PREFIX obo:
PREFIX rdf:
PREFIX rdfs:
PREFIX xsd:
obo:MI_1140 a rdfs:Class ;
rdfs:label "decarboxylation reaction" ;
rdfs:comment "Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1)." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000073 a rdfs:Class ;
rdfs:label "decrease" ;
rdfs:comment "a negative regulation that results in the decrease of one interactor volume. " ;
rdfs:subClassOf obo:INO_0000068 .
obo:OGG_0000000002 a rdfs:Class ;
rdfs:label "gene"@en ;
rdfs:comment "A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. " ;
rdfs:subClassOf obo:BFO_0000040 .
obo:BFO_0000034 a rdfs:Class ;
rdfs:label "function"@en ;
rdfs:subClassOf obo:BFO_0000016 .
obo:BFO_0000017 a rdfs:Class ;
rdfs:label "realizable entity"@en ;
rdfs:subClassOf obo:BFO_0000020 .
obo:MI_0558 a rdfs:Class ;
rdfs:label "deglycosylation reaction" ;
rdfs:comment "Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000089 a rdfs:Class ;
rdfs:label "co-regulation"@en ;
rdfs:comment "a regulation process that involves in two interactors co-regulate a third interactor. " ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000241 a rdfs:Class ;
rdfs:label "export" ;
rdfs:comment "a translocation that one interactor exports from one location" ;
rdfs:subClassOf obo:INO_0000176 .
obo:INO_0000122 a rdfs:Class ;
rdfs:label "induction" ;
rdfs:comment "a positive regulation that leads to the induction of a new interactor due to the presence of another interactor. " ;
rdfs:subClassOf obo:INO_0000117 .
obo:MI_2263 a rdfs:Class ;
rdfs:label "s-nitrosylation" ;
rdfs:comment "Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000111 a rdfs:Class ;
rdfs:label "protein heterodimerization" ;
rdfs:comment "a protein dimerization where two proteins are different. " ;
rdfs:subClassOf obo:INO_0000088 .
obo:INO_0000151 a rdfs:Class ;
rdfs:label "output interactor" ;
rdfs:comment "an interactor that is an output of an interaction." ;
rdfs:subClassOf obo:INO_0000016 .
obo:RO_0000087 a rdf:Property ;
rdfs:label "has role"@en ;
rdfs:comment "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en ;
rdfs:range .
obo:MI_1281 a rdfs:Class ;
rdfs:label "mutual suppression (complete)" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < ab = wt
OR
wt = ab < b <= a*
OR
a < wt = ab < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1280 .
obo:MI_0208 a rdfs:Class ;
rdfs:label "genetic interaction" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E""" ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000084 a rdfs:Class ;
rdfs:label "destabilization" ;
rdfs:comment "a negative regulation that results in a destabilization. " ;
rdfs:subClassOf obo:INO_0000068 .
obo:INO_0000147 a rdfs:Class ;
rdfs:label "motivator role"@en ;
rdfs:comment "an input interactor role that is borne by a material entity that motivates a process." ;
rdfs:subClassOf obo:INO_0000009 .
obo:BFO_0000054 a rdf:Property ;
rdfs:label "realized in"@en ;
rdfs:comment "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ;
rdfs:range .
obo:MI_1293 a rdfs:Class ;
rdfs:label "unilateral suppression (complete)" ;
rdfs:comment """An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab = b = wt [E = a]
OR
wt = b = ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1292 .
obo:INO_0000078 a rdfs:Class ;
rdfs:label "activation of gene transcription by high level protein"@en ;
rdfs:comment "an activation of gene transcription that is achieved by a high level of a protein" ;
rdfs:subClassOf obo:INO_0000051 .
obo:RO_0002213 a rdf:Property ;
rdfs:label "positively regulates"@en ;
rdfs:comment "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." ;
rdfs:range ;
rdfs:subPropertyOf obo:RO_0002304 , obo:RO_0002211 .
obo:RO_0002211 a rdf:Property ;
rdfs:label "regulates"@en ;
rdfs:comment "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." ;
rdfs:range ;
rdfs:subPropertyOf obo:RO_0002411 .
obo:INO_0000108 a rdfs:Class ;
rdfs:label "induction by binding to protein"@en ;
rdfs:comment "an induction that is achieved by binding to a protein" ;
rdfs:subClassOf obo:INO_0000122 .
obo:INO_0000095 a rdfs:Class ;
rdfs:label "gene expression down-regulation"@en ;
rdfs:comment "a negative regulation process that down-regulates gene expression level" ;
rdfs:subClassOf obo:INO_0000039 .
obo:RO_0002212 a rdf:Property ;
rdfs:label "negatively regulates"@en ;
rdfs:comment "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." ;
rdfs:range ;
rdfs:subPropertyOf obo:RO_0002305 , obo:RO_0002211 .
obo:MI_0915 a rdfs:Class ;
rdfs:label "physical association" ;
rdfs:comment "Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other." ;
rdfs:subClassOf obo:MI_0914 .
obo:MI_2252 a rdfs:Class ;
rdfs:label "guanine nucleotide exchange factor reaction" ;
rdfs:comment "The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000022 a rdfs:Class ;
rdfs:label "up-regulation of secretion"@en ;
rdfs:comment "an up-regulation that one interactor up-regulates the secretion of another interactor." ;
rdfs:subClassOf obo:INO_0000007 .
obo:BFO_0000030 a rdfs:Class ;
rdfs:label "object"@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:MI_1126 a rdfs:Class ;
rdfs:label "self interaction" ;
rdfs:comment "Intra-molecular interaction between two or more regions of the same molecule." ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_0407 a rdfs:Class ;
rdfs:label "direct interaction" ;
rdfs:comment "Interaction between molecules that are in direct contact with each other." ;
rdfs:subClassOf obo:MI_0915 .
obo:INO_0000133 a rdfs:Class ;
rdfs:label "host"@en ;
rdfs:comment "An organism bearing a host role." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:MI_1275 a rdfs:Class ;
rdfs:label "neutral epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
OR
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_0797 , obo:MI_0934 .
obo:MI_0213 a rdfs:Class ;
rdfs:label "methylation reaction" ;
rdfs:comment "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0202 a rdfs:Class ;
rdfs:label "depalmitoylation reaction" ;
rdfs:comment "S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues." ;
rdfs:subClassOf obo:MI_0212 .
obo:INO_0000173 a rdfs:Class ;
rdfs:label "gene transcription" ;
rdfs:comment "an interaction process that creates a complementary RNA copy of a sequence of DNA." ;
rdfs:subClassOf obo:INO_0000102 .
obo:RO_0002233 a rdf:Property ;
rdfs:label "has input"@en ;
rdfs:comment "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." ;
rdfs:range .
obo:MI_1286 a rdfs:Class ;
rdfs:label "over-suppression" ;
rdfs:comment """An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < wt < E
OR
E < wt < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0934 .
obo:INO_0000104 a rdfs:Class ;
rdfs:label "positive regulation of protein activity"@en ;
rdfs:comment "a regulation of protein activitiy process that involves a positive regulation" ;
rdfs:subClassOf obo:INO_0000055 .
obo:INO_0000144 a rdfs:Class ;
rdfs:label "negative regulator"@en ;
rdfs:comment "an interaction regulator that negatively regulates an interaction." ;
rdfs:subClassOf obo:INO_0000008 .
obo:MI_0910 a rdfs:Class ;
rdfs:label "nucleic acid cleavage" ;
rdfs:comment "Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments." ;
rdfs:subClassOf obo:MI_0194 .
obo:INO_0000116 a rdfs:Class ;
rdfs:label "immuno-precipitation" ;
rdfs:comment "a translocation that one interactor is precipitated based on an immunological precipitation process." ;
rdfs:subClassOf obo:INO_0000176 .
obo:INO_0000011 a rdfs:Class ;
rdfs:label "activator role"@en ;
rdfs:comment "a positive regulator role that is borne by a material entity that activates an interaction." ;
rdfs:subClassOf obo:INO_0000134 .
obo:MI_0198 a rdfs:Class ;
rdfs:label "defarnesylation reaction" ;
rdfs:comment "S-farnesyl-L-cysteined is cleaved and returns a C residue." ;
rdfs:subClassOf obo:MI_0212 .
obo:MI_0569 a rdfs:Class ;
rdfs:label "deneddylation reaction" ;
rdfs:comment "Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome." ;
rdfs:subClassOf obo:MI_0414 .
obo:PW_0000002 a rdfs:Class ;
rdfs:label "classic metabolic pathway" ;
rdfs:comment "The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics." ;
rdfs:subClassOf obo:INO_0000003 , obo:PW_0000001 .
obo:INO_0000027 a rdfs:Class ;
rdfs:label "cell-cell interaction"@en ;
rdfs:comment "a biological interaction that involves two cells as interactors." ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000040 a rdfs:Class ;
rdfs:label "human biochemical reaction"@en ;
rdfs:comment "a human molecular reaction that is specifically a biochemical reaction" ;
rdfs:subClassOf obo:INO_0000130 .
obo:INO_0000046 a rdfs:Class ;
rdfs:label "inhibition of gene transcription"@en ;
rdfs:comment "a negative regulation of gene transcription process that specifiies the negative regulation being an inhibition." ;
rdfs:subClassOf obo:INO_0000042 .
obo:INO_0000001 a rdfs:Class ;
rdfs:label "interaction network" ;
rdfs:comment "Interaction network is a process that includes a network of at least two interactions." ;
rdfs:subClassOf obo:BFO_0000015 .
obo:BFO_0000029 a rdfs:Class ;
rdfs:label "site"@en ;
rdfs:subClassOf obo:BFO_0000141 .
obo:NCBITaxon_562 a rdfs:Class ;
rdfs:label "Escherichia coli" ;
rdfs:subClassOf obo:NCBITaxon_2 .
