From 7cc9ebbd63e12d38f788b3ed7b09576ec2686289 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 5 Sep 2023 11:26:05 +0100 Subject: [PATCH] update imports --- src/ontology/components/hra_subset.owl | 198 +- src/ontology/imports/merged_import.owl | 5278 ++++++++--------- src/ontology/mappings/fbbt-mappings.sssom.tsv | 1 + 3 files changed, 2566 insertions(+), 2911 deletions(-) diff --git a/src/ontology/components/hra_subset.owl b/src/ontology/components/hra_subset.owl index 397996e3e2..351a387d6f 100644 --- a/src/ontology/components/hra_subset.owl +++ b/src/ontology/components/hra_subset.owl @@ -4186,15 +4186,6 @@ - - - - - - - - - @@ -4276,6 +4267,15 @@ + + + + + + + + + @@ -5059,6 +5059,15 @@ + + + + + + + + + @@ -5149,15 +5158,6 @@ - - - - - - - - - @@ -6193,15 +6193,6 @@ - - - - - - - - - @@ -6463,6 +6454,15 @@ + + + + + + + + + @@ -6715,6 +6715,15 @@ + + + + + + + + + @@ -7066,6 +7075,15 @@ + + + + + + + + + @@ -7759,15 +7777,6 @@ - - - - - - - - - @@ -9631,6 +9640,15 @@ + + + + + + + + + @@ -10108,15 +10126,6 @@ - - - - - - - - - @@ -10135,15 +10144,6 @@ - - - - - - - - - @@ -10567,15 +10567,6 @@ - - - - - - - - - @@ -10999,24 +10990,6 @@ - - - - - - - - - - - - - - - - - - @@ -11404,6 +11377,15 @@ + + + + + + + + + @@ -12547,15 +12529,6 @@ - - - - - - - - - @@ -12889,12 +12862,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 116edd67a0..f33da43dbb 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-07-24") + +Annotation(owl:versionInfo "2023-09-05") Declaration(Class()) Declaration(Class()) @@ -36,8 +36,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -937,7 +935,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -964,6 +961,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2000,6 +1998,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2142,7 +2142,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2196,6 +2195,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2203,7 +2203,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2216,7 +2215,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2227,10 +2225,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2328,7 +2326,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2378,6 +2375,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2410,6 +2410,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2875,7 +2879,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2949,9 +2952,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3018,6 +3021,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3042,6 +3047,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3119,7 +3126,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3308,12 +3315,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3357,7 +3362,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3515,9 +3519,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3597,7 +3598,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3629,6 +3629,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3867,10 +3868,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3882,8 +3879,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3893,23 +3890,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3970,10 +3959,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4299,6 +4284,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4397,7 +4383,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4472,6 +4457,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4567,6 +4553,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4578,6 +4565,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4604,6 +4592,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4663,6 +4652,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4678,8 +4668,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4719,6 +4707,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4888,8 +4879,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5063,6 +5052,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5155,6 +5145,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5363,7 +5356,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5444,8 +5436,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5472,6 +5464,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5763,6 +5756,18 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5804,7 +5809,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6211,7 +6215,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6219,11 +6225,14 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6240,19 +6249,22 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6268,6 +6280,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6281,6 +6294,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6290,6 +6306,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6309,10 +6329,16 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6422,8 +6448,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6647,7 +6671,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6844,6 +6867,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6979,10 +7003,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7021,16 +7047,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7045,8 +7067,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7174,7 +7194,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7277,9 +7296,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7518,10 +7534,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7551,6 +7569,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7580,6 +7600,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7626,11 +7647,13 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7702,6 +7725,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7724,6 +7748,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7742,6 +7768,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7750,10 +7778,18 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7808,7 +7844,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7847,6 +7886,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7871,6 +7914,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7987,7 +8033,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8005,6 +8054,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8016,13 +8066,14 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8121,6 +8172,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8176,9 +8230,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8231,6 +8282,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8315,6 +8367,13 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8365,6 +8424,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8386,7 +8446,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8446,7 +8505,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8508,6 +8566,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8575,6 +8636,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8595,6 +8659,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8621,6 +8688,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8634,6 +8702,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8648,9 +8719,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8727,6 +8795,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8755,6 +8826,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8769,7 +8843,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8786,6 +8859,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8814,7 +8890,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8825,7 +8900,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8842,7 +8917,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8964,6 +9038,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8987,9 +9063,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9004,6 +9077,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9016,6 +9092,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9027,6 +9104,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9035,12 +9115,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9260,9 +9340,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9363,7 +9444,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10743,6 +10823,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11387,6 +11468,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11735,7 +11817,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -11934,7 +12015,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -11961,7 +12041,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -11977,15 +12056,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12095,31 +12165,22 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12147,9 +12208,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12160,129 +12218,61 @@ Declaration(AnnotationProperty(owl:deprecated)) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ # Annotation Property: (example of usage) -AnnotationAssertion( "example of usage"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "example of usage"@en) AnnotationAssertion(rdfs:label "example of usage") # Annotation Property: (definition) -AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) -AnnotationAssertion( "2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") # Annotation Property: (editor note) -AnnotationAssertion( "editor note"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor note"@en) AnnotationAssertion(rdfs:label "editor note") -# Annotation Property: (has obsolescence reason) - -AnnotationAssertion( "has obsolescence reason"@en) -AnnotationAssertion( "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "has obsolescence reason"@en) - # Annotation Property: (curator note) -AnnotationAssertion( "curator note"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "curator note"@en) AnnotationAssertion(rdfs:label "curator note") # Annotation Property: (term tracker item) -AnnotationAssertion( "term tracker item"@en) -AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term."@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion( "IAO:0000233") AnnotationAssertion( "external") AnnotationAssertion( "term_tracker_item") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "term_tracker_item") -AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) -AnnotationAssertion(rdfs:label "term tracker item"@en) AnnotationAssertion(rdfs:label "term tracker item") # Annotation Property: (expand assertion to) -AnnotationAssertion( "expand assertion to"@en) -AnnotationAssertion( "ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" -"@en) -AnnotationAssertion( "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom."@en) -AnnotationAssertion( "Chris Mungall"@en) -AnnotationAssertion(rdfs:label "expand assertion to"@en) AnnotationAssertion(rdfs:label "expand assertion to") -# Annotation Property: (has ontology root term) +# Annotation Property: (preferred_root) -AnnotationAssertion( "has ontology root term"@en) -AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."@en) -AnnotationAssertion( "Nicolas Matentzoglu"@en) -AnnotationAssertion(rdfs:label "has ontology root term"@en) +AnnotationAssertion( "IAO:0000700") +AnnotationAssertion( "external") +AnnotationAssertion( "has_ontology_root_term") +AnnotationAssertion( "true"^^xsd:boolean) +AnnotationAssertion( "true"^^xsd:boolean) +AnnotationAssertion( "has_ontology_root_term") +AnnotationAssertion(rdfs:label "has ontology root term") AnnotationAssertion(rdfs:label "preferred_root") # Annotation Property: (term replaced by) -AnnotationAssertion( "term replaced by"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion(rdfs:label "term replaced by"@en) AnnotationAssertion(rdfs:label "term replaced by") # Annotation Property: (never in taxon) @@ -12659,18 +12649,10 @@ SubAnnotationPropertyOf( SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -12693,34 +12675,19 @@ AnnotationAssertion(rdfs:label (has_broad_synonym) -AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") -AnnotationAssertion(rdfs:label "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") # Annotation Property: (database_cross_reference) AnnotationAssertion(rdfs:label "database_cross_reference") -# Annotation Property: (has exact synonym) +# Annotation Property: (has_exact_synonym) -AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -AnnotationAssertion(rdfs:label "has exact synonym"@en) AnnotationAssertion(rdfs:label "has_exact_synonym") -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -# Annotation Property: (has narrow synonym) +# Annotation Property: (has_narrow_synonym) -AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") -AnnotationAssertion(rdfs:label "has narrow synonym"@en) AnnotationAssertion(rdfs:label "has_narrow_synonym") -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") # Annotation Property: (has_obo_format_version) @@ -12732,12 +12699,7 @@ AnnotationAssertion(rdfs:label (has_related_synonym) -AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") -AnnotationAssertion(rdfs:label "has related synonym"@en) AnnotationAssertion(rdfs:label "has_related_synonym") -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") # Annotation Property: (has_scope) @@ -12847,7 +12809,7 @@ AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) AnnotationAssertion( "is preceded by"@en) AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( "BFO:0000062") AnnotationAssertion( "external") AnnotationAssertion( "preceded_by") @@ -12904,8 +12866,6 @@ ObjectPropertyRange( "site of"@en) AnnotationAssertion( "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion( "BFO:0000067") -AnnotationAssertion( "contains_process") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "contains process"@en) @@ -13237,8 +13197,6 @@ TransitiveObjectProperty() AnnotationAssertion(Annotation( "BSPO:cjm") "X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.") AnnotationAssertion( "This was migrated from http://purl.obolibrary.org/obo/uberon/core#in_central_side_of in Uberon.") AnnotationAssertion( ) -AnnotationAssertion( "BSPO:0020001") -AnnotationAssertion( "in_central_side_of") AnnotationAssertion(rdfs:label "in central side of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) @@ -13298,8 +13256,6 @@ AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) AnnotationAssertion( "inheres_in"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0000052") -AnnotationAssertion( "characteristic_of") AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") AnnotationAssertion(rdfs:label "characteristic of"@en) SubObjectPropertyOf( ) @@ -13320,7 +13276,6 @@ AnnotationAssertion( "external") AnnotationAssertion( "bearer_of") AnnotationAssertion( "bearer_of") -AnnotationAssertion( "has_characteristic") AnnotationAssertion(rdfs:label "has characteristic"@en) AnnotationAssertion(rdfs:label "bearer of") InverseFunctionalObjectProperty() @@ -13353,7 +13308,7 @@ AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion( "RO:0000057") AnnotationAssertion( "external") AnnotationAssertion( "has_participant") @@ -13370,8 +13325,6 @@ AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) AnnotationAssertion( "function_of"@en) AnnotationAssertion( "is function of"@en) -AnnotationAssertion( "RO:0000079") -AnnotationAssertion( "function_of") AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") AnnotationAssertion(rdfs:label "function of"@en) SubObjectPropertyOf( ) @@ -13385,8 +13338,6 @@ AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) AnnotationAssertion( "is quality of"@en) AnnotationAssertion( "quality_of"@en) -AnnotationAssertion( "RO:0000080") -AnnotationAssertion( "quality_of") AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") AnnotationAssertion(rdfs:label "quality of"@en) SubObjectPropertyOf( ) @@ -13399,8 +13350,6 @@ AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) AnnotationAssertion( "is role of"@en) AnnotationAssertion( "role_of"@en) -AnnotationAssertion( "RO:0000081") -AnnotationAssertion( "role_of") AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") AnnotationAssertion(rdfs:label "role of"@en) SubObjectPropertyOf( ) @@ -13412,8 +13361,6 @@ AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) AnnotationAssertion( "has_function"@en) -AnnotationAssertion( "RO:0000085") -AnnotationAssertion( "has_function") AnnotationAssertion(rdfs:label "has function"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -13425,8 +13372,6 @@ AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) AnnotationAssertion( "has_quality"@en) -AnnotationAssertion( "RO:0000086") -AnnotationAssertion( "has_quality") AnnotationAssertion(rdfs:label "has quality"@en) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -13437,8 +13382,6 @@ AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) AnnotationAssertion( "has_role"@en) -AnnotationAssertion( "RO:0000087") -AnnotationAssertion( "has_role") AnnotationAssertion(rdfs:label "has role"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -13447,8 +13390,6 @@ ObjectPropertyRange( (has disposition) AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "RO:0000091") -AnnotationAssertion( "has_disposition") AnnotationAssertion(rdfs:label "has disposition"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13458,9 +13399,7 @@ ObjectPropertyRange( (disposition of) AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( "RO:0000092") AnnotationAssertion( ) -AnnotationAssertion( "disposition_of") AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") AnnotationAssertion(rdfs:label "disposition of"@en) SubObjectPropertyOf( ) @@ -13474,39 +13413,16 @@ AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion( "location_of"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0001015") -AnnotationAssertion( "location_of") AnnotationAssertion(rdfs:label "location of"@en) InverseObjectProperties( ) TransitiveObjectProperty() -# Object Property: (contained in) - -AnnotationAssertion( "contained in"@en) -AnnotationAssertion( "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):"@en) -AnnotationAssertion( "Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - "@en) -AnnotationAssertion( "Containment is location not involving parthood, and arises only where some immaterial continuant is involved.") -AnnotationAssertion( "contained_in"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0001018") -AnnotationAssertion( ) -AnnotationAssertion( "contained_in") -AnnotationAssertion(rdfs:label "contained in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (contains) +# Object Property: (obsolete contains) AnnotationAssertion( "contains"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0001019") -AnnotationAssertion( ) -AnnotationAssertion( "contains") -AnnotationAssertion(rdfs:label "contains"@en) +AnnotationAssertion(rdfs:label "obsolete contains") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (located in) @@ -13518,10 +13434,8 @@ AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion( "located_in"@en) AnnotationAssertion( ) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:located_in") -AnnotationAssertion( "RO:0001025") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:located_in") AnnotationAssertion( ) -AnnotationAssertion( "located_in") AnnotationAssertion(rdfs:label "located in"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Located_in"^^xsd:anyURI) TransitiveObjectProperty() @@ -13542,8 +13456,6 @@ AnnotationAssertion( "is boundary of"@en) AnnotationAssertion( "surface of"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002000") -AnnotationAssertion( "2D_boundary_of") AnnotationAssertion(rdfs:label "2D boundary of"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13558,8 +13470,6 @@ AnnotationAssertion( "has boundary"@en) AnnotationAssertion( "has_2D_boundary"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002002") -AnnotationAssertion( "has_2D_boundary") AnnotationAssertion(rdfs:label "has 2D boundary"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -13569,8 +13479,6 @@ ObjectPropertyRange( ) AnnotationAssertion( "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^xsd:anyURI) -AnnotationAssertion( "RO:0002005") -AnnotationAssertion( "innervated_by") AnnotationAssertion(rdfs:label "innervated_by"@en) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -13580,8 +13488,6 @@ ObjectPropertyRange( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002006") -AnnotationAssertion( "has_synaptic_terminal_of") AnnotationAssertion(rdfs:label "has synaptic terminal of"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13642,8 +13548,6 @@ SubObjectPropertyOf( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002015") -AnnotationAssertion( "has_positive_regulatory_component_activity") AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") AnnotationAssertion(rdfs:label "has positive regulatory component activity") SubObjectPropertyOf( ) @@ -13653,8 +13557,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002017") -AnnotationAssertion( "has_component_activity") AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") AnnotationAssertion(rdfs:label "has component activity") SubObjectPropertyOf( ) @@ -13664,8 +13566,6 @@ SubObjectPropertyOf( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002018") -AnnotationAssertion( "has_component_process") AnnotationAssertion(rdfs:label "has component process") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -13676,8 +13576,6 @@ ObjectPropertyRange( "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.") AnnotationAssertion( ) AnnotationAssertion( "2017-07-20T17:19:37Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002021") -AnnotationAssertion( "occurs_across") AnnotationAssertion(rdfs:label "occurs across") SubObjectPropertyOf( ) @@ -13685,8 +13583,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002022") -AnnotationAssertion( "directly_regulated_by") AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) 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.") AnnotationAssertion(rdfs:label "directly regulated by") SubObjectPropertyOf( ) @@ -13697,8 +13593,6 @@ InverseObjectProperties( ) "Process(P2) is directly negatively regulated by process(P1) 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 P2 directly negatively regulated by P1.") AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002023") -AnnotationAssertion( "directly_negatively_regulated_by") AnnotationAssertion(rdfs:label "directly negatively regulated by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13708,8 +13602,6 @@ InverseObjectProperties( ) "Process(P2) is directly postively regulated by process(P1) 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 P2 is directly postively regulated by P1.") AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002024") -AnnotationAssertion( "directly_positively_regulated_by") AnnotationAssertion(rdfs:label "directly positively regulated by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13719,8 +13611,6 @@ InverseObjectProperties( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") AnnotationAssertion( ) AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002025") -AnnotationAssertion( "has_effector_activity") AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") AnnotationAssertion(rdfs:label "has effector activity") SubObjectPropertyOf( ) @@ -13730,9 +13620,7 @@ FunctionalObjectProperty() AnnotationAssertion( "David Osumi-Sutherland") AnnotationAssertion( "<="@en) -AnnotationAssertion( "RO:0002081") AnnotationAssertion( ) -AnnotationAssertion( "before_or_simultaneous_with") AnnotationAssertion(rdfs:comment "Primitive instance level timing relation between events") AnnotationAssertion(rdfs:label "before or simultaneous with"@en) SubObjectPropertyOf( ) @@ -13742,9 +13630,7 @@ SubObjectPropertyOf( "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time.") AnnotationAssertion( ) AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "RO:0002082") AnnotationAssertion( ) -AnnotationAssertion( "simultaneous_with") AnnotationAssertion(rdfs:comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en) AnnotationAssertion(rdfs:label "simultaneous with"@en) SubObjectPropertyOf( ) @@ -13754,9 +13640,7 @@ TransitiveObjectProperty() # Object Property: (ends after) AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "RO:0002086") AnnotationAssertion( ) -AnnotationAssertion( "ends_after") AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) AnnotationAssertion(rdfs:label "ends after"@en) SubObjectPropertyOf( ) @@ -13801,8 +13685,6 @@ AnnotationAssertion( " some ( and some ?Y)") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002100") -AnnotationAssertion( "has_soma_location") AnnotationAssertion(rdfs:label "has soma location"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -13817,8 +13699,6 @@ AnnotationAssertion( " some ( that part_of some ( that has_part some ( that some Y?)))") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002103") -AnnotationAssertion( "synapsed_by") AnnotationAssertion(rdfs:label "synapsed by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13835,8 +13715,6 @@ AnnotationAssertion( ) AnnotationAssertion( " some ( and some ?Y)") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002104") -AnnotationAssertion( "has_plasma_membrane_part") AnnotationAssertion(rdfs:label "has plasma membrane part"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -13852,8 +13730,6 @@ AnnotationAssertion( " some ( that part_of some ( that some ( that some Y?)))") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002120") -AnnotationAssertion( "synapsed_to") AnnotationAssertion(rdfs:comment "N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -13874,8 +13750,6 @@ AnnotationAssertion( " some ( that some Y?)") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002130") -AnnotationAssertion( "has_synaptic_terminal_in") AnnotationAssertion(rdfs:label "has synaptic terminal in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -13911,8 +13785,6 @@ AnnotationAssertion( " some ( that ( some ( that some Y?)))") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002134") -AnnotationAssertion( "innervates") AnnotationAssertion(rdfs:label "innervates"@en) ObjectPropertyDomain( ) @@ -13924,8 +13796,6 @@ AnnotationAssertion( "connected to") AnnotationAssertion( "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002150") -AnnotationAssertion( "continuous_with") AnnotationAssertion(rdfs:label "continuous with"@en) AnnotationAssertion(rdfs:seeAlso "FMA:85972") SubObjectPropertyOf( ) @@ -13939,8 +13809,6 @@ AnnotationAssertion( "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.") AnnotationAssertion( "ancestral_stucture_of") AnnotationAssertion( "evolutionarily_descended_from") -AnnotationAssertion( "RO:0002156") -AnnotationAssertion( "derived_by_descent_from") AnnotationAssertion(rdfs:label "derived by descent from") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13950,9 +13818,7 @@ TransitiveObjectProperty() AnnotationAssertion( ) AnnotationAssertion( "inverse of derived by descent from") -AnnotationAssertion( "RO:0002157") AnnotationAssertion( ) -AnnotationAssertion( "has_derived_by_descendant") AnnotationAssertion(rdfs:label "has derived by descendant") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -13962,8 +13828,6 @@ TransitiveObjectProperty() AnnotationAssertion( ) AnnotationAssertion( "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.") AnnotationAssertion( "Consider obsoleting and merging with child relation, 'in homology relationship with'") -AnnotationAssertion( "RO:0002158") -AnnotationAssertion( "shares_ancestor_with") AnnotationAssertion(rdfs:comment "VBO calls this homologous_to") AnnotationAssertion(rdfs:label "shares ancestor with") SubObjectPropertyOf( ) @@ -13973,8 +13837,6 @@ TransitiveObjectProperty() # Object Property: (serially homologous to) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002159") -AnnotationAssertion( "serially_homologous_to") AnnotationAssertion(rdfs:label "serially homologous to") SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -13991,8 +13853,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002160") -AnnotationAssertion( "only_in_taxon") AnnotationAssertion(rdfs:label "only in taxon") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -14005,9 +13865,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002162") AnnotationAssertion( ) -AnnotationAssertion( "in_taxon") AnnotationAssertion(rdfs:comment "Connects a biological entity to its taxon of origin.") AnnotationAssertion(rdfs:label "in taxon") AnnotationAssertion(rdfs:seeAlso ) @@ -14023,9 +13881,7 @@ AnnotationAssertion( "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy") AnnotationAssertion( "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002163") AnnotationAssertion( ) -AnnotationAssertion( "spatially_disjoint_from") AnnotationAssertion(rdfs:label "spatially disjoint from") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -14035,8 +13891,6 @@ SubObjectPropertyOf( "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).") AnnotationAssertion( "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002170") -AnnotationAssertion( "connected_to") AnnotationAssertion(rdfs:label "connected to"@en) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^xsd:anyURI) @@ -14050,8 +13904,6 @@ AnnotationAssertion( "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).") AnnotationAssertion( "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002176") -AnnotationAssertion( "connects") AnnotationAssertion(rdfs:label "connects"@en) AnnotationAssertion(rdfs:label "connects") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^xsd:anyURI) @@ -14064,8 +13916,6 @@ ObjectPropertyRange( ObjectSomeValues AnnotationAssertion( "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.") AnnotationAssertion( "attached to part of (anatomical structure to anatomical structure)") -AnnotationAssertion( "RO:0002177") -AnnotationAssertion( "attached_to_part_of") AnnotationAssertion(rdfs:label "attached to part of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14077,8 +13927,6 @@ ObjectPropertyRange( "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.") AnnotationAssertion( "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002178") -AnnotationAssertion( "supplies") AnnotationAssertion(rdfs:label "supplies"@en) SubObjectPropertyOf( ) @@ -14087,8 +13935,6 @@ SubObjectPropertyOf( "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.") AnnotationAssertion( "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002179") -AnnotationAssertion( "drains") AnnotationAssertion(rdfs:label "drains"@en) SubObjectPropertyOf( ) @@ -14117,8 +13963,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002202") -AnnotationAssertion( "develops_from") AnnotationAssertion(rdfs:comment "This is the transitive form of the develops from relation") AnnotationAssertion(rdfs:label "develops from"@en) SubObjectPropertyOf( ) @@ -14134,9 +13978,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002203") AnnotationAssertion( ) -AnnotationAssertion( "develops_into") AnnotationAssertion(rdfs:label "develops into"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14149,8 +13991,6 @@ AnnotationAssertion( ) AnnotationAssertion( "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002206") -AnnotationAssertion( "expressed_in") AnnotationAssertion(rdfs:label "expressed in"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14166,9 +14006,7 @@ AnnotationAssertion( ) AnnotationAssertion( "FBbt") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002207") AnnotationAssertion( "has developmental precursor") -AnnotationAssertion( "directly_develops_from") AnnotationAssertion(rdfs:comment "TODO - add child relations from DOS") AnnotationAssertion(rdfs:label "directly develops from"@en) SubObjectPropertyOf( ) @@ -14181,9 +14019,7 @@ ObjectPropertyRange( ObjectUnionOf( ) AnnotationAssertion( "inverse of directly develops from") AnnotationAssertion( "developmental precursor of") -AnnotationAssertion( "RO:0002210") AnnotationAssertion( ) -AnnotationAssertion( "directly_develops_into") AnnotationAssertion(rdfs:label "directly develops into"@en) SubObjectPropertyOf( ) @@ -14297,8 +14133,6 @@ AnnotationAssertion( "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002219") -AnnotationAssertion( "surrounded_by") AnnotationAssertion(rdfs:label "surrounded by"@en) AnnotationAssertion(rdfs:label "surrounded by") SubObjectPropertyOf( ) @@ -14336,9 +14170,7 @@ AnnotationAssertion( "inverse of surrounded by") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002221") AnnotationAssertion( ) -AnnotationAssertion( "surrounds") AnnotationAssertion(rdfs:label "surrounds"@en) SubObjectPropertyOf( ) @@ -14349,9 +14181,7 @@ AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) -AnnotationAssertion( "RO:0002222") AnnotationAssertion( ) -AnnotationAssertion( "temporally_related_to") AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") AnnotationAssertion(rdfs:label "temporally related to"@en) ObjectPropertyDomain( ) @@ -14364,9 +14194,7 @@ AnnotationAssertion( ) AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "Allen") -AnnotationAssertion( "RO:0002223") AnnotationAssertion( ) -AnnotationAssertion( "starts") AnnotationAssertion(rdfs:label "starts"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14396,8 +14224,6 @@ TransitiveObjectProperty() AnnotationAssertion( ) AnnotationAssertion( "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002225") -AnnotationAssertion( "develops_from_part_of") AnnotationAssertion(rdfs:label "develops from part of"@en) SubObjectPropertyOf( ) @@ -14408,8 +14234,6 @@ AnnotationAssertion( ) AnnotationAssertion( "EHDAA2") AnnotationAssertion( "Jonathan Bard, EHDAA2") -AnnotationAssertion( "RO:0002226") -AnnotationAssertion( "develops_in") AnnotationAssertion(rdfs:label "develops in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -14420,9 +14244,7 @@ AnnotationAssertion( "inverse of ends with") AnnotationAssertion( ) AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "RO:0002229") AnnotationAssertion( ) -AnnotationAssertion( "ends") AnnotationAssertion(rdfs:label "ends"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14526,8 +14348,6 @@ InverseObjectProperties( "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.") AnnotationAssertion( "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002252") -AnnotationAssertion( "connecting_branch_of") AnnotationAssertion(rdfs:label "connecting branch of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -14538,9 +14358,7 @@ InverseObjectProperties( "inverse of connecting branch of") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002253") AnnotationAssertion( ) -AnnotationAssertion( "has_connecting_branch") AnnotationAssertion(rdfs:label "has connecting branch") SubObjectPropertyOf( ) @@ -14550,8 +14368,6 @@ AnnotationAssertion( ) AnnotationAssertion( "x has developmental contribution from y iff x has some part z such that z develops from y"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002254") -AnnotationAssertion( "has_developmental_contribution_from") AnnotationAssertion(rdfs:label "has developmental contribution from"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14563,9 +14379,7 @@ ObjectPropertyRange( ) AnnotationAssertion( "inverse of has developmental contribution from") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002255") AnnotationAssertion( ) -AnnotationAssertion( "developmentally_contributes_to") AnnotationAssertion(rdfs:label "developmentally contributes to"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14582,8 +14396,6 @@ AnnotationAssertion( " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)") AnnotationAssertion( "GO:0001759") AnnotationAssertion( "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]") -AnnotationAssertion( "RO:0002256") -AnnotationAssertion( "developmentally_induced_by") AnnotationAssertion(rdfs:label "developmentally induced by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14595,8 +14407,6 @@ ObjectPropertyRange( ) AnnotationAssertion( "Inverse of developmentally induced by"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002257") -AnnotationAssertion( "developmentally_induces") AnnotationAssertion(rdfs:label "developmentally induces"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14608,8 +14418,6 @@ AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion( ) AnnotationAssertion( "In general you should not use this relation to make assertions - use one of the more specific relations below this one") -AnnotationAssertion( "RO:0002258") -AnnotationAssertion( "developmentally_preceded_by") AnnotationAssertion(rdfs:comment "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from") AnnotationAssertion(rdfs:label "developmentally preceded by"@en) SubObjectPropertyOf( ) @@ -14621,9 +14429,7 @@ ObjectPropertyRange( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") -AnnotationAssertion( "RO:0002263") AnnotationAssertion( ) -AnnotationAssertion( "acts_upstream_of") AnnotationAssertion(rdfs:label "acts upstream of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -14632,10 +14438,8 @@ SubObjectPropertyOf( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") -AnnotationAssertion( "RO:0002264") AnnotationAssertion( "affects") AnnotationAssertion( ) -AnnotationAssertion( "acts_upstream_of_or_within") AnnotationAssertion(rdfs:label "acts upstream of or within") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -14647,8 +14451,6 @@ AnnotationAssertion( "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage") AnnotationAssertion( ) AnnotationAssertion( "replaces") -AnnotationAssertion( "RO:0002285") -AnnotationAssertion( "developmentally_replaces") AnnotationAssertion(rdfs:label "developmentally replaces"@en) SubObjectPropertyOf( ) @@ -14657,8 +14459,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "Inverse of developmentally preceded by") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002286") -AnnotationAssertion( "developmentally_succeeded_by") AnnotationAssertion(rdfs:label "developmentally succeeded by"@en) SubObjectPropertyOf( ) @@ -14667,8 +14467,6 @@ SubObjectPropertyOf( "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002287") -AnnotationAssertion( "part_of_developmental_precursor_of") AnnotationAssertion(rdfs:label "part of developmental precursor of"@en) SubObjectPropertyOf( ) @@ -14677,8 +14475,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002292") -AnnotationAssertion( "expresses") AnnotationAssertion(rdfs:label "expresses"@en) SubObjectPropertyOf( ) @@ -14819,8 +14615,6 @@ AnnotationAssertion( "inheres in part of") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002314") -AnnotationAssertion( "characteristic_of_part_of") AnnotationAssertion(rdfs:label "characteristic of part of"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -14849,8 +14643,6 @@ ObjectPropertyRange( "A relationship that holds via some environmental process") AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.") -AnnotationAssertion( "RO:0002320") -AnnotationAssertion( "evolutionarily_related_to") AnnotationAssertion(rdfs:label "evolutionarily related to"@en) # Object Property: (ecologically related to) @@ -14859,9 +14651,7 @@ AnnotationAssertion( "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6") AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions") -AnnotationAssertion( "RO:0002321") AnnotationAssertion( ) -AnnotationAssertion( "ecologically_related_to") AnnotationAssertion(rdfs:label "ecologically related to"@en) # Object Property: (confers advantage in) @@ -14869,9 +14659,7 @@ AnnotationAssertion(rdfs:label "ecol AnnotationAssertion( "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.") AnnotationAssertion( ) AnnotationAssertion( "adapted for") -AnnotationAssertion( "RO:0002322") AnnotationAssertion( ) -AnnotationAssertion( "confers_advantage_in") AnnotationAssertion(rdfs:label "confers advantage in"@en) SubObjectPropertyOf( ) @@ -14881,8 +14669,6 @@ AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002323") -AnnotationAssertion( "mereotopologically_related_to") AnnotationAssertion(rdfs:label "mereotopologically related to"@en) # Object Property: (developmentally related to) @@ -14890,8 +14676,6 @@ AnnotationAssertion(rdfs:label "mere AnnotationAssertion( "A relationship that holds between entities participating in some developmental process (GO:0032502)") AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development") -AnnotationAssertion( "RO:0002324") -AnnotationAssertion( "developmentally_related_to") AnnotationAssertion(rdfs:label "developmentally related to"@en) # Object Property: (enables) @@ -14905,9 +14689,7 @@ AnnotationAssertion( "is catalyzing") AnnotationAssertion( "is executing") AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") -AnnotationAssertion( "RO:0002327") AnnotationAssertion( ) -AnnotationAssertion( "enables") AnnotationAssertion(rdfs:label "enables"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -14918,8 +14700,6 @@ InverseObjectProperties( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") AnnotationAssertion( ) AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") -AnnotationAssertion( "RO:0002328") -AnnotationAssertion( "functionally_related_to") AnnotationAssertion(rdfs:label "functionally related to"@en) # Object Property: (part of structure that is capable of) @@ -14927,8 +14707,6 @@ AnnotationAssertion(rdfs:label "func AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") AnnotationAssertion( ) AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion( "RO:0002329") -AnnotationAssertion( "part_of_structure_that_is_capable_of") AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) SubObjectPropertyOf( ) @@ -14937,8 +14715,6 @@ SubObjectPropertyOf( "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.") AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism") -AnnotationAssertion( "RO:0002330") -AnnotationAssertion( "genomically_related_to") AnnotationAssertion(rdfs:label "genomically related to"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -14949,8 +14725,6 @@ AnnotationAssertion( ) AnnotationAssertion( "actively involved in") AnnotationAssertion( "enables part of") -AnnotationAssertion( "RO:0002331") -AnnotationAssertion( "involved_in") AnnotationAssertion(rdfs:label "involved in"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -14977,9 +14751,7 @@ ObjectPropertyRange( "inverse of enables") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002333") AnnotationAssertion( ) -AnnotationAssertion( "enabled_by") AnnotationAssertion(rdfs:label "enabled by"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -15033,8 +14805,6 @@ SubObjectPropertyOf( "A relationship that holds via some process of localization") AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is a grouping relation.") -AnnotationAssertion( "RO:0002337") -AnnotationAssertion( "related_via_localization_to") AnnotationAssertion(rdfs:label "related via localization to"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15128,8 +14898,6 @@ AnnotationAssertion( "member part of") AnnotationAssertion( "SIO") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002350") -AnnotationAssertion( "member_of") AnnotationAssertion(rdfs:label "member of"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15139,8 +14907,6 @@ InverseObjectProperties( "has member is a mereological relation between a collection and an item.") AnnotationAssertion( "SIO") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002351") -AnnotationAssertion( "has_member") AnnotationAssertion(rdfs:label "has member"@en) SubObjectPropertyOf( ) IrreflexiveObjectProperty() @@ -15149,10 +14915,8 @@ IrreflexiveObjectProperty() AnnotationAssertion( "inverse of has input") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002352") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "input_of") AnnotationAssertion(rdfs:label "input of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15175,8 +14939,6 @@ SubObjectPropertyOf( (formed as result of) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002354") -AnnotationAssertion( "formed_as_result_of") AnnotationAssertion(rdfs:label "formed as result of"@en) SubObjectPropertyOf( ) @@ -15185,9 +14947,7 @@ SubObjectPropertyOf( "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a") AnnotationAssertion( ) AnnotationAssertion( "attached to (anatomical structure to anatomical structure)") -AnnotationAssertion( "RO:0002371") AnnotationAssertion( ) -AnnotationAssertion( "attached_to") AnnotationAssertion(rdfs:label "attached to"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15198,8 +14958,6 @@ SymmetricObjectProperty() AnnotationAssertion( "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to."@en) AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Insertion_(anatomy)"@en) -AnnotationAssertion( "RO:0002372") -AnnotationAssertion( "has_muscle_origin") AnnotationAssertion(rdfs:label "has muscle origin"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -15211,8 +14969,6 @@ ObjectPropertyDomain(Annotation(rdfs:comment "We need to import uberon muscle to AnnotationAssertion( "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone."@en) AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Insertion_(anatomy)"@en) -AnnotationAssertion( "RO:0002373") -AnnotationAssertion( "has_muscle_insertion") AnnotationAssertion(rdfs:label "has muscle insertion"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -15227,8 +14983,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has fused element") -AnnotationAssertion( "RO:0002374") -AnnotationAssertion( "derived_from_ancestral_fusion_of") AnnotationAssertion(rdfs:comment "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B."