:mv]
is_a: VariO:0109 ! effect on protein processing

[Term]
id: VariO:0113
name: generation of a novel post translational modification site
def: "Variation generating a novel post translational modification site." [VariO:mv]
is_a: VariO:0107 ! effect on protein post translational modification

[Term]
id: VariO:0114
name: effect on amino acid size
def: "Variation affecting amino acid side chain size." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0115
name: effect on protein packing
def: "Variation affecting amino acid packing in folded protein." [VariO:mv]
is_a: VariO:0114 ! effect on amino acid size

[Term]
id: VariO:0116
name: protein cavity formation
def: "Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one." [VariO:mv]
is_a: VariO:0115 ! effect on protein packing

[Term]
id: VariO:0117
name: protein overpacking
def: "Variation causing over packing of amino acids due to replacement by larger amino acid side chain." [VariO:mv]
is_a: VariO:0115 ! effect on protein packing

[Term]
id: VariO:0118
name: effect on protein interaction site
def: "Variation affecting ligand binding amino acid(s) in protein." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0119
name: effect on protein binding site
def: "Variation affecting region on the surface of a protein that interacts with another molecule." [VariO:mv]
is_a: VariO:0118 ! effect on protein interaction site

[Term]
id: VariO:0120
name: effect on protein catalytic site
def: "Variation affecting amino acid(s) in protein catalytic site." [VariO:mv]
is_a: VariO:0118 ! effect on protein interaction site

[Term]
id: VariO:0121
name: effect on protein quaternary structure
def: "Variation affecting three dimensional structure of a protein complex." [VariO:mv]
is_a: VariO:0064 ! effect on protein 3D structure

[Term]
id: VariO:0122
name: effect on protein quaternary structure forming interaction
def: "Variation affecting interaction between protein subunits in quaternary structure." [VariO:mv]
is_a: VariO:0121 ! effect on protein quaternary structure

[Term]
id: VariO:0123
name: complex 3D structural change
def: "Complex change of protein three dimensional structure." [VariO:mv]
is_a: VariO:0064 ! effect on protein 3D structure

[Term]
id: VariO:0124
name: protein elongation
def: "Variation prolonging protein chain at an end." [VariO:mv]
is_a: VariO:0070 ! effect on protein tertiary structure

[Term]
id: VariO:0125
name: C-terminal protein elongation
def: "Addition of one or more amino acids to protein C-terminus." [VariO:mv]
is_a: VariO:0124 ! protein elongation

[Term]
id: VariO:0126
name: N-terminal protein elongation
def: "Addition of one or more amino acids to protein N-terminus." [VariO:mv]
is_a: VariO:0124 ! protein elongation

[Term]
id: VariO:0127
name: DNA variation origin
def: "Origin of DNA variation." [VariO:mv]
is_a: VariO:0129 ! DNA variation type
created_by: Mauno Vihnen
creation_date: 2013-10-11T08:46:32Z

[Term]
id: VariO:0128
name: variation affecting DNA
def: "Effects of a variation on DNA level." [VariO:mv]
is_a: VariO:0001 ! variation

[Term]
id: VariO:0129
name: DNA variation type
def: "Type of DNA variation. Describes origin and classification of a variant." [VariO:mv]
is_a: VariO:0128 ! variation affecting DNA

[Term]
id: VariO:0130
name: DNA variation of genetic origin
def: "DNA variation that has genetic origin." [VariO:mv]
is_a: VariO:0127 ! DNA variation origin

[Term]
id: VariO:0131
name: genomic variation
def: "Variation of genomic level." [VariO:mv]
is_a: VariO:0322 ! DNA variation classification

[Term]
id: VariO:0132
name: chromosomal variation
def: "Variation at chromosomal level." [VariO:mv]
is_a: VariO:0322 ! DNA variation classification

[Term]
id: VariO:0133
name: variation in chromosome number
def: "Variation affecting chromosome number." [VariO:mv]
synonym: "aneuploidy" RELATED []
is_a: VariO:0132 ! chromosomal variation

[Term]
id: VariO:0134
name: variation of chromosome structure
def: "Variation affecting structure of chromosome." [VariO:mv]
is_a: VariO:0132 ! chromosomal variation

[Term]
id: VariO:0135
name: DNA chain variation
def: "Variation at DNA chain." [VariO:mv]
is_a: VariO:0322 ! DNA variation classification

[Term]
id: VariO:0136
name: DNA substitution
def: "Substitution of a DNA nucleotide." [VariO:mv]
is_a: VariO:0135 ! DNA chain variation

[Term]
id: VariO:0137
name: effect on DNA stem
def: "Variation affecting hydrogen bonding in contiguous nested base pairs in DNA." [VariO:mv]
is_a: VariO:0171 ! effect on DNA secondary structure
created_by: Mauno Vihinen
creation_date: 2012-11-09T15:02:45Z

[Term]
id: VariO:0138
name: variant
def: "A genetic character, organism or individual with a difference to reference state." [VariO:mv]
is_a: VariO:0232 ! variation attribute
created_by: Mauno Vihinen
creation_date: 2012-11-11T19:43:00Z

[Term]
id: VariO:0139
name: mutation
def: "Any process generating variation." [VariO:mv]
is_a: VariO:0232 ! variation attribute
created_by: Mauno Vihinen
creation_date: 2012-11-11T19:43:39Z

[Term]
id: VariO:0140
name: not changed
def: "The observed feature is not changed in relation to the wild type form." [VariO:mv]
is_a: VariO:0289 ! quantity change
created_by: Mauno Vihinen
creation_date: 2012-11-11T19:46:40Z

[Term]
id: VariO:0141
name: DNA deletion
def: "Removal of one or more continuous nucleotides from DNA sequence." [VariO:mv]
synonym: "nucleotide deletion" EXACT []
is_a: VariO:0135 ! DNA chain variation

[Term]
id: VariO:0142
name: DNA insertion
def: "Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence." [VariO:mv]
synonym: "nucleotide insertion" EXACT []
is_a: VariO:0135 ! DNA chain variation

[Term]
id: VariO:0143
name: DNA indel
def: "A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s)." [VariO:mv]
is_a: VariO:0135 ! DNA chain variation

[Term]
id: VariO:0144
name: DNA translocation
def: "A continuous stretch of DNA sequence moved to a new position." [VariO:mv]
xref: MI:0593
xref: SO:0000199
is_a: VariO:0135 ! DNA chain variation

[Term]
id: VariO:0145
name: DNA inversion
def: "A continuous stretch of DNA sequence inserted to the same position in reverse orientation." [VariO:mv]
xref: SO:1000036
is_a: VariO:0144 ! DNA translocation

[Term]
id: VariO:0146
name: DNA variation of non-genetic origin
def: "DNA variation that does not have genetic origin." [VariO:mv]
is_a: VariO:0127 ! DNA variation origin

[Term]
id: VariO:0147
name: epigenetic DNA variation
def: "Heritable DNA variation of non-genetic origin." [VariO:mv]
is_a: VariO:0146 ! DNA variation of non-genetic origin

[Term]
id: VariO:0148
name: variation affecting DNA function
def: "Variation having effect on DNA function and usage." [VariO:mv]
is_a: VariO:0128 ! variation affecting DNA

[Term]
id: VariO:0149
name: effect on transcription
def: "Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA." [VariO:mv]
is_a: VariO:0148 ! variation affecting DNA function