obo:BFO_0000051 a rdf:Property ;
rdfs:label "has part"@en ;
rdfs:comment "a core relation that holds between a whole and its part"@en ;
rdfs:range ;
rdfs:subPropertyOf obo:RO_0002131 .
obo:INO_0000157 a rdfs:Class ;
rdfs:label "regulation" ;
rdfs:comment "A regulation represents a regulatory interaction between two interactors. " ;
rdfs:subClassOf obo:MI_0914 .
obo:INO_0000165 a rdfs:Class ;
rdfs:label "stabilization" ;
rdfs:comment "a postive interaction that one interactor increases the stability of another interactor. " ;
rdfs:subClassOf obo:INO_0000117 .
obo:MI_0216 a rdfs:Class ;
rdfs:label "palmitoylation reaction" ;
rdfs:comment "Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues." ;
rdfs:subClassOf obo:MI_0211 .
obo:MI_1139 a rdfs:Class ;
rdfs:label "carboxylation reaction" ;
rdfs:comment "Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000008 a rdfs:Class ;
rdfs:label "interaction regulator"@en ;
rdfs:comment "an interactor that regulates an interaction." ;
rdfs:subClassOf obo:INO_0000016 .
obo:GO_0018377 a rdfs:Class ;
rdfs:label "protein myristoylation" ;
rdfs:comment "The covalent attachment of a myristoyl group to a protein." ;
rdfs:subClassOf obo:MI_0211 .
obo:MI_0883 a rdfs:Class ;
rdfs:label "gtpase reaction" ;
rdfs:comment "Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate." ;
rdfs:subClassOf obo:MI_0881 .
obo:INO_0000105 a rdfs:Class ;
rdfs:label "host-pathogen interaction"@en ;
rdfs:comment "An interaction that involves a host (host organism or host cell) and pathogen organism at a specific condition." ;
rdfs:subClassOf obo:INO_0000002 .
obo:RO_0000057 a rdf:Property ;
rdfs:range .
obo:INO_0000154 a rdf:Property ;
rdfs:label "has interaction type"@en ;
rdfs:comment "An object property that represents a relation between an interaction process (domain) and another interaction process (range) where the interaction proces (domain) has a specific type of the other interaction process (range)" ;
rdfs:range .
obo:INO_0000016 a rdfs:Class ;
rdfs:label "interactor"@en ;
rdfs:comment "an interactor is a material entity that participates in an interaction." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:MI_1278 a rdfs:Class ;
rdfs:label "mutual enhancement" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a* <= b < wt [E = a*]
OR
wt < b <= a* < ab [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1271 .
obo:INO_0000035 a rdfs:Class ;
rdfs:label "autophosphorylation" ;
rdfs:comment "a phosphorylation process that adds a phosphate to a protein kinase (possibly affecting its activity) by virtue of its own enzymic activity. " ;
rdfs:subClassOf obo:GO_0016310 .
obo:MI_1289 a rdfs:Class ;
rdfs:label "phenotype bias" ;
rdfs:comment """An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (a < ab < b) AND (ab != wt)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0934 .
obo:GO_0012501 a rdfs:Class ;
rdfs:label "programmed cell death" ;
rdfs:comment "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." ;
rdfs:subClassOf obo:GO_0008219 .
obo:BFO_0000038 a rdfs:Class ;
rdfs:label "one-dimensional temporal region"@en ;
rdfs:subClassOf obo:BFO_0000008 .
obo:INO_0000023 a rdfs:Class ;
rdfs:label "human molecular interaction"@en ;
rdfs:comment "an interaction involving human molecules" ;
rdfs:subClassOf obo:INO_0000002 .
obo:MI_0914 a rdfs:Class ;
rdfs:label "association" ;
rdfs:comment "Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait." ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000119 a rdfs:Class ;
rdfs:label "inactivation" ;
rdfs:comment "a negative regulation that one interactor inactivates another." ;
rdfs:subClassOf obo:INO_0000068 .
obo:INO_0000100 a rdfs:Class ;
rdfs:label "regulation of assembly"@en ;
rdfs:comment "a regulation process where one gene product regulates an assembly process which forms an assembly having another gene product." ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000005 a rdfs:Class ;
rdfs:label "regulator role"@en ;
rdfs:comment "an regulator role that is borne by a material entity that regulates an interaction." ;
rdfs:subClassOf obo:INO_0000015 .
obo:MI_1280 a rdfs:Class ;
rdfs:label "mutual suppression" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab <= wt) [E = a*]
OR
(wt < b <= a*) AND (wt <= ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0796 .
obo:GO_0006461 a rdfs:Class ;
rdfs:subClassOf obo:MI_0407 .
obo:INO_0000062 a rdfs:Class ;
rdfs:label "costimulation" ;
rdfs:subClassOf obo:INO_0000169 .
obo:INO_0000056 a rdfs:Class ;
rdfs:label "downexpression"@en ;
rdfs:comment "a gene expression that has decreased volume. " ;
rdfs:subClassOf obo:INO_0000102 .
obo:INO_0000057 a rdfs:Class ;
rdfs:label "controling" ;
rdfs:comment "a regulation that one interactor controls the quality of another interactor to a specific range" ;
rdfs:subClassOf obo:INO_0000086 .
obo:INO_0000019 a rdfs:Class ;
rdfs:label "two-way interaction" ;
rdfs:comment "A two-way interaction is an interaction that includes two different directions among two interactors. " ;
rdfs:subClassOf obo:INO_0000002 .
obo:MI_0559 a rdfs:Class ;
rdfs:label "glycosylation reaction" ;
rdfs:comment "The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0987 a rdfs:Class ;
rdfs:label "rna strand elongation" ;
rdfs:comment "The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand." ;
rdfs:subClassOf obo:MI_0986 .
obo:BFO_0000141 a rdfs:Class ;
rdfs:label "immaterial entity"@en ;
rdfs:subClassOf obo:BFO_0000004 .
obo:MI_0796 a rdfs:Class ;
rdfs:label "suppression" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab <= wt [E = a*]
OR
wt <= ab < a* [E = a*]
where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0935 .
obo:INO_0000234 a rdfs:Class ;
rdfs:label "deregulation" ;
rdfs:comment "a negative regulation that results in the deregulation of one interactor on a process. " ;
rdfs:subClassOf obo:INO_0000068 .
obo:INO_0000068 a rdfs:Class ;
rdfs:label "negative regulation" ;
rdfs:comment "a regulation in which one interactor has a negative effect on another interactor " ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000051 a rdfs:Class ;
rdfs:label "activation of gene transcription"@en ;
rdfs:comment "a positive regulation of gene transcription process that inviolves an activation of the gene transcription." ;
rdfs:subClassOf obo:INO_0000049 .
obo:BFO_0000040 a rdfs:Class ;
rdfs:label "material entity"@en ;
rdfs:comment "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en ;
rdfs:subClassOf obo:BFO_0000004 .
obo:INO_0000067 a rdfs:Class ;
rdfs:label "negative regulation of protein activity"@en ;
rdfs:comment "a regulation of protein activitiy process that involves a negative regulation" ;
rdfs:subClassOf obo:INO_0000055 .
obo:INO_0000012 a rdfs:Class ;
rdfs:label "mutual information network" ;
rdfs:comment "an interaction network model that is represented by at least two mutual information interactions." ;
rdfs:subClassOf obo:INO_0000158 .
obo:INO_0000176 a rdfs:Class ;
rdfs:label "translocation" ;
rdfs:comment "A process that changes the location of a material entity." ;
rdfs:subClassOf obo:BFO_0000015 .
obo:NCBITaxon_2157 a rdfs:Class ;
rdfs:label "Archaea" ;
rdfs:subClassOf obo:LifO_0000005 .
obo:MI_0572 a rdfs:Class ;
rdfs:label "dna cleavage" ;
rdfs:comment "Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments." ;
rdfs:subClassOf obo:MI_0910 .
obo:IDO_0000629 a rdfs:Class ;
rdfs:label "host role"@en ;
rdfs:comment "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism."@en ;
rdfs:subClassOf obo:BFO_0000023 .
obo:INO_0000030 a rdfs:Class ;
rdfs:label "gene-enviroment interaction"@en ;
rdfs:comment "an interaction that involves a gene and its environment (e.g., calcium in blood). " ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000013 a rdfs:Class ;
rdfs:label "node" ;
rdfs:comment "a node is an object that represents an interactor in a graph of an interaction or interaction network." ;
rdfs:subClassOf obo:BFO_0000030 .
obo:MI_1287 a rdfs:Class ;
rdfs:label "mutual over-suppression" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < wt < ab [E = a*]
OR
ab < wt < b <= a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1286 .
obo:INO_0000041 a rdfs:Class ;
rdfs:label "physical entity - obsolete"@en ;
rdfs:comment "Obsolete note: This class is replaced by CHEBI term: molecular entity" ;
rdfs:subClassOf obo:INO_0000159 .
obo:CL_0000000 a rdfs:Class ;
rdfs:label "cell" ;
rdfs:comment "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:INO_0000132 a rdfs:Class ;
rdfs:label "small molecule"@en ;
rdfs:subClassOf obo:CHEBI_23367 .
obo:INO_0000024 a rdfs:Class ;
rdfs:label "activation" ;
rdfs:comment "a positive regulation that one interactor activates another. " ;
rdfs:subClassOf obo:INO_0000117 .
obo:INO_0000172 a rdfs:Class ;
rdfs:label "transactivation" ;
rdfs:comment "a gene expression regulation that leads to an increased rate of gene expression triggered either by biological processes or by artificial means." ;
rdfs:subClassOf obo:INO_0000044 .