@en) AnnotationAssertion(rdfs:label "derived from ancestral fusion of"@en) SubObjectPropertyOf( ) @@ -15241,8 +14995,6 @@ AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships") AnnotationAssertion( "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002375") -AnnotationAssertion( "in_branching_relationship_with") AnnotationAssertion(rdfs:label "in branching relationship with"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/170"^^xsd:anyURI) @@ -15263,9 +15015,7 @@ AnnotationAssertion( "http://en.wikipedia.org/wiki/Tributary") AnnotationAssertion( "http://www.medindia.net/glossary/venous_tributary.htm") AnnotationAssertion( "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^xsd:anyURI) -AnnotationAssertion( "RO:0002376") AnnotationAssertion( ) -AnnotationAssertion( "tributary_of") AnnotationAssertion(rdfs:label "tributary of"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "http://en.wikipedia.org/wiki/Tributary"^^xsd:anyURI) @@ -15278,8 +15028,6 @@ AnnotationAssertion( "x spatially_coextensive_with y if and inly if x and y have the same location") AnnotationAssertion( ) AnnotationAssertion( "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios") -AnnotationAssertion( "RO:0002379") -AnnotationAssertion( "spatially_coextensive_with") AnnotationAssertion(rdfs:label "spatially coextensive with"@en) SubObjectPropertyOf( ) @@ -15288,9 +15036,7 @@ SubObjectPropertyOf( "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S") AnnotationAssertion( "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002380") AnnotationAssertion( ) -AnnotationAssertion( "branching_part_of") AnnotationAssertion(rdfs:label "branching part of"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "FMA:85994") @@ -15304,8 +15050,6 @@ ObjectPropertyRange( ObjectSomeValues AnnotationAssertion( ) AnnotationAssertion( "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)."@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002384") -AnnotationAssertion( "has_developmental_potential_involving") AnnotationAssertion(rdfs:label "has developmental potential involving"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15316,8 +15060,6 @@ ObjectPropertyRange( ) AnnotationAssertion( "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002385") -AnnotationAssertion( "has_potential_to_developmentally_contribute_to") AnnotationAssertion(rdfs:label "has potential to developmentally contribute to"@en) SubObjectPropertyOf( ) @@ -15326,8 +15068,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002386") -AnnotationAssertion( "has_potential_to_developmentally_induce") AnnotationAssertion(rdfs:label "has potential to developmentally induce"@en) SubObjectPropertyOf( ) @@ -15336,8 +15076,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "x has the potential to develop into y iff x develops into y or if x is capable of developing into y"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002387") -AnnotationAssertion( "has_potential_to_develop_into") AnnotationAssertion(rdfs:label "has potential to develop into"@en) SubObjectPropertyOf( ) @@ -15346,8 +15084,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y"@en) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002388") -AnnotationAssertion( "has_potential_to_directly_develop_into") AnnotationAssertion(rdfs:label "has potential to directly develop into"@en) SubObjectPropertyOf( ) @@ -15386,8 +15122,6 @@ AnnotationAssertion( ) AnnotationAssertion( "indirectly activates") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002407") -AnnotationAssertion( "indirectly_positively_regulates") AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -15400,8 +15134,6 @@ AnnotationAssertion( ) AnnotationAssertion( "indirectly inhibits") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002409") -AnnotationAssertion( "indirectly_negatively_regulates") AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -15428,8 +15160,6 @@ For the third, we consider the effect of the upstream process on the output(s) o Each of these 3 primitives can be composed to yield a cross-product of different relation types.") AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion( "RO:0002410") -AnnotationAssertion( "causally_related_to") AnnotationAssertion(rdfs:label "causally related to"@en) # Object Property: (causally upstream of) @@ -15496,8 +15226,6 @@ TransitiveObjectProperty() AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002428") -AnnotationAssertion( "involved_in_regulation_of") AnnotationAssertion(rdfs:label "involved in regulation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15507,8 +15235,6 @@ SubObjectPropertyOf( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002429") -AnnotationAssertion( "involved_in_positive_regulation_of") AnnotationAssertion(rdfs:label "involved in positive regulation of") SubObjectPropertyOf( ) @@ -15517,8 +15243,6 @@ SubObjectPropertyOf( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002430") -AnnotationAssertion( "involved_in_negative_regulation_of") AnnotationAssertion(rdfs:label "involved in negative regulation of") SubObjectPropertyOf( ) @@ -15528,8 +15252,6 @@ AnnotationAssertion( "OWL does not allow defining object properties via a Union") AnnotationAssertion( ) AnnotationAssertion( "involved in or reguates") -AnnotationAssertion( "RO:0002431") -AnnotationAssertion( "involved_in_or_involved_in_regulation_of") AnnotationAssertion(rdfs:label "involved in or involved in regulation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15541,9 +15263,7 @@ AnnotationAssertion( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") AnnotationAssertion( ) AnnotationAssertion( "executes activity in") -AnnotationAssertion( "RO:0002432") AnnotationAssertion( "enables activity in") -AnnotationAssertion( "is_active_in") AnnotationAssertion(rdfs:comment "") AnnotationAssertion(rdfs:label "is active in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Is_active_in"^^xsd:anyURI) @@ -15554,8 +15274,6 @@ SubObjectPropertyOf( "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002433") -AnnotationAssertion( "contributes_to_morphology_of") AnnotationAssertion(rdfs:label "contributes to morphology of") SubObjectPropertyOf( ) @@ -15566,10 +15284,8 @@ AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") AnnotationAssertion( ) AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") -AnnotationAssertion( "RO:0002434") AnnotationAssertion( "in pairwise interaction with") AnnotationAssertion( ) -AnnotationAssertion( "interacts_with") AnnotationAssertion(rdfs:label "interacts with") AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) @@ -15583,8 +15299,6 @@ AnnotationAssertion( ) AnnotationAssertion( "binds") AnnotationAssertion( "molecularly binds with") -AnnotationAssertion( "RO:0002436") -AnnotationAssertion( "molecularly_interacts_with") AnnotationAssertion(rdfs:label "molecularly interacts with") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) @@ -15596,8 +15310,6 @@ SymmetricObjectProperty() AnnotationAssertion( "Axiomatization to GO to be added later") AnnotationAssertion( ) AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") -AnnotationAssertion( "RO:0002447") -AnnotationAssertion( "phosphorylates") AnnotationAssertion(rdfs:label "phosphorylates") SubObjectPropertyOf( ) @@ -15608,9 +15320,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002448") AnnotationAssertion( "molecularly controls") -AnnotationAssertion( "directly_regulates_activity_of") AnnotationAssertion(rdfs:label "directly regulates activity of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15624,9 +15334,7 @@ For example, A and B may be gene products and binding of B by A negatively regul AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "directly inhibits") -AnnotationAssertion( "RO:0002449") AnnotationAssertion( "molecularly decreases activity of") -AnnotationAssertion( "directly_negatively_regulates_activity_of") AnnotationAssertion(rdfs:label "directly negatively regulates activity of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15639,9 +15347,7 @@ For example, A and B may be gene products and binding of B by A positively regul AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "directly activates") -AnnotationAssertion( "RO:0002450") AnnotationAssertion( "molecularly increases activity of") -AnnotationAssertion( "directly_positively_regulates_activity_of") AnnotationAssertion(rdfs:label "directly positively regulates activity of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15651,8 +15357,6 @@ ObjectPropertyRange( ) AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") -AnnotationAssertion( "RO:0002464") -AnnotationAssertion( "helper_property_(not_for_use_in_curation)") AnnotationAssertion(rdfs:label "helper property (not for use in curation)") # Object Property: (composed primarily of) @@ -15662,9 +15366,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002473") AnnotationAssertion( ) -AnnotationAssertion( "composed_primarily_of") AnnotationAssertion(rdfs:label "composed primarily of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15676,8 +15378,6 @@ AnnotationAssertion( "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d") AnnotationAssertion( ) AnnotationAssertion( "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.") -AnnotationAssertion( "RO:0002476") -AnnotationAssertion( "child_nucleus_of") AnnotationAssertion(rdfs:label "child nucleus of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15687,8 +15387,6 @@ ObjectPropertyRange( "A child nucleus relationship in which the cells are part of a hermaphroditic organism") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002477") -AnnotationAssertion( "child_nucleus_of_in_hermaphrodite") AnnotationAssertion(rdfs:label "child nucleus of in hermaphrodite") SubObjectPropertyOf( ) @@ -15696,8 +15394,6 @@ SubObjectPropertyOf( "A child nucleus relationship in which the cells are part of a male organism") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002478") -AnnotationAssertion( "child_nucleus_of_in_male") AnnotationAssertion(rdfs:label "child nucleus of in male") SubObjectPropertyOf( ) @@ -15705,9 +15401,7 @@ SubObjectPropertyOf( "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002479") AnnotationAssertion( ) -AnnotationAssertion( "has_part_that_occurs_in") AnnotationAssertion(rdfs:label "has part that occurs in") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15715,8 +15409,6 @@ ObjectPropertyRange( (is kinase activity) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002481") -AnnotationAssertion( "is_kinase_activity") AnnotationAssertion(rdfs:label "is kinase activity") SubObjectPropertyOf( ) @@ -15724,8 +15416,6 @@ SubObjectPropertyOf( "See notes for inverse relation") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002485") -AnnotationAssertion( "receives_input_from") AnnotationAssertion(rdfs:label "receives input from") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15734,8 +15424,6 @@ InverseObjectProperties( "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002486") -AnnotationAssertion( "sends_output_to") AnnotationAssertion(rdfs:label "sends output to") SubObjectPropertyOf( ) @@ -15743,8 +15431,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.") -AnnotationAssertion( "RO:0002487") -AnnotationAssertion( "relation_between_physical_entity_and_a_process_or_stage") AnnotationAssertion(rdfs:label "relation between physical entity and a process or stage") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15753,8 +15439,6 @@ ObjectPropertyRange( "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002488") -AnnotationAssertion( "existence_starts_during") AnnotationAssertion(rdfs:label "existence starts during") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15763,8 +15447,6 @@ SubObjectPropertyOf( "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002489") -AnnotationAssertion( "existence_starts_with") AnnotationAssertion(rdfs:label "existence starts with") SubObjectPropertyOf( ) @@ -15772,8 +15454,6 @@ SubObjectPropertyOf( "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002490") -AnnotationAssertion( "existence_overlaps") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence overlaps") SubObjectPropertyOf( ) @@ -15782,9 +15462,7 @@ SubObjectPropertyOf( "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002491") AnnotationAssertion( "exists during") -AnnotationAssertion( "existence_starts_and_ends_during") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence starts and ends during") SubObjectPropertyOf( ) @@ -15794,8 +15472,6 @@ SubObjectPropertyOf( "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002492") -AnnotationAssertion( "existence_ends_during") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends during") SubObjectPropertyOf( ) @@ -15805,8 +15481,6 @@ SubObjectPropertyOf( "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002493") -AnnotationAssertion( "existence_ends_with") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends with") SubObjectPropertyOf( ) @@ -15815,8 +15489,6 @@ SubObjectPropertyOf( "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002494") -AnnotationAssertion( "transformation_of") AnnotationAssertion(rdfs:label "transformation of") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15826,8 +15498,6 @@ TransitiveObjectProperty() AnnotationAssertion( "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002495") -AnnotationAssertion( "immediate_transformation_of") AnnotationAssertion(rdfs:label "immediate transformation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15836,8 +15506,6 @@ SubObjectPropertyOf( "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002496") -AnnotationAssertion( "existence_starts_during_or_after") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence starts during or after") SubObjectPropertyOf( ) @@ -15846,8 +15514,6 @@ SubObjectPropertyOf( "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002497") -AnnotationAssertion( "existence_ends_during_or_before") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends during or before") SubObjectPropertyOf( ) @@ -15856,8 +15522,6 @@ SubObjectPropertyOf( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002500") -AnnotationAssertion( "causal_agent_in_process") AnnotationAssertion(rdfs:label "causal agent in process") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15868,8 +15532,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion( "RO:0002501") -AnnotationAssertion( "causal_relation_between_processes") AnnotationAssertion(rdfs:label "causal relation between processes") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15878,8 +15540,6 @@ ObjectPropertyRange( (depends on) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002502") -AnnotationAssertion( "depends_on") AnnotationAssertion(rdfs:label "depends on") AnnotationAssertion(rdfs:seeAlso ) @@ -15889,8 +15549,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion( "RO:0002506") -AnnotationAssertion( "causal_relation_between_entities") AnnotationAssertion(rdfs:label "causal relation between entities") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15903,8 +15561,6 @@ AnnotationAssertion( ) AnnotationAssertion( "has supporting framework") AnnotationAssertion( "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).") -AnnotationAssertion( "RO:0002551") -AnnotationAssertion( "has_skeleton") AnnotationAssertion(rdfs:label "has skeleton") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15918,8 +15574,6 @@ ObjectPropertyRange(Annotation( "Thi AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally influenced by (entity-centric)") -AnnotationAssertion( "RO:0002559") -AnnotationAssertion( "causally_influenced_by") AnnotationAssertion(rdfs:label "causally influenced by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15927,8 +15581,6 @@ InverseObjectProperties( (interaction relation helper property) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002563") -AnnotationAssertion( "interaction_relation_helper_property") AnnotationAssertion(rdfs:label "interaction relation helper property") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) @@ -15937,8 +15589,6 @@ SubObjectPropertyOf( (molecular interaction relation helper property) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002564") -AnnotationAssertion( "molecular_interaction_relation_helper_property") AnnotationAssertion(rdfs:label "molecular interaction relation helper property") SubObjectPropertyOf( ) @@ -15964,8 +15614,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally influences (entity-centric)") -AnnotationAssertion( "RO:0002566") -AnnotationAssertion( "causally_influences") AnnotationAssertion(rdfs:label "causally influences") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15976,8 +15624,6 @@ ObjectPropertyRange( "A relation that holds between elements of a musculoskeletal system or its analogs.") AnnotationAssertion( ) AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.") -AnnotationAssertion( "RO:0002567") -AnnotationAssertion( "biomechanically_related_to") AnnotationAssertion(rdfs:label "biomechanically related to") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15988,8 +15634,6 @@ ObjectPropertyRange( "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.") AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Antagonist_(muscle)") -AnnotationAssertion( "RO:0002568") -AnnotationAssertion( "has_muscle_antagonist") AnnotationAssertion(rdfs:label "has muscle antagonist") SubObjectPropertyOf( ) @@ -15997,10 +15641,8 @@ SubObjectPropertyOf( "inverse of branching part of") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002569") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "has_branching_part") AnnotationAssertion(rdfs:label "has branching part") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16012,9 +15654,7 @@ AnnotationAssertion( ) AnnotationAssertion( "UBERON:cjm") AnnotationAssertion( "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.") -AnnotationAssertion( "RO:0002570") AnnotationAssertion( ) -AnnotationAssertion( "conduit_for") AnnotationAssertion(rdfs:label "conduit for") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16025,9 +15665,7 @@ ObjectPropertyRange( "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002571") AnnotationAssertion( ) -AnnotationAssertion( "lumen_of") AnnotationAssertion(rdfs:label "lumen of") SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -16036,9 +15674,7 @@ ObjectPropertyRange( "s is luminal space of x iff s is lumen_of x and s is an immaterial entity") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002572") AnnotationAssertion( ) -AnnotationAssertion( "luminal_space_of") AnnotationAssertion(rdfs:label "luminal space of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16047,9 +15683,7 @@ ObjectPropertyDomain( "inverse of has skeleton") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002576") AnnotationAssertion( ) -AnnotationAssertion( "skeleton_of") AnnotationAssertion(rdfs:label "skeleton of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16078,8 +15712,6 @@ SubObjectPropertyOf( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002584") -AnnotationAssertion( "has_part_structure_that_is_capable_of") AnnotationAssertion(rdfs:label "has part structure that is capable of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16087,8 +15719,6 @@ SubObjectPropertyOf( (results in breakdown of) AnnotationAssertion( "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p") -AnnotationAssertion( "RO:0002586") -AnnotationAssertion( "results_in_breakdown_of") AnnotationAssertion(rdfs:label "results in breakdown of") SubObjectPropertyOf( ) @@ -16132,8 +15762,6 @@ AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002595") -AnnotationAssertion( "causal_relation_between_material_entity_and_a_process") AnnotationAssertion(rdfs:label "causal relation between material entity and a process") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16144,8 +15772,6 @@ ObjectPropertyRange( "pyrethroid -> growth") AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002596") -AnnotationAssertion( "capable_of_regulating") AnnotationAssertion(rdfs:label "capable of regulating") SubObjectPropertyOf( ) @@ -16153,8 +15779,6 @@ SubObjectPropertyOf( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002597") -AnnotationAssertion( "capable_of_negatively_regulating") AnnotationAssertion(rdfs:label "capable of negatively regulating") SubObjectPropertyOf( ) @@ -16163,8 +15787,6 @@ SubObjectPropertyOf( "renin -> arteriolar smooth muscle contraction") AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002598") -AnnotationAssertion( "capable_of_positively_regulating") AnnotationAssertion(rdfs:label "capable of positively regulating") SubObjectPropertyOf( ) @@ -16179,14 +15801,6 @@ AnnotationAssertion( "process has causal agent") SubObjectPropertyOf( ) -# Object Property: (correlated with) - -AnnotationAssertion( "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.") -AnnotationAssertion( "Groups both positive and negative correlation") -AnnotationAssertion( "RO:0002610") -AnnotationAssertion( "correlated_with") -AnnotationAssertion(rdfs:label "correlated with") - # Object Property: (directly positively regulates) AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") @@ -16301,8 +15915,6 @@ SubObjectPropertyOf( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") AnnotationAssertion( ) AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0004031") -AnnotationAssertion( "enables_subfunction") AnnotationAssertion(rdfs:label "enables subfunction") SubObjectPropertyOf( ) @@ -16311,9 +15923,7 @@ SubObjectPropertyOf( ) AnnotationAssertion( ) AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0004032") AnnotationAssertion( ) -AnnotationAssertion( "acts_upstream_of_or_within,_positive_effect") AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16323,9 +15933,7 @@ SubObjectPropertyOf( ) AnnotationAssertion( ) AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0004033") AnnotationAssertion( ) -AnnotationAssertion( "acts_upstream_of_or_within,_negative_effect") AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16336,9 +15944,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0004034") AnnotationAssertion( ) -AnnotationAssertion( "acts_upstream_of,_positive_effect") AnnotationAssertion(rdfs:label "acts upstream of, positive effect") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16350,9 +15956,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0004035") AnnotationAssertion( ) -AnnotationAssertion( "acts_upstream_of,_negative_effect") AnnotationAssertion(rdfs:label "acts upstream of, negative effect") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16363,8 +15967,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0004046") -AnnotationAssertion( "causally_upstream_of_or_within,_negative_effect") AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16374,8 +15976,6 @@ SubObjectPropertyOf( ) AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0004047") -AnnotationAssertion( "causally_upstream_of_or_within,_positive_effect") AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -16384,8 +15984,6 @@ SubObjectPropertyOf( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0011002") -AnnotationAssertion( "regulates_activity_of") AnnotationAssertion(rdfs:label "regulates activity of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16427,8 +16025,6 @@ SubObjectPropertyOf( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0012011") -AnnotationAssertion( "indirectly_causally_upstream_of") AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) SubObjectPropertyOf( ) @@ -16437,8 +16033,6 @@ SubObjectPropertyOf( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0012012") -AnnotationAssertion( "indirectly_regulates") AnnotationAssertion(rdfs:label "indirectly regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16448,17 +16042,13 @@ SubObjectPropertyOf( "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.") AnnotationAssertion( ) AnnotationAssertion( "2020-07-17T09:26:52Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0013001") AnnotationAssertion( "has synaptic input or output in") -AnnotationAssertion( "has_synaptic_IO_in_region") AnnotationAssertion(rdfs:label "has synaptic IO in region"@en) SubObjectPropertyOf( ) # Object Property: (different in magnitude relative to) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") -AnnotationAssertion( "RO:0015006") -AnnotationAssertion( "different_in_magnitude_relative_to") AnnotationAssertion(rdfs:label "different in magnitude relative to") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16466,8 +16056,6 @@ ObjectPropertyRange( (increased in magnitude relative to) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") -AnnotationAssertion( "RO:0015007") -AnnotationAssertion( "increased_in_magnitude_relative_to") AnnotationAssertion(rdfs:comment "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.") AnnotationAssertion(rdfs:label "increased in magnitude relative to") SubObjectPropertyOf( ) @@ -16477,8 +16065,6 @@ ObjectPropertyRange( (has cross section) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.") -AnnotationAssertion( "RO:0015011") -AnnotationAssertion( "has_cross_section") AnnotationAssertion(rdfs:comment "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.") AnnotationAssertion(rdfs:label "has cross section") @@ -16488,8 +16074,6 @@ AnnotationAssertion( "PMID:19243617") "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0015015") -AnnotationAssertion( "has_high_plasma_membrane_amount") AnnotationAssertion(rdfs:label "has high plasma membrane amount") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16500,8 +16084,6 @@ AnnotationAssertion( "PMID:19243617") "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0015016") -AnnotationAssertion( "has_low_plasma_membrane_amount") AnnotationAssertion(rdfs:label "has low plasma membrane amount") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16514,24 +16096,10 @@ AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") -AnnotationAssertion( "RO:0017001") -AnnotationAssertion( "device_utilizes_material") AnnotationAssertion(rdfs:label "device utilizes material"@en) -# Object Property: (positively correlated with) - -AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion( "directly correlated with"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0017003") -AnnotationAssertion( "positively_correlated_with") -AnnotationAssertion(rdfs:label "positively correlated with"@en) -SubObjectPropertyOf( ) -SymmetricObjectProperty() -ReflexiveObjectProperty() - # Object Property: (regulates characteristic) AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") @@ -16890,22 +16458,6 @@ AnnotationAssertion( "CARO:0000000") AnnotationAssertion(rdfs:label "anatomical entity") -# Class: (anatomical structure) - -AnnotationAssertion(Annotation( "CC:DOS") "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") -AnnotationAssertion( "spatial") -AnnotationAssertion( "CARO:0000003") -AnnotationAssertion(rdfs:label "anatomical structure") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion(Annotation( "CC:DOS") "An anatomical entity that has mass.") -AnnotationAssertion( "spatial") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) - # Class: (electron) AnnotationAssertion( "Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.") @@ -30961,6 +30513,7 @@ AnnotationAssertion( "mature oocyte") AnnotationAssertion( "ovum") AnnotationAssertion(rdfs:label "egg cell") +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Egg_cell.svg"^^xsd:anyURI) SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -31043,9 +30596,9 @@ AnnotationAssertion( "FMA:86475") AnnotationAssertion( "MESH:D006412") AnnotationAssertion( "VHOG:0001485") -AnnotationAssertion( "HSC") AnnotationAssertion( "blood forming stem cell") AnnotationAssertion( "hemopoietic stem cell") +AnnotationAssertion(Annotation( ) "HSC") AnnotationAssertion( "colony forming unit hematopoietic") AnnotationAssertion( ) AnnotationAssertion( ) @@ -31060,8 +30613,8 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:add") Annotation( "ISBN:0721601464") "A progenitor cell committed to the erythroid lineage.") AnnotationAssertion( "BTO:0004911") -AnnotationAssertion( "BFU-E") -AnnotationAssertion( "CFU-E") +AnnotationAssertion(Annotation( ) "BFU-E") +AnnotationAssertion(Annotation( ) "CFU-E") AnnotationAssertion( "blast forming unit erythroid") AnnotationAssertion( "burst forming unit erythroid") AnnotationAssertion( "colony forming unit erythroid") @@ -31088,7 +30641,7 @@ DisjointClasses( "GOC:add") Annotation( "PMID:1104740") Annotation( "http://en.wikipedia.org/wiki/Monoblast") Annotation( "http://www.copewithcytokines.de") "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.") AnnotationAssertion( "CALOHA:TS-1195") AnnotationAssertion( "FMA:83553") -AnnotationAssertion( "CFU-M") +AnnotationAssertion(Annotation( ) "CFU-M") AnnotationAssertion( "colony forming unit macrophage") AnnotationAssertion( "colony forming unit monocyte") AnnotationAssertion( "monocyte stem cell") @@ -31114,10 +30667,10 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0878932437") Annotation( "MESH:D023461") "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0004730") -AnnotationAssertion(Annotation( "ISBN:0878932437") "CMP") AnnotationAssertion( "common myeloid precursor") -AnnotationAssertion(Annotation( "ISBN:0878932437") "CFU-GEMM") -AnnotationAssertion(Annotation( "ISBN:0878932437") "CFU-S") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CMP") AnnotationAssertion(Annotation( "ISBN:0878932437") "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte") AnnotationAssertion(Annotation( "ISBN:0878932437") "multipotential myeloid stem cell") AnnotationAssertion(Annotation( "ISBN:0878932437") "myeloid stem cell") @@ -31154,11 +30707,11 @@ DisjointClasses( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "PMID:10407577") Annotation( "PMID:16551251") "A oligopotent progenitor cell committed to the lymphoid lineage.") AnnotationAssertion( ) -AnnotationAssertion( "CLP") AnnotationAssertion( "common lymphocyte precursor") AnnotationAssertion( "common lymphocyte progenitor") AnnotationAssertion( "common lymphoid precursor") -AnnotationAssertion( "ELP") +AnnotationAssertion(Annotation( ) "CLP") +AnnotationAssertion(Annotation( ) "ELP") AnnotationAssertion( "committed lymphopoietic stem cell") AnnotationAssertion( "early lymphocyte progenitor") AnnotationAssertion( "lymphoid stem cell") @@ -31309,6 +30862,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell") +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Epithelial_cells.svg"^^xsd:anyURI) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -31532,7 +31086,6 @@ AnnotationAssertion( "sensory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (bipolar neuron) @@ -31724,12 +31277,12 @@ AnnotationAssertion(Annotation( "BTO:0002625") AnnotationAssertion( "BTO:0003298") AnnotationAssertion( "FMA:70546") -AnnotationAssertion( "BMSC") AnnotationAssertion( "bone marrow stromal cells") AnnotationAssertion( "colony-forming unit-fibroblast") AnnotationAssertion(Annotation( "PMID:11378515") "marrow stromal cells") -AnnotationAssertion( "CFU-F") -AnnotationAssertion(Annotation( "PMID:11378515") "MSC") +AnnotationAssertion(Annotation( ) "BMSC") +AnnotationAssertion(Annotation( ) "CFU-F") +AnnotationAssertion(Annotation( "PMID:11378515") Annotation( ) "MSC") AnnotationAssertion( "mesenchymal precursor cell") AnnotationAssertion(Annotation( "MESH:D044982") Annotation( ) "mesenchymal progenitor cells") AnnotationAssertion( "mesenchymal stem cell") @@ -31799,7 +31352,7 @@ SubClassOf( ObjectSomeValuesFrom( (professional antigen presenting cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response.") -AnnotationAssertion( "APC") +AnnotationAssertion(Annotation( ) "APC") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells.") AnnotationAssertion(rdfs:label "professional antigen presenting cell") @@ -31943,12 +31496,6 @@ AnnotationAssertion(rdfs:label "gobl SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (acid secreting cell) - -AnnotationAssertion(rdfs:label "acid secreting cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) - # Class: (parietal cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0517223651") "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl.") @@ -31957,8 +31504,9 @@ AnnotationAssertion( "oxyntic cell") AnnotationAssertion(rdfs:label "parietal cell") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocrine cell) @@ -32197,6 +31745,7 @@ AnnotationAssertion( "muscle fiber") AnnotationAssertion( "myocyte") AnnotationAssertion(rdfs:label "muscle cell") +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Muscle_cells.svg"^^xsd:anyURI) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -32261,6 +31810,15 @@ AnnotationAssertion(rdfs:label "sens EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (pain receptor cell) + +AnnotationAssertion(Annotation( "MESH:D009619") "The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings.") +AnnotationAssertion(Annotation(rdfs:seeAlso "https://meshb.nlm.nih.gov/record/ui?ui=D009619"^^xsd:anyURI) "nociceptor") +AnnotationAssertion(Annotation(rdfs:seeAlso "https://www.thefreedictionary.com/nocireceptor"^^xsd:anyURI) "nocireceptor") +AnnotationAssertion(rdfs:comment "Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship") +AnnotationAssertion(rdfs:label "pain receptor cell") +SubClassOf( ) + # Class: (mechanoreceptor cell) AnnotationAssertion(Annotation( "MESH:D008465") "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.") @@ -32320,6 +31878,7 @@ AnnotationAssertion( "CALOHA:TS-0868") AnnotationAssertion( "FMA:86740") AnnotationAssertion(rdfs:label "photoreceptor cell") +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -32738,7 +32297,7 @@ EquivalentClasses( ObjectIntersection # Class: (migratory neural crest cell) -AnnotationAssertion(Annotation( "MESH:A16.254.600") "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.") +AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2015.02.017") "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.") AnnotationAssertion( "FMA:86667") AnnotationAssertion(rdfs:label "migratory neural crest cell") SubClassOf( ) @@ -32876,6 +32435,7 @@ AnnotationAssertion( "vascular associated smooth muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (epidermal cell) @@ -33370,11 +32930,13 @@ DisjointClasses( "GOC:tfm") Annotation( "ISBN:0323052908") "A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.") AnnotationAssertion( ) AnnotationAssertion( "FMA:83043") -AnnotationAssertion( "plasmidotrophoblast") -AnnotationAssertion( "syncytial trophoblast") -AnnotationAssertion( "syntrophoblast") +AnnotationAssertion(Annotation( "PMID:11787150") "syncytial trophoblast cell") +AnnotationAssertion(Annotation( "PMID:21733368") "syncytiotrophoblastic cell") +AnnotationAssertion( "plasmidotrophoblast cell") +AnnotationAssertion( "syntrophoblast cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "syncytiotrophoblast cell") +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/2100") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -33410,7 +32972,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.") AnnotationAssertion(rdfs:label "neuron") -SubClassOf( ) +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Neuron_cells.svg"^^xsd:anyURI) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -33447,7 +33009,7 @@ DisjointClasses( (proerythroblast) -AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "MESH:A11.118.290.350.200") Annotation( "PMID:1638021") "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.") +AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMID:1638021") "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.") AnnotationAssertion( "FMA:83518") AnnotationAssertion(Annotation( "ISBN:0721601464") "rubriblast") AnnotationAssertion( "pronormoblast") @@ -33463,6 +33025,7 @@ AnnotationAssertion( "metazoan cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "animal cell") +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Animal_cells.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -33563,12 +33126,12 @@ DisjointClasses( "GOC:amm") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "GO_REF:0000031") Annotation( "ISBN:0721601464") Annotation( "MESH:D055014") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") Annotation( "PMID:16551251") Annotation( "PMID:16647566") Annotation( "http://en.wikipedia.org/wiki/CFU-GM") Annotation( "http://www.copewithcytokines.de") "A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.") AnnotationAssertion( ) AnnotationAssertion(Annotation( "http://www.copewithcytokines.de") "CFU-C , Colony forming unit in culture") -AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") "CFU-GM") -AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") "GMP") AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") "colony forming unit granulocyte macrophage") AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") "granulocyte-macrophage progenitor") AnnotationAssertion( "granulocyte/monocyte precursor") AnnotationAssertion( "granulocyte/monocyte progenitor") +AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") Annotation( ) "CFU-GM") +AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") Annotation( ) "GMP") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.") AnnotationAssertion(rdfs:label "granulocyte monocyte progenitor cell") @@ -33643,9 +33206,10 @@ SubClassOf( ObjectSomeValuesFrom( (amine precursor uptake and decarboxylation cell) -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") Annotation( "MESH:A11.070") "A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell.") AnnotationAssertion( "BTO:0003866") AnnotationAssertion( "FMA:83114") +AnnotationAssertion( "MESH:D001078") AnnotationAssertion( "APUD cell") AnnotationAssertion(rdfs:label "amine precursor uptake and decarboxylation cell") SubClassOf( ) @@ -33731,7 +33295,7 @@ SubClassOf( ObjectSomeValuesFrom( (odontoclast) -AnnotationAssertion(Annotation( "GOC:add") Annotation( "MESH:A11.329.679") "A specialized osteoclast associated with the absorption and removal of cementum.") +AnnotationAssertion(Annotation( "GOC:add") "A specialized osteoclast associated with the absorption and removal of cementum.") AnnotationAssertion( "BTO:0002516") AnnotationAssertion( "FMA:83027") AnnotationAssertion(rdfs:label "odontoclast") @@ -33747,8 +33311,8 @@ EquivalentClasses( ObjectIntersection # Class: (enucleate erythrocyte) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") "An erythrocyte lacking a nucleus.") -AnnotationAssertion( "RBC") AnnotationAssertion( "red blood cell") +AnnotationAssertion(Annotation( ) "RBC") AnnotationAssertion(rdfs:label "enucleate erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -33815,10 +33379,17 @@ SubClassOf( ObjectSomeValuesFrom( (olfactory granule cell) -AnnotationAssertion(Annotation( "GOC:mah") "Granule cell that is part of the olfactory bulb.") +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "doi:10.1038/s41598-018-27692-8") "A granule cell that has a soma located in an olfactory bulb granule cell layer. An olfactory granule cell is an interneuron that lacks an axon, makes reciprocal dendro-dendritic synapses with mitral cells and tufted cells and is involved in the fine spatio-temporal tuning of the responses of these principal olfactory bulb neurons to odors.") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-018-27692-8") "olfactory bulb granule cell") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-018-27692-8") rdfs:comment "Granule cells are the most abundant neuronal population in the olfactory bulb and are continuously renewed throughout life.") AnnotationAssertion(rdfs:label "olfactory granule cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transporting cell) @@ -34154,6 +33725,8 @@ SubClassOf( (choroid plexus epithelial cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") Annotation( "JB:jb") Annotation( "PMID:9550134") "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord.") +AnnotationAssertion( "2023-08-04T08:48:30Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "DOI:10.1101/2022.10.12.511898") "choroid plexus cell") AnnotationAssertion( "FMA:70549") AnnotationAssertion( "epithelial cell of choroid plexus") AnnotationAssertion(rdfs:label "choroid plexus epithelial cell") @@ -34858,6 +34431,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "perivascular macrophage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (myeloid suppressor cell) @@ -34903,10 +34477,10 @@ SubClassOf( ObjectSomeValuesFrom( (early lymphoid progenitor) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:pam") Annotation( "GOC:tfm") Annotation( "GO_REF:0000031") Annotation( "PMID:19022770") "A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative.") -AnnotationAssertion( "ELP") -AnnotationAssertion( "LMPP") AnnotationAssertion( "lymphoid-primed multipotent progenitor") -AnnotationAssertion(Annotation( "PMID:18371378") "GMLP") +AnnotationAssertion(Annotation( ) "ELP") +AnnotationAssertion(Annotation( "PMID:18371378") Annotation( ) "GMLP") +AnnotationAssertion(Annotation( ) "LMPP") AnnotationAssertion(rdfs:comment "Markers are associated with mouse cells. ELP transcription factors include E2A-positive, Ikaros-positive, EBF-negative, Pax5-negative, PU.1-negative.") AnnotationAssertion(rdfs:label "early lymphoid progenitor") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -35455,10 +35029,10 @@ SubClassOf( (common myeloid progenitor, CD34-positive) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "ISBN:0878932437") Annotation( "PMCID:PMC2212039") Annotation( "PMID:10724173") Annotation( "PMID:16551251") Annotation( "PMID:16647566") "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1.") -AnnotationAssertion(Annotation( "ISBN:0878932437") "CMP") AnnotationAssertion( "common myeloid precursor, CD34-positive") -AnnotationAssertion(Annotation( "ISBN:0878932437") "CFU-GEMM") -AnnotationAssertion(Annotation( "ISBN:0878932437") "CFU-S") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CMP") AnnotationAssertion(Annotation( "ISBN:0878932437") "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte") AnnotationAssertion(Annotation( "ISBN:0878932437") "multipotential myeloid stem cell") AnnotationAssertion(Annotation( "ISBN:0878932437") "myeloid stem cell") @@ -35483,8 +35057,8 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:add") Annotation( "ISBN:0721601464") "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).") AnnotationAssertion( "BTO:0004911") -AnnotationAssertion( "BFU-E") -AnnotationAssertion( "CFU-E") +AnnotationAssertion(Annotation( ) "BFU-E") +AnnotationAssertion(Annotation( ) "CFU-E") AnnotationAssertion( "blast forming unit erythroid") AnnotationAssertion( "burst forming unit erythroid") AnnotationAssertion( "colony forming unit erythroid") @@ -36835,7 +36409,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-08-30T02:00:42Z") AnnotationAssertion( "FMA:86577") -AnnotationAssertion(Annotation( "PMID:18442648") Annotation( ) "HpSC") +AnnotationAssertion(Annotation( "PMID:18442648") Annotation( ) "HpSC") AnnotationAssertion(rdfs:label "hepatic stem cell") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/800") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -37983,11 +37557,11 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2010-11-10T02:51:34Z") -AnnotationAssertion(Annotation( "PMID:24133281") "O-2A/OPC") -AnnotationAssertion(Annotation( "PMID:11756508") "O2A/OPC") AnnotationAssertion(Annotation( "PMID:2253328") "oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell") AnnotationAssertion(Annotation( ) Annotation( "PMID:24133281") "oligodendrocyte/type-2 astrocyte progenitor cell") AnnotationAssertion( "MESH:D000073637") +AnnotationAssertion(Annotation( "PMID:24133281") Annotation( ) "O-2A/OPC") +AnnotationAssertion(Annotation( "PMID:11756508") Annotation( ) "O2A/OPC") AnnotationAssertion( ) AnnotationAssertion(Annotation( "ISBN:9780702028991") Annotation( "PMID:10704434") Annotation( "PMID:2182078") rdfs:comment "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991).") AnnotationAssertion(rdfs:label "oligodendrocyte precursor cell") @@ -39166,8 +38740,8 @@ SubClassOf(Annotation( AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:19745164") "A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart.") AnnotationAssertion( ) AnnotationAssertion( "2011-07-11T03:15:38Z") -AnnotationAssertion(Annotation( "PMID:19745164") "CPC") AnnotationAssertion(Annotation( "PMID:17519333") Annotation( "PMID:19745164") "cardiovascular progenitor cell") +AnnotationAssertion(Annotation( "PMID:19745164") Annotation( ) "CPC") AnnotationAssertion(rdfs:comment "Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell.") AnnotationAssertion(rdfs:label "cardioblast") SubClassOf( ) @@ -39256,10 +38830,10 @@ SubClassOf( (multi-ciliated epithelial cell) AnnotationAssertion(Annotation( "CL:CVS") "A ciliated epithelial cell with many cilia.") -AnnotationAssertion( "MCC"@en) AnnotationAssertion( "multi-ciliated cell"@en) AnnotationAssertion( "multiciliated cell"@en) AnnotationAssertion( "multiciliated epithelial cell"@en) +AnnotationAssertion(Annotation( ) "MCC"@en) AnnotationAssertion(rdfs:label "multi-ciliated epithelial cell") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -39553,6 +39127,7 @@ AnnotationAssertion( "mural cell"@en) SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (microcirculation associated smooth muscle cell) @@ -40838,10 +40413,17 @@ EquivalentClasses( ObjectIntersection # Class: (lung neuroendocrine cell) +AnnotationAssertion(Annotation( "PMID:33355253") Annotation( "doi:10.3109/01902148209069653") Annotation( "doi:10.7554/eLife.78216") "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( "PMID:33355253") "pulmonary neuroendocrine cell") +AnnotationAssertion(Annotation( "PMID:33355253") Annotation( ) "PNEC") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior lateral line nerve glial cell) @@ -42857,6 +42439,20 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mitral cell) + +AnnotationAssertion(Annotation( "MP:0009954") "The large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex.") +AnnotationAssertion(rdfs:label "mitral cell") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (olfactory bulb tufted cell) + +AnnotationAssertion(Annotation( "MP:0009955") "The principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala.") +AnnotationAssertion(rdfs:label "olfactory bulb tufted cell") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (parvocellular neurosecretory cell) AnnotationAssertion(Annotation( "MP:0010125") "The secretory neurons of the paraventricular nucleus that synthesize and secrete vasopressin, corticotropin-releasing factor (CRF) and thyrotropin-releasing hormone (TRH) into blood vessels in the hypothalamo-pituitary portal system.") @@ -44235,15 +43831,6 @@ AnnotationAssertion( "brain vascular cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (choroid plexus cell) - -AnnotationAssertion(Annotation( "DOI:10.1101/2022.10.12.511898") "A cell that is part of the choroid plexus.