[Term]
id: VariO:0150
name: effect on DNA information transfer
def: "Variation affecting information transfer of DNA." [VariO:mv]
is_a: VariO:0148 ! variation affecting DNA function

[Term]
id: VariO:0151
name: defect in DNA repair
def: "Variation affecting the process of restoring DNA after damage." [VariO:mv]
xref: GO:0006281
xref: Wikipedia:DNA_repair
is_a: VariO:0148 ! variation affecting DNA function

[Term]
id: VariO:0152
name: effect on regulatory function of DNA
def: "Variation affecting regulatory function of DNA." [VariO:mv]
is_a: VariO:0148 ! variation affecting DNA function

[Term]
id: VariO:0153
name: effect on promoter activity
def: "Variation affecting promoter activity on DNA expression." [VariO:mv]
is_a: VariO:0152 ! effect on regulatory function of DNA

[Term]
id: VariO:0154
name: defective DNA replication
def: "Variation originating from semiconservative DNA strand synthesis. The template for replication is either DNA or RNA molecule." [VariO:mv]
is_a: VariO:0148 ! variation affecting DNA function

[Term]
id: VariO:0155
name: variation affecting DNA structure
def: "Variation affecting structure of DNA." [VariO:mv]
is_a: VariO:0128 ! variation affecting DNA

[Term]
id: VariO:0156
name: epigenetic DNA modification
def: "Hereditary variation of DNA not affecting primary sequence." [VariO:mv]
is_a: VariO:0155 ! variation affecting DNA structure

[Term]
id: VariO:0157
name: epigenetic DNA methylation
def: "Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression." [VariO:mv]
is_a: VariO:0156 ! epigenetic DNA modification

[Term]
id: VariO:0158
name: chromatin remodeling
def: "Dynamic chromatin structural change." [VariO:mv]
synonym: "chromatin modeling" EXACT [GO:0006338]
synonym: "chromatin remodelling" EXACT [GO:0006338]
xref: GO:0006338
is_a: VariO:0156 ! epigenetic DNA modification

[Term]
id: VariO:0159
name: affected DNA level
def: "Affected level of DNA." [VariO:mv]
is_a: VariO:0155 ! variation affecting DNA structure

[Term]
id: VariO:0160
name: DNA chain affected
def: "Variation effect on DNA level." [VariO:mv]
is_a: VariO:0159 ! affected DNA level

[Term]
id: VariO:0161
name: variation in intron
def: "Variation located in intron." [VariO:mv]
xref: SO:0001627
is_a: VariO:0160 ! DNA chain affected

[Term]
id: VariO:0162
name: variation in exon
def: "Variation located in exon." [VariO:mv]
is_a: VariO:0160 ! DNA chain affected

[Term]
id: VariO:0163
name: variation at intergenic DNA
def: "Variation located in intergenic DNA." [VariO:mv]
xref: SO:0001628
is_a: VariO:0160 ! DNA chain affected

[Term]
id: VariO:0164
name: chromosome affected
def: "Variation effect on chromosome level." [VariO:mv]
is_a: VariO:0159 ! affected DNA level

[Term]
id: VariO:0165
name: genome affected
def: "Variation effect on genome level." [VariO:mv]
is_a: VariO:0159 ! affected DNA level

[Term]
id: VariO:0166
name: gene structure variation
def: "Variation affecting gene structure." [VariO:mv]
is_a: VariO:0155 ! variation affecting DNA structure

[Term]
id: VariO:0167
name: gene fusion
def: "Variation fusing two genes." [VariO:mv]
xref: SO:0001565
is_a: VariO:0166 ! gene structure variation

[Term]
id: VariO:0168
name: gene deletion
def: "Variation deleting gene." [VariO:mv]
is_a: VariO:0166 ! gene structure variation

[Term]
id: VariO:0169
name: complete gene deletion
def: "Variation deleting complete gene." [VariO:mv]
is_a: VariO:0168 ! gene deletion

[Term]
id: VariO:0170
name: partial gene deletion
def: "Variation deleting part of a gene." [VariO:mv]
is_a: VariO:0168 ! gene deletion

[Term]
id: VariO:0171
name: effect on DNA secondary structure
def: "Variation affecting DNA secondary structure." [VariO:mv]
is_a: VariO:0155 ! variation affecting DNA structure

[Term]
id: VariO:0172
name: artificial DNA variation
def: "Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA." [VariO:mv]
is_a: VariO:0146 ! DNA variation of non-genetic origin
created_by: Mauno Vihnen
creation_date: 2012-11-16T08:44:55Z

[Term]
id: VariO:0173
name: effect on DNA G quartet
def: "Variation affecting G-quartet of four stranded DNA structure." [VariO:mv]
is_a: VariO:0171 ! effect on DNA secondary structure

[Term]
id: VariO:0174
name: effect on i motif
def: "Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly." [VariO:mv]
is_a: VariO:0171 ! effect on DNA secondary structure

[Term]
id: VariO:0175
name: effect on triple-stranded DNA
def: "Variation affecting DNA helix formed of three strands." [VariO:mv]
is_a: VariO:0171 ! effect on DNA secondary structure

[Term]
id: VariO:0176
name: chromosome variation
def: "Variation affecting chromosome." [VariO:mv]
xref: SO:0000240
is_a: VariO:0155 ! variation affecting DNA structure

[Term]
id: VariO:0177
name: telomere length change
def: "Variation affecting length of telomere sequence." [VariO:mv]
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0178
name: telomere shortening
def: "Variation shortening length of telomere sequence." [VariO:mv]
is_a: VariO:0177 ! telomere length change

[Term]
id: VariO:0179
name: telomere extension
def: "Variation extending length of telomere sequence." [VariO:mv]
is_a: VariO:0177 ! telomere length change

[Term]
id: VariO:0180
name: chromosome structure variation
def: "Variation affecting structure of chromosome." [VariO:mv]
xref: SO:1000183
is_a: VariO:0176 ! chromosome variation

[Term]
id: VariO:0181
name: isochromosome
def: "Chromosome lacking one arm with duplication of the other arm." [VariO:mv]
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0182
name: ring chromosome
def: "Circular chromosome with ends joined." [VariO:mv]
xref: SO:1000045
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0183
name: chromosomal amplification
def: "Increase in the frequency of a chromosomal region." [VariO:mv]
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0184
name: interspersed repeat
def: "Copies of a chromosomal region of length greater than one scattered to genome sequence." [VariO:mv]
xref: SO:0000658
is_a: VariO:0183 ! chromosomal amplification

[Term]
id: VariO:0185
name: tandem repeat
def: "Adjacent copies of a chromosomal region of length greater than 1." [VariO:mv]
xref: SO:0000705
is_a: VariO:0183 ! chromosomal amplification

[Term]
id: VariO:0186
name: minisatellite
def: "Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs." [VariO:mv]
is_a: VariO:0185 ! tandem repeat

[Term]
id: VariO:0187
name: copy number variation
def: "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." [VariO:mv]
xref: SO:0001019
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0188
name: microsatellite
def: "Tandem repetitive sequence consisting of units of two to six base pair." [VariO:mv]
is_a: VariO:0185 ! tandem repeat

[Term]
id: VariO:0189
name: trinucleotide expansion
def: "Tandem repetitive sequence consisting of three nucleotide units." [VariO:mv]
is_a: VariO:0188 ! microsatellite

