Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) Prefix(rdfs:=) Ontology( Annotation( "OBO-Edit 2.3.1") Annotation( "23:11:2018 15:56") Annotation( "variation_ontology") Annotation( "1.2") Annotation( "med-mnv") Annotation(rdfs:comment "A Variation Ontology") Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) 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############################ # Annotation Properties ############################ # Annotation Property: (definition) AnnotationAssertion(rdfs:label "definition") # Annotation Property: (database_cross_reference) AnnotationAssertion(rdfs:label "database_cross_reference") # Annotation Property: (has_exact_synonym) AnnotationAssertion(rdfs:label "has_exact_synonym") # Annotation Property: (has_obo_format_version) AnnotationAssertion(rdfs:label "has_obo_format_version") # Annotation Property: (has_obo_namespace) AnnotationAssertion(rdfs:label "has_obo_namespace") # Annotation Property: (has_related_synonym) AnnotationAssertion(rdfs:label "has_related_synonym") ############################ # Object Properties ############################ # Object Property: (adjacent_to) AnnotationAssertion(Annotation( "SO:ke") "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "adjacent_to") AnnotationAssertion(rdfs:label "adjacent_to") # Object Property: (associated_with) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "associated_with") AnnotationAssertion(rdfs:comment "This relationship is vague and up for discussion.") AnnotationAssertion(rdfs:label "associated_with") # Object Property: (complete_evidence_for_feature) AnnotationAssertion(Annotation( "SO:ke") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "complete_evidence_for_feature") AnnotationAssertion(rdfs: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.") AnnotationAssertion(rdfs:label "complete_evidence_for_feature") TransitiveObjectProperty() # Object Property: (contains) AnnotationAssertion(Annotation( "PSI-MOD:ref") "'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "contains") AnnotationAssertion(rdfs:comment "The inverse relationship to \"part of\".") AnnotationAssertion(rdfs:label "contains") TransitiveObjectProperty() # Object Property: (derives_from) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "derives_from") AnnotationAssertion(rdfs:label "derives_from") TransitiveObjectProperty() # Object Property: (evidence_for_feature) AnnotationAssertion(Annotation( "SO:ke") "B is evidence_for_feature A, if an instance of B supports the existence of A.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "evidence_for_feature") AnnotationAssertion(rdfs: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.") AnnotationAssertion(rdfs:label "evidence_for_feature") TransitiveObjectProperty() # Object Property: (genome_of) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "genome_of") AnnotationAssertion(rdfs:label "genome_of") # Object Property: (has functional parent) AnnotationAssertion(Annotation( "PSI-MOD:ref") "'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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "has_functional_parent") AnnotationAssertion(rdfs:comment "This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.") AnnotationAssertion(rdfs:label "has functional parent") TransitiveObjectProperty() # Object Property: (has_origin) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "has_origin") AnnotationAssertion(rdfs:label "has_origin") # Object Property: (has_part) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "has_part") AnnotationAssertion(rdfs:label "has_part") # Object Property: (has_quality) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "has_quality") AnnotationAssertion(rdfs:comment "The relationship between a feature and an attribute.") AnnotationAssertion(rdfs:label "has_quality") # Object Property: (member_of) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "member_of") AnnotationAssertion(rdfs: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.") AnnotationAssertion(rdfs:label "member_of") TransitiveObjectProperty() # Object Property: (negatively_regulates) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "negatively_regulates") AnnotationAssertion(rdfs:label "negatively_regulates") # Object Property: (non_functional_homolog_of) AnnotationAssertion(Annotation( "SO:ke") "A relationship between a pseudogenic feature and its functional ancestor.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "non_functional_homolog_of") AnnotationAssertion(rdfs:label "non_functional_homolog_of") # Object Property: (part_of) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "part_of") AnnotationAssertion(rdfs:label "part_of") TransitiveObjectProperty() # Object Property: (partial_evidence_for_feature) AnnotationAssertion(Annotation( "SO:ke") "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "partial_evidence_for_feature") AnnotationAssertion(rdfs:label "partial_evidence_for_feature") # Object Property: (position_of) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "position_of") AnnotationAssertion(rdfs:label "position_of") # Object Property: (positively_regulates) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "positively_regulates") AnnotationAssertion(rdfs:label "positively_regulates") # Object Property: (regulates) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "regulates") AnnotationAssertion(rdfs:label "regulates") # Object Property: (sequence_of) AnnotationAssertion( "variation_ontology") AnnotationAssertion( "sequence_of") AnnotationAssertion(rdfs:label "sequence_of") # Object Property: (variant_of) AnnotationAssertion(Annotation( "SO:immuno_workshop") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "variant_of") AnnotationAssertion(rdfs:comment "Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.") AnnotationAssertion(rdfs:label "variant_of") ############################ # Classes ############################ # Class: (variation) AnnotationAssertion(Annotation( "VariO:mv") "Alteration in DNA, RNA or protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0001") AnnotationAssertion(rdfs:label "variation") # Class: (variation affecting protein) AnnotationAssertion(Annotation( "VariO:mv") "Effects of a variation on protein level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0002") AnnotationAssertion(rdfs:label "variation affecting protein") SubClassOf( ) # Class: (variation affecting protein function) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on protein function.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0003") AnnotationAssertion(rdfs:label "variation affecting protein function") SubClassOf( ) # Class: (effect on protein movement) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on the movement of a protein along filament of a polymeric molecule.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0004") AnnotationAssertion(rdfs:label "effect on protein movement") SubClassOf( ) # Class: (effect on protein storage) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0005") AnnotationAssertion(rdfs:label "effect on protein storage") SubClassOf( ) # Class: (effect on structural protein) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0006") AnnotationAssertion(rdfs:label "effect on structural protein") SubClassOf( ) # Class: (effect on protein recognition) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on selective non-covalent interaction of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0007") AnnotationAssertion(rdfs:label "effect on protein recognition") SubClassOf( ) # Class: (effect on catalytic protein function) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on catalytic function of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0008") AnnotationAssertion(rdfs:label "effect on catalytic protein function") SubClassOf( ) # Class: (effect on transport function of protein) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0009") AnnotationAssertion(rdfs:label "effect on transport function of protein") SubClassOf( ) # Class: (effect on RNA abundance) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting abundance of produced RNA molecules.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0010") AnnotationAssertion(rdfs:label "effect on RNA abundance") SubClassOf( ) # Class: (effect on protein information transfer) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0011") AnnotationAssertion(rdfs:label "effect on protein information transfer") SubClassOf( ) # Class: (protein variation type) AnnotationAssertion(Annotation( "VariO:mv") "Type of protein variation. Describes origin and classification of a variant.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0012") AnnotationAssertion(rdfs:label "protein variation type") SubClassOf( ) # Class: (protein variation of genetic origin) AnnotationAssertion(Annotation( "VariO:mv") "Protein variation that has genetic origin.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0013") AnnotationAssertion(rdfs:label "protein variation of genetic origin") SubClassOf( ) # Class: (amino acid deletion) AnnotationAssertion(Annotation( "VariO:mv") "Removal of one or more continuous amino acids from protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0014") AnnotationAssertion(rdfs:label "amino acid deletion") SubClassOf( ) # Class: (protein truncation) AnnotationAssertion(Annotation( "VariO:mv") "Shortening of protein sequence from terminus.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0015") AnnotationAssertion(rdfs:label "protein truncation") SubClassOf( ) # Class: (sequence retaining amino acid deletion) AnnotationAssertion(Annotation( "VariO:mv") "Deletion of one or more amino acids from a protein, without affecting the sequence after deletion.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0016") AnnotationAssertion(rdfs:label "sequence retaining amino acid deletion") SubClassOf( ) # Class: (nonsynonymous variation) AnnotationAssertion(Annotation( "Vario:mv") "mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-06-04T13:23:24Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0017") AnnotationAssertion(rdfs:label "nonsynonymous variation") SubClassOf( ) # Class: (amino acid insertion) AnnotationAssertion(Annotation( "VariO:mv") "Addition of one or more amino acids to protein sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0018") AnnotationAssertion(rdfs:label "amino acid insertion") SubClassOf( ) # Class: (amphigoric amino acid insertion) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0019") AnnotationAssertion(rdfs:label "amphigoric amino acid insertion") SubClassOf( ) # Class: (sequence retaining amino acid insertion) AnnotationAssertion(Annotation( "VariO:mv") "Insertion of one or more amino acids to the protein without affecting the sequence after insertion.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0020") AnnotationAssertion(rdfs:label "sequence retaining amino acid insertion") SubClassOf( ) # Class: (amino acid substitution) AnnotationAssertion(Annotation( "VariO:mv") "Substitution of an amino acid in protein.") AnnotationAssertion( "SO:0001606") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0021") AnnotationAssertion(rdfs:label "amino acid substitution") SubClassOf( ) # Class: (amino acid indel) AnnotationAssertion(Annotation( "VariO:mv") "A complex protein variation consisting of both amino acid insertion(s) and deletion(s).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0022") AnnotationAssertion(rdfs:label "amino acid indel") SubClassOf( ) # Class: (amphigoric amino acid indel) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-03-06T10:59:41Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0023") AnnotationAssertion(rdfs:label "amphigoric amino acid indel") SubClassOf( ) # Class: (variation emerging at protein level) AnnotationAssertion(Annotation( "VariO:mv") "Protein variation that does not have genetic origin being modified at protein level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0024") AnnotationAssertion(rdfs:label "variation emerging at protein level") SubClassOf( ) # Class: (epigenetic protein variation) AnnotationAssertion(Annotation( "VariO:mv") "Heritable protein variation of non-genetic origin.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0025") AnnotationAssertion(rdfs:label "epigenetic protein variation") SubClassOf( ) # Class: (protein structural inheritance) AnnotationAssertion(Annotation( "VariO:mv") "Inheritance of protein or protein complex structure without involvement of genetic information.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0026") AnnotationAssertion(rdfs:label "protein structural inheritance") SubClassOf( ) # Class: (proteinaceous infection) AnnotationAssertion(Annotation( "VariO:mv") "Protein conformation change induced by structurally modified protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0027") AnnotationAssertion(rdfs:label "proteinaceous infection") SubClassOf( ) # Class: (post translational modification) AnnotationAssertion(Annotation( "VariO:mv") "Protein molecule chemically modified after translation.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0028") AnnotationAssertion(rdfs:label "post translational modification") SubClassOf( ) # Class: (sequence retaining amino acid indel) AnnotationAssertion(Annotation( "VariO:mv") "Amino acid indel without affecting the sequence after the indel position.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-03-06T11:04:21Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0029") AnnotationAssertion(rdfs:label "sequence retaining amino acid indel") SubClassOf( ) # Class: (in-frame indel) AnnotationAssertion(Annotation( "VariO:mv") "RNA indel not affecting reading frame after indel position.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-06-14T10:03:57Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0030") AnnotationAssertion(rdfs:label "in-frame indel") SubClassOf( ) # Class: (out-of-frame indel) AnnotationAssertion(Annotation( "VariO:mv") "RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-06-14T10:03:57Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0031") AnnotationAssertion(rdfs:label "out-of-frame indel") SubClassOf( ) # Class: (variation affecting protein property) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting characteristic property of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0032") AnnotationAssertion(rdfs:label "variation affecting protein property") SubClassOf( ) # Class: (effect on protein subcellular localization) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on the targeting of a protein within a cell or cellular compartment.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0033") AnnotationAssertion(rdfs:label "effect on protein subcellular localization") SubClassOf( ) # Class: (effect on protein stability) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on stability of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0034") AnnotationAssertion(rdfs:label "effect on protein stability") SubClassOf( ) # Class: (effect on protein solubility) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on the potential of protein to dissolve in a liquid.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0035") AnnotationAssertion(rdfs:label "effect on protein solubility") SubClassOf( ) # Class: (effect on protein inclusion body formation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting the formation of particles of aggregated proteins.") AnnotationAssertion( "GO:0016234") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0036") AnnotationAssertion(rdfs:label "effect on protein inclusion body formation") SubClassOf( ) # Class: (covariant position) AnnotationAssertion(Annotation( "VariO:mv") "Variation at a covarying sequence position.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2014-01-16T14:03:51Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0037") AnnotationAssertion(rdfs:label "covariant position") SubClassOf( ) # Class: (effect on protein aggregation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein aggregation tendency.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0038") AnnotationAssertion(rdfs:label "effect on protein aggregation") SubClassOf( ) # Class: (protein function change) AnnotationAssertion(Annotation( "VariO:mv") "Type of protein function affecting variation.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0039") AnnotationAssertion(rdfs:label "protein function change") SubClassOf( ) # Class: (protein gain of function) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation causing new or enhanced protein activity.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0040") AnnotationAssertion(rdfs:label "protein gain of function") SubClassOf( ) # Class: (neomorphic protein variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation generates new protein function.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0041") AnnotationAssertion(rdfs:label "neomorphic protein variation") SubClassOf( ) # Class: (antimorphic protein variation) AnnotationAssertion(Annotation( "VariO:mv") "Dominant variation that acts to opposite direction than the normal protein.") AnnotationAssertion( "dominant negative protein variation") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0042") AnnotationAssertion(rdfs:label "antimorphic protein variation") SubClassOf( ) # Class: (protein loss of function) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation reducing or abolishing protein activity.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0043") AnnotationAssertion(rdfs:label "protein loss of function") SubClassOf( ) # Class: (effect on protein accessibility) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation to the accessibility of protein region to solvent.