obo:BFO_0000023 a rdfs:Class ;
rdfs:label "role"@en ;
rdfs:comment "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en ;
rdfs:subClassOf obo:BFO_0000017 .
obo:INO_0000063 a rdfs:Class ;
rdfs:label "cell-environment interaction"@en ;
rdfs:comment "an interaction that involves a cell and its environment as interactors" ;
rdfs:subClassOf obo:INO_0000002 .
obo:MI_0194 a rdfs:Class ;
rdfs:label "cleavage reaction" ;
rdfs:comment "Covalent bond breakage in a molecule leading to the formation of smaller molecules." ;
rdfs:subClassOf obo:MI_0414 .
obo:GO_0008150 a rdfs:Class ;
rdfs:label "biological_process" ;
rdfs:comment "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." ;
rdfs:subClassOf obo:BFO_0000015 .
obo:MI_0571 a rdfs:Class ;
rdfs:label "mrna cleavage" ;
rdfs:comment "Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." ;
rdfs:subClassOf obo:MI_0902 .
obo:MI_0212 a rdfs:Class ;
rdfs:label "lipoprotein cleavage reaction" ;
rdfs:comment "Cleavage of a lipid group covalently bound to a protein residue." ;
rdfs:subClassOf obo:MI_0194 .
obo:MI_1355 a rdfs:Class ;
rdfs:label "lipid cleavage" ;
rdfs:comment "Reaction monitoring the cleavage (hydrolysis) or a lipid molecule." ;
rdfs:subClassOf obo:MI_0194 .
obo:INO_0000045 a rdfs:Class ;
rdfs:label "protein translation"@en ;
rdfs:comment "a gene expression process that results in protein production from a gene DNA sequence. " ;
rdfs:subClassOf obo:INO_0000102 .
obo:INO_0000110 a rdfs:Class ;
rdfs:label "human molecular degradation"@en ;
rdfs:subClassOf obo:INO_0000130 .
obo:INO_0000096 a rdfs:Class ;
rdfs:label "induction of production"@en ;
rdfs:comment "an induction that leads to the production of an entity" ;
rdfs:subClassOf obo:INO_0000122 .
obo:INO_0000034 a rdfs:Class ;
rdfs:label "regulation of translation"@en ;
rdfs:comment "a gene expression regulation process that involves the regulation of a protein translation process." ;
rdfs:subClassOf obo:INO_0000044 .
obo:INO_0000077 a rdfs:Class ;
rdfs:label "co-regulation of transcription"@en ;
rdfs:comment "a regulation of transcription process where two or more regulators regulate a gene transcription" ;
rdfs:subClassOf obo:INO_0000032 .
obo:MI_2272 a rdfs:Class ;
rdfs:label "tyrosinylation" ;
rdfs:comment "Reversible reaction that add a tyrosine residue to an amino-acid." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000150 a rdfs:Class ;
rdfs:label "hygiene factor role"@en ;
rdfs:comment "an input interactor role that is borne by a material entity (e.g. status, job security, salary and fringe benefits) that do not motivate if present, but, if absent, result in demotivation." ;
rdfs:subClassOf obo:INO_0000009 .
obo:INO_0000146 a rdfs:Class ;
rdfs:label "macrophage-pathogen interaction"@en ;
rdfs:comment "An host cell-pathogen interaction where the host is a macrophage cell" ;
rdfs:subClassOf obo:INO_0000107 .
obo:MI_0197 a rdfs:Class ;
rdfs:label "deacetylation reaction" ;
rdfs:comment "N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1276 a rdfs:Class ;
rdfs:label "opposing epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1275 , obo:MI_1284 .
obo:MI_0408 a rdfs:Class ;
rdfs:label "disulfide bond" ;
rdfs:comment "Covalent bond mediated by 2 sulfur atoms." ;
rdfs:subClassOf obo:MI_0195 .
obo:MI_1251 a rdfs:Class ;
rdfs:label "methylmalonyl-CoA isomerase reaction" ;
rdfs:comment "The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2." ;
rdfs:subClassOf obo:MI_1250 .
obo:INO_0000121 a rdfs:Class ;
rdfs:label "human molecular synthesis"@en ;
rdfs:subClassOf obo:INO_0000023 .
obo:INO_0000002 a rdfs:Class ;
rdfs:label "interaction" ;
rdfs:comment "Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another. "@en ;
rdfs:subClassOf obo:BFO_0000015 .
obo:BFO_0000016 a rdfs:Class ;
rdfs:label "disposition"@en ;
rdfs:subClassOf obo:BFO_0000017 .
obo:IAO_0000030 a rdfs:Class ;
rdfs:label "information content entity"@en ;
rdfs:comment "A generically dependent continuant that is about some thing."@en ;
rdfs:subClassOf obo:BFO_0000031 .
obo:MI_1127 a rdfs:Class ;
rdfs:label "putative self interaction" ;
rdfs:comment "Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules." ;
rdfs:subClassOf obo:MI_0407 .
obo:INO_0000052 a rdfs:Class ;
rdfs:label "activation of gene transcription by low level protein"@en ;
rdfs:comment "an activation of gene transcription that is achieved by a low level of a protein" ;
rdfs:subClassOf obo:INO_0000051 .
obo:MI_0201 a rdfs:Class ;
rdfs:label "demyristoylation reaction" ;
rdfs:comment "N6-myristoyl-L-lysine is cleaved and returns a K residue." ;
rdfs:subClassOf obo:MI_0212 .
obo:MI_2280 a rdfs:Class ;
rdfs:label "deamidation reaction" ;
rdfs:comment "Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline)." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000059 a rdfs:Class ;
rdfs:label "cooperation" ;
rdfs:comment "an indirect association that one interactor cooperates with another interactor in a specfiic process. " ;
rdfs:subClassOf obo:MI_0914 .
obo:NCBITaxon_1773 a rdfs:Class ;
rdfs:label "Mycobacterium tuberculosis" ;
rdfs:subClassOf obo:NCBITaxon_2 .
obo:INO_0000143 a rdfs:Class ;
rdfs:label "host-pathogen mutant interaction"@en ;
rdfs:comment "An host-pathogen interaction where the pathogen is a gene mutant" ;
rdfs:subClassOf obo:INO_0000105 .
obo:MI_1273 a rdfs:Class ;
rdfs:label "maximal epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab = a* < b < wt
OR
wt < b < a* = ab
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1272 , obo:MI_1284 .
obo:INO_0000103 a rdfs:Class ;
rdfs:label "accessory regulation" ;
rdfs:comment "a positive regulation that one interactor facilitates a phenomenon such as a phenotype. This is an accessory effect not a major one. " ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000135 a rdfs:Class ;
rdfs:label "pathway step"@en ;
rdfs:comment "An data item that indicates the step number of a pathway." ;
rdfs:subClassOf obo:IAO_0000027 .
obo:MI_1294 a rdfs:Class ;
rdfs:label "unilateral suppression (partial)" ;
rdfs:comment """An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab < b = wt [E = a]
OR
wt = b < ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1292 .
obo:PW_0000001 a rdfs:Class ;
rdfs:label "pathway" ;
rdfs:comment "A pathway is a set of inter-connected reactions and interactions whose delineation and scope are used as a model for exploring and studying, describing and understanding the working of and relationships between biomolecules within a context." ;
rdfs:subClassOf obo:INO_0000001 .
obo:MI_1284 a rdfs:Class ;
rdfs:label "quantitative epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_0797 .
obo:INO_0000088 a rdfs:Class ;
rdfs:label "protein dimerization" ;
rdfs:comment "a protein complex assembly that involves two proteins that form a dimer. " ;
rdfs:subClassOf obo:GO_0006461 .
obo:MI_0971 a rdfs:Class ;
rdfs:label "phosphopantetheinylation" ;
rdfs:comment "The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000125 a rdfs:Class ;
rdfs:label "input interactor" ;
rdfs:comment "an interactor that is an input of an interaction." ;
rdfs:subClassOf obo:INO_0000016 .
obo:NCBITaxon_9606 a rdfs:Class ;
rdfs:label "Homo sapiens" ;
rdfs:subClassOf obo:NCBITaxon_2759 .
obo:INO_0000070 a rdfs:Class ;
rdfs:label "inhibition of protein activity"@en ;
rdfs:comment "a negative regulation of protein activitiy process that involves an inhibition of a protein activity" ;
rdfs:subClassOf obo:INO_0000067 .
obo:MI_1279 a rdfs:Class ;
rdfs:label "unilateral enhancement" ;
rdfs:comment """An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a < b = wt [E = a]
OR
wt = b < a < ab [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1271 .
obo:INO_0000033 a rdfs:Class ;
rdfs:label "attenuation" ;
rdfs:comment "a negative regulation that attenuates the virulence of a pathogenic microbe. " ;
rdfs:subClassOf obo:INO_0000068 .
obo:BFO_0000001 a rdfs:Class ;
rdfs:label "entity"@en .
obo:CL_0000235 a rdfs:Class ;
rdfs:label "macrophage" ;
rdfs:comment "A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." ;
rdfs:subClassOf obo:BFO_0000040 , obo:CL_0000000 .
obo:INO_0000081 a rdfs:Class ;
rdfs:label "activation of gene transcription by phosphorylated protein"@en ;
rdfs:comment "an activation of gene transcription that is achieved by a phosphorylated protein" ;
rdfs:subClassOf obo:INO_0000051 .
obo:INO_0000049 a rdfs:Class ;
rdfs:label "positive regulation of gene transcription"@en ;
rdfs:comment "a regulation of transcription process that inviolves a positive regulation." ;
rdfs:subClassOf obo:INO_0000032 .
obo:INO_0000114 a rdfs:Class ;
rdfs:label "overexpression" ;
rdfs:comment "a gene expression that has increased volume. " ;
rdfs:subClassOf obo:INO_0000102 .