[Term]
id: VariO:0190
name: mononucleotide expansion
def: "Tandem repetitive sequence consisting of one nucleotide type." [VariO:mv]
is_a: VariO:0188 ! microsatellite

[Term]
id: VariO:0191
name: tetranucleotide expansion
def: "Tandem repetitive sequence consisting of four nucleotide units." [VariO:mv]
is_a: VariO:0188 ! microsatellite

[Term]
id: VariO:0192
name: mobile genetic element insertion
def: "Mobile genetic element incorporated into chromosome." [VariO:mv]
is_a: VariO:0183 ! chromosomal amplification

[Term]
id: VariO:0193
name: chromosomal deletion
def: "Deletion of chromosomal region." [VariO:mv]
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0194
name: interstitial deletion
def: "Deletion of chromosomal region not including terminus." [VariO:mv]
is_a: VariO:0193 ! chromosomal deletion

[Term]
id: VariO:0195
name: terminal deletion
def: "Deletion of chromosomal region from the end of chromosome arm." [VariO:mv]
is_a: VariO:0193 ! chromosomal deletion

[Term]
id: VariO:0196
name: complex chromosomal variation
def: "Chromosome structure variation with four or more breakpoints." [SO:ke, VariO:mv]
xref: SO:1000146
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0197
name: chromosomal translocation
def: "Translocation of chromosomal region." [VariO:mv]
xref: SO:0000199
is_a: VariO:0180 ! chromosome structure variation

[Term]
id: VariO:0198
name: intrachromosomal translocation
def: "Translocation of chromosomal region within a chromosome." [VariO:mv]
is_a: VariO:0197 ! chromosomal translocation

[Term]
id: VariO:0199
name: chromosomal inversion
def: "Intrachromosomal variation where a chromosomal region is inserted in reverse direction." [VariO:mv]
is_a: VariO:0198 ! intrachromosomal translocation

[Term]
id: VariO:0200
name: paracentric inversion
def: "Chromosomal inversion within a chromosome arm." [VariO:mv]
xref: SO:1000047
is_a: VariO:0199 ! chromosomal inversion

[Term]
id: VariO:0201
name: pericentric inversion
def: "Chromosomal inversion including centromere." [VariO:mv]
xref: SO:1000046
is_a: VariO:0199 ! chromosomal inversion

[Term]
id: VariO:0202
name: interchromosomal translocation
def: "Translocation of chromosomal region to another chromosome." [VariO:mv]
is_a: VariO:0197 ! chromosomal translocation

[Term]
id: VariO:0203
name: reciprocal chromosomal translocation
def: "Switching of chromosomal regions between two chromosomes." [VariO:mv]
xref: SO:1000048
is_a: VariO:0202 ! interchromosomal translocation

[Term]
id: VariO:0204
name: Robertsonian translocation
def: "Fusion of long arms of two acrocentric chromosomes having very short p arms." [VariO:mv]
xref: SO:1000043
is_a: VariO:0202 ! interchromosomal translocation

[Term]
id: VariO:0205
name: uncharacterized chromosomal variation
def: "Chromosomal variation of uncharacterized type." [VariO:mv]
xref: SO:1000170
is_a: VariO:0176 ! chromosome variation

[Term]
id: VariO:0206
name: chromosome number variation
def: "Variation affecting the number of chromosomes." [VariO:mv]
synonym: "aneuploidy" EXACT []
is_a: VariO:0176 ! chromosome variation

[Term]
id: VariO:0207
name: trisomy
def: "Three copies of a chromosome in a cell or organism." [VariO:mv]
is_a: VariO:0206 ! chromosome number variation

[Term]
id: VariO:0208
name: disomy
def: "Two copies of a chromosome in a cell or organism ." [VariO:mv]
is_a: VariO:0206 ! chromosome number variation

[Term]
id: VariO:0209
name: uniparental disomy
def: "Both copies of a chromosome or a part of it in diploid cell or organism are from one parent." [VariO:mv]
is_a: VariO:0208 ! disomy

[Term]
id: VariO:0210
name: isodisomy
def: "Uniparental disomy with duplication of a single chromosome from one parent." [VariO:mv]
is_a: VariO:0209 ! uniparental disomy

[Term]
id: VariO:0211
name: heterodisomy
def: "Uniparental disomy with both homologous chromosomes from one parent." [VariO:mv]
is_a: VariO:0209 ! uniparental disomy

[Term]
id: VariO:0212
name: nullisomy
def: "No copies of a chromosome in a cell or organism." [VariO:mv]
is_a: VariO:0206 ! chromosome number variation

[Term]
id: VariO:0213
name: tetrasomy
def: "Four copies of a chromosome in a cell or organism." [VariO:mv]
is_a: VariO:0206 ! chromosome number variation

[Term]
id: VariO:0214
name: monosomy
def: "One copy of a chromosome in a cell or organism." [VariO:mv]
is_a: VariO:0206 ! chromosome number variation

[Term]
id: VariO:0215
name: chromosome set number variation
def: "Variation affecting number of entire chromosome sets." [VariO:mv]
synonym: "euploidy" EXACT []
is_a: VariO:0155 ! variation affecting DNA structure

[Term]
id: VariO:0216
name: diploidy
def: "Variation with two sets of chromosomes." [VariO:mv]
is_a: VariO:0215 ! chromosome set number variation

[Term]
id: VariO:0217
name: tetraploidy
def: "Variation with four sets of chromosomes." [VariO:mv]
is_a: VariO:0215 ! chromosome set number variation
created_by: Mauno
creation_date: 2011-03-04T12:19:35Z

[Term]
id: VariO:0218
name: polyploidy
def: "Variation with several sets of chromosomes." [VariO:mv]
is_a: VariO:0215 ! chromosome set number variation

[Term]
id: VariO:0219
name: autopolyploidy
def: "Variation with several sets of chromosomes originating from the same organism." [VariO:mv]
is_a: VariO:0218 ! polyploidy

[Term]
id: VariO:0220
name: allopolyploidy
def: "Variation with several sets of chromosomes originating from a different organism." [VariO:mv]
is_a: VariO:0218 ! polyploidy

[Term]
id: VariO:0221
name: nulliploidy
def: "Variation without chromosomes." [VariO:mv]
is_a: VariO:0215 ! chromosome set number variation

[Term]
id: VariO:0222
name: triploidy
def: "Variation with three sets of chromosomes." [VariO:mv]
is_a: VariO:0215 ! chromosome set number variation

[Term]
id: VariO:0223
name: pentaploidy
def: "Variation with five sets of chromosomes." [VariO:mv]
is_a: VariO:0215 ! chromosome set number variation

[Term]
id: VariO:0224
name: hexaploidy
def: "Variation with six sets of chromosomes." [VariO:mv]
is_a: VariO:0215 ! chromosome set number variation

[Term]
id: VariO:0225
name: monoploidy
def: "Variation with a single set of chromosomes." [VariO:mv]
synonym: "haploidy" EXACT []
is_a: VariO:0215 ! chromosome set number variation

[Term]
id: VariO:0226
name: chromatin structure variation
def: "Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins." [VariO:mv]
is_a: VariO:0155 ! variation affecting DNA structure

[Term]
id: VariO:0227
name: variation affecting DNA property
def: "Variation affecting characteristic property of DNA." [VariO:mv]
is_a: VariO:0128 ! variation affecting DNA