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0044") AnnotationAssertion(rdfs:label "effect on protein accessibility") SubClassOf( ) # Class: (variation exposing buried region) AnnotationAssertion(Annotation( "VariO:mv") "Variation exposing buried region.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0045") AnnotationAssertion(rdfs:label "variation exposing buried region") SubClassOf( ) # Class: (variation burying exposed region) AnnotationAssertion(Annotation( "VariO:mv") "Variation leading to burying of exposed region.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0046") AnnotationAssertion(rdfs:label "variation burying exposed region") SubClassOf( ) # Class: (association of protein variation to pathogenicity) AnnotationAssertion(Annotation( "VariO:mv") "Implication of a protein variant to pathogenicity.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0047") AnnotationAssertion(rdfs:label "association of protein variation to pathogenicity") SubClassOf( ) # Class: (effect on protein charge) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on charge in protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0048") AnnotationAssertion(rdfs:label "effect on protein charge") SubClassOf( ) # Class: (effect on protein electrostatics) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting electrostatics of the protein surface.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0049") AnnotationAssertion(rdfs:label "effect on protein electrostatics") SubClassOf( ) # Class: (effect on protein isoelectric point) AnnotationAssertion(Annotation( "VariO:mv") "Variation changing protein isoelectric point.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0050") AnnotationAssertion(rdfs:label "effect on protein isoelectric point") SubClassOf( ) # Class: (effect on protein degradation) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on degradation of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0051") AnnotationAssertion(rdfs:label "effect on protein degradation") SubClassOf( ) # Class: (effect on protein abundance) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting abundance of produced protein molecules.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0052") AnnotationAssertion(rdfs:label "effect on protein abundance") SubClassOf( ) # Class: (effect on protein activity) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on activity of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0053") AnnotationAssertion(rdfs:label "effect on protein activity") SubClassOf( ) # Class: (effect on protein affinity) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on protein affinity to binding molecule(s).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0054") AnnotationAssertion(rdfs:label "effect on protein affinity") SubClassOf( ) # Class: (effect on protein specificity) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on substrate binding specificity of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0055") AnnotationAssertion(rdfs:label "effect on protein specificity") SubClassOf( ) # Class: (effect on enzyme reaction kinetics) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation to enzyme reaction kinetics.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0056") AnnotationAssertion(rdfs:label "effect on enzyme reaction kinetics") SubClassOf( ) # Class: (conservation of protein variation site) AnnotationAssertion(Annotation( "VariO:mv") "Conservation of the variant site in related protein sequences.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0057") AnnotationAssertion(rdfs:label "conservation of protein variation site") SubClassOf( ) # Class: (effect on protein interaction) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on the interaction of protein with its partner.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0058") AnnotationAssertion(rdfs:label "effect on protein interaction") SubClassOf( ) # Class: (effect on protein contact energy) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on contact energy between interacting molecules.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0059") AnnotationAssertion(rdfs:label "effect on protein contact energy") SubClassOf( ) # Class: (variation affecting protein structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting structure of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0060") AnnotationAssertion(rdfs:label "variation affecting protein structure") SubClassOf( ) # Class: (epigenetic protein modification) AnnotationAssertion(Annotation( "VariO:mv") "Hereditary protein structure modification of non-genetic origin.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0061") AnnotationAssertion(rdfs:label "epigenetic protein modification") SubClassOf( ) # Class: (prion formation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting the formation of infectious protein having misfolded structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0062") AnnotationAssertion(rdfs:label "prion formation") SubClassOf( ) # Class: (epigenetic protein complex structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting heritable protein complex structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0063") AnnotationAssertion(rdfs:label "epigenetic protein complex structure") SubClassOf( ) # Class: (effect on protein 3D structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein three dimensional structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0064") AnnotationAssertion(rdfs:label "effect on protein 3D structure") SubClassOf( ) # Class: (effect on protein dynamics) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting dynamics in protein structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0065") AnnotationAssertion(rdfs:label "effect on protein dynamics") SubClassOf( ) # Class: (effect on structural flexibility) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein structural flexibility.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0066") AnnotationAssertion(rdfs:label "effect on structural flexibility") SubClassOf( ) # Class: (effect on induced fit) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting induced fit of protein binding to its partner.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0067") AnnotationAssertion(rdfs:label "effect on induced fit") SubClassOf( ) # Class: (effect on structural disorder) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein structural disorder.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0068") AnnotationAssertion(rdfs:label "effect on structural disorder") SubClassOf( ) # Class: (effect on allosteric site) AnnotationAssertion(Annotation( "VariO:mv") "Variation in affecting protein allosteric site.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0069") AnnotationAssertion(rdfs:label "effect on allosteric site") SubClassOf( ) # Class: (effect on protein tertiary structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein three dimensional structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0070") AnnotationAssertion(rdfs:label "effect on protein tertiary structure") SubClassOf( ) # Class: (effect on protein folding rate) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting rate of protein folding.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0071") AnnotationAssertion(rdfs:label "effect on protein folding rate") SubClassOf( ) # Class: (extrachromosomal DNA affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation effect on nonchromosomal DNA.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-11-09T14:16:30Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0072") AnnotationAssertion(rdfs:label "extrachromosomal DNA affected") SubClassOf( ) # Class: (effect to protein fold) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein tertiary structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0073") AnnotationAssertion(rdfs:label "effect to protein fold") SubClassOf( ) # Class: (protein conformational change) AnnotationAssertion(Annotation( "VariO:mv") "Variation changing protein conformation.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0074") AnnotationAssertion(rdfs:label "protein conformational change") SubClassOf( ) # Class: (global protein conformation change) AnnotationAssertion(Annotation( "VariO:mv") "Variation causing large overall protein conformational change.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0075") AnnotationAssertion(rdfs:label "global protein conformation change") SubClassOf( ) # Class: (local protein conformation change) AnnotationAssertion(Annotation( "VariO:mv") "Variation causing local and minor conformational change.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0076") AnnotationAssertion(rdfs:label "local protein conformation change") SubClassOf( ) # Class: (changed domain orientation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein structure due to alteration to domain orientation.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0077") AnnotationAssertion(rdfs:label "changed domain orientation") SubClassOf( ) # Class: (effect on protein disulphide formation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting formation of intramolecular disulphide bonds.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0078") AnnotationAssertion(rdfs:label "effect on protein disulphide formation") SubClassOf( ) # Class: (effect on protein secondary structural element) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein secondary structural element of local ordered structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0079") AnnotationAssertion(rdfs:label "effect on protein secondary structural element") SubClassOf( ) # Class: (effect on protein helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting secondary structure conformation where the peptide backbone forms a coil.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0080") AnnotationAssertion(rdfs:label "effect on protein helix") SubClassOf( ) # Class: (effect on left handed protein helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein left handed helix turning anticlockwise.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0081") AnnotationAssertion(rdfs:label "effect on left handed protein helix") SubClassOf( ) # Class: (effect on right handed protein helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0082") AnnotationAssertion(rdfs:label "effect on right handed protein helix") SubClassOf( ) # Class: (effect on pi helix) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0083") AnnotationAssertion(rdfs:label "effect on pi helix") SubClassOf( ) # Class: (effect on three ten helix) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0084") AnnotationAssertion(rdfs:label "effect on three ten helix") SubClassOf( ) # Class: (effect on alpha helix) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0085") AnnotationAssertion(rdfs:label "effect on alpha helix") SubClassOf( ) # Class: (effect on protein beta strand) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting extended protein backbone structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0086") AnnotationAssertion(rdfs:label "effect on protein beta strand") SubClassOf( ) # Class: (effect on protein antiparallel beta strand) AnnotationAssertion(Annotation( "VariO:mv") "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).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0087") AnnotationAssertion(rdfs:comment "Range.") AnnotationAssertion(rdfs:label "effect on protein antiparallel beta strand") SubClassOf( ) # Class: (effect on protein parallel beta strand) AnnotationAssertion(Annotation( "VariO:mv") "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).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0088") AnnotationAssertion(rdfs:comment "Range.") AnnotationAssertion(rdfs:label "effect on protein parallel beta strand") SubClassOf( ) # Class: (effect on protein turn motif) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein backbone turn motif.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0089") AnnotationAssertion(rdfs:label "effect on protein turn motif") SubClassOf( ) # Class: (effect on protein alpha beta motif) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0090") AnnotationAssertion(rdfs:label "effect on protein alpha beta motif") SubClassOf( ) # Class: (effect on protein beta turn) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0091") AnnotationAssertion(rdfs:label "effect on protein beta turn") SubClassOf( ) # Class: (effect on protein st motif) AnnotationAssertion(Annotation( "VariO:mv") "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).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0092") AnnotationAssertion(rdfs:label "effect on protein st motif") SubClassOf( ) # Class: (effect on protein st staple) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0093") AnnotationAssertion(rdfs:label "effect on protein st staple") SubClassOf( ) # Class: (effect on protein gamma turn) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0094") AnnotationAssertion(rdfs:label "effect on protein gamma turn") SubClassOf( ) # Class: (effect on protein st turn) AnnotationAssertion(Annotation( "VariO:mv") "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).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0095") AnnotationAssertion(rdfs:label "effect on protein st turn") SubClassOf( ) # Class: (effect on protein schellman loop) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0096") AnnotationAssertion(rdfs:label "effect on protein schellman loop") SubClassOf( ) # Class: (effect on protein nest motif) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0097") AnnotationAssertion(rdfs:label "effect on protein nest motif") SubClassOf( ) # Class: (effect on protein niche motif) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0098") AnnotationAssertion(rdfs:label "effect on protein niche motif") SubClassOf( ) # Class: (effect on protein asx motif) AnnotationAssertion(Annotation( "VariO:mv") "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).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0099") AnnotationAssertion(rdfs:label "effect on protein asx motif") SubClassOf( ) # Class: (effect on protein beta bulge) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0100") AnnotationAssertion(rdfs:label "effect on protein beta bulge") SubClassOf( ) # Class: (effect on protein asx turn) AnnotationAssertion(Annotation( "VariO:mv") "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).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0101") AnnotationAssertion(rdfs:label "effect on protein asx turn") SubClassOf( ) # Class: (effect on protein beta bulge loop) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0102") AnnotationAssertion(rdfs:label "effect on protein beta bulge loop") SubClassOf( ) # Class: (effect on protein coil) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting irregular, unstructured region of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0103") AnnotationAssertion(rdfs:label "effect on protein coil") SubClassOf( ) # Class: (effect on transmembrane polypeptide) AnnotationAssertion(Annotation( "VariO:mv") "Variation altering membrane spanning protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0104") AnnotationAssertion(rdfs:label "effect on transmembrane polypeptide") SubClassOf( ) # Class: (effect on membrane protein extramembrane region) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting region not traversing the lipid bilayer in a membrane protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0105") AnnotationAssertion(rdfs:label "effect on membrane protein extramembrane region") SubClassOf( ) # Class: (effect on membrane protein intramembrane region) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting region present in the lipid bilayer in a membrane protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0106") AnnotationAssertion(rdfs:label "effect on membrane protein intramembrane region") SubClassOf( ) # Class: (effect on protein post translational modification) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting the covalent alteration of protein amino acid by post translational process.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0107") AnnotationAssertion(rdfs:label "effect on protein post translational modification") SubClassOf( ) # Class: (deletion of a post translational modification site) AnnotationAssertion(Annotation( "VariO:mv") "Variation causing deletion of a post translational modification site.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0108") AnnotationAssertion(rdfs:label "deletion of a post translational modification site") SubClassOf( ) # Class: (effect on protein processing) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting site of protein maturation by cleavage of peptide bond(s).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0109") AnnotationAssertion(rdfs:label "effect on protein processing") SubClassOf( ) # Class: (effect on protein splicing) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting post-translational removal of peptide sequences from within a protein sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0110") AnnotationAssertion(rdfs:label "effect on protein splicing") SubClassOf( ) # Class: (variation generating a novel protein processing site) AnnotationAssertion(Annotation( "VariO:mv") "Variation that generates a novel protein processing site.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0111") AnnotationAssertion(rdfs:label "variation generating a novel protein processing site") SubClassOf( ) # Class: (variation preventing polypeptide processing) AnnotationAssertion(Annotation( "VariO:mv") "Variation causing prevention of polypeptide processing.