obo:INO_0000038 a rdfs:Class ;
rdfs:label "positive regulation of gene expression"@en ;
rdfs:comment "a regulation process that positively regulates gene expression level" ;
rdfs:subClassOf obo:INO_0000044 .
obo:IDO_0000528 a rdfs:Class ;
rdfs:label "pathogen"@en ;
rdfs:comment "A material entity with a pathogenic disposition."@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:INO_0000127 a rdfs:Class ;
rdfs:label "human molecular modulation"@en ;
rdfs:subClassOf obo:INO_0000101 .
obo:INO_0000055 a rdfs:Class ;
rdfs:label "regulation of protein activity"@en ;
rdfs:comment "a regulation process that regulates an activity of a protein" ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000140 a rdfs:Class ;
rdfs:label "neutralization" ;
rdfs:comment "a biochemical reaction that one interactor neutrolizes another. " ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_0945 a rdfs:Class ;
rdfs:label "oxidoreductase activity electron transfer reaction" ;
rdfs:comment "An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000066 a rdfs:Class ;
rdfs:label "immunological cross-reaction" ;
rdfs:subClassOf obo:INO_0000054 .
obo:MI_0556 a rdfs:Class ;
rdfs:label "transglutamination reaction" ;
rdfs:comment "Gln-Lys cross-link catalyzed by a transglutaminase." ;
rdfs:subClassOf obo:MI_0195 .
obo:INO_0000312 a rdfs:Class ;
rdfs:label "gene-protein interaction" ;
rdfs:comment "an interaction that involves in a gene DNA and a protein" ;
rdfs:subClassOf obo:INO_0000002 .
obo:BFO_0000004 a rdfs:Class ;
rdfs:label "independent continuant"@en ;
rdfs:comment "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en ;
rdfs:subClassOf obo:BFO_0000002 .
obo:BFO_0000015 a rdfs:Class ;
rdfs:label "process"@en ;
rdfs:comment "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en ;
rdfs:subClassOf obo:BFO_0000003 .
obo:MI_0200 a rdfs:Class ;
rdfs:label "degeranylation reaction" ;
rdfs:comment "S-geranylgeranyl-L-cysteine is cleaved and returns a C residue." ;
rdfs:subClassOf obo:MI_0212 .
obo:GO_0016310 a rdfs:Class ;
rdfs:label "phosphorylation" ;
rdfs:comment "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide." ;
rdfs:subClassOf obo:INO_0000007 .
obo:INO_0000018 a rdfs:Class ;
rdfs:label "organism-organism interaction"@en ;
rdfs:comment "a biological interaction that occurs in the organism level. " ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000244 a rdfs:Class ;
rdfs:label "secretion" ;
rdfs:comment "a translocation that one interactor secretes from the inside of another interactor" ;
rdfs:subClassOf obo:INO_0000176 .
obo:MI_1027 a rdfs:Class ;
rdfs:label "diphtamidation reaction" ;
rdfs:comment "A modification that converts an L-histidine residue to diphthamide." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000044 a rdfs:Class ;
rdfs:label "gene expression regulation"@en ;
rdfs:comment "a regulation process that regulates gene expression level" ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000007 a rdfs:Class ;
rdfs:label "up-regulation"@en ;
rdfs:comment "a positive regulation that one interactor up-regulates another." ;
rdfs:subClassOf obo:INO_0000117 .
obo:MI_0567 a rdfs:Class ;
rdfs:label "neddylation reaction" ;
rdfs:comment "Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000138 a rdfs:Class ;
rdfs:label "macrophage-pathogen PPI inducing cell death"@en ;
rdfs:comment "A macrophage-pathogen protein-protein interaction that induces cell death." ;
rdfs:subClassOf obo:INO_0000113 .
obo:RO_0002411 a rdf:Property ;
rdfs:label "causally upstream of"@en ;
rdfs:comment "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" ;
rdfs:range ;
rdfs:subPropertyOf obo:RO_0002418 , obo:BFO_0000063 .
obo:INO_0000085 a rdfs:Class ;
rdfs:label "gene expression inhibition"@en ;
rdfs:comment "a negative regulation process that inhibits gene expression level" ;
rdfs:subClassOf obo:INO_0000039 .
obo:INO_0000149 a rdfs:Class ;
rdfs:label "prevention" ;
rdfs:subClassOf obo:INO_0000068 .
obo:MI_0935 a rdfs:Class ;
rdfs:label "positive genetic interaction" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E < ab <= wt
OR
wt <= ab < E
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:INO_0000074 a rdfs:Class ;
rdfs:label "negative regulation of transcription by binding to promoter"@en ;
rdfs:comment "a regulation of transcription by binding to promoter that is further classified as a positive regulation" ;
rdfs:subClassOf obo:INO_0000071 .
obo:INO_0000109 a rdfs:Class ;
rdfs:label "macrophage-pathogen interaction"@en ;
rdfs:comment "An host cell-pathogen interaction where the host cell is a macrophage."@en ;
rdfs:subClassOf obo:INO_0000107 .
obo:INO_0000158 a rdfs:Class ;
rdfs:label "interaction network model"@en ;
rdfs:comment "An information content entity that models interaction network" ;
rdfs:subClassOf obo:IAO_0000030 .
obo:GO_0051259 a rdfs:Class ;
rdfs:label "protein complex oligomerization" ;
rdfs:comment "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." ;
rdfs:subClassOf obo:GO_0008150 .
obo:INO_0000169 a rdfs:Class ;
rdfs:label "synergization" ;
rdfs:comment "a regulation process that involves in two interactors that are synergized in affecting a phenomenon (e.g., phenotype)." ;
rdfs:subClassOf obo:INO_0000089 .
obo:MI_0795 a rdfs:Class ;
rdfs:label "asynthetic" ;
rdfs:comment """An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a = b = ab != wt
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0935 .
obo:CHEBI_23367 a rdfs:Class ;
rdfs:label "molecular entity" ;
rdfs:comment "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:MI_0902 a rdfs:Class ;
rdfs:label "rna cleavage" ;
rdfs:comment "Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner." ;
rdfs:subClassOf obo:MI_0910 .
obo:INO_0000092 a rdfs:Class ;
rdfs:label "dissociation" ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_1310 a rdfs:Class ;
rdfs:label "de-ADP-ribosylation reaction" ;
rdfs:comment "Measure of hydrolytic reactions that release ADP-ribose." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0844 a rdfs:Class ;
rdfs:label "phosphotransfer reaction" ;
rdfs:comment "Reaction where a phosphate is transferred between two proteins of a phosphorelay system." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000029 a rdfs:Class ;
rdfs:label "antagonism" ;
rdfs:comment "a biochemical binding where a substance binds to the same site an agonist would bind to without causing activation of the receptor" ;
rdfs:subClassOf obo:MI_0407 .
obo:INO_0000099 a rdfs:Class ;
rdfs:label "hydrogen binding"@en ;
rdfs:comment "Interaction leading to the formation of hydrogen bond between two molecules" ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_0209 a rdfs:Class ;
rdfs:label "geranylgeranylation reaction" ;
rdfs:comment "Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue." ;
rdfs:subClassOf obo:MI_0211 .
obo:INO_0000069 a rdfs:Class ;
rdfs:label "chemical reaction catalyst role"@en ;
rdfs:comment "an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself." ;
rdfs:subClassOf obo:INO_0000015 .
obo:BFO_0000008 a rdfs:Class ;
rdfs:label "temporal region"@en ;
rdfs:subClassOf obo:BFO_0000003 .
obo:INO_0000058 a rdfs:Class ;
rdfs:label "conversion" ;
rdfs:comment "a direct physical association that one interactor is converted from another interactor. " ;
rdfs:subClassOf obo:MI_0407 .
obo:INO_0000093 a rdfs:Class ;
rdfs:label "down-regulation" ;
rdfs:comment "a negative regulation that one interactor down-regulates another." ;
rdfs:subClassOf obo:INO_0000068 .
obo:INO_0000102 a rdfs:Class ;
rdfs:label "gene expression" ;
rdfs:comment "a biological interaction that uses the information from a gene to synthesize a functional gene product. " ;
rdfs:subClassOf obo:INO_0000002 .
obo:BFO_0000002 a rdfs:Class ;
rdfs:label "continuant"@en ;
rdfs:subClassOf obo:BFO_0000001 .
obo:MI_0217 a rdfs:Class ;
rdfs:label "phosphorylation reaction" ;
rdfs:comment "Reversible reaction that can affect D,C,H,S,T,Y,R residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0206 a rdfs:Class ;
rdfs:label "farnesylation reaction" ;
rdfs:comment "Reversible reaction that can affect C residue." ;
rdfs:subClassOf obo:MI_0211 .
obo:INO_0000090 a rdfs:Class ;
rdfs:label "molecular complex"@en ;
rdfs:subClassOf obo:CHEBI_23367 .
obo:INO_0000142 a rdfs:Class ;
rdfs:label "oxidation" ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000311 a rdfs:Class ;
rdfs:label "protein-protein interaction" ;
rdfs:comment "an interaction between two proteins. " ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000003 a rdfs:Class ;
rdfs:label "pathway" ;
rdfs:comment "an interaction network that includes at least two interactions and has a start point(s) and an end point(s). " ;
rdfs:subClassOf obo:INO_0000001 .
obo:MI_0195 a rdfs:Class ;
rdfs:label "covalent binding" ;
rdfs:comment "Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners." ;
rdfs:subClassOf obo:MI_0407 .
obo:INO_0000131 a rdfs:Class ;
rdfs:label "human molecular template reaction"@en ;
rdfs:subClassOf obo:INO_0000023 .