[Term]
id: VariO:0228
name: protein fusion
def: "Fusion of two protein chains. Produced from fusion gene of two joined genes." [VariO:mv]
is_a: VariO:0124 ! protein elongation
created_by: Mauno Vihnen
creation_date: 2012-12-11T08:59:44Z

[Term]
id: VariO:0229
name: association of DNA variation to pathogenicity
def: "Implication of a DNA variant to pathogenicity." [VariO:mv]
is_a: VariO:0227 ! variation affecting DNA property

[Term]
id: VariO:0230
name: effect on DNA interaction
def: "Variation affecting interaction of DNA with its partner." [VariO:mv]
is_a: VariO:0227 ! variation affecting DNA property

[Term]
id: VariO:0231
name: conservation of DNA variation site
def: "Conservation of the variation site in related DNA sequences." [VariO:mv]
is_a: VariO:0227 ! variation affecting DNA property

[Term]
id: VariO:0232
name: variation attribute
def: "Attributes define and modulate terms at other levels." [VariO:mv]
is_a: VariO:0001 ! variation

[Term]
id: VariO:0233
name: conservation
def: "Sequence conservation attribute." [VariO:mv]
is_a: VariO:0232 ! variation attribute

[Term]
id: VariO:0234
name: conserved region
def: "Variation at a region of sequence similarity in multiple sequence alignment of related sequences." [VariO:mv]
is_a: VariO:0233 ! conservation

[Term]
id: VariO:0235
name: invariant region
def: "Variation at invariant sequence region in multiple sequence alignment of related sequences." [VariO:mv]
is_a: VariO:0233 ! conservation

[Term]
id: VariO:0236
name: interaction
def: "Mutual or reciprocal action or influence that happens at a given place and time between participating molecules." [src_code:NR, VariO:mv]
is_a: VariO:0232 ! variation attribute

[Term]
id: VariO:0237
name: genetic interaction
def: "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." [PMID:16527956, VariO:mv]
xref: MI:0208
is_a: VariO:0236 ! interaction

[Term]
id: VariO:0238
name: genetic interaction defined by inequality
def: "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." [PMID:14755292, VariO:mv]
synonym: "genetic inequality" EXACT [MI:0931]
xref: MI:0931
is_a: VariO:0237 ! genetic interaction

[Term]
id: VariO:0239
name: single nonmonotonic genetic interaction defined by inequality
def: "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." [PMID:15833125]
synonym: "single nonmonotonic" EXACT [MI:0800]
synonym: "single nonmonotonic genetic interaction (sensu inequality)" EXACT [MI:0800]
xref: MI:0800
is_a: VariO:0238 ! genetic interaction defined by inequality

[Term]
id: VariO:0240
name: missing protein
def: "Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism." [VariO:mv]
is_a: VariO:0325 ! protein variation classification
created_by: Mauno Vihnen
creation_date: 2012-12-11T13:07:02Z

[Term]
id: VariO:0241
name: RNA translocation
def: "A continuous stretch of RNA sequence moved to a new position." [VariO:mv]
is_a: VariO:0328 ! RNA variation classification
created_by: Mauno Vihnen
creation_date: 2012-12-18T16:17:33Z

[Term]
id: VariO:0242
name: conditional genetic interaction defined by inequality
def: "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." [PMID:15833125, VariO:mv]
synonym: "conditional" EXACT [MI:0798]
synonym: "conditional genetic interaction (sensu inequality)" EXACT [MI:0798]
xref: MI:0798
is_a: VariO:0238 ! genetic interaction defined by inequality

[Term]
id: VariO:0243
name: additive genetic interaction defined by inequality
def: "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." [PMID:15833125, VariO:mv]
synonym: "additive" EXACT [MI:0799]
synonym: "additive genetic interaction (sensu inequality)" EXACT [MI:0799]
xref: MI:0799
is_a: VariO:0238 ! genetic interaction defined by inequality

[Term]
id: VariO:0244
name: RNA inversion
def: "A continuous stretch of RNA sequence inserted to the same position in reverse orientation." [VriO:mv]
is_a: VariO:0241 ! RNA translocation
created_by: Mauno Vihnen
creation_date: 2012-12-18T16:17:33Z

[Term]
id: VariO:0245
name: missing RNA
def: "Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site." [VariO:mv]
is_a: VariO:0328 ! RNA variation classification
created_by: Mauno Vihnen
creation_date: 2013-01-04T09:23:09Z

[Term]
id: VariO:0246
name: artificial protein variation
def: "Protein variation generated on purpose." [VariO:mv]
is_a: VariO:0024 ! variation emerging at protein level
created_by: gerard
creation_date: 2013-02-01T11:24:30Z

[Term]
id: VariO:0247
name: artificial RNA variation
def: "RNA variation generated on purpose." [VariO:mv]
is_a: VariO:0333 ! variation emerging at RNA level
created_by: gerard
creation_date: 2013-02-01T11:27:07Z

[Term]
id: VariO:0248
name: positive genetic interaction
def: "The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b." [PMID:14755292, VariO:mv]
synonym: "positive gent int" EXACT [MI:0935]
xref: MI:0935
is_a: VariO:0237 ! genetic interaction

[Term]
id: VariO:0249
name: double nonmonotonic genetic interaction defined by inequality
def: "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." [PMID:15833125, VariO:mv]
synonym: "double nonmonotonic" EXACT [MI:0801]
synonym: "double nonmonotonic genetic interaction (sensu inequality)" EXACT [MI:0801]
xref: MI:0801
is_a: VariO:0238 ! genetic interaction defined by inequality
is_a: VariO:0248 ! positive genetic interaction

[Term]
id: VariO:0250
name: epistatic genetic interaction
def: "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." [PMID:11988766]
synonym: "epistatis" EXACT [MI:0930]
xref: MI:0930
is_a: VariO:0248 ! positive genetic interaction

[Term]
id: VariO:0251
name: epistatic genetic interaction defined by inequality
def: "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)." [PMID:15833125, VariO:mv]
synonym: "epistatic" EXACT [MI:0797]
synonym: "epistatic genetic interaction (sensu inequality)" EXACT [MI:0797]
xref: MI:0797
is_a: VariO:0238 ! genetic interaction defined by inequality
is_a: VariO:0250 ! epistatic genetic interaction

[Term]
id: VariO:0252
name: asynthetic genetic interaction defined by inequality
def: "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." [PMID:15833125]
synonym: "asynthetic" EXACT [MI:0795]
synonym: "asynthetic genetic interaction (sensu inequality)" EXACT [MI:0795]
xref: MI:0795
is_a: VariO:0238 ! genetic interaction defined by inequality
is_a: VariO:0250 ! epistatic genetic interaction

[Term]
id: VariO:0253
name: suppressive genetic interaction defined by inequality
def: "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." [PMID:15833125, VariO:mv]
synonym: "suppression" EXACT [MI:0796]
synonym: "suppressive genetic interaction (sensu inequality)" EXACT [MI:0796]
xref: MI:0796
is_a: VariO:0238 ! genetic interaction defined by inequality
is_a: VariO:0250 ! epistatic genetic interaction

[Term]
id: VariO:0254
name: neutral genetic interaction
def: "The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b." [PMID:14755292, VariO:mv]
synonym: "neutral gent int" EXACT [MI:0934]
xref: MI:0934
is_a: VariO:0237 ! genetic interaction