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0112") AnnotationAssertion(rdfs:label "variation preventing polypeptide processing") SubClassOf( ) # Class: (generation of a novel post translational modification site) AnnotationAssertion(Annotation( "VariO:mv") "Variation generating a novel post translational modification site.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0113") AnnotationAssertion(rdfs:label "generation of a novel post translational modification site") SubClassOf( ) # Class: (effect on amino acid size) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting amino acid side chain size.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0114") AnnotationAssertion(rdfs:label "effect on amino acid size") SubClassOf( ) # Class: (effect on protein packing) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting amino acid packing in folded protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0115") AnnotationAssertion(rdfs:label "effect on protein packing") SubClassOf( ) # Class: (protein cavity formation) AnnotationAssertion(Annotation( "VariO:mv") "Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0116") AnnotationAssertion(rdfs:label "protein cavity formation") SubClassOf( ) # Class: (protein overpacking) AnnotationAssertion(Annotation( "VariO:mv") "Variation causing over packing of amino acids due to replacement by larger amino acid side chain.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0117") AnnotationAssertion(rdfs:label "protein overpacking") SubClassOf( ) # Class: (effect on protein interaction site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting ligand binding amino acid(s) in protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0118") AnnotationAssertion(rdfs:label "effect on protein interaction site") SubClassOf( ) # Class: (effect on protein binding site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting region on the surface of a protein that interacts with another molecule.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0119") AnnotationAssertion(rdfs:label "effect on protein binding site") SubClassOf( ) # Class: (effect on protein catalytic site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting amino acid(s) in protein catalytic site.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0120") AnnotationAssertion(rdfs:label "effect on protein catalytic site") SubClassOf( ) # Class: (effect on protein quaternary structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting three dimensional structure of a protein complex.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0121") AnnotationAssertion(rdfs:label "effect on protein quaternary structure") SubClassOf( ) # Class: (effect on protein quaternary structure forming interaction) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting interaction between protein subunits in quaternary structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0122") AnnotationAssertion(rdfs:label "effect on protein quaternary structure forming interaction") SubClassOf( ) # Class: (complex 3D structural change) AnnotationAssertion(Annotation( "VariO:mv") "Complex change of protein three dimensional structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0123") AnnotationAssertion(rdfs:label "complex 3D structural change") SubClassOf( ) # Class: (protein elongation) AnnotationAssertion(Annotation( "VariO:mv") "Variation prolonging protein chain at an end.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0124") AnnotationAssertion(rdfs:label "protein elongation") SubClassOf( ) # Class: (C-terminal protein elongation) AnnotationAssertion(Annotation( "VariO:mv") "Addition of one or more amino acids to protein C-terminus.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0125") AnnotationAssertion(rdfs:label "C-terminal protein elongation") SubClassOf( ) # Class: (N-terminal protein elongation) AnnotationAssertion(Annotation( "VariO:mv") "Addition of one or more amino acids to protein N-terminus.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0126") AnnotationAssertion(rdfs:label "N-terminal protein elongation") SubClassOf( ) # Class: (DNA variation origin) AnnotationAssertion(Annotation( "VariO:mv") "Origin of DNA variation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-10-11T08:46:32Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0127") AnnotationAssertion(rdfs:label "DNA variation origin") SubClassOf( ) # Class: (variation affecting DNA) AnnotationAssertion(Annotation( "VariO:mv") "Effects of a variation on DNA level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0128") AnnotationAssertion(rdfs:label "variation affecting DNA") SubClassOf( ) # Class: (DNA variation type) AnnotationAssertion(Annotation( "VariO:mv") "Type of DNA variation. Describes origin and classification of a variant.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0129") AnnotationAssertion(rdfs:label "DNA variation type") SubClassOf( ) # Class: (DNA variation of genetic origin) AnnotationAssertion(Annotation( "VariO:mv") "DNA variation that has genetic origin.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0130") AnnotationAssertion(rdfs:label "DNA variation of genetic origin") SubClassOf( ) # Class: (genomic variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation of genomic level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0131") AnnotationAssertion(rdfs:label "genomic variation") SubClassOf( ) # Class: (chromosomal variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation at chromosomal level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0132") AnnotationAssertion(rdfs:label "chromosomal variation") SubClassOf( ) # Class: (variation of chromosome number) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting chromosome number.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "aneuploidy") AnnotationAssertion( "VariO:0133") AnnotationAssertion(rdfs:label "variation of chromosome number") SubClassOf( ) # Class: (variation of chromosome structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting structure of chromosome.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0134") AnnotationAssertion(rdfs:label "variation of chromosome structure") SubClassOf( ) # Class: (DNA chain variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation at DNA chain.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0135") AnnotationAssertion(rdfs:label "DNA chain variation") SubClassOf( ) # Class: (DNA substitution) AnnotationAssertion(Annotation( "VariO:mv") "Substitution of a DNA nucleotide.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0136") AnnotationAssertion(rdfs:label "DNA substitution") SubClassOf( ) # Class: (effect on RNA tertiary structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA tertiary structure.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-04-26T12:45:52Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0137") AnnotationAssertion(rdfs:label "effect on RNA tertiary structure") SubClassOf( ) # Class: (variant) AnnotationAssertion(Annotation( "VariO:mv") "A genetic character, organism or individual with a difference to reference state.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-11-11T19:43:00Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0138") AnnotationAssertion(rdfs:label "variant") SubClassOf( ) # Class: (mutation) AnnotationAssertion(Annotation( "VariO:mv") "Any process generating variation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-11-11T19:43:39Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0139") AnnotationAssertion(rdfs:label "mutation") SubClassOf( ) # Class: (not changed) AnnotationAssertion(Annotation( "VariO:mv") "The observed feature is not changed in relation to the wild type form.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-11-11T19:46:40Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0140") AnnotationAssertion(rdfs:label "not changed") SubClassOf( ) # Class: (DNA deletion) AnnotationAssertion(Annotation( "VariO:mv") "Removal of one or more continuous nucleotides from DNA sequence.") AnnotationAssertion( "nucleotide deletion") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0141") AnnotationAssertion(rdfs:label "DNA deletion") SubClassOf( ) # Class: (DNA insertion) AnnotationAssertion(Annotation( "VariO:mv") "Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence.") AnnotationAssertion( "nucleotide insertion") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0142") AnnotationAssertion(rdfs:label "DNA insertion") SubClassOf( ) # Class: (DNA indel) AnnotationAssertion(Annotation( "VariO:mv") "A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0143") AnnotationAssertion(rdfs:label "DNA indel") SubClassOf( ) # Class: (DNA translocation) AnnotationAssertion(Annotation( "VariO:mv") "A continuous stretch of DNA sequence moved to a new position within a chromosome.") AnnotationAssertion( "MI:0593") AnnotationAssertion( "SO:0000199") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0144") AnnotationAssertion(rdfs:label "DNA translocation") SubClassOf( ) # Class: (DNA inversion) AnnotationAssertion(Annotation( "VariO:mv") "A continuous stretch of DNA sequence inserted to the same position in reverse orientation.") AnnotationAssertion( "SO:1000036") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0145") AnnotationAssertion(rdfs:label "DNA inversion") SubClassOf( ) # Class: (DNA variation of non-genetic origin) AnnotationAssertion(Annotation( "VariO:mv") "DNA variation that does not have genetic origin.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0146") AnnotationAssertion(rdfs:label "DNA variation of non-genetic origin") SubClassOf( ) # Class: (epigenetic DNA variation) AnnotationAssertion(Annotation( "VariO:mv") "Heritable DNA variation of non-genetic origin.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0147") AnnotationAssertion(rdfs:label "epigenetic DNA variation") SubClassOf( ) # Class: (variation affecting DNA function) AnnotationAssertion(Annotation( "VariO:mv") "Variation having effect on DNA function and usage.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0148") AnnotationAssertion(rdfs:label "variation affecting DNA function") SubClassOf( ) # Class: (effect on transcription) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0149") AnnotationAssertion(rdfs:label "effect on transcription") SubClassOf( ) # Class: (effect on DNA information transfer) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting information transfer of DNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0150") AnnotationAssertion(rdfs:label "effect on DNA information transfer") SubClassOf( ) # Class: (effect on DNA repair) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting the process of restoring DNA after damage.") AnnotationAssertion( "GO:0006281") AnnotationAssertion( "Wikipedia:DNA_repair") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0151") AnnotationAssertion(rdfs:label "effect on DNA repair") SubClassOf( ) # Class: (effect on regulatory function of DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting regulatory function of DNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0152") AnnotationAssertion(rdfs:label "effect on regulatory function of DNA") SubClassOf( ) # Class: (chromatin variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting chromatin.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-03-05T16:05:29Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0153") AnnotationAssertion(rdfs:label "chromatin variation") SubClassOf( ) # Class: (effect on DNA replication) AnnotationAssertion(Annotation( "VariO:mv") "Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0154") AnnotationAssertion(rdfs:label "effect on DNA replication") SubClassOf( ) # Class: (variation affecting DNA structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting structure of DNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0155") AnnotationAssertion(rdfs:label "variation affecting DNA structure") SubClassOf( ) # Class: (epigenetic DNA modification) AnnotationAssertion(Annotation( "VariO:mv") "Hereditary variation of DNA not affecting primary sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0156") AnnotationAssertion(rdfs:label "epigenetic DNA modification") SubClassOf( ) # Class: (epigenetic DNA methylation) AnnotationAssertion(Annotation( "VariO:mv") "Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0157") AnnotationAssertion(rdfs:label "epigenetic DNA methylation") SubClassOf( ) # Class: (nucleosome positioning) AnnotationAssertion(Annotation( "VariO:mv") "Positioning of nucleosomes to DNA strand.") AnnotationAssertion(Annotation( "GO:0006338") "chromatin modeling") AnnotationAssertion(Annotation( "GO:0006338") "chromatin remodelling") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0158") AnnotationAssertion(rdfs:label "nucleosome positioning") SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (affected DNA level) AnnotationAssertion(Annotation( "VariO:mv") "Affected level of DNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0159") AnnotationAssertion(rdfs:label "affected DNA level") SubClassOf( ) # Class: (DNA chain affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation effect on DNA level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0160") AnnotationAssertion(rdfs:label "DNA chain affected") SubClassOf( ) # Class: (variation in intron) AnnotationAssertion(Annotation( "VariO:mv") "Variation located in intron.") AnnotationAssertion( "SO:0001627") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0161") AnnotationAssertion(rdfs:label "variation in intron") SubClassOf( ) # Class: (variation in exon) AnnotationAssertion(Annotation( "VariO:mv") "Variation located in exon.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0162") AnnotationAssertion(rdfs:label "variation in exon") SubClassOf( ) # Class: (variation at intergenic DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation located in intergenic DNA.") AnnotationAssertion( "SO:0001628") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0163") AnnotationAssertion(rdfs:label "variation at intergenic DNA") SubClassOf( ) # Class: (chromosome affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation effect on chromosome level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0164") AnnotationAssertion(rdfs:label "chromosome affected") SubClassOf( ) # Class: (genome affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation effect on genome level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0165") AnnotationAssertion(rdfs:label "genome affected") SubClassOf( ) # Class: (immunological receptor gene rearrangement) AnnotationAssertion(Annotation( "VariO:mv") "Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-22T19:10:52Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0166") AnnotationAssertion(rdfs:label "immunological receptor gene rearrangement") SubClassOf( ) # Class: (effect on DNA form) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting DNA structural form.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T12:52:26Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0167") AnnotationAssertion(rdfs:label "effect on DNA form") SubClassOf( ) # Class: (somatic hypermutation) AnnotationAssertion(Annotation( "VariO:mv") "Immunoglobulin diversification mechanism by producing variations to antigen variable regions.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-22T19:12:51Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0168") AnnotationAssertion(rdfs:label "somatic hypermutation") SubClassOf( ) # Class: (class switch recombination) AnnotationAssertion(Annotation( "VariO:mv") "Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-22T19:12:51Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0169") AnnotationAssertion(rdfs:label "class switch recombination") SubClassOf( ) # Class: (immunological receptor gene conversion) AnnotationAssertion(Annotation( "VariO:mv") "Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-22T19:12:51Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0170") AnnotationAssertion(rdfs:label "immunological receptor gene conversion") SubClassOf( ) # Class: (effect on DNA tertiary structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting DNA tertiary structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0171") AnnotationAssertion(rdfs:label "effect on DNA tertiary structure") SubClassOf( ) # Class: (artificial DNA variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-11-16T08:44:55Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0172") AnnotationAssertion(rdfs:label "artificial DNA variation") SubClassOf( ) # Class: (effect on nucleic acid G-quadruplex) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0173") AnnotationAssertion(rdfs:label "effect on nucleic acid G-quadruplex") SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (effect on i motif) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0174") AnnotationAssertion(rdfs:label "effect on i motif") SubClassOf( ) # Class: (effect on DNA triple helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting DNA helix formed of three strands.