obo:MI_1143 a rdfs:Class ;
rdfs:label "aminoacylation reaction" ;
rdfs:comment "Aminoacylation is the process of adding an aminoacyl group to a compound." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1290 a rdfs:Class ;
rdfs:label "suppression (complete)" ;
rdfs:comment """An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
wt = ab != a = E
where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0796 .
obo:INO_0000120 a rdfs:Class ;
rdfs:label "increase" ;
rdfs:comment "a positive regulation that leads to the increase of a quality of an entity." ;
rdfs:subClassOf obo:INO_0000117 .
obo:INO_0000171 a rdfs:Class ;
rdfs:label "termination" ;
rdfs:comment "a negative regulation that leads to a process termination." ;
rdfs:subClassOf obo:INO_0000068 .
obo:IDO_0000405 a rdfs:Class ;
rdfs:label "pathogen role"@en ;
rdfs:comment "A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition."@en ;
rdfs:subClassOf obo:BFO_0000023 .
obo:INO_0000014 a rdfs:Class ;
rdfs:label "edge" ;
rdfs:comment "an edge is an object that represents a graphic line that links two interactors in an interaction. " ;
rdfs:subClassOf obo:BFO_0000030 .
obo:MI_1288 a rdfs:Class ;
rdfs:label "over-suppression-enhancement" ;
rdfs:comment """An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b < ab
OR
ab < a < wt < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0934 .
obo:MI_1295 a rdfs:Class ;
rdfs:label "unilateral over-suppression" ;
rdfs:comment """An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E = a < b = wt < ab
OR
ab < wt = b < a = E
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1286 .
obo:INO_0000106 a rdfs:Class ;
rdfs:label "gene fusion" ;
rdfs:comment "a genetic interaction that forms a hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion." ;
rdfs:subClassOf obo:MI_0208 .
obo:MI_1272 a rdfs:Class ;
rdfs:label "positive epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0797 , obo:MI_0935 .
obo:PR_000000001 a rdfs:Class ;
rdfs:label "protein" ;
rdfs:comment "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." ;
rdfs:subClassOf obo:CHEBI_23367 .
obo:MI_1283 a rdfs:Class ;
rdfs:label "suppression-enhancement" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < b < wt [E = a*]
OR
wt < b < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1282 .
obo:INO_0000025 a rdfs:Class ;
rdfs:label "gene-cell interaction"@en ;
rdfs:comment "an interaction that includes a gene and a cell as interactors." ;
rdfs:subClassOf obo:INO_0000002 .
obo:GO_0006915 a rdfs:Class ;
rdfs:label "apoptotic process" ;
rdfs:comment "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." ;
rdfs:subClassOf obo:GO_0012501 .
obo:INO_0000071 a rdfs:Class ;
rdfs:label "regulation of transcription by binding to promoter"@en ;
rdfs:comment "a regulation of transcription process that occurs through the binding to a promotor of a gene" ;
rdfs:subClassOf obo:INO_0000079 .
obo:INO_0000047 a rdfs:Class ;
rdfs:label "chemical reaction catalyst"@en ;
rdfs:comment "an interactor that starts or speeds up a chemical reaction while undergoing no permanent change itself." ;
rdfs:subClassOf obo:INO_0000016 .
obo:GO_0006473 a rdfs:Class ;
rdfs:label "protein acetylation" ;
rdfs:comment "The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." ;
rdfs:subClassOf obo:INO_0000022 .
obo:MI_0211 a rdfs:Class ;
rdfs:label "lipid addition" ;
rdfs:comment "Covalent or non covalent binding of lipid group on a protein residue." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1277 a rdfs:Class ;
rdfs:label "qualitative epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_1275 .
obo:MI_1250 a rdfs:Class ;
rdfs:label "isomerase reaction" ;
rdfs:comment "The catalysis of the structural rearrangement of isomers." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000155 a rdfs:Class ;
rdfs:label "recruitment" ;
rdfs:comment "a positive regulation that leads the recruitment of one interactor from one location to another. " ;
rdfs:subClassOf obo:INO_0000157 .
obo:BFO_0000019 a rdfs:Class ;
rdfs:label "quality"@en ;
rdfs:subClassOf obo:BFO_0000020 .
obo:INO_0000156 a rdfs:Class ;
rdfs:label "epithelial cell-pathogen protein-protein interaction"@en ;
rdfs:subClassOf obo:INO_0000152 .
obo:INO_0000060 a rdfs:Class ;
rdfs:label "coprecipitation" ;
rdfs:comment "a colocalization that two interactors are precipitated together." ;
rdfs:subClassOf obo:MI_0403 .
obo:INO_0000174 a rdfs:Class ;
rdfs:label "genetic transduction" ;
rdfs:comment "a cell-cell interaction that transfers viral, bacterial, or both bacterial and viral DNA from one cell to another using a bacteriophage vector. " ;
rdfs:subClassOf obo:INO_0000027 .
obo:MI_0794 a rdfs:Class ;
rdfs:label "synthetic" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (to any degree) as a result of any of the individual perturbations.
wt = a = b = E (not=) ab""" ;
rdfs:subClassOf obo:MI_0933 .
obo:INO_0000028 a rdfs:Class ;
rdfs:label "protein activation by mutant"@en ;
rdfs:comment "an activation process where one protein is activated by a gene mutant" ;
rdfs:subClassOf obo:INO_0000026 .
obo:INO_0000117 a rdfs:Class ;
rdfs:label "positive regulation" ;
rdfs:subClassOf obo:INO_0000157 .
obo:MI_0570 a rdfs:Class ;
rdfs:label "protein cleavage" ;
rdfs:comment "Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation." ;
rdfs:subClassOf obo:MI_0194 .
obo:CHEBI_33696 a rdfs:Class ;
rdfs:label "nucleic acid" ;
rdfs:comment "A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid." ;
rdfs:subClassOf obo:CHEBI_23367 .
obo:BFO_0000020 a rdfs:Class ;
rdfs:label "specifically dependent continuant"@en ;
rdfs:comment "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en ;
rdfs:subClassOf obo:BFO_0000002 .
obo:INO_0000159 a rdfs:Class ;
rdfs:label "obsolete class"@en .
obo:INO_0000043 a rdfs:Class ;
rdfs:label "negative regulation of protein translation"@en ;
rdfs:comment "a negative regulation process that down-regulates protein translation level" ;
rdfs:subClassOf obo:INO_0000034 .
obo:INO_0000128 a rdfs:Class ;
rdfs:label "human template reaction regulation"@en ;
rdfs:subClassOf obo:INO_0000101 .
obo:INO_0000152 a rdfs:Class ;
rdfs:label "epithelial cell-pathogen interaction" ;
rdfs:comment "An host cell-pathogen interaction where the host is an epithelial cell"@en ;
rdfs:subClassOf obo:INO_0000107 .
obo:NCBITaxon_2759 a rdfs:Class ;
rdfs:label "Eukaryota" ;
rdfs:subClassOf obo:LifO_0000005 .
obo:INO_0000098 a rdfs:Class ;
rdfs:label "bacterial conjugation"@en ;
rdfs:comment "a cell-cell interaction that the transfers genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells." ;
rdfs:subClassOf obo:INO_0000027 .
obo:MI_0985 a rdfs:Class ;
rdfs:label "deamination reaction" ;
rdfs:comment "The removal of an amine group from a molecule." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0557 a rdfs:Class ;
rdfs:label "adp ribosylation reaction" ;
rdfs:comment "Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000017 a rdfs:Class ;
rdfs:label "activator"@en ;
rdfs:comment "a positive interaction regulator that activates an interaction." ;
rdfs:subClassOf obo:INO_0000141 .
obo:MI_0934 a rdfs:Class ;
rdfs:label "neutral genetic interaction" ;
rdfs:comment """An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b [ab != E]
OR
With respect to two qualitatively different phenotypes, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:INO_0000113 a rdfs:Class ;
rdfs:label "macrophage-pathogen protein-protein interaction"@en ;
rdfs:comment "A macrophage-pathogen interaction that involves a macrophage protein and a pathogen protein." ;
rdfs:subClassOf obo:INO_0000109 .
obo:MI_1146 a rdfs:Class ;
rdfs:label "phospholipase reaction" ;
rdfs:comment "Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2273 a rdfs:Class ;
rdfs:label "tyrosination" ;
rdfs:comment "Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin." ;
rdfs:subClassOf obo:MI_2272 .
obo:GO_0008219 a rdfs:Class ;
rdfs:label "cell death" ;
rdfs:comment "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538)." ;
rdfs:subClassOf obo:GO_0008150 .
obo:INO_0000065 a rdfs:Class ;
rdfs:label "organism-environment interaction"@en ;
rdfs:comment "an interaction that involves an organism and its environment as interactors" ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000076 a rdfs:Class ;
rdfs:label "biochemical degradation" ;
rdfs:comment "an enzymatic reaction that leads to the breakdown of a biochemical entity. " ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000037 a rdfs:Class ;
rdfs:label "regulation of gene activation"@en ;
rdfs:comment "a regulation process that regulates the activation of a gene so that the gene is expressed at a particular time" ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000048 a rdfs:Class ;
rdfs:label "coimmunoprecipitation" ;
rdfs:comment "a coprecipitation that occurs through an immunoprecipitation process." ;
rdfs:subClassOf obo:INO_0000060 .
obo:MI_0882 a rdfs:Class ;
rdfs:label "atpase reaction" ;
rdfs:comment "Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate." ;
rdfs:subClassOf obo:MI_0881 .
obo:MI_0220 a rdfs:Class ;
rdfs:label "ubiquitination reaction" ;
rdfs:comment "Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1110 a rdfs:Class ;
rdfs:label "predicted interaction" ;
rdfs:comment "Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method." ;
rdfs:subClassOf obo:INO_0000002 .