[Term]
id: VariO:0255
name: noninteractive genetic interaction defined by inequality
def: "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." [PMID:15833125, VariO:mv]
synonym: "noninteractive" EXACT [MI:0932]
synonym: "noninteractive genetic interaction (sensu inequality)" EXACT [MI:0932]
xref: MI:0932
is_a: VariO:0238 ! genetic interaction defined by inequality
is_a: VariO:0254 ! neutral genetic interaction

[Term]
id: VariO:0256
name: negative genetic interaction
def: "The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b." [PMID:14755292, VariO:mv]
synonym: "negative gen int" EXACT [MI:0933]
xref: MI:0933
is_a: VariO:0237 ! genetic interaction

[Term]
id: VariO:0257
name: synthetic genetic interaction defined by inequality
def: "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." [PMID:15833125]
synonym: "synthetic" EXACT [MI:0794]
synonym: "synthetic genetic interaction (sensu inequality)" EXACT [MI:0794]
xref: MI:0794
is_a: VariO:0238 ! genetic interaction defined by inequality
is_a: VariO:0256 ! negative genetic interaction

[Term]
id: VariO:0258
name: structural level of interaction
def: "Molecular structural level of interaction." [VariO:mv]
is_a: VariO:0236 ! interaction

[Term]
id: VariO:0259
name: intermolecular interaction
def: "Interaction between molecules." [VariO:mv]
is_a: VariO:0258 ! structural level of interaction

[Term]
id: VariO:0260
name: intramolecular interaction
def: "Interaction within a molecule." [VariO:mv]
is_a: VariO:0258 ! structural level of interaction

[Term]
id: VariO:0261
name: colocalization
def: "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." [PMID:14755292]
xref: MI:0403
is_a: VariO:0236 ! interaction

[Term]
id: VariO:0262
name: interactor
def: "Entity participating in a physical or functional interaction." [SBO:0000336]
xref: SBO:0000336
is_a: VariO:0236 ! interaction

[Term]
id: VariO:0263
name: small molecule
def: "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." [PMID:14755292]
xref: MI:0328
is_a: VariO:0262 ! interactor

[Term]
id: VariO:0264
name: metal
def: "Metal atom." [CHEBI:33521]
xref: CHEBI:33521
is_a: VariO:0263 ! small molecule

[Term]
id: VariO:0265
name: solvent
def: "A liquid that can dissolve other substances (solutes) without any change in their chemical composition." [CHEBI:46787]
xref: CHEBI:46787
is_a: VariO:0263 ! small molecule

[Term]
id: VariO:0266
name: water
def: "An inorganic hydroxy compound that has formula H2O." [CHEBI:15377]
xref: CHEBI:15377
is_a: VariO:0265 ! solvent

[Term]
id: VariO:0267
name: complex
def: "Set of interacting molecules that can be copurified." [PMID:14755292]
xref: MI:0314
is_a: VariO:0262 ! interactor

[Term]
id: VariO:0268
name: ribonucleoprotein complex
def: "A macromolecular complex containing both protein and RNA molecules." [PMID:14755292]
synonym: "ribonucleoprot compl" EXACT [MI:0316]
xref: MI:0316
is_a: VariO:0267 ! complex

[Term]
id: VariO:0269
name: protein complex
def: "A stable set of interacting proteins that can be copurified and operate as a functional unit." [PMID:14755292]
synonym: "protein-protein complex" EXACT [GO:0043234]
xref: GO:0043234
xref: MI:0315
is_a: VariO:0267 ! complex

[Term]
id: VariO:0270
name: protein dna complex
def: "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." [PMID:14755292]
xref: MI:0233
is_a: VariO:0267 ! complex

[Term]
id: VariO:0271
name: unknown participant
def: "Any type of molecule, including complexes, that may be observed but not identified." [PMID:14755292]
xref: MI:0329
is_a: VariO:0262 ! interactor

[Term]
id: VariO:0272
name: gene
def: "Interactor of genetic interaction." [MI:0000704]
xref: MI:0250
is_a: VariO:0262 ! interactor

[Term]
id: VariO:0273
name: biopolymer
def: "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds." [PMID:14577292]
xref: MI:0383
is_a: VariO:0262 ! interactor

[Term]
id: VariO:0274
name: nucleic acid
def: "Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages." [PMID:14755292]
xref: GO:0005561
xref: MI:0318
is_a: VariO:0273 ! biopolymer

[Term]
id: VariO:0275
name: peptide
def: "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." [PMID:14755292]
synonym: "oligopeptide" EXACT [MI:0327]
synonym: "polypeptide" EXACT [MI:0327]
xref: MI:0327
is_a: VariO:0273 ! biopolymer

[Term]
id: VariO:0276
name: polysaccharide
def: "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." [PMID:14755292]
xref: MI:0904
is_a: VariO:0273 ! biopolymer

[Term]
id: VariO:0277
name: protein
def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence." [PMID:14755292]
xref: GO:0003675
xref: MI:0326
is_a: VariO:0273 ! biopolymer

[Term]
id: VariO:0278
name: association
def: "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." [PMID:14755292]
xref: MI:0914
is_a: VariO:0236 ! interaction

[Term]
id: VariO:0279
name: interaction physical force
def: "Interaction physical force." [VariO:mv]
is_a: VariO:0236 ! interaction

[Term]
id: VariO:0280
name: covalent bond
def: "A chemical link between two atoms in which electrons are shared between them." [http://chemistry.about.com/od/chemistryglossary/a/covalentbonddef.htm]
is_a: VariO:0279 ! interaction physical force

[Term]
id: VariO:0281
name: disulphide bridge
def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain." [EBIBS:GAR, UniProt:curation_manual, VariO:mv]
xref: SO:0001088
is_a: VariO:0280 ! covalent bond

[Term]
id: VariO:0282
name: non covalent bond
def: "Interaction between biochemical entities that results in the formation of a non-covalent bond." [VariO:mv]
xref: SBO:0000177
is_a: VariO:0279 ! interaction physical force

[Term]
id: VariO:0283
name: hydrogen bond
def: "Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom." [VariO:mv]
synonym: "H-bond" RELATED [FIX:0000503]
xref: FIX:0000503
xref: http://chemistry.about.com/od/chemistryglossary/g/hbond.htm
is_a: VariO:0282 ! non covalent bond

[Term]
id: VariO:0284
name: hydrogen bond network
def: "Network of interactions formed by several hydrogen bonds." [VariO:mv]
is_a: VariO:0283 ! hydrogen bond

[Term]
id: VariO:0285
name: hydrophobic interaction
def: "Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction." [http://medical-dictionary.thefreedictionary.com/Hydrophobic+Interaction]
is_a: VariO:0282 ! non covalent bond

[Term]
id: VariO:0286
name: salt bridge
def: "Interaction between charged groups." [VariO:mv]
is_a: VariO:0282 ! non covalent bond

[Term]
id: VariO:0287
name: van der Waals interaction
def: "Weak attractive electrical force between neutral groups or molecules." [VariO:mv]
xref: FIX:0000506
is_a: VariO:0282 ! non covalent bond

[Term]
id: VariO:0288
name: electrostatic interaction
def: "Attraction between two electrically charged groups or molecules." [VariO:mv]
is_a: VariO:0282 ! non covalent bond

[Term]
id: VariO:0289
name: quantity change
def: "Quantity attribute." [VariO:mv]
is_a: VariO:0232 ! variation attribute

[Term]
id: VariO:0290
name: decreased
def: "The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.)." [SGD:curators]
xref: APO:0000003
is_a: VariO:0289 ! quantity change