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0175") AnnotationAssertion(rdfs:label "effect on DNA triple helix") SubClassOf( ) # Class: (chromosome variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting chromosome.") AnnotationAssertion( "SO:0000240") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0176") AnnotationAssertion(rdfs:label "chromosome variation") SubClassOf( ) # Class: (telomere length change) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting length of telomere sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0177") AnnotationAssertion(rdfs:label "telomere length change") SubClassOf( ) # Class: (telomere shortening) AnnotationAssertion(Annotation( "VariO:mv") "Variation shortening length of telomere sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0178") AnnotationAssertion(rdfs:label "telomere shortening") SubClassOf( ) # Class: (telomere extension) AnnotationAssertion(Annotation( "VariO:mv") "Variation extending length of telomere sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0179") AnnotationAssertion(rdfs:label "telomere extension") SubClassOf( ) # Class: (chromosome structure variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting structure of chromosome.") AnnotationAssertion( "SO:1000183") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0180") AnnotationAssertion(rdfs:label "chromosome structure variation") SubClassOf( ) # Class: (isochromosome) AnnotationAssertion(Annotation( "VariO:mv") "Chromosome lacking one arm with duplication of the other arm.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0181") AnnotationAssertion(rdfs:label "isochromosome") SubClassOf( ) # Class: (ring chromosome) AnnotationAssertion(Annotation( "VariO:mv") "Circular chromosome with ends joined.") AnnotationAssertion( "SO:1000045") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0182") AnnotationAssertion(rdfs:label "ring chromosome") SubClassOf( ) # Class: (chromosomal amplification) AnnotationAssertion(Annotation( "VariO:mv") "Increase in the frequency of a chromosomal region.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0183") AnnotationAssertion(rdfs:label "chromosomal amplification") SubClassOf( ) # Class: (interspersed repeat) AnnotationAssertion(Annotation( "VariO:mv") "Copies of a chromosomal region of length greater than one scattered to genome sequence.") AnnotationAssertion( "SO:0000658") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0184") AnnotationAssertion(rdfs:label "interspersed repeat") SubClassOf( ) # Class: (tandem repeat) AnnotationAssertion(Annotation( "VariO:mv") "Adjacent copies of a chromosomal region of length greater than 1.") AnnotationAssertion( "SO:0000705") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0185") AnnotationAssertion(rdfs:label "tandem repeat") SubClassOf( ) # Class: (minisatellite) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0186") AnnotationAssertion(rdfs:label "minisatellite") SubClassOf( ) # Class: (copy number variation) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "SO:0001019") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0187") AnnotationAssertion(rdfs:label "copy number variation") SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (microsatellite) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of units of two to six base pair.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0188") AnnotationAssertion(rdfs:label "microsatellite") SubClassOf( ) # Class: (trinucleotide expansion) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of three nucleotide units.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0189") AnnotationAssertion(rdfs:label "trinucleotide expansion") SubClassOf( ) # Class: (mononucleotide expansion) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of one nucleotide type.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0190") AnnotationAssertion(rdfs:label "mononucleotide expansion") SubClassOf( ) # Class: (tetranucleotide expansion) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of four nucleotide units.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0191") AnnotationAssertion(rdfs:label "tetranucleotide expansion") SubClassOf( ) # Class: (DNA mobile genetic element insertion) AnnotationAssertion(Annotation( "VariO:mv") "Mobile genetic element incorporated into chromosome.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0192") AnnotationAssertion(rdfs:label "DNA mobile genetic element insertion") SubClassOf( ) # Class: (chromosomal deletion) AnnotationAssertion(Annotation( "VariO:mv") "Deletion of chromosomal region.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0193") AnnotationAssertion(rdfs:label "chromosomal deletion") SubClassOf( ) # Class: (interstitial deletion) AnnotationAssertion(Annotation( "VariO:mv") "Deletion of chromosomal region not including terminus.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0194") AnnotationAssertion(rdfs:label "interstitial deletion") SubClassOf( ) # Class: (terminal deletion) AnnotationAssertion(Annotation( "VariO:mv") "Deletion of chromosomal region from the end of chromosome arm.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0195") AnnotationAssertion(rdfs:label "terminal deletion") SubClassOf( ) # Class: (complex chromosomal variation) AnnotationAssertion(Annotation( "SO:ke") Annotation( "VariO:mv") "Chromosome structure variation with four or more breakpoints.") AnnotationAssertion( "SO:1000146") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0196") AnnotationAssertion(rdfs:label "complex chromosomal variation") SubClassOf( ) # Class: (chromosomal translocation) AnnotationAssertion(Annotation( "VariO:mv") "Translocation of chromosomal region.") AnnotationAssertion( "SO:0000199") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0197") AnnotationAssertion(rdfs:label "chromosomal translocation") SubClassOf( ) # Class: (intrachromosomal translocation) AnnotationAssertion(Annotation( "VariO:mv") "Translocation of chromosomal region within a chromosome.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0198") AnnotationAssertion(rdfs:label "intrachromosomal translocation") SubClassOf( ) # Class: (chromosomal inversion) AnnotationAssertion(Annotation( "VariO:mv") "Intrachromosomal variation where a chromosomal region is inserted in reverse direction.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0199") AnnotationAssertion(rdfs:label "chromosomal inversion") SubClassOf( ) # Class: (paracentric inversion) AnnotationAssertion(Annotation( "VariO:mv") "Chromosomal inversion within a chromosome arm.") AnnotationAssertion( "SO:1000047") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0200") AnnotationAssertion(rdfs:label "paracentric inversion") SubClassOf( ) # Class: (pericentric inversion) AnnotationAssertion(Annotation( "VariO:mv") "Chromosomal inversion including centromere.") AnnotationAssertion( "SO:1000046") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0201") AnnotationAssertion(rdfs:label "pericentric inversion") SubClassOf( ) # Class: (interchromosomal translocation) AnnotationAssertion(Annotation( "VariO:mv") "Translocation of chromosomal region to another chromosome.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0202") AnnotationAssertion(rdfs:label "interchromosomal translocation") SubClassOf( ) # Class: (reciprocal chromosomal translocation) AnnotationAssertion(Annotation( "VariO:mv") "Switching of chromosomal regions between nonhomologous chromosomes.") AnnotationAssertion( "SO:1000048") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0203") AnnotationAssertion(rdfs:label "reciprocal chromosomal translocation") SubClassOf( ) # Class: (Robertsonian translocation) AnnotationAssertion(Annotation( "VariO:mv") "Fusion of long arms of two acrocentric chromosomes having very short p arms.") AnnotationAssertion( "SO:1000043") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0204") AnnotationAssertion(rdfs:label "Robertsonian translocation") SubClassOf( ) # Class: (dinucleotide expansion) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of two nucleotide units.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-17T10:53:06Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0205") AnnotationAssertion(rdfs:label "dinucleotide expansion") SubClassOf( ) # Class: (chromosome number variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting the number of chromosomes.") AnnotationAssertion( "aneuploidy") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0206") AnnotationAssertion(rdfs:label "chromosome number variation") SubClassOf( ) # Class: (trisomy) AnnotationAssertion(Annotation( "VariO:mv") "Three copies of a chromosome in a cell or organism.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0207") AnnotationAssertion(rdfs:label "trisomy") SubClassOf( ) # Class: (disomy) AnnotationAssertion(Annotation( "VariO:mv") "Two copies of a chromosome in a cell or organism .") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0208") AnnotationAssertion(rdfs:label "disomy") SubClassOf( ) # Class: (uniparental disomy) AnnotationAssertion(Annotation( "VariO:mv") "Both copies of a chromosome or a part of it in diploid cell or organism are from one parent.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0209") AnnotationAssertion(rdfs:label "uniparental disomy") SubClassOf( ) # Class: (isodisomy) AnnotationAssertion(Annotation( "VariO:mv") "Uniparental disomy with duplication of a single chromosome from one parent.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0210") AnnotationAssertion(rdfs:label "isodisomy") SubClassOf( ) # Class: (heterodisomy) AnnotationAssertion(Annotation( "VariO:mv") "Pair of non-identical chromosomes inherited from one parent.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0211") AnnotationAssertion(rdfs:label "heterodisomy") SubClassOf( ) # Class: (nullisomy) AnnotationAssertion(Annotation( "VariO:mv") "No copies of a chromosome in a cell or organism.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0212") AnnotationAssertion(rdfs:label "nullisomy") SubClassOf( ) # Class: (tetrasomy) AnnotationAssertion(Annotation( "VariO:mv") "Four copies of a chromosome in a cell or organism.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0213") AnnotationAssertion(rdfs:label "tetrasomy") SubClassOf( ) # Class: (monosomy) AnnotationAssertion(Annotation( "VariO:mv") "One copy of a chromosome in a cell or organism.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0214") AnnotationAssertion(rdfs:label "monosomy") SubClassOf( ) # Class: (chromosome set number variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting number of entire chromosome sets.") AnnotationAssertion( "euploidy") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0215") AnnotationAssertion(rdfs:label "chromosome set number variation") SubClassOf( ) # Class: (diploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with two sets of chromosomes.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0216") AnnotationAssertion(rdfs:label "diploidy") SubClassOf( ) # Class: (tetraploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with four sets of chromosomes.") AnnotationAssertion( "Mauno") AnnotationAssertion( "2011-03-04T12:19:35Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0217") AnnotationAssertion(rdfs:label "tetraploidy") SubClassOf( ) # Class: (polyploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with several sets of chromosomes.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0218") AnnotationAssertion(rdfs:label "polyploidy") SubClassOf( ) # Class: (autopolyploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with several sets of chromosomes originating from the same organism.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0219") AnnotationAssertion(rdfs:label "autopolyploidy") SubClassOf( ) # Class: (allopolyploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with several sets of chromosomes originating from a different organism.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0220") AnnotationAssertion(rdfs:label "allopolyploidy") SubClassOf( ) # Class: (nulliploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation without chromosomes.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0221") AnnotationAssertion(rdfs:label "nulliploidy") SubClassOf( ) # Class: (triploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with three sets of chromosomes.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0222") AnnotationAssertion(rdfs:label "triploidy") SubClassOf( ) # Class: (pentaploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with five sets of chromosomes.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0223") AnnotationAssertion(rdfs:label "pentaploidy") SubClassOf( ) # Class: (hexaploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with six sets of chromosomes.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0224") AnnotationAssertion(rdfs:label "hexaploidy") SubClassOf( ) # Class: (monoploidy) AnnotationAssertion(Annotation( "VariO:mv") "Variation with a single set of chromosomes.") AnnotationAssertion( "haploidy") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0225") AnnotationAssertion(rdfs:label "monoploidy") SubClassOf( ) # Class: (chromatin structure variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0226") AnnotationAssertion(rdfs:label "chromatin structure variation") SubClassOf( ) # Class: (variation affecting DNA property) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting characteristic property of DNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0227") AnnotationAssertion(rdfs:label "variation affecting DNA property") SubClassOf( ) # Class: (protein fusion) AnnotationAssertion(Annotation( "VariO:mv") "Fusion of two protein chains. Produced from fusion gene of two joined genes.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-12-11T08:59:44Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0228") AnnotationAssertion(rdfs:label "protein fusion") SubClassOf( ) # Class: (association of DNA variation to pathogenicity) AnnotationAssertion(Annotation( "VariO:mv") "Implication of a DNA variant to pathogenicity.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0229") AnnotationAssertion(rdfs:label "association of DNA variation to pathogenicity") SubClassOf( ) # Class: (effect on DNA interaction) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting interaction of DNA with its partner.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0230") AnnotationAssertion(rdfs:label "effect on DNA interaction") SubClassOf( ) # Class: (conservation of DNA variation site) AnnotationAssertion(Annotation( "VariO:mv") "Conservation of the variation site in related DNA sequences.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0231") AnnotationAssertion(rdfs:label "conservation of DNA variation site") SubClassOf( ) # Class: (variation attribute) AnnotationAssertion(Annotation( "VariO:mv") "Attributes define and modulate terms at other levels.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0232") AnnotationAssertion(rdfs:label "variation attribute") SubClassOf( ) # Class: (conservation) AnnotationAssertion(Annotation( "VariO:mv") "Sequence conservation attribute.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0233") AnnotationAssertion(rdfs:label "conservation") SubClassOf( ) # Class: (conserved region) AnnotationAssertion(Annotation( "VariO:mv") "Variation at a region of sequence similarity in multiple sequence alignment of related sequences.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0234") AnnotationAssertion(rdfs:label "conserved region") SubClassOf( ) # Class: (invariant region) AnnotationAssertion(Annotation( "VariO:mv") "Variation at invariant sequence region in multiple sequence alignment of related sequences.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0235") AnnotationAssertion(rdfs:label "invariant region") SubClassOf( ) # Class: (interaction) AnnotationAssertion(Annotation( "VariO:mv") Annotation( "src_code:NR") "Mutual or reciprocal action or influence that happens at a given place and time between participating molecules.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0236") AnnotationAssertion(rdfs:label "interaction") SubClassOf( ) # Class: (genetic interaction) AnnotationAssertion(Annotation( "PMID:16527956") Annotation( "VariO:mv") "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.") AnnotationAssertion( "MI:0208") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0237") AnnotationAssertion(rdfs:label "genetic interaction") SubClassOf( ) # Class: (genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:14755292") Annotation( "VariO:mv") "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.") AnnotationAssertion( "MI:0931") AnnotationAssertion(Annotation( "MI:0931") "genetic inequality") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0238") AnnotationAssertion(rdfs:label "genetic interaction defined by inequality") SubClassOf( ) # Class: (single nonmonotonic genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") "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.") AnnotationAssertion( "MI:0800") AnnotationAssertion(Annotation( "MI:0800") "single nonmonotonic") AnnotationAssertion(Annotation( "MI:0800") "single nonmonotonic genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0239") AnnotationAssertion(rdfs:label "single nonmonotonic genetic interaction defined by inequality") SubClassOf( ) # Class: (missing protein) AnnotationAssertion(Annotation( "VariO:mv") "Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-12-11T13:07:02Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0240") AnnotationAssertion(rdfs:label "missing protein") SubClassOf( ) # Class: (RNA translocation) AnnotationAssertion(Annotation( "VariO:mv") "A continuous stretch of RNA sequence moved to a new position.