obo:MI_0568 a rdfs:Class ;
rdfs:label "desumoylation reaction" ;
rdfs:comment "Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000124 a rdfs:Class ;
rdfs:label "inhibition" ;
rdfs:comment "a negative regulation that one interactor inhibites another." ;
rdfs:subClassOf obo:INO_0000068 .
obo:LifO_0000005 a rdfs:Class ;
rdfs:label "organism"@en ;
rdfs:comment "An organism is an individual entity that exhibits the properties of life, including reproduction, growth and development, maintenance, and response to stimuli. All organisms are composed of one or more cells." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:MI_0871 a rdfs:Class ;
rdfs:label "demethylation reaction" ;
rdfs:comment "The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000032 a rdfs:Class ;
rdfs:label "regulation of transcription"@en ;
rdfs:comment "a gene expression regulation process that involves the regulation of a gene transcription." ;
rdfs:subClassOf obo:INO_0000044 .
obo:INO_0000054 a rdfs:Class ;
rdfs:label "antigen-antibody interaction" ;
rdfs:comment "a direct interaction where an antigen interacts with an antibody physically." ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_0403 a rdfs:Class ;
rdfs:label "colocalization" ;
rdfs:comment "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." ;
rdfs:subClassOf obo:INO_0000002 .
obo:INO_0000026 a rdfs:Class ;
rdfs:label "protein activation"@en ;
rdfs:comment "an activation process where one protein is activated by a material entity" ;
rdfs:subClassOf obo:INO_0000024 .
obo:MI_0207 a rdfs:Class ;
rdfs:label "formylation reaction" ;
rdfs:comment "Reaction that can affect K or G residues. Reside is functionalised with a formyl group." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000010 a rdfs:Class ;
rdfs:label "output interactor role" ;
rdfs:comment "an interactor role that is borne by a material entity that acts as an output of an interaction." ;
rdfs:subClassOf obo:INO_0000015 .
obo:MI_1291 a rdfs:Class ;
rdfs:label "suppression (partial)" ;
rdfs:comment """An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, \"wild type\" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < wt [E = a*]
OR
wt < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0796 .
obo:INO_0000021 a rdfs:Class ;
rdfs:label "human molecular pathway"@en ;
rdfs:comment "a pathway that exists in human body." ;
rdfs:subClassOf obo:INO_0000003 .
obo:PW_0000003 a rdfs:Class ;
rdfs:label "signaling pathway" ;
rdfs:comment "The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways." ;
rdfs:subClassOf obo:INO_0000003 , obo:PW_0000001 .
obo:INO_0000137 a rdfs:Class ;
rdfs:label "negative regulator role"@en ;
rdfs:comment "an interactor role that is borne by a material entity that negatively regulates an interaction." ;
rdfs:subClassOf obo:INO_0000005 .
obo:INO_0000009 a rdfs:Class ;
rdfs:label "input interactor role" ;
rdfs:comment "an interactor role that is borne by a material entity that acts as an input of an interaction." ;
rdfs:subClassOf obo:INO_0000015 .
obo:MI_1292 a rdfs:Class ;
rdfs:label "unilateral suppression" ;
rdfs:comment """An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab <= b = wt [E = a]
OR
wt = b <= ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0796 .
obo:MI_1230 a rdfs:Class ;
rdfs:label "uridylation reaction" ;
rdfs:comment "The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166)." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0881 a rdfs:Class ;
rdfs:label "nucleoside triphosphatase reaction" ;
rdfs:comment "Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000148 a rdfs:Class ;
rdfs:label "precedence" ;
rdfs:comment "an indirect association that one interactor is preceded by another interactor. " ;
rdfs:subClassOf obo:MI_0914 .
obo:MI_0933 a rdfs:Class ;
rdfs:label "negative genetic interaction" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E <= wt
OR
wt <= E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:INO_0000015 a rdfs:Class ;
rdfs:label "interactor role" ;
rdfs:comment "a role that is borne by a material entity to act as a participant in an interaction process." ;
rdfs:subClassOf obo:BFO_0000023 .
obo:MI_1282 a rdfs:Class ;
rdfs:label "mutual suppression (partial)" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab < wt) [E = a*]
OR
(wt < b <= a*) AND (wt < ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1280 .
obo:INO_0000086 a rdfs:Class ;
rdfs:label "dominant regulation" ;
rdfs:comment "a regulation that one interactor has a dominant effect on the quality of another interactor. This differs from the accessory regulation. " ;
rdfs:subClassOf obo:INO_0000157 .
obo:INO_0000004 a rdfs:Class ;
rdfs:label "Bayesian network" ;
rdfs:comment "an interaction network model that is represented by a probabilistic graphical model (a type of statistical model) that represents a set of random variables and their conditional dependencies via a directed acyclic graph (DAG)." ;
rdfs:subClassOf obo:INO_0000158 .
obo:INO_0000083 a rdfs:Class ;
rdfs:label "human molecular catalysis"@en ;
rdfs:subClassOf obo:INO_0000101 .
obo:INO_0000107 a rdfs:Class ;
rdfs:label "host cell-pathogen interaction"@en ;
rdfs:comment "An host-pathogen interaction where the host is a cell." ;
rdfs:subClassOf obo:INO_0000105 .
obo:INO_0000075 a rdfs:Class ;
rdfs:label "gene activation"@en ;
rdfs:comment "a positive regulation of gene expression process that activates a gene so that the gene is expressed at a particular time" ;
rdfs:subClassOf obo:INO_0000038 .
obo:INO_0000039 a rdfs:Class ;
rdfs:label "negative regulation of gene expression"@en ;
rdfs:comment "a regulation process that negatively regulates gene expression level" ;
rdfs:subClassOf obo:INO_0000044 .
obo:BFO_0000148 a rdfs:Class ;
rdfs:label "zero-dimensional temporal region"@en ;
rdfs:subClassOf obo:BFO_0000008 .
obo:INO_0000130 a rdfs:Class ;
rdfs:label "human molecular conversion"@en ;
rdfs:comment "a human molecular interaction where one molecule converts to another molecule." ;
rdfs:subClassOf obo:INO_0000023 .
obo:INO_0000097 a rdfs:Class ;
rdfs:label "elimination" ;
rdfs:comment "a negative regulation that one interactor eliminates another." ;
rdfs:subClassOf obo:INO_0000068 .
obo:MI_0192 a rdfs:Class ;
rdfs:label "acetylation reaction" ;
rdfs:comment "Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:PW_0000013 a rdfs:Class ;
rdfs:label "disease pathway" ;
rdfs:comment "Complex human diseases encompass a spectrum of genetic and environmental attributes that together affect the normal functioning of several molecular and cellular pathways. Their combined and accumulated effect is manifested in the anomalous phenotype of the complex condition." ;
rdfs:subClassOf obo:INO_0000003 , obo:PW_0000001 .
obo:INO_0000231 a rdfs:Class ;
rdfs:label "co-expression" ;
rdfs:subClassOf obo:INO_0000061 .
obo:INO_0000141 a rdfs:Class ;
rdfs:label "positive regulator"@en ;
rdfs:comment "an interaction regulator that positively regulates an interaction." ;
rdfs:subClassOf obo:INO_0000008 .
obo:INO_0000101 a rdfs:Class ;
rdfs:label "human molecular control interaction"@en ;
rdfs:comment "a human molecular interaction where one molecule controls another molecule." ;
rdfs:subClassOf obo:INO_0000023 .
obo:INO_0000126 a rdfs:Class ;
rdfs:label "interference" ;
rdfs:comment "a negative regulation that one interactor interferes a process. " ;
rdfs:subClassOf obo:INO_0000068 .
obo:MI_1271 a rdfs:Class ;
rdfs:label "enhancement" ;
rdfs:comment """An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E < wt
OR
wt < E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0933 .
obo:MI_1327 a rdfs:Class ;
rdfs:label "sulfurtransfer reaction" ;
rdfs:comment "Reaction where a sulfate group is transferred between two proteins" ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000115 a rdfs:Class ;
rdfs:label "hyperphosphorylation" ;
rdfs:subClassOf obo:GO_0016310 .
obo:MI_1148 a rdfs:Class ;
rdfs:label "ampylation reaction" ;
rdfs:comment """AMPylation, previously known as adenylylation, is formation of a
phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys
(RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.""" ;
rdfs:subClassOf obo:MI_0414 .
obo:BFO_0000003 a rdfs:Class ;
rdfs:label "occurrent"@en ;
rdfs:subClassOf obo:BFO_0000001 .
obo:MI_1274 a rdfs:Class ;
rdfs:label "minimal epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab = b < wt
OR
wt < b = ab < a*
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1272 , obo:MI_1282 , obo:MI_1284 .
obo:PW_0000754 a rdfs:Class ;
rdfs:label "drug pathway" ;
rdfs:comment "The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. The systems involved in drug processing and responses are also those handling exogenous, xenobiotic compounds in the cellular detoxification pathway. The distinction between a random encounter with a foreign compound and the processing of a substance administered for treatment along with the importance of genetic variation for the individual responses to particular drugs warrant their separate consideration." ;
rdfs:subClassOf obo:INO_0000003 , obo:PW_0000001 .
obo:MI_0203 a rdfs:Class ;
rdfs:label "dephosphorylation reaction" ;
rdfs:comment "Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:CHEBI_16991 a rdfs:Class ;
rdfs:label "deoxyribonucleic acid" ;
rdfs:comment "High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms." ;
rdfs:subClassOf obo:CHEBI_33696 .
obo:INO_0000072 a rdfs:Class ;
rdfs:label "positive regulation of transcription by binding to promoter"@en ;
rdfs:comment "a regulation of transcription by binding to promoter that is further classified as a positive regulation" ;
rdfs:subClassOf obo:INO_0000071 .