[Term]
id: VariO:0291
name: increased
def: "The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.)." [SGD:curators]
xref: APO:0000004
is_a: VariO:0289 ! quantity change

[Term]
id: VariO:0292
name: missing
def: "The observed feature is missing compared to that in the wild type." [VariO:mv]
is_a: VariO:0289 ! quantity change

[Term]
id: VariO:0293
name: pathogenicity association
def: "Pathogenicity attribute." [VariO:mv]
is_a: VariO:0232 ! variation attribute

[Term]
id: VariO:0294
name: disease causing
def: "Variation is causative of disease." [VariO:mv]
is_a: VariO:0293 ! pathogenicity association

[Term]
id: VariO:0295
name: not related to clinical phenotype
def: "Variation is not related to clinical phenotype." [VariO:mv]
is_a: VariO:0293 ! pathogenicity association

[Term]
id: VariO:0296
name: disease associated
def: "Variation is disease related." [VariO:mv]
is_a: VariO:0293 ! pathogenicity association

[Term]
id: VariO:0297
name: variation affecting RNA
def: "Effects of a variation on RNA level." [VariO:mv]
is_a: VariO:0001 ! variation

[Term]
id: VariO:0298
name: variation affecting RNA property
def: "Variation affecting characteristic property of RNA." [VariO:mv]
is_a: VariO:0297 ! variation affecting RNA

[Term]
id: VariO:0299
name: effect on RNA degradation
def: "Variation affecting degradation of RNA." [VariO:mv]
is_a: VariO:0298 ! variation affecting RNA property

[Term]
id: VariO:0300
name: effect on RNA folding
def: "Variation affecting folding of RNA." [VariO:mv]
is_a: VariO:0298 ! variation affecting RNA property

[Term]
id: VariO:0301
name: effect on RNA stability
def: "Variation affecting stability of transcript." [VariO:mv]
xref: SO:0001546
is_a: VariO:0298 ! variation affecting RNA property

[Term]
id: VariO:0302
name: conservation of RNA variation site
def: "Conservation of the variation site in related RNA sequences." [VariO:mv]
is_a: VariO:0298 ! variation affecting RNA property

[Term]
id: VariO:0303
name: polysomy
def: "An excess of a particular chromosome in a cell or organism." [VariO:mv]
is_a: VariO:0206 ! chromosome number variation
created_by: gerard
creation_date: 2013-02-01T11:30:39Z

[Term]
id: VariO:0304
name: association of RNA variation to pathogenicity
def: "Implication of an RNA variant to pathogenicity." [VariO:mv]
is_a: VariO:0298 ! variation affecting RNA property

[Term]
id: VariO:0305
name: effect on RNA interaction
def: "Variation affecting interaction of RNA with its partner." [VariO:mv]
is_a: VariO:0298 ! variation affecting RNA property

[Term]
id: VariO:0306
name: RNA variation type
def: "Type of RNA variation. Describes origin and classification of a variant." [VariO:mv]
is_a: VariO:0297 ! variation affecting RNA

[Term]
id: VariO:0307
name: RNA variation of genetic origin
def: "RNA variation that has genetic origin." [VariO:mv]
is_a: VariO:0324 ! RNA variation origin

[Term]
id: VariO:0308
name: missense variation
def: "Nucleotide change in the mRNA triplet codon codes for another amino acid." [VariO:mv]
is_a: VariO:0312 ! RNA substitution

[Term]
id: VariO:0309
name: termination codon change
def: "RNA nucleotide change in termination codon." [VariO:mv]
xref: SO:0001590
is_a: VariO:0328 ! RNA variation classification

[Term]
id: VariO:0310
name: nonsense variation
def: "Nucleotide change in the mRNA codon triplet creates a terminator codon." [VariO:mv]
is_a: VariO:0312 ! RNA substitution

[Term]
id: VariO:0311
name: RNA indel
def: "A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s)." [VariO:mv]
is_a: VariO:0328 ! RNA variation classification

[Term]
id: VariO:0312
name: RNA substitution
def: "Substitution of RNA nucleotide." [VariO:mv]
is_a: VariO:0328 ! RNA variation classification

[Term]
id: VariO:0313
name: transition
def: "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." [VariO:mv]
relationship: part_of VariO:0136 ! DNA substitution
relationship: part_of VariO:0312 ! RNA substitution

[Term]
id: VariO:0314
name: pyrimidine transition
def: "A substitution of a pyrimidine, C or T (or U), for another pyrimidine." [VariO:mv]
is_a: VariO:0313 ! transition

[Term]
id: VariO:0315
name: purine transition
def: "A substitution of a purine, A or G, for another purine." [VariO:mv]
is_a: VariO:0313 ! transition

[Term]
id: VariO:0316
name: transversion
def: "Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa." [VariO:mv]
xref: http://en.wikipedia.org/wiki/Transversion "wiki"
relationship: part_of VariO:0136 ! DNA substitution
relationship: part_of VariO:0312 ! RNA substitution

[Term]
id: VariO:0317
name: initiation codon change
def: "RNA nucleotide change in the initiation codon." [VariO:mv]
xref: SO:0001582
is_a: VariO:0328 ! RNA variation classification

[Term]
id: VariO:0318
name: silent variation
def: "RNA variation that does not change the encoded amino acid." [VariO:mv]
is_a: VariO:0312 ! RNA substitution

[Term]
id: VariO:0319
name: RNA deletion
def: "One or more continuous nucleotides are missing from RNA sequence." [VariO:mv]
is_a: VariO:0328 ! RNA variation classification

[Term]
id: VariO:0320
name: in-frame deletion
def: "Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained." [VariO:mv]
is_a: VariO:0319 ! RNA deletion

[Term]
id: VariO:0321
name: out-of-frame deletion
def: "Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame." [VariO:mv]
is_a: VariO:0319 ! RNA deletion

[Term]
id: VariO:0322
name: DNA variation classification
def: "Classification of DNA variation." [VariO:mv]
is_a: VariO:0129 ! DNA variation type
created_by: Mauno Vihnen
creation_date: 2013-10-11T08:46:32Z

[Term]
id: VariO:0323
name: protein variation origin
def: "Origin of protein variation." [VariO:mv]
is_a: VariO:0012 ! protein variation type
created_by: Mauno Vihnen
creation_date: 2013-10-11T08:53:23Z

[Term]
id: VariO:0324
name: RNA variation origin
def: "Origin of RNA variation." [VariO:mv]
is_a: VariO:0306 ! RNA variation type
created_by: Mauno Vihnen
creation_date: 2013-10-11T09:04:23Z

[Term]
id: VariO:0325
name: protein variation classification
def: "Classification of protein variation." [VariO:mv]
is_a: VariO:0012 ! protein variation type
created_by: Mauno Vihnen
creation_date: 2013-10-11T08:59:04Z

[Term]
id: VariO:0326
name: RNA insertion
def: "Addition of one or more nucleotides between adjacent nucleotides in RNA sequence." [VariO:mv]
is_a: VariO:0328 ! RNA variation classification

[Term]
id: VariO:0327
name: out-of-frame insertion
def: "Insertion of nucleotide(s) causing alteration of mRNA reading frame." [VariO:mv]
is_a: VariO:0326 ! RNA insertion

[Term]
id: VariO:0328
name: RNA variation classification
def: "Classification of RNA variation." [VariO:mv]
is_a: VariO:0306 ! RNA variation type
created_by: Mauno Vihnen
creation_date: 2013-10-11T09:05:02Z