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-12-18T16:17:33Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0241") AnnotationAssertion(rdfs:label "RNA translocation") SubClassOf( ) # Class: (conditional genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") Annotation( "VariO:mv") "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.") AnnotationAssertion( "MI:0798") AnnotationAssertion(Annotation( "MI:0798") "conditional") AnnotationAssertion(Annotation( "MI:0798") "conditional genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0242") AnnotationAssertion(rdfs:label "conditional genetic interaction defined by inequality") SubClassOf( ) # Class: (additive genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") Annotation( "VariO:mv") "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.") AnnotationAssertion( "MI:0799") AnnotationAssertion(Annotation( "MI:0799") "additive") AnnotationAssertion(Annotation( "MI:0799") "additive genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0243") AnnotationAssertion(rdfs:label "additive genetic interaction defined by inequality") SubClassOf( ) # Class: (RNA inversion) AnnotationAssertion(Annotation( "VriO:mv") "A continuous stretch of RNA sequence inserted to the same position in reverse orientation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2012-12-18T16:17:33Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0244") AnnotationAssertion(rdfs:label "RNA inversion") SubClassOf( ) # Class: (missing RNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-01-04T09:23:09Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0245") AnnotationAssertion(rdfs:label "missing RNA") SubClassOf( ) # Class: (artificial protein variation) AnnotationAssertion(Annotation( "VariO:mv") "Protein variation generated on purpose.") AnnotationAssertion( "gerard") AnnotationAssertion( "2013-02-01T11:24:30Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0246") AnnotationAssertion(rdfs:label "artificial protein variation") SubClassOf( ) # Class: (artificial RNA variation) AnnotationAssertion(Annotation( "VariO:mv") "RNA variation generated on purpose.") AnnotationAssertion( "gerard") AnnotationAssertion( "2013-02-01T11:27:07Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0247") AnnotationAssertion(rdfs:label "artificial RNA variation") SubClassOf( ) # Class: (positive genetic interaction) AnnotationAssertion(Annotation( "PMID:14755292") Annotation( "VariO:mv") "The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b.") AnnotationAssertion( "MI:0935") AnnotationAssertion(Annotation( "MI:0935") "positive gent int") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0248") AnnotationAssertion(rdfs:label "positive genetic interaction") SubClassOf( ) # Class: (double nonmonotonic genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") Annotation( "VariO:mv") "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.") AnnotationAssertion( "MI:0801") AnnotationAssertion(Annotation( "MI:0801") "double nonmonotonic") AnnotationAssertion(Annotation( "MI:0801") "double nonmonotonic genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0249") AnnotationAssertion(rdfs:label "double nonmonotonic genetic interaction defined by inequality") SubClassOf( ) SubClassOf( ) # Class: (epistatic genetic interaction) AnnotationAssertion(Annotation( "PMID:11988766") "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.") AnnotationAssertion( "MI:0930") AnnotationAssertion(Annotation( "MI:0930") "epistatis") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0250") AnnotationAssertion(rdfs:label "epistatic genetic interaction") SubClassOf( ) # Class: (epistatic genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") Annotation( "VariO:mv") "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).") AnnotationAssertion( "MI:0797") AnnotationAssertion(Annotation( "MI:0797") "epistatic") AnnotationAssertion(Annotation( "MI:0797") "epistatic genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0251") AnnotationAssertion(rdfs:label "epistatic genetic interaction defined by inequality") SubClassOf( ) SubClassOf( ) # Class: (asynthetic genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") "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.") AnnotationAssertion( "MI:0795") AnnotationAssertion(Annotation( "MI:0795") "asynthetic") AnnotationAssertion(Annotation( "MI:0795") "asynthetic genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0252") AnnotationAssertion(rdfs:label "asynthetic genetic interaction defined by inequality") SubClassOf( ) SubClassOf( ) # Class: (suppressive genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") Annotation( "VariO:mv") "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.") AnnotationAssertion( "MI:0796") AnnotationAssertion(Annotation( "MI:0796") "suppression") AnnotationAssertion(Annotation( "MI:0796") "suppressive genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0253") AnnotationAssertion(rdfs:label "suppressive genetic interaction defined by inequality") SubClassOf( ) SubClassOf( ) # Class: (neutral genetic interaction) AnnotationAssertion(Annotation( "PMID:14755292") Annotation( "VariO:mv") "The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b.") AnnotationAssertion( "MI:0934") AnnotationAssertion(Annotation( "MI:0934") "neutral gent int") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0254") AnnotationAssertion(rdfs:label "neutral genetic interaction") SubClassOf( ) # Class: (noninteractive genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") Annotation( "VariO:mv") "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.") AnnotationAssertion( "MI:0932") AnnotationAssertion(Annotation( "MI:0932") "noninteractive") AnnotationAssertion(Annotation( "MI:0932") "noninteractive genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0255") AnnotationAssertion(rdfs:label "noninteractive genetic interaction defined by inequality") SubClassOf( ) SubClassOf( ) # Class: (negative genetic interaction) AnnotationAssertion(Annotation( "PMID:14755292") Annotation( "VariO:mv") "The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b.") AnnotationAssertion( "MI:0933") AnnotationAssertion(Annotation( "MI:0933") "negative gen int") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0256") AnnotationAssertion(rdfs:label "negative genetic interaction") SubClassOf( ) # Class: (synthetic genetic interaction defined by inequality) AnnotationAssertion(Annotation( "PMID:15833125") "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.") AnnotationAssertion( "MI:0794") AnnotationAssertion(Annotation( "MI:0794") "synthetic") AnnotationAssertion(Annotation( "MI:0794") "synthetic genetic interaction (sensu inequality)") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0257") AnnotationAssertion(rdfs:label "synthetic genetic interaction defined by inequality") SubClassOf( ) SubClassOf( ) # Class: (structural level of interaction) AnnotationAssertion(Annotation( "VariO:mv") "Molecular structural level of interaction.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0258") AnnotationAssertion(rdfs:label "structural level of interaction") SubClassOf( ) # Class: (intermolecular interaction) AnnotationAssertion(Annotation( "VariO:mv") "Interaction between molecules.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0259") AnnotationAssertion(rdfs:label "intermolecular interaction") SubClassOf( ) # Class: (intramolecular interaction) AnnotationAssertion(Annotation( "VariO:mv") "Interaction within a molecule.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0260") AnnotationAssertion(rdfs:label "intramolecular interaction") SubClassOf( ) # Class: (colocalization) AnnotationAssertion(Annotation( "PMID:14755292") "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.") AnnotationAssertion( "MI:0403") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0261") AnnotationAssertion(rdfs:label "colocalization") SubClassOf( ) # Class: (interactor) AnnotationAssertion(Annotation( "SBO:0000336") "Entity participating in a physical or functional interaction.") AnnotationAssertion( "SBO:0000336") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0262") AnnotationAssertion(rdfs:label "interactor") SubClassOf( ) # Class: (small molecule) AnnotationAssertion(Annotation( "PMID:14755292") "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.") AnnotationAssertion( "MI:0328") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0263") AnnotationAssertion(rdfs:label "small molecule") SubClassOf( ) # Class: (metal) AnnotationAssertion(Annotation( "CHEBI:33521") "Metal atom.") AnnotationAssertion( "CHEBI:33521") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0264") AnnotationAssertion(rdfs:label "metal") SubClassOf( ) # Class: (solvent) AnnotationAssertion(Annotation( "CHEBI:46787") "A liquid that can dissolve other substances (solutes) without any change in their chemical composition.") AnnotationAssertion( "CHEBI:46787") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0265") AnnotationAssertion(rdfs:label "solvent") SubClassOf( ) # Class: (water) AnnotationAssertion(Annotation( "CHEBI:15377") "An inorganic hydroxy compound that has formula H2O.") AnnotationAssertion( "CHEBI:15377") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0266") AnnotationAssertion(rdfs:label "water") SubClassOf( ) # Class: (complex) AnnotationAssertion(Annotation( "PMID:14755292") "Set of interacting molecules that can be copurified.") AnnotationAssertion( "MI:0314") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0267") AnnotationAssertion(rdfs:label "complex") SubClassOf( ) # Class: (ribonucleoprotein complex) AnnotationAssertion(Annotation( "PMID:14755292") "A macromolecular complex containing both protein and RNA molecules.") AnnotationAssertion( "MI:0316") AnnotationAssertion(Annotation( "MI:0316") "ribonucleoprot compl") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0268") AnnotationAssertion(rdfs:label "ribonucleoprotein complex") SubClassOf( ) # Class: (protein complex) AnnotationAssertion(Annotation( "PMID:14755292") "A stable set of interacting proteins that can be copurified and operate as a functional unit.") AnnotationAssertion( "GO:0043234") AnnotationAssertion( "MI:0315") AnnotationAssertion(Annotation( "GO:0043234") "protein-protein complex") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0269") AnnotationAssertion(rdfs:label "protein complex") SubClassOf( ) # Class: (protein dna complex) AnnotationAssertion(Annotation( "PMID:14755292") "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.") AnnotationAssertion( "MI:0233") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0270") AnnotationAssertion(rdfs:label "protein dna complex") SubClassOf( ) # Class: (unknown participant) AnnotationAssertion(Annotation( "PMID:14755292") "Any type of molecule, including complexes, that may be observed but not identified.") AnnotationAssertion( "MI:0329") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0271") AnnotationAssertion(rdfs:label "unknown participant") SubClassOf( ) # Class: (gene) AnnotationAssertion(Annotation( "MI:0000704") "Interactor of genetic interaction.") AnnotationAssertion( "MI:0250") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0272") AnnotationAssertion(rdfs:label "gene") SubClassOf( ) # Class: (biopolymer) AnnotationAssertion(Annotation( "PMID:14577292") "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.") AnnotationAssertion( "MI:0383") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0273") AnnotationAssertion(rdfs:label "biopolymer") SubClassOf( ) # Class: (nucleic acid) AnnotationAssertion(Annotation( "PMID:14755292") "Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages.") AnnotationAssertion( "GO:0005561") AnnotationAssertion( "MI:0318") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0274") AnnotationAssertion(rdfs:label "nucleic acid") SubClassOf( ) # Class: (peptide) AnnotationAssertion(Annotation( "PMID:14755292") "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.") AnnotationAssertion( "MI:0327") AnnotationAssertion(Annotation( "MI:0327") "oligopeptide") AnnotationAssertion(Annotation( "MI:0327") "polypeptide") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0275") AnnotationAssertion(rdfs:label "peptide") SubClassOf( ) # Class: (polysaccharide) AnnotationAssertion(Annotation( "PMID:14755292") "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.") AnnotationAssertion( "MI:0904") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0276") AnnotationAssertion(rdfs:label "polysaccharide") SubClassOf( ) # Class: (protein) AnnotationAssertion(Annotation( "PMID:14755292") "A linear polymer of amino acids joined by peptide bonds in a specific sequence.") AnnotationAssertion( "GO:0003675") AnnotationAssertion( "MI:0326") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0277") AnnotationAssertion(rdfs:label "protein") SubClassOf( ) # Class: (association) AnnotationAssertion(Annotation( "PMID:14755292") "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.") AnnotationAssertion( "MI:0914") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0278") AnnotationAssertion(rdfs:label "association") SubClassOf( ) # Class: (interaction physical force) AnnotationAssertion(Annotation( "VariO:mv") "Interaction physical force.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0279") AnnotationAssertion(rdfs:label "interaction physical force") SubClassOf( ) # Class: (covalent bond) AnnotationAssertion(Annotation( "http://chemistry.about.com/od/chemistryglossary/a/covalentbonddef.htm") "A chemical link between two atoms in which electrons are shared between them.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0280") AnnotationAssertion(rdfs:label "covalent bond") SubClassOf( ) # Class: (disulphide bridge) AnnotationAssertion(Annotation( "EBIBS:GAR") Annotation( "UniProt:curation_manual") Annotation( "VariO:mv") "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain.") AnnotationAssertion( "SO:0001088") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0281") AnnotationAssertion(rdfs:label "disulphide bridge") SubClassOf( ) # Class: (non covalent bond) AnnotationAssertion(Annotation( "VariO:mv") "Interaction between biochemical entities that results in the formation of a non-covalent bond.") AnnotationAssertion( "SBO:0000177") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0282") AnnotationAssertion(rdfs:label "non covalent bond") SubClassOf( ) # Class: (hydrogen bond) AnnotationAssertion(Annotation( "VariO:mv") "Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom.") AnnotationAssertion( "FIX:0000503") AnnotationAssertion( "http://chemistry.about.com/od/chemistryglossary/g/hbond.htm") AnnotationAssertion( "variation_ontology") AnnotationAssertion(Annotation( "FIX:0000503") "H-bond") AnnotationAssertion( "VariO:0283") AnnotationAssertion(rdfs:label "hydrogen bond") SubClassOf( ) # Class: (hydrogen bond network) AnnotationAssertion(Annotation( "VariO:mv") "Network of interactions formed by several hydrogen bonds.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0284") AnnotationAssertion(rdfs:label "hydrogen bond network") SubClassOf( ) # Class: (hydrophobic interaction) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/Hydrophobic+Interaction") "Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0285") AnnotationAssertion(rdfs:label "hydrophobic interaction") SubClassOf( ) # Class: (salt bridge) AnnotationAssertion(Annotation( "VariO:mv") "Interaction between charged groups.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0286") AnnotationAssertion(rdfs:label "salt bridge") SubClassOf( ) # Class: (van der Waals interaction) AnnotationAssertion(Annotation( "VariO:mv") "Weak attractive electrical force between neutral groups or molecules.") AnnotationAssertion( "FIX:0000506") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0287") AnnotationAssertion(rdfs:label "van der Waals interaction") SubClassOf( ) # Class: (electrostatic interaction) AnnotationAssertion(Annotation( "VariO:mv") "Attraction between two electrically charged groups or molecules.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0288") AnnotationAssertion(rdfs:label "electrostatic interaction") SubClassOf( ) # Class: (quantity change) AnnotationAssertion(Annotation( "VariO:mv") "Quantity attribute.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0289") AnnotationAssertion(rdfs:label "quantity change") SubClassOf( ) # Class: (decreased) AnnotationAssertion(Annotation( "SGD:curators") "The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.).") AnnotationAssertion( "APO:0000003") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0290") AnnotationAssertion(rdfs:label "decreased") SubClassOf( ) # Class: (increased) AnnotationAssertion(Annotation( "SGD:curators") "The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.).") AnnotationAssertion( "APO:0000004") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0291") AnnotationAssertion(rdfs:label "increased") SubClassOf( ) # Class: (missing) AnnotationAssertion(Annotation( "VariO:mv") "The observed feature is missing compared to that in the wild type.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0292") AnnotationAssertion(rdfs:label "missing") SubClassOf( ) # Class: (pathogenicity association) AnnotationAssertion(Annotation( "VariO:mv") "Pathogenicity attribute.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0293") AnnotationAssertion(rdfs:label "pathogenicity association") SubClassOf( ) # Class: (disease causing) AnnotationAssertion(Annotation( "VariO:mv") "Variation is causative of disease.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0294") AnnotationAssertion(rdfs:label "disease causing") SubClassOf( ) # Class: (not related to clinical phenotype) AnnotationAssertion(Annotation( "VariO:mv") "Variation is not related to clinical phenotype.