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "choroid plexus cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (mammillary body neuron) AnnotationAssertion(Annotation( "DOI:10.1101/2022.10.12.511898") "A neuron that has its soma located in the mammillary body.") @@ -44743,6 +44330,14 @@ AnnotationAssertion(Annotation( "catecholaminergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (perivascular cell) + +AnnotationAssertion(Annotation( "PMID:24928499") Annotation( "PMID:27889329") "A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics.") +AnnotationAssertion( ) +AnnotationAssertion( "2023-08-22T13:40:28Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "perivascular cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (enteroglial cell) AnnotationAssertion(Annotation( "PMID:16336493") Annotation( "PMID:17483847") Annotation( "PMID:25975510") "Glial cell that provides support to the enteric nervous system. It is involved in enteric neurotransmission, in maintaining the integrity of the mucosal barrier of the gut and serves as a link between the nervous and immune systems of the gut. In enteric nerve strands, glial processes ensheath multiaxonal bundles which distinguishes enteric glia from all other peripheral glia. Ultrastructurally, the most conspicuous trait of an enteroglial cell is the presence of 10 nm filaments, which criss-cross the cell body, form axial bundles in the processes and appear to firmly anchor the cells to the ganglionic surfaces. Similar to astrocytes, their main constituent is glial fibrillary acidic protein (GFAP).") @@ -44823,25 +44418,6 @@ AnnotationAssertion( "transition metal ion transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (autophagosome assembly) - -AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "PMID:9412464") "The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.") -AnnotationAssertion(Annotation( "GOC:autophagy") "autophagic vacuole assembly") -AnnotationAssertion( "autophagosome biosynthesis") -AnnotationAssertion( "autophagosome formation") -AnnotationAssertion( "PAS formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:mah") "autophagic vacuole formation") -AnnotationAssertion( "GO:0000045") -AnnotationAssertion(rdfs:label "autophagosome assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (mitotic sister chromatid segregation) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:jl") "The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.") @@ -44986,17 +44562,6 @@ AnnotationAssertion( "lytic vacuole") SubClassOf( ) -# Class: (autophagosome membrane) - -AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "GOC:isa_complete") "The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.") -AnnotationAssertion(Annotation( "GOC:autophagy") "autophagic vacuole membrane") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0000421") -AnnotationAssertion(rdfs:label "autophagosome membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (embryonic axis specification) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:go_curators") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo.") @@ -45121,14 +44686,6 @@ AnnotationAssertion( "cell morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (cell morphogenesis involved in differentiation) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0000904") -AnnotationAssertion(rdfs:label "cell morphogenesis involved in differentiation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (response to acid chemical) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:rn") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form.") @@ -45166,6 +44723,20 @@ AnnotationAssertion(rdfs:label "ossi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (neurotransmitter uptake) + +AnnotationAssertion(Annotation( "ISBN:0123668387") "The directed movement of neurotransmitters into neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters.") +AnnotationAssertion( "neurotransmitter recycling") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "neurotransmitter import") +AnnotationAssertion( "neurotransmitter import into glial cell") +AnnotationAssertion( "neurotransmitter import into neuron") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0001504") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "neurotransmitter uptake") +SubClassOf( ) +SubClassOf( ) + # Class: (regulation of neurotransmitter levels) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates levels of neurotransmitter.") @@ -46259,7 +45830,7 @@ AnnotationAssertion( "See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19', 'TS5, trophectoderm ; EMAP:28' and 'TS6, trophectoderm ; EMAP:39'.") AnnotationAssertion(rdfs:label "trophectodermal cellular morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -46396,17 +45967,6 @@ AnnotationAssertion(rdfs:label "resp EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (Mullerian duct regression) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12368913") "The process in which the Mullerian ducts, primordia of the oviducts, uterus and upper vagina, undergo regression in male embryos.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0001880") -AnnotationAssertion(rdfs:label "Mullerian duct regression") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nucleoside binding) AnnotationAssertion(Annotation( "GOC:hjd") "Binding to a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.") @@ -46966,6 +46526,74 @@ AnnotationAssertion( "regulation of sodium ion transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of L-glutamate import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of L-glutamate import into a cell.") +AnnotationAssertion( "al") +AnnotationAssertion( "2012-06-13T07:34:08Z") +AnnotationAssertion( "GO:1900920") +AnnotationAssertion( "regulation of L-glutamate import") +AnnotationAssertion( "regulation of L-glutamate transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of L-glutamate uptake") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0002036") +AnnotationAssertion(rdfs:label "regulation of L-glutamate import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of L-glutamate import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of L-glutamate import into a cell.") +AnnotationAssertion( "al") +AnnotationAssertion( "2012-06-13T07:34:30Z") +AnnotationAssertion( "GO:1900921") +AnnotationAssertion( "down regulation of L-glutamate transport") +AnnotationAssertion( "down-regulation of L-glutamate transport") +AnnotationAssertion( "downregulation of L-glutamate transport") +AnnotationAssertion( "negative regulation of L-glutamate import") +AnnotationAssertion( "negative regulation of L-glutamate transport") +AnnotationAssertion( "regulation of L-glutamate import") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of L-glutamate import") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of L-glutamate import") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of L-glutamate import") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of L-glutamate import") +AnnotationAssertion( "inhibition of L-glutamate transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of L-glutamate uptake") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of L-glutamate uptake") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of L-glutamate uptake") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of L-glutamate uptake") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of L-glutamate uptake") +AnnotationAssertion( "GO:0002037") +AnnotationAssertion(rdfs:label "negative regulation of L-glutamate import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of L-glutamate import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of L-glutamate import into a cell.") +AnnotationAssertion( "al") +AnnotationAssertion( "2012-06-13T07:34:38Z") +AnnotationAssertion( "GO:1900922") +AnnotationAssertion( "positive regulation of L-glutamate import") +AnnotationAssertion( "positive regulation of L-glutamate transport") +AnnotationAssertion( "up regulation of L-glutamate transport") +AnnotationAssertion( "upregulation of L-glutamate transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of L-glutamate import") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of L-glutamate import") +AnnotationAssertion( "up-regulation of L-glutamate transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of L-glutamate import") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of L-glutamate import") +AnnotationAssertion( "activation of L-glutamate transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of L-glutamate uptake") +AnnotationAssertion( "stimulation of L-glutamate transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of L-glutamate uptake") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of L-glutamate uptake") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of L-glutamate uptake") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of L-glutamate uptake") +AnnotationAssertion( "GO:0002038") +AnnotationAssertion(rdfs:label "positive regulation of L-glutamate import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (positive regulation of neuroblast proliferation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that activates or increases the rate of neuroblast proliferation.") @@ -47305,6 +46933,55 @@ AnnotationAssertion(rdfs:label "male EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (cytoplasmic translation) + +AnnotationAssertion(Annotation( "GOC:hjd") "The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.") +AnnotationAssertion( "hjd") +AnnotationAssertion( "2011-06-09T03:11:53Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0002181") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term applies to translation performed by cytoplasmic ribosomes, which is distinct from translation performed by organellar ribosomes. For mitochondrial translation, consider GO:0032543 'mitochondrial translation' or its child terms.") +AnnotationAssertion(rdfs:label "cytoplasmic translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (cytoplasmic translational elongation) + +AnnotationAssertion(Annotation( "GOC:hjd") "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in the cytoplasm.") +AnnotationAssertion( "hjd") +AnnotationAssertion( "2011-06-09T03:14:42Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0002182") +AnnotationAssertion(rdfs:label "cytoplasmic translational elongation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (cytoplasmic translational initiation) + +AnnotationAssertion(Annotation( "GOC:hjd") "The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.") +AnnotationAssertion( "hjd") +AnnotationAssertion( "2011-06-09T03:15:48Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0002183") +AnnotationAssertion(rdfs:label "cytoplasmic translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (cytoplasmic translational termination) + +AnnotationAssertion(Annotation( "GOC:hjd") "The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon.") +AnnotationAssertion( "hjd") +AnnotationAssertion( "2011-06-09T03:17:13Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0002184") +AnnotationAssertion(rdfs:label "cytoplasmic translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (somatic diversification of immune receptors) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") Annotation( "PMID:16102575") Annotation( "PMID:16166509") "The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences.") @@ -52446,7 +52123,7 @@ AnnotationAssertion( "GO:0003382") AnnotationAssertion(rdfs:label "epithelial cell morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell-cell signaling involved in amphid sensory organ development) @@ -52884,9 +52561,8 @@ SubClassOf( ObjectSomeValuesFrom( (protein kinase activity) -AnnotationAssertion(Annotation( "MetaCyc:PROTEIN-KINASE-RXN") "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.") +AnnotationAssertion(Annotation( "PMID:25399640") "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.") AnnotationAssertion( "GO:0050222") -AnnotationAssertion( "MetaCyc:PROTEIN-KINASE-RXN") AnnotationAssertion(Annotation(rdfs:label "INF-gamma induced phosphorylation of L13a") "Reactome:R-HSA-156832") AnnotationAssertion(Annotation(rdfs:label "IRAK1 phosphorylates Pellino") "Reactome:R-HSA-937034") AnnotationAssertion(Annotation(rdfs:label "Unknown kinase phosphorylates NICD4") "Reactome:R-HSA-9604606") @@ -52902,512 +52578,6 @@ SubClassOf( ) SubClassOf( ) -# Class: (protein serine/threonine kinase activity) - -AnnotationAssertion(Annotation( "GOC:bf") Annotation( "PMID:2956925") "Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20114"^^xsd:anyURI) -AnnotationAssertion( "GO:0004695") -AnnotationAssertion( "GO:0004696") -AnnotationAssertion( "GO:0004700") -AnnotationAssertion( "GO:0106311") -AnnotationAssertion(Annotation( "skos:exactMatch") "EC:2.7.11.1") -AnnotationAssertion(Annotation(rdfs:label "PDPK1 phosphorylates AKT2") "Reactome:R-HSA-109702") -AnnotationAssertion(Annotation(rdfs:label "MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y427-SHC1") "Reactome:R-HSA-109822") -AnnotationAssertion(Annotation(rdfs:label "MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y-IRS1,p-Y-IRS2") "Reactome:R-HSA-109823") -AnnotationAssertion(Annotation(rdfs:label "MAP2K1 phosphorylates MAPK3") "Reactome:R-HSA-109860") -AnnotationAssertion(Annotation(rdfs:label "MAP2K2 phosphorylates MAPK1") "Reactome:R-HSA-109862") -AnnotationAssertion(Annotation(rdfs:label "PKA phosphorylates CREB1") "Reactome:R-HSA-111919") -AnnotationAssertion(Annotation(rdfs:label "PKC phosphorylates GRK2") "Reactome:R-HSA-111970") -AnnotationAssertion(Annotation(rdfs:label "Inactivation of MAP2K1 by CDK1") "Reactome:R-HSA-112342") -AnnotationAssertion(Annotation(rdfs:label "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex") "Reactome:R-HSA-112381") -AnnotationAssertion(Annotation(rdfs:label "PRKCB (PKC-beta) phosphorylates CARMA1") "Reactome:R-HSA-1168635") -AnnotationAssertion(Annotation(rdfs:label "Activated IKK phosphorylates I-kappaB") "Reactome:R-HSA-1168638") -AnnotationAssertion(Annotation(rdfs:label "TAK1 associated with the CBM complex phosphorylates IKKbeta") "Reactome:R-HSA-1168641") -AnnotationAssertion(Annotation(rdfs:label "ACVR2A,B (ActRIIA,B) phosphorylates ACVR1B (ActRIB, ALK4) in