[Term]
id: VariO:0329
name: mistranscribed RNA
def: "RNA variation due to defective fidelity of transcription." [VariO:mv]
is_a: VariO:0333 ! variation emerging at RNA level
created_by: Mauno Vihnen
creation_date: 2014-10-23T00:29:53Z

[Term]
id: VariO:0330
name: mistranslated protein
def: "Protein variation due to defective fidelity of translation." [VariO:mv]
is_a: VariO:0024 ! variation emerging at protein level
created_by: Mauno Vihnen
creation_date: 2014-10-23T00:31:56Z

[Term]
id: VariO:0331
name: misreplicated DNA
def: "DNA variation due to defective fidelity of replication." [VariO:mv]
is_a: VariO:0146 ! DNA variation of non-genetic origin
created_by: Mauno Vihnen
creation_date: 2014-10-23T00:41:03Z

[Term]
id: VariO:0332
name: in-frame insertion
def: "Insertion of nucleotides in multiples of three so that the reading frame is retained." [VariO:mv]
is_a: VariO:0326 ! RNA insertion

[Term]
id: VariO:0333
name: variation emerging at RNA level
def: "RNA variation that does not have genetic origin being modified at RNA level." [VariO:mv]
is_a: VariO:0324 ! RNA variation origin

[Term]
id: VariO:0334
name: edited RNA
def: "Post transcriptionally chemically modified RNA." [VariO:mv]
is_a: VariO:0333 ! variation emerging at RNA level

[Term]
id: VariO:0335
name: decayed RNA
def: "RNA molecule destroyed due to appearance of a premature termination codon." [VariO:mv]
is_a: VariO:0333 ! variation emerging at RNA level

[Term]
id: VariO:0336
name: modified RNA
def: "Post transcriptionally modified RNA." [VariO:mv]
is_a: VariO:0333 ! variation emerging at RNA level

[Term]
id: VariO:0337
name: modified DNA
def: "DNA variation due to biological, chemical, physical or other modification." [VariO:mv]
is_a: VariO:0146 ! DNA variation of non-genetic origin
created_by: Mauno Vihnen
creation_date: 2014-10-23T00:42:47Z

[Term]
id: VariO:0338
name: variation affecting RNA structure
def: "Variation affecting structure of RNA." [VariO:mv]
is_a: VariO:0297 ! variation affecting RNA

[Term]
id: VariO:0339
name: effect on RNA editing
def: "Variation affecting chemical modification of RNA transcript by RNA editing mechanism." [VariO:mv]
is_a: VariO:0338 ! variation affecting RNA structure

[Term]
id: VariO:0340
name: effect on RNA substitution editing
def: "Variation affecting RNA editing process of chemical modification of a nucleotide in RNA." [VariO:mv]
is_a: VariO:0339 ! effect on RNA editing

[Term]
id: VariO:0341
name: effect on RNA insertion editing
def: "Variation affecting insertion of one or more nucleotides to RNA by RNA editing process." [VariO:mv]
is_a: VariO:0339 ! effect on RNA editing

[Term]
id: VariO:0342
name: effect on RNA deletion editing
def: "Effect on deletion of one or more nucleotides from RNA by RNA editing process." [VariO:mv]
is_a: VariO:0339 ! effect on RNA editing

[Term]
id: VariO:0344
name: RNA degradation by decay
def: "Variation causing degradation of RNA." [VariO:mv]
is_a: VariO:0299 ! effect on RNA degradation

[Term]
id: VariO:0345
name: RNA degradation by nonstop-mediated decay
def: "Variation causing nonstop-mediated RNA decay." [VariO:mv]
is_a: VariO:0344 ! RNA degradation by decay

[Term]
id: VariO:0346
name: RNA degradation by no-go mediated decay
def: "Variation causing no-go mediated RNA decay." [VariO:mv]
is_a: VariO:0344 ! RNA degradation by decay

[Term]
id: VariO:0347
name: RNA degradation by nonsense-mediated decay
def: "Variation causing nonsense-mediated decay of RNA due to premature translation termination codon." [VariO:mv]
is_a: VariO:0344 ! RNA degradation by decay

[Term]
id: VariO:0348
name: RNA modification by nonsense-associated altered splicing
def: "Variation causing nonsense-associated altered RNA splicing." [VariO:mv]
is_a: VariO:0338 ! variation affecting RNA structure

[Term]
id: VariO:0349
name: affected RNA level
def: "Affected level of RNA." [VariO:mv]
is_a: VariO:0338 ! variation affecting RNA structure

[Term]
id: VariO:0350
name: non-protein coding RNA sequence
def: "Variation affecting RNA sequence not coding for protein." [VariO:mv]
is_a: VariO:0349 ! affected RNA level

[Term]
id: VariO:0351
name: protein coding RNA sequence
def: "Variation affecting RNA sequence coding for protein." [VariO:mv]
is_a: VariO:0349 ! affected RNA level

[Term]
id: VariO:0352
name: coding RNA sequence
def: "Variation affecting region coding for protein in protein coding RNA." [VariO:mv]
is_a: VariO:0351 ! protein coding RNA sequence

[Term]
id: VariO:0353
name: non-coding region of protein coding RNA sequence
def: "Variation affecting region not coding for protein in protein coding RNA." [VariO:mv]
is_a: VariO:0351 ! protein coding RNA sequence

[Term]
id: VariO:0354
name: effect on RNA maturation
def: "Variation affecting maturation of RNA." [VariO:mv]
is_a: VariO:0338 ! variation affecting RNA structure

[Term]
id: VariO:0355
name: effect on RNA polyadenylation
def: "Variation affecting enzymatic addition of adenylyl residues to the 3' end of RNA molecule." [VariO:mv]
is_a: VariO:0354 ! effect on RNA maturation

[Term]
id: VariO:0356
name: effect on alternative polyadenylation
def: "Variation affecting polyadenylation of RNA molecule at alternative site." [VariO:mv]
is_a: VariO:0355 ! effect on RNA polyadenylation

[Term]
id: VariO:0357
name: effect on RNA five prime capping
def: "Variation affecting modification of five prime nucleotide in RNA by adding guanine nucleotide with five prime to five prime linkage." [VariO:mv]
is_a: VariO:0354 ! effect on RNA maturation

[Term]
id: VariO:0358
name: effect on RNA three prime end processing
def: "Variation affecting three prime end processing of RNA." [VariO:mv]
is_a: VariO:0354 ! effect on RNA maturation

[Term]
id: VariO:0359
name: effect on RNA modification
def: "Variation affecting covalent modification of RNA during maturation." [VariO:mv]
is_a: VariO:0354 ! effect on RNA maturation

[Term]
id: VariO:0360
name: effect on RNA base modification
def: "Variation affecting post transcriptional modification of RNA base." [VariO:mv]
is_a: VariO:0359 ! effect on RNA modification

[Term]
id: VariO:0361
name: effect on RNA nucleoside sugar modification
def: "Variation affecting post transcriptional modification of RNA nucleoside sugar." [VariO:mv]
is_a: VariO:0359 ! effect on RNA modification

[Term]
id: VariO:0362
name: effect on RNA splicing
def: "Variation affecting RNA splicing." [VariO:mv]
xref: SO:0001568
is_a: VariO:0354 ! effect on RNA maturation