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0295") AnnotationAssertion(rdfs:label "not related to clinical phenotype") SubClassOf( ) # Class: (disease associated) AnnotationAssertion(Annotation( "VariO:mv") "Variation is disease related.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0296") AnnotationAssertion(rdfs:label "disease associated") SubClassOf( ) # Class: (variation affecting RNA) AnnotationAssertion(Annotation( "VariO:mv") "Effects of a variation on RNA level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0297") AnnotationAssertion(rdfs:label "variation affecting RNA") SubClassOf( ) # Class: (variation affecting RNA property) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting characteristic property of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0298") AnnotationAssertion(rdfs:label "variation affecting RNA property") SubClassOf( ) # Class: (effect on RNA degradation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting degradation of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0299") AnnotationAssertion(rdfs:label "effect on RNA degradation") SubClassOf( ) # Class: (effect on RNA folding) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting folding of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0300") AnnotationAssertion(rdfs:label "effect on RNA folding") SubClassOf( ) # Class: (effect on RNA stability) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting stability of transcript.") AnnotationAssertion( "SO:0001546") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0301") AnnotationAssertion(rdfs:label "effect on RNA stability") SubClassOf( ) # Class: (conservation of RNA variation site) AnnotationAssertion(Annotation( "VariO:mv") "Conservation of the variation site in related RNA sequences.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0302") AnnotationAssertion(rdfs:label "conservation of RNA variation site") SubClassOf( ) # Class: (polysomy) AnnotationAssertion(Annotation( "VariO:mv") "An excess of a particular chromosome in a cell or organism.") AnnotationAssertion( "gerard") AnnotationAssertion( "2013-02-01T11:30:39Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0303") AnnotationAssertion(rdfs:label "polysomy") SubClassOf( ) # Class: (association of RNA variation to pathogenicity) AnnotationAssertion(Annotation( "VariO:mv") "Implication of an RNA variant to pathogenicity.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0304") AnnotationAssertion(rdfs:label "association of RNA variation to pathogenicity") SubClassOf( ) # Class: (effect on RNA interaction) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting interaction of RNA with its partner.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0305") AnnotationAssertion(rdfs:label "effect on RNA interaction") SubClassOf( ) # Class: (RNA variation type) AnnotationAssertion(Annotation( "VariO:mv") "Type of RNA variation. Describes origin and classification of a variant.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0306") AnnotationAssertion(rdfs:label "RNA variation type") SubClassOf( ) # Class: (RNA variation of genetic origin) AnnotationAssertion(Annotation( "VariO:mv") "RNA variation that has genetic origin.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0307") AnnotationAssertion(rdfs:label "RNA variation of genetic origin") SubClassOf( ) # Class: (missense variation) AnnotationAssertion(Annotation( "VariO:mv") "Nucleotide change in the mRNA triplet codon codes for another amino acid.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0308") AnnotationAssertion(rdfs:label "missense variation") SubClassOf( ) # Class: (termination codon change) AnnotationAssertion(Annotation( "VariO:mv") "RNA nucleotide change in termination codon.") AnnotationAssertion( "SO:0001590") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0309") AnnotationAssertion(rdfs:label "termination codon change") SubClassOf( ) # Class: (nonsense variation) AnnotationAssertion(Annotation( "VariO:mv") "Nucleotide change in the mRNA codon triplet creates a terminator codon.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0310") AnnotationAssertion(rdfs:label "nonsense variation") SubClassOf( ) # Class: (RNA indel) AnnotationAssertion(Annotation( "VariO:mv") "A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s).") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0311") AnnotationAssertion(rdfs:label "RNA indel") SubClassOf( ) # Class: (RNA substitution) AnnotationAssertion(Annotation( "VariO:mv") "Substitution of RNA nucleotide.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0312") AnnotationAssertion(rdfs:label "RNA substitution") SubClassOf( ) # Class: (transition) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0313") AnnotationAssertion(rdfs:label "transition") SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom(owl:topObjectProperty )) # Class: (pyrimidine transition) AnnotationAssertion(Annotation( "VariO:mv") "A substitution of a pyrimidine, C or T (or U), for another pyrimidine.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0314") AnnotationAssertion(rdfs:label "pyrimidine transition") SubClassOf( ) # Class: (purine transition) AnnotationAssertion(Annotation( "VariO:mv") "A substitution of a purine, A or G, for another purine.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0315") AnnotationAssertion(rdfs:label "purine transition") SubClassOf( ) # Class: (transversion) AnnotationAssertion(Annotation( "VariO:mv") "Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa.") AnnotationAssertion(Annotation(rdfs:label "wiki") "http://en.wikipedia.org/wiki/Transversion") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0316") AnnotationAssertion(rdfs:label "transversion") SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (initiation codon change) AnnotationAssertion(Annotation( "VariO:mv") "RNA nucleotide change in the initiation codon.") AnnotationAssertion( "SO:0001582") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0317") AnnotationAssertion(rdfs:label "initiation codon change") SubClassOf( ) # Class: (silent variation) AnnotationAssertion(Annotation( "VariO:mv") "RNA variation that does not change the encoded amino acid.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0318") AnnotationAssertion(rdfs:label "silent variation") SubClassOf( ) # Class: (RNA deletion) AnnotationAssertion(Annotation( "VariO:mv") "One or more continuous nucleotides are missing from RNA sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0319") AnnotationAssertion(rdfs:label "RNA deletion") SubClassOf( ) # Class: (in-frame deletion) AnnotationAssertion(Annotation( "VariO:mv") "Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0320") AnnotationAssertion(rdfs:label "in-frame deletion") SubClassOf( ) # Class: (out-of-frame deletion) AnnotationAssertion(Annotation( "VariO:mv") "Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0321") AnnotationAssertion(rdfs:label "out-of-frame deletion") SubClassOf( ) # Class: (DNA variation classification) AnnotationAssertion(Annotation( "VariO:mv") "Classification of DNA variation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-10-11T08:46:32Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0322") AnnotationAssertion(rdfs:label "DNA variation classification") SubClassOf( ) # Class: (protein variation origin) AnnotationAssertion(Annotation( "VariO:mv") "Origin of protein variation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-10-11T08:53:23Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0323") AnnotationAssertion(rdfs:label "protein variation origin") SubClassOf( ) # Class: (RNA variation origin) AnnotationAssertion(Annotation( "VariO:mv") "Origin of RNA variation.") AnnotationAssertion( "2013-10-11T09:04:23Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0324") AnnotationAssertion(rdfs:label "RNA variation origin") SubClassOf( ) # Class: (protein variation classification) AnnotationAssertion(Annotation( "VariO:mv") "Classification of protein variation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-10-11T08:59:04Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0325") AnnotationAssertion(rdfs:label "protein variation classification") SubClassOf( ) # Class: (RNA insertion) AnnotationAssertion(Annotation( "VariO:mv") "Addition of one or more nucleotides between adjacent nucleotides in RNA sequence.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0326") AnnotationAssertion(rdfs:label "RNA insertion") SubClassOf( ) # Class: (out-of-frame insertion) AnnotationAssertion(Annotation( "VariO:mv") "Insertion of nucleotide(s) causing alteration of mRNA reading frame.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0327") AnnotationAssertion(rdfs:label "out-of-frame insertion") SubClassOf( ) # Class: (RNA variation classification) AnnotationAssertion(Annotation( "VariO:mv") "Classification of RNA variation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2013-10-11T09:05:02Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0328") AnnotationAssertion(rdfs:label "RNA variation classification") SubClassOf( ) # Class: (alternative RNA form) AnnotationAssertion(Annotation( "VariO:mv") "RNA variation due to defective fidelity of transcription.") AnnotationAssertion( "2014-10-23T00:29:53Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0329") AnnotationAssertion(rdfs:label "alternative RNA form") SubClassOf( ) # Class: (mistranslated protein) AnnotationAssertion(Annotation( "VariO:mv") "Protein variation due to defective fidelity of translation.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2014-10-23T00:31:56Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0330") AnnotationAssertion(rdfs:label "mistranslated protein") SubClassOf( ) # Class: (alternative form of mRNA) AnnotationAssertion(Annotation( "VariO:mv") "Alternative form of mRNA molecule.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-04-26T14:47:12Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0331") AnnotationAssertion(rdfs:label "alternative form of mRNA") SubClassOf( ) # Class: (in-frame insertion) AnnotationAssertion(Annotation( "VariO:mv") "Insertion of nucleotides in multiples of three so that the reading frame is retained.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0332") AnnotationAssertion(rdfs:label "in-frame insertion") SubClassOf( ) # Class: (RNA variation of non-genetic origin) AnnotationAssertion(Annotation( "VariO:mv") "RNA variation that does not have genetic origin being modified at RNA level.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0333") AnnotationAssertion(rdfs:label "RNA variation of non-genetic origin") SubClassOf( ) # Class: (RNA splicing change) AnnotationAssertion(Annotation( "VariO:mv") "Change to RNA splicing.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0334") AnnotationAssertion(rdfs:label "RNA splicing change") SubClassOf( ) # Class: (decayed RNA) AnnotationAssertion(Annotation( "VariO:mv") "RNA molecule destroyed due to appearance of a premature termination codon.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0335") AnnotationAssertion(rdfs:label "decayed RNA") SubClassOf( ) # Class: (modified RNA) AnnotationAssertion(Annotation( "VariO:mv") "Post transcriptionally modified RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0336") AnnotationAssertion(rdfs:label "modified RNA") SubClassOf( ) # Class: (modified DNA) AnnotationAssertion(Annotation( "VariO:mv") "DNA variation due to biological, chemical, physical or other modification.") AnnotationAssertion( "Mauno Vihinen") AnnotationAssertion( "2014-10-23T00:42:47Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0337") AnnotationAssertion(rdfs:label "modified DNA") SubClassOf( ) # Class: (variation affecting RNA structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting structure of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0338") AnnotationAssertion(rdfs:label "variation affecting RNA structure") SubClassOf( ) # Class: (synonymous variation) AnnotationAssertion(Annotation( "VariO:mv") "mRNA variation not affecting the sequence of the translated protein.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-06-04T13:23:24Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0343") AnnotationAssertion(rdfs:label "synonymous variation") SubClassOf( ) # Class: (affected RNA type) AnnotationAssertion(Annotation( "VariO:mv") "Affected type of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0349") AnnotationAssertion(rdfs:label "affected RNA type") SubClassOf( ) # Class: (non-protein coding RNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA not coding for protein.") AnnotationAssertion( "ncRNA") AnnotationAssertion( "non-coding RNA ncRNA") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0350") AnnotationAssertion(rdfs:label "non-protein coding RNA") SubClassOf( ) # Class: (protein coding RNA) AnnotationAssertion(Annotation( "VariO:mv") "RNA coding for protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0351") AnnotationAssertion(rdfs:label "protein coding RNA") SubClassOf( ) # Class: (coding region of mRNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting region coding for protein in protein coding RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0352") AnnotationAssertion(rdfs:label "coding region of mRNA") SubClassOf( ) # Class: (non-coding region of mRNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting region not coding for protein in protein coding mRNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0353") AnnotationAssertion(rdfs:label "non-coding region of mRNA") SubClassOf( ) # Class: (effect on post transcriptional RNA modification) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting post transcriptional RNA modification.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0354") AnnotationAssertion(rdfs:label "effect on post transcriptional RNA modification") SubClassOf( ) # Class: (alternatively polyadenylated mRNA) AnnotationAssertion(Annotation( "VariO:mv") "Polyadenylation of mRNA molecule at alternative site.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0356") AnnotationAssertion(rdfs:label "alternatively polyadenylated mRNA") SubClassOf( ) # Class: (RNA sugar variation) AnnotationAssertion(Annotation( "VariO:mv") "Post transcriptional modification of RNA nucleoside sugar.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0361") AnnotationAssertion(rdfs:label "RNA sugar variation") SubClassOf( ) # Class: (effect on RNA splicing) AnnotationAssertion(Annotation( "VariO:mv") "Effect to process where introns in mRNA are cut away from exons.") AnnotationAssertion( "SO:0001568") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0362") AnnotationAssertion(rdfs:label "effect on RNA splicing") SubClassOf( ) # Class: (effect on RNA localization) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting cellular localization of RNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-05-07T11:20:14Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0363") AnnotationAssertion(rdfs:label "effect on RNA localization") SubClassOf( ) # Class: (effect on RNA aggregation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting aggregation tendency of RNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-05-07T11:20:14Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0364") AnnotationAssertion(rdfs:label "effect on RNA aggregation") SubClassOf( ) # Class: (effect on cis splicing) AnnotationAssertion(Annotation( "VariO:mv") "Intronic splicing within an RNA molecule.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0365") AnnotationAssertion(rdfs:label "effect on cis splicing") SubClassOf( ) # Class: (variation at recursive splice site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting splicing at recursive splice site which subdivides a large intron.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0366") AnnotationAssertion(rdfs:label "variation at recursive splice site") SubClassOf( ) # Class: (variation at five prime splice site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting intronic region bordering exon or retained RNA region, at the five prime end of the intron.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0367") AnnotationAssertion(rdfs:label "variation at five prime splice site") SubClassOf( ) # Class: (variation at canonical five prime splice site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting canonical prime splice site at five prime end.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0368") AnnotationAssertion(rdfs:label "variation at canonical five prime splice site") SubClassOf( ) # Class: (variation at non canonical five prime splice site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting non canonical splice site at five prime end.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0369") AnnotationAssertion(rdfs:label "variation at non canonical five prime splice site") SubClassOf( ) # Class: (variation at three prime splice site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting intronic region bordering the exon or retained RNA region, at the 3' edge of the intron.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0370") AnnotationAssertion(rdfs:label "variation at three prime splice site") SubClassOf( ) # Class: (variation at non canonical three prime splice site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting non canonical splice site at three prime end.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0371") AnnotationAssertion(rdfs:label "variation at non canonical three prime splice site") SubClassOf( ) # Class: (variation at canonical three prime splice site) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting canonical splice site at three prime end.