obo:MI_1237 a rdfs:Class ;
rdfs:label "proline isomerization reaction" ;
rdfs:comment "The conversion between cis- and trans- peptide bonds formed by the amine group of a proline." ;
rdfs:subClassOf obo:MI_1250 .
obo:INO_0000094 a rdfs:Class ;
rdfs:label "gene expression up-regulation"@en ;
rdfs:comment "a positive regulation of gene expression process that up-regulates gene expression level" ;
rdfs:subClassOf obo:INO_0000038 .
obo:INO_0000091 a rdfs:Class ;
rdfs:label "disruption" ;
rdfs:comment "a negative regulation that results in a disruption." ;
rdfs:subClassOf obo:INO_0000068 .
obo:MI_0199 a rdfs:Class ;
rdfs:label "deformylation reaction" ;
rdfs:comment "N6-formyl-L-lysine is cleaved and returns a K residue." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0214 a rdfs:Class ;
rdfs:label "myristoylation reaction" ;
rdfs:comment "Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues." ;
rdfs:subClassOf obo:MI_0211 .
obo:INO_0000050 a rdfs:Class ;
rdfs:label "competition" ;
rdfs:comment "an indirect association that one interactor competes with another interactor in a specfiic process. " ;
rdfs:subClassOf obo:MI_0914 .
obo:INO_0000134 a rdfs:Class ;
rdfs:label "positive regulator role"@en ;
rdfs:comment "an interactor role that is borne by a material entity that positively regulates an interaction." ;
rdfs:subClassOf obo:INO_0000005 .
obo:INO_0000053 a rdfs:Class ;
rdfs:label "positive regulation of protein translation"@en ;
rdfs:comment "a regulation of translation process that positively regulates protein translation level" ;
rdfs:subClassOf obo:INO_0000034 .
obo:INO_0000242 a rdfs:Class ;
rdfs:label "import" ;
rdfs:comment "a translocation that one interactor imports from one location" ;
rdfs:subClassOf obo:INO_0000176 .
obo:CHEBI_33697 a rdfs:Class ;
rdfs:label "ribonucleic acid" ;
rdfs:comment "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins." ;
rdfs:subClassOf obo:CHEBI_33696 .
obo:INO_0000235 a rdfs:Class ;
rdfs:label "one-way interaction" ;
rdfs:comment "A one-way interaction is an interaction that shows one direction between interactors." ;
rdfs:subClassOf obo:INO_0000002 .
obo:MI_0566 a rdfs:Class ;
rdfs:label "sumoylation reaction" ;
rdfs:comment "Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000061 a rdfs:Class ;
rdfs:label "correlation" ;
rdfs:comment "an indirect association that two interactors are correlated in a process without defined influence of each other. " ;
rdfs:subClassOf obo:MI_0914 .
obo:MI_0193 a rdfs:Class ;
rdfs:label "amidation reaction" ;
rdfs:comment "Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000145 a rdfs:Class ;
rdfs:label "deactivator role"@en ;
rdfs:comment "a negative regulator role that is borne by a material entity that deactivates, inhibits, blocks, or disrupts the action of a biological agent (e.g., enzyme)." ;
rdfs:subClassOf obo:INO_0000137 .
obo:CL_0000066 a rdfs:Class ;
rdfs:label "epithelial cell" ;
rdfs:comment "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." ;
rdfs:subClassOf obo:CL_0000000 .
obo:MI_0210 a rdfs:Class ;
rdfs:label "hydroxylation reaction" ;
rdfs:comment "Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0701 a rdfs:Class ;
rdfs:label "dna strand elongation" ;
rdfs:comment "The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand." ;
rdfs:subClassOf obo:MI_0986 .
obo:MI_0986 a rdfs:Class ;
rdfs:label "nucleic acid strand elongation reaction" ;
rdfs:comment "The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase." ;
rdfs:subClassOf obo:MI_0414 .
obo:INO_0000112 a rdfs:Class ;
rdfs:label "protein homodimerization" ;
rdfs:comment "a protein dimerization where two proteins are the same. " ;
rdfs:subClassOf obo:INO_0000088 .
obo:BFO_0000031 a rdfs:Class ;
rdfs:label "generically dependent continuant"@en ;
rdfs:comment "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en ;
rdfs:subClassOf obo:BFO_0000002 .
obo:PW_0000004 a rdfs:Class ;
rdfs:label "regulatory pathway" ;
rdfs:comment "The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning." ;
rdfs:subClassOf obo:INO_0000003 , obo:PW_0000001 .
obo:INO_0000153 a rdfs:Class ;
rdfs:label "reactivation" ;
rdfs:comment "an activation that repeats." ;
rdfs:subClassOf obo:INO_0000024 .
obo:INO_0000178 a rdfs:Class ;
rdfs:label "tyrosine-phosphorylation" ;
rdfs:subClassOf obo:GO_0016310 .
obo:INO_0000064 a rdfs:Class ;
rdfs:label "cross-immunoprecipitation interaction" ;
rdfs:comment "an immuno-precipitation that one interactor is precipitated based on an cross- immunological precipitation process." ;
rdfs:subClassOf obo:INO_0000116 .
obo:INO_0000118 a rdfs:Class ;
rdfs:label "impairment" ;
rdfs:comment "A negative regulation that disables, damages, or impairs the functioning of another entity." ;
rdfs:subClassOf obo:INO_0000068 .
obo:MI_0414 a rdfs:Class ;
rdfs:label "enzymatic reaction" ;
rdfs:comment "terms aiming to represent biochemical reactions referring to their resulting product modifications." ;
rdfs:subClassOf obo:MI_0407 .
obo:INO_0000129 a rdfs:Class ;
rdfs:label "host gene mutant-pathogen interaction"@en ;
rdfs:comment "An host-pathogen interaction where the host is a gene mutant" ;
rdfs:subClassOf obo:INO_0000105 .
a rdfs:Class ;
rdfs:comment "An unconstrained type or object" .
obo:MI_0932 a rdfs:Class ;
rdfs:label "noninteractive" ;
rdfs:comment "The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype." ;
rdfs:subClassOf obo:MI_0934 .
obo:INO_0000123 a rdfs:Class ;
rdfs:label "human molecular regulatory reaction"@en ;
rdfs:subClassOf obo:INO_0000023 .
obo:IAO_0000027 a rdfs:Class ;
rdfs:label "data item"@en ;
rdfs:comment "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en ;
rdfs:subClassOf obo:IAO_0000030 .
obo:NCBITaxon_2 a rdfs:Class ;
rdfs:label "Bacteria" ;
rdfs:subClassOf obo:LifO_0000005 .
obo:MI_0797 a rdfs:Class ;
rdfs:label "epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:INO_0000079 a rdfs:Class ;
rdfs:label "promoter-based regulation of transcription"@en ;
rdfs:comment "a regulation of transcription process through binding to a promoter or regulating the promoter binding activity" ;
rdfs:subClassOf obo:INO_0000032 .
obo:INO_0000042 a rdfs:Class ;
rdfs:label "negative regulation of gene transcription"@en ;
rdfs:comment "a negative regulation process that down-regulates gene expression level" ;
rdfs:subClassOf obo:INO_0000032 .
obo:INO_0000031 a rdfs:Class ;
rdfs:label "regulation of protein location"@en ;
rdfs:comment "a regulation process that regulates the location of a protein" ;
rdfs:subClassOf obo:INO_0000157 .
obo:MI_0204 a rdfs:Class ;
rdfs:label "deubiquitination reaction" ;
rdfs:comment "Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:BFO_0000050 a rdf:Property ;
rdfs:label "part of"@en ;
rdfs:comment "a core relation that holds between a part and its whole"@en ;
rdfs:seeAlso , , ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002131 .
obo:BFO_0000062 a rdf:Property ;
rdfs:label "preceded by"@en ;
rdfs:comment "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002086 .
obo:BFO_0000063 a rdf:Property ;
rdfs:label "precedes"@en ;
rdfs:comment "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:BFO_0000179 a rdf:Property ;
rdfs:label "BFO OWL specification label"@en ;
rdfs:comment "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en ;
rdfs:range xsd:string .
obo:BFO_0000180 a rdf:Property ;
rdfs:label "BFO CLIF specification label"@en ;
rdfs:comment "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en ;
rdfs:range xsd:string .
obo:IAO_0000111 a rdf:Property ;
rdfs:label "editor preferred term"@en ;
rdfs:comment "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en ;
rdfs:range xsd:string .
obo:IAO_0000112 a rdf:Property ;
rdfs:label "example of usage"@en ;
rdfs:comment "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en ;
rdfs:range xsd:string .
obo:IAO_0000114 a rdf:Property ;
rdfs:label "has curation status"@en ;
rdfs:range xsd:string .
obo:IAO_0000115 a rdf:Property ;
rdfs:label "textual definition" ;
rdfs:comment "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en ;
rdfs:range xsd:string .
obo:IAO_0000116 a rdf:Property ;
rdfs:label "editor note"@en ;
rdfs:comment "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ;
rdfs:range xsd:string .
obo:IAO_0000117 a rdf:Property ;
rdfs:label "term editor"@en ;
rdfs:comment "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en ;
rdfs:range xsd:string .
obo:IAO_0000118 a rdf:Property ;
rdfs:label "alternative term"@en ;
rdfs:comment "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ;
rdfs:range xsd:string .
obo:IAO_0000119 a rdf:Property ;
rdfs:label "definition source"@en ;
rdfs:comment "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en ;
rdfs:range xsd:string .
obo:IAO_0000232 a rdf:Property ;
rdfs:label "curator note"@en ;
rdfs:comment "An administrative note of use for a curator but of no use for a user"@en ;
rdfs:range xsd:string .