[Term]
id: VariO:0364
name: intron gain
def: "Variant causing gain of new intron." [VariO:mv]
xref: SO:0001573
is_a: VariO:0362 ! effect on RNA splicing

[Term]
id: VariO:0365
name: variation affecting cis splicing
def: "Variation modifying intronic splicing within a mRNA molecule." [VariO:mv]
is_a: VariO:0362 ! effect on RNA splicing

[Term]
id: VariO:0366
name: variation at recursive splice site
def: "Variation affecting recursive splice site which subdivides a large intron." [VariO:mv]
is_a: VariO:0365 ! variation affecting cis splicing

[Term]
id: VariO:0367
name: variation at five prime cis splice site
def: "Variation affecting intronic two base pair region bordering exon, at the five prime end of the intron." [VariO:mv]
is_a: VariO:0365 ! variation affecting cis splicing

[Term]
id: VariO:0368
name: variation at canonical five prime splice site
def: "Variation affecting canonical five prime splice site." [VariO:mv]
is_a: VariO:0367 ! variation at five prime cis splice site

[Term]
id: VariO:0369
name: variation at non canonical five prime splice site
def: "Variation affecting non canonical five prime splice site." [VariO:mv]
is_a: VariO:0367 ! variation at five prime cis splice site

[Term]
id: VariO:0370
name: variation at three prime cis splice site
def: "Variation affecting intronic two base pair region bordering the exon, at the 3' edge of the intron." [VariO:mv]
is_a: VariO:0365 ! variation affecting cis splicing

[Term]
id: VariO:0371
name: variation at non canonical three prime splice site
def: "Variation affecting non canonical three prime splice site." [VariO:mv]
is_a: VariO:0370 ! variation at three prime cis splice site

[Term]
id: VariO:0372
name: variation at canonical three prime splice site
def: "Variation affecting canonical three prime splice site." [VariO:mv]
is_a: VariO:0370 ! variation at three prime cis splice site

[Term]
id: VariO:0373
name: cryptic splice site activation
def: "Variation generating new splice site." [VariO:mv]
xref: SO:0001569
is_a: VariO:0362 ! effect on RNA splicing

[Term]
id: VariO:0374
name: cryptic splice donor activation
def: "A variation activating new splice donor site." [VariO:mv]
xref: SO:0001571
is_a: VariO:0373 ! cryptic splice site activation

[Term]
id: VariO:0375
name: cryptic splice acceptor activation
def: "Variation activating new splice acceptor site." [VariO:mv]
xref: SO:0001570
is_a: VariO:0373 ! cryptic splice site activation

[Term]
id: VariO:0376
name: variation affecting trans splicing
def: "Variation affecting splicing and ligation of two different mRNA molecules." [VariO:mv]
is_a: VariO:0362 ! effect on RNA splicing

[Term]
id: VariO:0381
name: exon loss
def: "Variation causing exon loss." [VariO:mv]
xref: SO:0001572
is_a: VariO:0362 ! effect on RNA splicing

[Term]
id: VariO:0382
name: variation to RNA secondary structure
def: "Variation affecting RNA secondary structure." [VariO:mv]
is_a: VariO:0338 ! variation affecting RNA structure

[Term]
id: VariO:0383
name: effect on RNA multiloop
def: "Variation affecting closed RNA structure in which at least two double stranded regions meet." [VariO:mv]
is_a: VariO:0382 ! variation to RNA secondary structure

[Term]
id: VariO:0384
name: effect on RNA bulge
def: "Variation affecting RNA structure in which nucleotides in one strand do not form base pairs." [VariO:mv]
is_a: VariO:0382 ! variation to RNA secondary structure

[Term]
id: VariO:0385
name: effect on RNA interior loop
def: "Variation affecting RNA structure in which both the strands do not form base pairs." [VariO:mv]
is_a: VariO:0382 ! variation to RNA secondary structure

[Term]
id: VariO:0386
name: effect on RNA stem
def: "Variation affecting hydrogen bonding in contiguous nested base pairs in RNA." [VariO:mv]
is_a: VariO:0382 ! variation to RNA secondary structure

[Term]
id: VariO:0387
name: effect on RNA hairpin loop
def: "Variation affecting loop connecting adjacent regions forming helix in RNA." [VariO:mv]
is_a: VariO:0382 ! variation to RNA secondary structure

[Term]
id: VariO:0396
name: variation affecting RNA function
def: "Variation having effect on RNA function and usage." [VariO:mv]
is_a: VariO:0297 ! variation affecting RNA

[Term]
id: VariO:0397
name: effect on RNA splicing function
def: "Variation affecting splicing function of RNA." [VariO:mv]
is_a: VariO:0396 ! variation affecting RNA function

[Term]
id: VariO:0398
name: effect on catalytic RNA activity
def: "Variation affecting catalytic function of RNA." [VariO:mv]
is_a: VariO:0396 ! variation affecting RNA function

[Term]
id: VariO:0399
name: effect on translation
def: "Variation affecting translation of protein." [VariO:mv]
is_a: VariO:0396 ! variation affecting RNA function

[Term]
id: VariO:0400
name: effect on regulatory function of RNA
def: "Variation affecting regulatory function of RNA." [VariO:mv]
is_a: VariO:0396 ! variation affecting RNA function

[Term]
id: VariO:0401
name: effect on amino acid transfer of RNA
def: "Variation affecting RNA function in amino acid transfer." [VariO:mv]
is_a: VariO:0396 ! variation affecting RNA function

[Term]
id: VariO:0402
name: effect on RNA information transfer
def: "Variation affecting information transfer by RNA." [VariO:mv]
is_a: VariO:0396 ! variation affecting RNA function

[Typedef]
id: adjacent_to
name: adjacent_to
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke]

[Typedef]
id: associated_with
name: associated_with
comment: This relationship is vague and up for discussion.

[Typedef]
id: complete_evidence_for_feature
name: complete_evidence_for_feature
def: "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." [SO:ke]
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.
is_transitive: true

[Typedef]
id: contains
name: contains
def: "'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'." [PSI-MOD:ref]
comment: The inverse relationship to "part of".
is_transitive: true

[Typedef]
id: derives_from
name: derives_from
is_transitive: true

[Typedef]
id: evidence_for_feature
name: evidence_for_feature
def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke]
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.
is_transitive: true

[Typedef]
id: genome_of
name: genome_of

[Typedef]
id: has_functional_parent
name: has functional parent
def: "'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." [PSI-MOD:ref]
comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.
is_transitive: true

[Typedef]
id: has_origin
name: has_origin

[Typedef]
id: has_part
name: has_part

[Typedef]
id: has_quality
name: has_quality
comment: The relationship between a feature and an attribute.

[Typedef]
id: member_of
name: 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.
is_transitive: true

[Typedef]
id: negatively_regulates
name: negatively_regulates

[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]

[Typedef]
id: part_of
name: part_of
is_transitive: true

[Typedef]
id: partial_evidence_for_feature
name: partial_evidence_for_feature
def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke]

[Typedef]
id: position_of
name: position_of

[Typedef]
id: positively_regulates
name: positively_regulates

[Typedef]
id: regulates
name: regulates
transitive_over: part_of ! part_of

[Typedef]
id: sequence_of
name: sequence_of

[Typedef]
id: variant_of
name: variant_of
def: "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." [SO:immuno_workshop]
comment: Added to SO during the immunology workshop, June 2007.  This relationship was approved by Barry Smith.