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0372") AnnotationAssertion(rdfs:label "variation at canonical three prime splice site") SubClassOf( ) # Class: (cryptic splice site activation) AnnotationAssertion(Annotation( "VariO:mv") "Activation of new splice site.") AnnotationAssertion( "SO:0001569") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0373") AnnotationAssertion(rdfs:label "cryptic splice site activation") SubClassOf( ) # Class: (cryptic splice donor activation) AnnotationAssertion(Annotation( "VariO:mv") "Activation of new splice donor site.") AnnotationAssertion( "SO:0001571") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0374") AnnotationAssertion(rdfs:label "cryptic splice donor activation") SubClassOf( ) # Class: (cryptic splice acceptor activation) AnnotationAssertion(Annotation( "VariO:mv") "Activation of new splice acceptor site.") AnnotationAssertion( "SO:0001570") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0375") AnnotationAssertion(rdfs:label "cryptic splice acceptor activation") SubClassOf( ) # Class: (effect on trans splicing) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting splicing and ligation different RNA molecules.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0376") AnnotationAssertion(rdfs:label "effect on trans splicing") SubClassOf( ) # Class: (retrotransposon insertion) AnnotationAssertion(Annotation( "VariO:mv") "Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-08-26T12:50:29Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0377") AnnotationAssertion(rdfs:label "retrotransposon insertion") SubClassOf( ) # Class: (DNA transposon) AnnotationAssertion(Annotation( "VariO:mv") "Insertion of a DNA transposable element into chromosome.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-08-26T12:50:29Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0378") AnnotationAssertion(rdfs:label "DNA transposon") SubClassOf( ) # Class: (LINE) AnnotationAssertion(Annotation( "VariO:mv") "Long interspersed nuclear element generated by retrotransposition.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-08-26T12:51:03Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0379") AnnotationAssertion(rdfs:label "LINE") SubClassOf( ) # Class: (SINE) AnnotationAssertion(Annotation( "VariO:mv") "Short interspersed nuclear element generated by retrotransposition. Length below 500 bp.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-08-26T12:51:03Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0380") AnnotationAssertion(rdfs:label "SINE") SubClassOf( ) # Class: (effect on RNA double helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA double helix.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-05-07T11:22:31Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0381") AnnotationAssertion(rdfs:label "effect on RNA double helix") SubClassOf( ) # Class: (effect on RNA secondary structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA secondary structure.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0382") AnnotationAssertion(rdfs:label "effect on RNA secondary structure") SubClassOf( ) # Class: (effect on RNA multiloop) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting closed RNA structure in which at least two double stranded regions meet.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0383") AnnotationAssertion(rdfs:label "effect on RNA multiloop") SubClassOf( ) # Class: (effect on RNA bulge) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA structure in which nucleotides in one strand do not form base pairs.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0384") AnnotationAssertion(rdfs:label "effect on RNA bulge") SubClassOf( ) # Class: (effect on RNA interior loop) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA structure in which both the strands do not form base pairs.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0385") AnnotationAssertion(rdfs:label "effect on RNA interior loop") SubClassOf( ) # Class: (effect on RNA stem) AnnotationAssertion(Annotation( "VariO:mv") "Variation effecting hydrogen bonding in contiguous nested base pairs in RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0386") AnnotationAssertion(rdfs:label "effect on RNA stem") SubClassOf( ) # Class: (effect on RNA hairpin loop) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting loop connecting adjacent regions forming helix in RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0387") AnnotationAssertion(rdfs:label "effect on RNA hairpin loop") SubClassOf( ) # Class: (LTR) AnnotationAssertion(Annotation( "VariO:mv") "Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-08-26T12:51:03Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0388") AnnotationAssertion(rdfs:label "LTR") SubClassOf( ) # Class: (pentanucleotide expansion) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of five nucleotide units.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-17T10:55:04Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0389") AnnotationAssertion(rdfs:label "pentanucleotide expansion") SubClassOf( ) # Class: (effect on DNA double helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting DNA double helical structure.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T12:53:57Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0390") AnnotationAssertion(rdfs:label "effect on DNA double helix") SubClassOf( ) # Class: (plasmid affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation effect on independently replicating small DNA molecule.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-18T20:15:22Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0391") AnnotationAssertion(rdfs:label "plasmid affected") SubClassOf( ) # Class: (insertion sequence) AnnotationAssertion(Annotation( "VariO:mv") "Simple, relatively short transposable element. IS elements contain only transposition related genes.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-18T20:28:19Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0392") AnnotationAssertion(rdfs:label "insertion sequence") SubClassOf( ) # Class: (epigenetic RNA variation) AnnotationAssertion(Annotation( "VariO:mv") "RNA variation of epigenetic origin.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-05-07T11:43:50Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0393") AnnotationAssertion(rdfs:label "epigenetic RNA variation") SubClassOf( ) # Class: (effect on DNA cruciform) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-18T20:44:08Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0394") AnnotationAssertion(rdfs:label "effect on DNA cruciform") SubClassOf( ) # Class: (variation affecting RNA function) AnnotationAssertion(Annotation( "VariO:mv") "Variation having effect on RNA function and usage.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0396") AnnotationAssertion(rdfs:label "variation affecting RNA function") SubClassOf( ) # Class: (effect on RNA splicing function) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting splicing function of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0397") AnnotationAssertion(rdfs:label "effect on RNA splicing function") SubClassOf( ) # Class: (effect on catalytic RNA activity) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting catalytic function of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0398") AnnotationAssertion(rdfs:label "effect on catalytic RNA activity") SubClassOf( ) # Class: (effect on translation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting translation of protein.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0399") AnnotationAssertion(rdfs:label "effect on translation") SubClassOf( ) # Class: (effect on regulatory function of RNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting regulatory function of RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0400") AnnotationAssertion(rdfs:label "effect on regulatory function of RNA") SubClassOf( ) # Class: (effect on amino acid transfer of RNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA function in amino acid transfer.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0401") AnnotationAssertion(rdfs:label "effect on amino acid transfer of RNA") SubClassOf( ) # Class: (effect on RNA information transfer) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting information transfer by RNA.") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0402") AnnotationAssertion(rdfs:label "effect on RNA information transfer") SubClassOf( ) # Class: (group I intron) AnnotationAssertion(Annotation( "VariO:mv") "Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-21T10:06:37Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0403") AnnotationAssertion(rdfs:label "group I intron") SubClassOf( ) # Class: (group II intron) AnnotationAssertion(Annotation( "VariO:mv") "Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-21T10:06:37Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0404") AnnotationAssertion(rdfs:label "group II intron") SubClassOf( ) # Class: (dicentric translocation) AnnotationAssertion(Annotation( "VariO:mv") "Fusion of two chromosome segments both containing a centromere.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-22T19:15:03Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0405") AnnotationAssertion(rdfs:label "dicentric translocation") SubClassOf( ) # Class: (edited DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation generated by chromosome editing.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-22T19:20:45Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0407") AnnotationAssertion(rdfs:label "edited DNA") SubClassOf( ) # Class: (RNA chimera) AnnotationAssertion(Annotation( "VariO:mv") "Fusion transcript of exons from two or more genes.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-24T13:21:02Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0408") AnnotationAssertion(rdfs:label "RNA chimera") SubClassOf( ) # Class: (frameshifted RNA) AnnotationAssertion(Annotation( "VariO:mv") "Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-09-24T13:21:02Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0409") AnnotationAssertion(rdfs:label "frameshifted RNA") SubClassOf( ) # Class: (effect on single stranded DNA structure) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting single stranded DNA structure.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-11-08T10:04:23Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0410") AnnotationAssertion(rdfs:label "effect on single stranded DNA structure") SubClassOf( ) # Class: (alternatively spliced RNA) AnnotationAssertion(Annotation( "VariO:mv") "mRNA molecule matured by splicing at an alternative site.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2015-10-13T19:36:23Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0411") AnnotationAssertion(rdfs:label "alternatively spliced RNA") SubClassOf( ) # Class: (effect on catalytic DNA activity) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting catalytic function of DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2016-11-29T11:11:11Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0412") AnnotationAssertion(rdfs:label "effect on catalytic DNA activity") SubClassOf( ) # Class: (effect on A DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting A form of right-handed DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T12:55:40Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0413") AnnotationAssertion(rdfs:label "effect on A DNA") SubClassOf( ) # Class: (effect on B DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting B form of right-handed DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T12:55:40Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0414") AnnotationAssertion(rdfs:label "effect on B DNA") SubClassOf( ) # Class: (effect on C DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting C form of right-handed DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T12:55:40Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0415") AnnotationAssertion(rdfs:label "effect on C DNA") SubClassOf( ) # Class: (effect on L DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting L form of right-handed DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T12:55:40Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0416") AnnotationAssertion(rdfs:label "effect on L DNA") SubClassOf( ) # Class: (effect on S DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting S form of right-handed DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T12:55:40Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0417") AnnotationAssertion(rdfs:label "effect on S DNA") SubClassOf( ) # Class: (effect on D DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting D form of right-handed DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:10:01Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0418") AnnotationAssertion(rdfs:label "effect on D DNA") SubClassOf( ) # Class: (effect on H DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting H form of intramolecular triple helical DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:14:56Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0419") AnnotationAssertion(rdfs:label "effect on H DNA") SubClassOf( ) # Class: (effect on four-stranded DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting four-stranded DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:17:51Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0420") AnnotationAssertion(rdfs:label "effect on four-stranded DNA") SubClassOf( ) # Class: (effect on Z DNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting Z form of left-handed DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:20:36Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0421") AnnotationAssertion(rdfs:label "effect on Z DNA") SubClassOf( ) # Class: (effect on intramolecular DNA triple helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:22:35Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0422") AnnotationAssertion(rdfs:label "effect on intramolecular DNA triple helix") SubClassOf( ) # Class: (effect on intermolecular DNA triple helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:24:18Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0423") AnnotationAssertion(rdfs:label "effect on intermolecular DNA triple helix") SubClassOf( ) # Class: (effect on DNA-RNA hybrid) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting DNA-RNA hybrid.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:29:46Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0424") AnnotationAssertion(rdfs:label "effect on DNA-RNA hybrid") SubClassOf( ) SubClassOf( ) # Class: (effect on RNA triple helix) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting RNA helix formed of three strands.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:48:49Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0425") AnnotationAssertion(rdfs:label "effect on RNA triple helix") SubClassOf( ) # Class: (effect on four-stranded RNA) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting four-stranded RNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-16T13:48:49Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0426") AnnotationAssertion(rdfs:label "effect on four-stranded RNA") SubClassOf( ) # Class: (type of chromosomal amplification) AnnotationAssertion(Annotation( "VariO:mv") "Classification of chromosomal amplification type.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-17T09:34:30Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0427") AnnotationAssertion(rdfs:label "type of chromosomal amplification") SubClassOf( ) # Class: (genome variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting genome.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-23T09:01:36Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0428") AnnotationAssertion(rdfs:label "genome variation") SubClassOf( ) # Class: (complex genomic variation) AnnotationAssertion(Annotation( "VariO:mv") "Chromosome structure variation due to several breakpoints.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-23T09:03:57Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0429") AnnotationAssertion(rdfs:label "complex genomic variation") SubClassOf( ) # Class: (nucleotide expansion) AnnotationAssertion(Annotation( "VariO:mv") "Repetitive sequence consisting of one more nucleotide units.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-23T09:09:22Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0430") AnnotationAssertion(rdfs:label "nucleotide expansion") SubClassOf( ) # Class: (effect on R loop) AnnotationAssertion(Annotation( "VariO:mv") "Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-23T09:32:22Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0431") AnnotationAssertion(rdfs:label "effect on R loop") SubClassOf( ) # Class: (effect on T loop) AnnotationAssertion(Annotation( "VariO:mv") "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.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-23T09:34:30Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0432") AnnotationAssertion(rdfs:label "effect on T loop") SubClassOf( ) # Class: (effect on D loop) AnnotationAssertion(Annotation( "VariO:mv") "Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-01-23T09:45:49Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0433") AnnotationAssertion(rdfs:label "effect on D loop") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (DNA sugar variation) AnnotationAssertion(Annotation( "VariO:mv") "Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-03-23T10:54:09Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0434") AnnotationAssertion(rdfs:label "DNA sugar variation") SubClassOf( ) # Class: (effect on protein reaction kinetics) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation to protein reaction kinetics.