obo:IAO_0000412 a rdf:Property ;
rdfs:label "imported from"@en ;
rdfs:range xsd:string .
obo:IAO_0000424 a rdf:Property ;
rdfs:label "expand expression to"@en ;
rdfs:range xsd:string .
obo:IAO_0000589 a rdf:Property ;
rdfs:label "OBO foundry unique label"@en ;
rdfs:range xsd:string .
obo:IAO_0000600 a rdf:Property ;
rdfs:label "elucidation"@en ;
rdfs:range xsd:string .
obo:IAO_0000601 a rdf:Property ;
rdfs:label "has associated axiom(nl)"@en ;
rdfs:range xsd:string .
obo:IAO_0000602 a rdf:Property ;
rdfs:label "has associated axiom(fol)"@en ;
rdfs:range xsd:string .
obo:INO_0000006 a rdf:Property ;
rdfs:label "has literature mining keywords"@en ;
rdfs:comment "an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition. " ;
rdfs:range xsd:string .
obo:INO_0000020 a rdf:Property ;
rdfs:label "has activator"@en ;
rdfs:comment "an object property between an activation process and a material entity that acts as an activator during the process." ;
rdfs:range .
obo:INO_0000036 a rdf:Property ;
rdfs:label "example of literature mining keyword usage"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:IAO_0000112 .
obo:INO_0000080 a rdf:Property ;
rdfs:label "has_controller"@en ;
rdfs:range .
obo:INO_0000082 a rdf:Property ;
rdfs:label "controls"@en ;
rdfs:range .
obo:INO_0000087 a rdf:Property ;
rdfs:label "has keyword dependency pattern"@en ;
rdfs:comment "an annotation property that specifies the dependency pattern of the literature keywords that match to the ontology interaction type." ;
rdfs:range xsd:string .
obo:INO_0000136 a rdf:Property ;
rdfs:label "has_next_step"@en ;
rdfs:range .
obo:INO_0000139 a rdf:Property ;
rdfs:label "lacks part"@en ;
rdfs:range .
obo:INO_0000160 a rdf:Property ;
rdfs:label "has coefficient"@en ;
rdfs:comment "An data property that represents the coefficient value in a chemical reaction equation. Specifically, the cofficent is the number in front of a formula in a chemical equation." ;
rdfs:range .
obo:RO_0001900 a rdf:Property ;
rdfs:label "temporal interpretation"@en ;
rdfs:comment "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." ;
rdfs:seeAlso , ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002422 .
obo:RO_0002081 a rdf:Property ;
rdfs:label "before or simultaneous with"@en ;
rdfs:comment "Primitive instance level timing relation between events" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:RO_0002082 a rdf:Property ;
rdfs:label "simultaneous with"@en ;
rdfs:comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002081 .
obo:RO_0002083 a rdf:Property ;
rdfs:label "before"@en ;
rdfs:comment "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002081 .
obo:RO_0002084 a rdf:Property ;
rdfs:label "during which ends"@en ;
rdfs:comment "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:RO_0002085 a rdf:Property ;
rdfs:label "encompasses"@en ;
rdfs:comment "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002088 .
obo:RO_0002086 a rdf:Property ;
rdfs:label "ends after"@en ;
rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:RO_0002087 a rdf:Property ;
rdfs:label "immediately preceded by"@en ;
rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:BFO_0000062 .
obo:RO_0002088 a rdf:Property ;
rdfs:label "during which starts"@en ;
rdfs:comment "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:RO_0002089 a rdf:Property ;
rdfs:label "starts before"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:RO_0002090 a rdf:Property ;
rdfs:label "immediately precedes"@en ;
rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:BFO_0000063 .
obo:RO_0002091 a rdf:Property ;
rdfs:label "starts during"@en ;
rdfs:comment "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:RO_0002092 a rdf:Property ;
rdfs:label "happens during"@en ;
rdfs:comment "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002093 , obo:RO_0002091 .
obo:RO_0002093 a rdf:Property ;
rdfs:label "ends during"@en ;
rdfs:comment "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). "@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 .
obo:RO_0002131 a rdf:Property ;
rdfs:label "overlaps"@en ;
rdfs:comment "x overlaps y if and only if there exists some z such that x has part z and z part of y" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002323 .
obo:RO_0002222 a rdf:Property ;
rdfs:label "temporally related to"@en ;
rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ;
rdfs:range .
obo:RO_0002223 a rdf:Property ;
rdfs:label "starts"@en ;
rdfs:comment "inverse of starts with" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 , obo:BFO_0000050 .
obo:RO_0002224 a rdf:Property ;
rdfs:label "starts with"@en ;
rdfs:comment "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 , obo:BFO_0000051 .
obo:RO_0002229 a rdf:Property ;
rdfs:label "ends"@en ;
rdfs:comment "inverse of ends with" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 , obo:BFO_0000050 .
obo:RO_0002230 a rdf:Property ;
rdfs:label "ends with"@en ;
rdfs:comment "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002222 , obo:BFO_0000051 .
obo:RO_0002234 a rdf:Property ;
rdfs:label "has output"@en ;
rdfs:comment "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." ;
rdfs:range .
obo:RO_0002304 a rdf:Property ;
rdfs:label "causally upstream of, positive effect" ;
rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0004047 , obo:RO_0002411 .
obo:RO_0002305 a rdf:Property ;
rdfs:label "causally upstream of, negative effect" ;
rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0004046 , obo:RO_0002411 .
obo:RO_0002323 a rdf:Property ;
rdfs:label "mereotopologically related to"@en ;
rdfs:comment "A mereological relationship or a topological relationship" ;
rdfs:range .
obo:RO_0002404 a rdf:Property ;
rdfs:label "causally downstream of"@en ;
rdfs:comment "inverse of upstream of" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002427 , obo:BFO_0000062 .
obo:RO_0002405 a rdf:Property ;
rdfs:label "immediately causally downstream of"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002404 , obo:RO_0002087 .
obo:RO_0002406 a rdf:Property ;
rdfs:label "directly activates"@en ;
rdfs:comment "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002629 .
obo:RO_0002407 a rdf:Property ;
rdfs:label "indirectly activates"@en ;
rdfs:comment "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002213 .
obo:RO_0002408 a rdf:Property ;
rdfs:label "directly inhibits"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002630 .
obo:RO_0002409 a rdf:Property ;
rdfs:label "indirectly inhibits"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002212 .
obo:RO_0002410 a rdf:Property ;
rdfs:label "causally related to"@en ;
rdfs:comment "This relation groups causal relations between material entities and causal relations between processes" ;
rdfs:range .
obo:RO_0002412 a rdf:Property ;
rdfs:label "immediately causally upstream of"@en ;
rdfs:comment "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002411 , obo:RO_0002090 .
obo:RO_0002413 a rdf:Property ;
rdfs:label "directly provides input for"@en ;
rdfs:comment "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002414 , obo:RO_0002412 .
obo:RO_0002414 a rdf:Property ;
rdfs:label "transitively provides input for"@en ;
rdfs:comment "transitive form of directly_provides_input_for" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002411 .
obo:RO_0002416 a rdf:Property ;
rdfs:label "logical macro assertion"@en ;
rdfs:comment "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." ;
rdfs:seeAlso ;
rdfs:range xsd:string .
obo:RO_0002418 a rdf:Property ;
rdfs:label "causally upstream of or within" ;
rdfs:comment "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002501 .
obo:RO_0002421 a rdf:Property ;
rdfs:label "logical macro assertion on a property"@en ;
rdfs:comment "A logical macro assertion whose domain is an IRI for a property" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002416 .
obo:RO_0002422 a rdf:Property ;
rdfs:label "logical macro assertion on an object property"@en ;
rdfs:comment "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002421 .
obo:RO_0002423 a rdf:Property ;
rdfs:label "logical macro assertion on an annotation property"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002421 .
obo:RO_0002427 a rdf:Property ;
rdfs:label "causally downstream of or within" ;
rdfs:comment "inverse of causally upstream of or within" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002501 .
obo:RO_0002501 a rdf:Property ;
rdfs:label "causal relation between processes" ;
rdfs:comment "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002410 .
obo:RO_0002575 a rdf:Property ;
rdfs:label "is direct form of" ;
rdfs:comment "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" ;
rdfs:seeAlso ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002422 .
obo:RO_0002578 a rdf:Property ;
rdfs:label "directly regulates" ;
rdfs:comment "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002412 , obo:RO_0002211 .
obo:RO_0002579 a rdf:Property ;
rdfs:label "is indirect form of" ;
rdfs:comment "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" ;
rdfs:seeAlso ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002422 .
obo:RO_0002629 a rdf:Property ;
rdfs:label "directly positively regulates" ;
rdfs:comment "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002578 , obo:RO_0002213 .
obo:RO_0002630 a rdf:Property ;
rdfs:label "directly negatively regulates" ;
rdfs:comment "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002578 , obo:RO_0002212 .
obo:RO_0004046 a rdf:Property ;
rdfs:label "causally upstream of or within, negative effect" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002418 .
obo:RO_0004047 a rdf:Property ;
rdfs:label "causally upstream of or within, positive effect" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002418 .
obo:RO_0004048 a rdf:Property ;
rdfs:label "is directional form of" ;
rdfs:comment "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002422 .
obo:RO_0004049 a rdf:Property ;
rdfs:label "is positive form of" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0004048 .
obo:RO_0004050 a rdf:Property ;
rdfs:label "is negative form of" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0004048 .
obo:RO_0040042 a rdf:Property ;
rdfs:label "is homeomorphic for" ;
rdfs:comment "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C." ;
rdfs:seeAlso ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002422 .
a rdf:Property ;
rdfs:label "has_rank" ;
rdfs:comment "A metadata relation between a class and its taxonomic rank (eg species, family)" ;
rdfs:range xsd:string .