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-04-28T14:52:51Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0435") AnnotationAssertion(rdfs:label "effect on protein reaction kinetics") SubClassOf( ) # Class: (mature RNA) AnnotationAssertion(Annotation( "VariO:mv") "Completely processed RNA molecule.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-04-28T14:58:30Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0436") AnnotationAssertion(rdfs:label "mature RNA") SubClassOf( ) # Class: (alternatively initiated mRNA) AnnotationAssertion(Annotation( "VariO:mv") "RNA variation causing alternative translation initiation.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-04-28T16:01:26Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0437") AnnotationAssertion(rdfs:label "alternatively initiated mRNA") SubClassOf( ) # Class: (epigenetic RNA modification) AnnotationAssertion(Annotation( "VariO:mv") "Epigenetic modification of RNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-05-07T14:40:53Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0438") AnnotationAssertion(rdfs:label "epigenetic RNA modification") SubClassOf( ) # Class: (effect on RNA activity) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on RNA activity.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-04-28T16:23:47Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0439") AnnotationAssertion(rdfs:label "effect on RNA activity") SubClassOf( ) # Class: (effect on RNA reaction kinetics) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on RNA reaction kinetics.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-04-28T16:26:01Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0440") AnnotationAssertion(rdfs:label "effect on RNA reaction kinetics") SubClassOf( ) # Class: (effect on RNA affinity) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on RNA affinity to binding molecule(s).") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-04-28T16:26:01Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0441") AnnotationAssertion(rdfs:label "effect on RNA affinity") SubClassOf( ) # Class: (effect on RNA specificity) AnnotationAssertion(Annotation( "VariO:mv") "Effect of variation on substrate binding specificity of RNA.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-04-28T16:26:01Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0442") AnnotationAssertion(rdfs:label "effect on RNA specificity") SubClassOf( ) # Class: (alternatively initiated protein) AnnotationAssertion(Annotation( "VariO:mv") "Protein variant originating from alternative translation initiation.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-05-03T09:09:05Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0443") AnnotationAssertion(rdfs:label "alternatively initiated protein") SubClassOf( ) # Class: (de novo variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-01-08T11:31:50Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0444") AnnotationAssertion(rdfs:label "de novo variation") SubClassOf( ) # Class: (germinal variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation that has been inherited from a germline cell.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-12-15T09:58:57Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "germline variation") AnnotationAssertion( "VariO:0445") AnnotationAssertion(rdfs:label "germinal variation") SubClassOf( ) # Class: (somatic variation) AnnotationAssertion(Annotation( "VariO:mv") "Variation that has its origin in a cell in soma.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-12-15T09:58:57Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0446") AnnotationAssertion(rdfs:label "somatic variation") SubClassOf( ) # Class: (immunological recognition molecule diversification) AnnotationAssertion(Annotation( "VariO:mv") "Processes that recombine and modify genes coding for immunological recognition molecules (antigens, B- and T-cell receptors, MCH type I and II molecules).") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2017-12-15T10:47:27Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0447") AnnotationAssertion(rdfs:label "immunological recognition molecule diversification") SubClassOf( ) # Class: (organellar DNA affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation effect on DNA within cellular compartment.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-02-01T12:42:12Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0448") AnnotationAssertion(rdfs:label "organellar DNA affected") SubClassOf( ) # Class: (extrachromosomal circular DNA) AnnotationAssertion(Annotation( "VariO:mv") "Circular DNA molecule not part of the chromosomes.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-02-01T12:47:35Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0449") AnnotationAssertion(rdfs:label "extrachromosomal circular DNA") SubClassOf( ) # Class: (mitochondrial DNA affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting DNA within mitochondria.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-02-01T12:52:27Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0450") AnnotationAssertion(rdfs:label "mitochondrial DNA affected") SubClassOf( ) # Class: (plastid DNA affected) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting DNA within plastids e.g. chloroplasts.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-02-01T12:53:15Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0451") AnnotationAssertion(rdfs:label "plastid DNA affected") SubClassOf( ) # Class: (heptanucleotide expansion) AnnotationAssertion(Annotation( "VariO:mv") "Tandem repetitive sequence consisting of six nucleotide units.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-02-01T14:49:25Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0452") AnnotationAssertion(rdfs:label "heptanucleotide expansion") SubClassOf( ) # Class: (histone modification) AnnotationAssertion(Annotation( "VariO:mv") "Epigenetic modification of histone.") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-02-06T09:08:59Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0453") AnnotationAssertion(rdfs:label "histone modification") SubClassOf( ) # Class: (variation at topology associating domain) AnnotationAssertion(Annotation( "VariO:mv") "Variation affecting topology associating domain (TAD).") AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-03-05T16:55:07Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0454") AnnotationAssertion(rdfs:label "variation at topology associating domain") SubClassOf( ) # Class: (effect on A motif) AnnotationAssertion( "med-mnv") AnnotationAssertion( "2018-11-08T10:05:56Z") AnnotationAssertion( "variation_ontology") AnnotationAssertion( "VariO:0455") AnnotationAssertion(rdfs:label "effect on A motif") SubClassOf( ) # Class: (RNA genome) AnnotationAssertion( "Genome composed of RNA molecule.") AnnotationAssertion(rdfs:label "RNA genome"@en) SubClassOf( ) # Class: (RNA virus genome) AnnotationAssertion( "Genome for a RNA virus.") AnnotationAssertion(rdfs:label "RNA virus genome"@en) SubClassOf( ) # Class: (viroid genome) AnnotationAssertion( "Genome for an infectious particle.") AnnotationAssertion(rdfs:label "viroid genome"@en) SubClassOf( ) # Class: (satelletite genome) AnnotationAssertion( "Genome for a subviral agent.") AnnotationAssertion(rdfs:label "satelletite genome"@en) SubClassOf( ) # Class: (pre-mRNA) AnnotationAssertion( "Unprocessed mRNA.") AnnotationAssertion(rdfs:label "pre-mRNA"@en) SubClassOf( ) # Class: (mRNA) AnnotationAssertion( "Mature mRNA.") AnnotationAssertion(rdfs:label "mRNA"@en) SubClassOf( ) # Class: (circular RNA) AnnotationAssertion( "Covalently closed single-stranded RNA chain.") AnnotationAssertion( "circRNA") AnnotationAssertion(rdfs:label "circular RNA"@en) SubClassOf( ) # Class: (antisense RNA) AnnotationAssertion( "Single-stranded non-coding RNA compelementary to a mRNA or part of it.") AnnotationAssertion(rdfs:label "antisense RNA"@en) SubClassOf( ) # Class: (non-coding sense RNA) AnnotationAssertion( "Single-stranded noncoding RNA overlapping with mRNA but not coding for a protein.") AnnotationAssertion(rdfs:label "non-coding sense RNA"@en) SubClassOf( ) # Class: (functional non-coding RNA) AnnotationAssertion( "Non-coding RNA with a function.") AnnotationAssertion(rdfs:label "functional non-coding RNA"@en) SubClassOf( ) # Class: (retrotransposon RNA intermediate) AnnotationAssertion( "RNA intermediate of a retrotransposon.") AnnotationAssertion( "class I transposable element transposon via RNA intermediate") AnnotationAssertion(rdfs:label "retrotransposon RNA intermediate"@en) SubClassOf( ) # Class: (translation related non-coding RNA) AnnotationAssertion( "RNA involved in protein synthesis.") AnnotationAssertion(rdfs:label "translation related non-coding RNA"@en) SubClassOf( ) # Class: (transfer RNA) AnnotationAssertion( "Transfer RNA involved in protein synthesis. Modiefied tRNA contains amino acid and carries it to ribosome.") AnnotationAssertion( "tRNA") AnnotationAssertion(rdfs:label "transfer RNA"@en) SubClassOf( ) # Class: (large subunit ribosomal RNA) AnnotationAssertion( "Non-coding RNA that is a constituent of the large ribosomal subunit.") AnnotationAssertion( "LSU RNA") AnnotationAssertion(rdfs:label "large subunit ribosomal RNA"@en) SubClassOf( ) # Class: (small subunit ribosomal RNA) AnnotationAssertion( "Non-coding RNA that is a constituent of the small ribosomal unit.") AnnotationAssertion( "SSU RNA") AnnotationAssertion(rdfs:label "small subunit ribosomal RNA"@en) SubClassOf( ) # Class: (intron) AnnotationAssertion( "Intervening region ithat is spliced off during RNA maturation.") AnnotationAssertion(rdfs:label "intron"@en) SubClassOf( ) # Class: (self-splicing intron) AnnotationAssertion( "Intron with an intrinsic splicing activity.") AnnotationAssertion(rdfs:label "self-splicing intron"@en) SubClassOf( ) # Class: (spliceosomal intron) AnnotationAssertion( "Intron removed by spliceosome.") AnnotationAssertion(rdfs:label "spliceosomal intron"@en) SubClassOf( ) # Class: (intron retention) AnnotationAssertion( "Inclusion intron sequence to mRNA.") AnnotationAssertion(rdfs:label "intron retention") AnnotationAssertion(owl:backwardCompatibleWith "targeting RNA"@en) SubClassOf( ) # Class: (telomerase RNA) AnnotationAssertion( "Non-coding RNA component of telomerase.") AnnotationAssertion(rdfs:label "telomerase RNA"@en) SubClassOf( ) # Class: (catalytic RNA) AnnotationAssertion( "RNA with catalytic activity.") AnnotationAssertion(rdfs:label "catalytic RNA"@en) SubClassOf( ) # Class: (regulatory RNA) AnnotationAssertion( "RNA with regulatory activity.") AnnotationAssertion(rdfs:label "regulatory RNA"@en) SubClassOf( ) # Class: (microRNA) AnnotationAssertion( "Short non-coding RNA that binds to complementary region in mRNA and silences and regulates gene expression.") AnnotationAssertion( "miRNA") AnnotationAssertion(rdfs:label "microRNA"@en) SubClassOf( ) # Class: (small intervening RNA) AnnotationAssertion( "Short double-stranded non-coding RNA regulating gene expresion by causing degration of mRNA with complementary sequence.") AnnotationAssertion( "siRNA") AnnotationAssertion(rdfs:label "small intervening RNA"@en) SubClassOf( ) # Class: (piwi-interacting RNA) AnnotationAssertion( "Non-coding RNA binding to piwi-superfamily Argonaute proteins to silence transposons, repeat-derived transcripts and genetic elements.") AnnotationAssertion( "piRNA") AnnotationAssertion(rdfs:label "piwi-interacting RNA"@en) SubClassOf( ) # Class: (signal recognition particle RNA) AnnotationAssertion( "Non-coding RNA component of signal recognition particle.") AnnotationAssertion(rdfs:label "signal recognition particle RNA"@en) SubClassOf( ) # Class: (X-chromosome inactivation center RNA) AnnotationAssertion( "Non-coding RNA component of X-inactivation center.") AnnotationAssertion(rdfs:label "X-chromosome inactivation center RNA"@en) SubClassOf( ) # Class: (RNA editing related RNA) AnnotationAssertion( "Non-coding RNA component of editosome complex.") AnnotationAssertion(rdfs:label "RNA editing related RNA"@en) SubClassOf( ) # Class: (DNA editing related RNA) AnnotationAssertion( "Non-coding RNA component of DNA editing complex.") AnnotationAssertion(rdfs:label "DNA editing related RNA"@en) SubClassOf( ) # Class: (spliceosomal RNA) AnnotationAssertion( "Non-coding RNA component of spliceosome.") AnnotationAssertion(rdfs:label "spliceosomal RNA"@en) SubClassOf( ) # Class: (location or origin of non-coding RNA) AnnotationAssertion(rdfs:label "location or origin of non-coding RNA"@en) SubClassOf( ) # Class: (nuclear non-coding RNA) AnnotationAssertion( "Non-coding RNA in nucleus.") AnnotationAssertion(rdfs:label "nuclear non-coding RNA"@en) SubClassOf( ) # Class: (mitochondrial non-coding RNA) AnnotationAssertion( "Non-coding RNA in mitochondrion.") AnnotationAssertion(rdfs:label "mitochondrial non-coding RNA"@en) SubClassOf( ) # Class: (chromatin related non-coding RNA) AnnotationAssertion( "Non-coding RNA related to chromatin.") AnnotationAssertion(rdfs:label "chromatin related non-coding RNA"@en) SubClassOf( ) # Class: (centromeric non-coding RNA) AnnotationAssertion( "Non-coding RNA related to centromere.") AnnotationAssertion(rdfs:label "centromeric non-coding RNA"@en) SubClassOf( ) # Class: (size of non-coding RNA) AnnotationAssertion( "Classification of non-coding RNA based on the length.") AnnotationAssertion(rdfs:label "size of non-coding RNA"@en) SubClassOf( ) # Class: (short non-coding RNA) AnnotationAssertion( "Non-coding RNA shorter than 200 nucleotides or base pairs.") AnnotationAssertion( "small non-coding RNA sRNA") AnnotationAssertion(rdfs:label "short non-coding RNA"@en) SubClassOf( ) # Class: (ribosomal RNA) AnnotationAssertion( "Non-coding RNA constituent of ribosome.") AnnotationAssertion( "rRNA") AnnotationAssertion(rdfs:label "ribosomal RNA"@en) SubClassOf( ) # Class: (long non-coding RNA) AnnotationAssertion( "Non-coding RNA longer than 200 nucleotides or base pairs.") AnnotationAssertion( "large non-coding RNA lncRNA") AnnotationAssertion(rdfs:label "long non-coding RNA"@en) SubClassOf( ) # Class: (very long non-coding RNA) AnnotationAssertion( "Non-coding RNA longer than 10 kb.") AnnotationAssertion( "vlnicRNA") AnnotationAssertion(rdfs:label "very long non-coding RNA"@en) SubClassOf( ) # Class: (exon) AnnotationAssertion( "Transcript region that is part in mature mRNA.") AnnotationAssertion( "") AnnotationAssertion(rdfs:label "exon"@en) SubClassOf( ) # Class: (alternatively terminated mRNA) AnnotationAssertion( "Variation causing alternative mRNA termination.") AnnotationAssertion(rdfs:label "alternatively terminated mRNA"@en) SubClassOf( ) # Class: (effect on RNA modification) AnnotationAssertion( "Variation affecting post transcriptional RNA modification.") AnnotationAssertion(rdfs:label "effect on RNA modification"@en) SubClassOf( ) # Class: (modified mRNA nucleotide) AnnotationAssertion( "Post transcriptionally modified nucleotide in mRNA.") AnnotationAssertion(rdfs:label "modified mRNA nucleotide"@en) SubClassOf( ) # Class: (effect on RNA pseudoknot) AnnotationAssertion( "Variation affecting RNA stucture containing at teast two stem loops where part of one stem is intercalated to the other stem.") AnnotationAssertion(rdfs:label "effect on RNA pseudoknot"@en) SubClassOf( ) # Class: (RNA fragment) AnnotationAssertion( "RNA produced by degradation of processing of an RNA molecule.") AnnotationAssertion(rdfs:label "RNA fragment"@en) SubClassOf( ) # Class: (exon skipping) AnnotationAssertion( "Variation where an exon is completele cleaved out from a mature transcript.") AnnotationAssertion(rdfs:label "exon skipping"@en) SubClassOf( ) # Class: (loss of exon fragment) AnnotationAssertion( "Transcript from which part of an exon is missing.") AnnotationAssertion(rdfs:label "loss of exon fragment"@en) SubClassOf( ) # Class: (inclusion of cryptic exon) AnnotationAssertion( "Transcript that includes a cryptic exon from the middle of intron.") AnnotationAssertion(rdfs:label "inclusion of cryptic exon"@en) SubClassOf( ) # Class: (inclusion of intron fragment) AnnotationAssertion( "Transcript that contains and additional stretch from intron.") AnnotationAssertion(rdfs:label "inclusion of intron fragment"@en) SubClassOf( ) # Class: (affected splice site) AnnotationAssertion( "Type of variation affecting splice site.") AnnotationAssertion(rdfs:label "affected splice site"@en) SubClassOf( ) # Class: (effect on mode of splicing) AnnotationAssertion( "Variation affecting the type of RNA splicing.") AnnotationAssertion(rdfs:label "effect on mode of splicing"@en) SubClassOf( ) # Class: (effect on co-transcriptional splicing) AnnotationAssertion( "Variation affecting splicing occurring simultnaeously with transcription.") AnnotationAssertion(rdfs:label "effect on co-transcriptional splicing"@en) SubClassOf( ) # Class: (effect on non-sequential splicing) AnnotationAssertion( "Variation affecting splicing that does not occur in sequential order.") AnnotationAssertion(rdfs:label "effect on non-sequential splicing"@en) SubClassOf( ) # Class: (effect on recursive splicing) AnnotationAssertion( "Variation affecting intron splicing that occurs in several splicing events.") AnnotationAssertion(rdfs:label "effect on recursive splicing"@en) SubClassOf( ) # Class: (mutually exclusive exon) AnnotationAssertion( "Only one of two exons is incluided into mRNA.") AnnotationAssertion( "snoRNA") AnnotationAssertion(rdfs:label "mutually exclusive exon"@en) SubClassOf( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) )