response to Activin") "Reactome:R-HSA-1181149") -AnnotationAssertion(Annotation(rdfs:label "Type II Activin Receptor (ActRII/ACVR2) phosphorylates Type I Activin Receptor (ActRIB/ACVR1B) in response to NODAL") "Reactome:R-HSA-1181156") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of R-SMAD2/3 by NODAL receptor") "Reactome:R-HSA-1181355") -AnnotationAssertion(Annotation(rdfs:label "Type II Activin Receptor (ActRIIB/ACVR2B) phosphorylates Type I Activin Receptor (ActRIC/ACVR1C) in response to NODAL") "Reactome:R-HSA-1225894") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of USP8 by P-AKT") "Reactome:R-HSA-1358791") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LIN52 component of MuvB by DYRK1A") "Reactome:R-HSA-1362270") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of DLC2 by MAPK8") "Reactome:R-HSA-139908") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of BIM by JNK") "Reactome:R-HSA-139918") -AnnotationAssertion(Annotation(rdfs:label "p-AKT1,p-AKT2 phosphorylates AS160 (TBC1D4)") "Reactome:R-HSA-1445144") -AnnotationAssertion(Annotation(rdfs:label "p-AKT2 phosphorylates Myosin 5A") "Reactome:R-HSA-1449597") -AnnotationAssertion(Annotation(rdfs:label "AMPK-alpha2 phosphorylates TBC1D1") "Reactome:R-HSA-1454699") -AnnotationAssertion(Annotation(rdfs:label "p-AKT2 phosphorylates RGC2") "Reactome:R-HSA-1458463") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of SMAD2,3 by Activin:Activin Receptor") "Reactome:R-HSA-1549526") -AnnotationAssertion(Annotation(rdfs:label "Regulation of KIF23 (MKLP1) by phosphorylation") "Reactome:R-HSA-156673") -AnnotationAssertion(Annotation(rdfs:label "Activation of Cdc25C") "Reactome:R-HSA-156678") -AnnotationAssertion(Annotation(rdfs:label "PLK1 phosphorylates NUDC") "Reactome:R-HSA-156682") -AnnotationAssertion(Annotation(rdfs:label "Inactivation of Wee1 kinase") "Reactome:R-HSA-156699") -AnnotationAssertion(Annotation(rdfs:label "Regulation of KIF20A (MKL2) by phosphorylation") "Reactome:R-HSA-156723") -AnnotationAssertion(Annotation(rdfs:label "p38 MAPK phosphorylates PPARGC1A") "Reactome:R-HSA-1592233") -AnnotationAssertion(Annotation(rdfs:label "p-T309,S474-AKT2:PIP3 phosphorylates PDE3B") "Reactome:R-HSA-162363") -AnnotationAssertion(Annotation(rdfs:label "Inactivation of Myt1 kinase") "Reactome:R-HSA-162657") -AnnotationAssertion(Annotation(rdfs:label "Down Regulation of Emi1 through Phosphorylation of Emi1") "Reactome:R-HSA-163010") -AnnotationAssertion(Annotation(rdfs:label "ULK1 phosphorylates AMBRA1:BECN1 complex") "Reactome:R-HSA-1632857") -AnnotationAssertion(Annotation(rdfs:label "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP") "Reactome:R-HSA-163416") -AnnotationAssertion(Annotation(rdfs:label "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP") "Reactome:R-HSA-163418") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of cohesin by PLK1 at centromeres") "Reactome:R-HSA-1638803") -AnnotationAssertion(Annotation(rdfs:label "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer") "Reactome:R-HSA-164151") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of TSC2 by PKB") "Reactome:R-HSA-165162") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of complexed TSC2 by PKB") "Reactome:R-HSA-165182") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of 4E-BP1 by activated mTORC1") "Reactome:R-HSA-165692") -AnnotationAssertion(Annotation(rdfs:label "mTORC1 phosphorylation of RPS6KB1 (S6K)") "Reactome:R-HSA-165718") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Ribosomal protein S6 by activated S6K1") "Reactome:R-HSA-165726") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation and inactivation of eEF2K by activated S6K1") "Reactome:R-HSA-165758") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation and activation of eIF4G by activated S6K1") "Reactome:R-HSA-165766") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation and activation of eIF4B by activated S6K1") "Reactome:R-HSA-165777") -AnnotationAssertion(Annotation(rdfs:label "First phosphorylation of IRAK1 by IRAK4 bound to activated TLR:MyD88:Mal") "Reactome:R-HSA-166119") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of IRF-3/IRF7 and their release from the activated TLR complex") "Reactome:R-HSA-166245") -AnnotationAssertion(Annotation(rdfs:label "Second phosphorylation of IRAK1 by IRAK4 bound to activated TLR:MyD88:TIRAP") "Reactome:R-HSA-166284") -AnnotationAssertion(Annotation(rdfs:label "Multiple IRAK1 autophosphorylation steps") "Reactome:R-HSA-166286") -AnnotationAssertion(Annotation(rdfs:label "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex") "Reactome:R-HSA-167084") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation (Ser5) of RNA pol II CTD") "Reactome:R-HSA-167098") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylated MAPKs phosphorylate ATF-2") "Reactome:R-HSA-168053") -AnnotationAssertion(Annotation(rdfs:label "Active IKK Complex phosphorylates NF-kappa-B inhibitor") "Reactome:R-HSA-168140") -AnnotationAssertion(Annotation(rdfs:label "Activated TAK1 mediates phosphorylation of the IKK Complex") "Reactome:R-HSA-168184") -AnnotationAssertion(Annotation(rdfs:label "Myt-1 mediated phosphorylation of Cyclin B:Cdc2 complexes") "Reactome:R-HSA-170055") -AnnotationAssertion(Annotation(rdfs:label "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes") "Reactome:R-HSA-170076") -AnnotationAssertion(Annotation(rdfs:label "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes") "Reactome:R-HSA-170087") -AnnotationAssertion(Annotation(rdfs:label "Myt-1 mediated phosphorylation of Cyclin A:Cdc2") "Reactome:R-HSA-170116") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Cyclin B1 in the CRS domain") "Reactome:R-HSA-170126") -AnnotationAssertion(Annotation(rdfs:label "FRS2 is phosphorylated by active TrkA receptor") "Reactome:R-HSA-170977") -AnnotationAssertion(Annotation(rdfs:label "Free APC/C phosphorylated by Plk1") "Reactome:R-HSA-174119") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of the Emi1 DSGxxS degron by Plk1") "Reactome:R-HSA-174174") -AnnotationAssertion(Annotation(rdfs:label "Recruitment and activation of Chk1") "Reactome:R-HSA-176116") -AnnotationAssertion(Annotation(rdfs:label "Activation of claspin") "Reactome:R-HSA-176298") -AnnotationAssertion(Annotation(rdfs:label "p38 MAPK phosphorylates MAPKAPK2, MAPKAPK3") "Reactome:R-HSA-187688") -AnnotationAssertion(Annotation(rdfs:label "CAK-mediated phosphorylation of Cyclin A:Cdk2") "Reactome:R-HSA-187949") -AnnotationAssertion(Annotation(rdfs:label "CAK-mediated phosphorylation of Cyclin E:Cdk2") "Reactome:R-HSA-188350") -AnnotationAssertion(Annotation(rdfs:label "IRAK is activated") "Reactome:R-HSA-193647") -AnnotationAssertion(Annotation(rdfs:label "IKKbeta phosphorylates IkB causing NF-kB to dissociate") "Reactome:R-HSA-193705") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of APC component of the destruction complex") "Reactome:R-HSA-195275") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3") "Reactome:R-HSA-195283") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3") "Reactome:R-HSA-195287") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3") "Reactome:R-HSA-195300") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of beta-catenin at Ser45 by CK1 alpha") "Reactome:R-HSA-195318") -AnnotationAssertion(Annotation(rdfs:label "PDPK1 phosphorylates AKT at T308") "Reactome:R-HSA-198270") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates BAD") "Reactome:R-HSA-198347") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates GSK3") "Reactome:R-HSA-198371") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates MDM2") "Reactome:R-HSA-198599") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates TSC2, inhibiting it") "Reactome:R-HSA-198609") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates IKKalpha") "Reactome:R-HSA-198611") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates p21Cip1 and p27Kip1") "Reactome:R-HSA-198613") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates caspase-9") "Reactome:R-HSA-198621") -AnnotationAssertion(Annotation(rdfs:label "TORC2 (mTOR) phosphorylates AKT at S473") "Reactome:R-HSA-198640") -AnnotationAssertion(Annotation(rdfs:label "p38MAPK phosphorylates MSK1") "Reactome:R-HSA-198669") -AnnotationAssertion(Annotation(rdfs:label "ERK1/2 activates ELK1") "Reactome:R-HSA-198731") -AnnotationAssertion(Annotation(rdfs:label "ERK1/2/5 activate RSK1/2/3") "Reactome:R-HSA-198746") -AnnotationAssertion(Annotation(rdfs:label "ERK1/2 phosphorylates MSK1") "Reactome:R-HSA-198756") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates CREB1") "Reactome:R-HSA-199298") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates FOXO transcription factors") "Reactome:R-HSA-199299") -AnnotationAssertion(Annotation(rdfs:label "AKT can phosphorylate RSK") "Reactome:R-HSA-199839") -AnnotationAssertion(Annotation(rdfs:label "AKT can phosphorylate NR4A1 (NUR77)") "Reactome:R-HSA-199863") -AnnotationAssertion(Annotation(rdfs:label "RSK1/2/3 phosphorylates CREB at Serine 133") "Reactome:R-HSA-199895") -AnnotationAssertion(Annotation(rdfs:label "MSK1 activates ATF1") "Reactome:R-HSA-199910") -AnnotationAssertion(Annotation(rdfs:label "MAPKAPK2 phosphorylates CREB at Serine 133") "Reactome:R-HSA-199917") -AnnotationAssertion(Annotation(rdfs:label "ERK5 activates the transcription factor MEF2") "Reactome:R-HSA-199929") -AnnotationAssertion(Annotation(rdfs:label "MSK1 activates CREB") "Reactome:R-HSA-199935") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates AKT1S1 (PRAS40)") "Reactome:R-HSA-200143") -AnnotationAssertion(Annotation(rdfs:label "Activation of cytosolic AMPK by phosphorylation") "Reactome:R-HSA-200421") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LRP5/6 cytoplasmic domain by membrane-associated GSK3beta") "Reactome:R-HSA-201677") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LRP5/6 cytoplasmic domain by CSNKI") "Reactome:R-HSA-201691") -AnnotationAssertion(Annotation(rdfs:label "CSNK2-mediated phosphorylation of DVL") "Reactome:R-HSA-201717") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of PKC theta") "Reactome:R-HSA-202222") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of CARMA1") "Reactome:R-HSA-202437") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Bcl10") "Reactome:R-HSA-202459") -AnnotationAssertion(Annotation(rdfs:label "Activation of IKK complex") "Reactome:R-HSA-202500") -AnnotationAssertion(Annotation(rdfs:label "Activation of TAK1-TAB2 complex") "Reactome:R-HSA-202510") -AnnotationAssertion(Annotation(rdfs:label "p-S177,S181-IKKB:IKKA:pUb-NEMO phosphorylates IkB-alpha:NF-kB") "Reactome:R-HSA-202541") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of STK4 (MST1) and SAV1 by STK4") "Reactome:R-HSA-2028284") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LATS1 and 2 by p-STK4 (p-MST1)") "Reactome:R-HSA-2028555") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of YAP by LATS2") "Reactome:R-HSA-2028583") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LATS1 and 2 by p-STK3 (p-MST2)") "Reactome:R-HSA-2028589") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of STK3 (MST2) and SAV1 by STK3") "Reactome:R-HSA-2028591") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of YAP by LATS1") "Reactome:R-HSA-2028598") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MOB1A and B by p-STK4 (p-MST1)") "Reactome:R-HSA-2028629") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MOB1A and B by p-STK3 (p-MST2)") "Reactome:R-HSA-2028635") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of WWTR1 (TAZ) by LATS2") "Reactome:R-HSA-2028661") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MOB1A and B by p-STK4(MST1)/N") "Reactome:R-HSA-2028670") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LATS1 and 2 by p-STK3 (MST2)/N") "Reactome:R-HSA-2028673") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MOB1A and B by p-STK3(MST2)/N") "Reactome:R-HSA-2028675") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LATS1 and 2 by p-STK4(MST1)/N") "Reactome:R-HSA-2028679") -AnnotationAssertion(Annotation(rdfs:label "Autophosphorylation of PAK1") "Reactome:R-HSA-2029454") -AnnotationAssertion(Annotation(rdfs:label "PAK1 phosphorylates LIMK1") "Reactome:R-HSA-2029460") -AnnotationAssertion(Annotation(rdfs:label "p-ERK phosphorylates WAVEs and ABI") "Reactome:R-HSA-2029469") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of WWTR1 (TAZ) by LATS1") "Reactome:R-HSA-2060328") -AnnotationAssertion(Annotation(rdfs:label "IKBA is phosphorylated by Phospho IKKB kinase") "Reactome:R-HSA-209087") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates FOXO1A") "Reactome:R-HSA-211164") -AnnotationAssertion(Annotation(rdfs:label "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197") "Reactome:R-HSA-211583") -AnnotationAssertion(Annotation(rdfs:label "Autophosphorylation of PAK-2p34 in the activation loop") "Reactome:R-HSA-211650") -AnnotationAssertion(Annotation(rdfs:label "MASTL (GWL) phosphorylates ARPP19") "Reactome:R-HSA-2168079") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of SMAD2 and SMAD3 linker regions by CDK8 or CDK9") "Reactome:R-HSA-2176475") -AnnotationAssertion(Annotation(rdfs:label "PLK1 phosphorylates GORASP1") "Reactome:R-HSA-2214351") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant is phosphorylated by TORC2 complex") "Reactome:R-HSA-2243938") -AnnotationAssertion(Annotation(rdfs:label "PDPK1 phosphorylates AKT1 E17K mutant") "Reactome:R-HSA-2243942") -AnnotationAssertion(Annotation(rdfs:label "PLK1 hyperphosphorylates Condensin II complex") "Reactome:R-HSA-2294580") -AnnotationAssertion(Annotation(rdfs:label "IRF3 is phosphorylated by TBK1") "Reactome:R-HSA-2396007") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates BAD") "Reactome:R-HSA-2399941") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates GSK3") "Reactome:R-HSA-2399966") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates p21Cip1 and p27Kip1") "Reactome:R-HSA-2399969") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates AKT1S1 (PRAS40)") "Reactome:R-HSA-2399977") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates MDM2") "Reactome:R-HSA-2399981") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates TSC2, inhibiting it") "Reactome:R-HSA-2399982") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates caspase-9") "Reactome:R-HSA-2399985") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates NR4A1 (NUR77)") "Reactome:R-HSA-2399988") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates forkhead box transcription factors") "Reactome:R-HSA-2399992") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates CREB1") "Reactome:R-HSA-2399996") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates RSK") "Reactome:R-HSA-2399999") -AnnotationAssertion(Annotation(rdfs:label "AKT1 E17K mutant phosphorylates CHUK (IKKalpha)") "Reactome:R-HSA-2400001") -AnnotationAssertion(Annotation(rdfs:label "MAPK3-3 or MAPK1 phosphorylate GORASP2") "Reactome:R-HSA-2422927") -AnnotationAssertion(Annotation(rdfs:label "MASTL phosphorylates ENSA") "Reactome:R-HSA-2430535") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of cohesin by PLK1 at chromosomal arms") "Reactome:R-HSA-2466068") -AnnotationAssertion(Annotation(rdfs:label "ACVR2A,B (ActRIIA,B) phosphorylates ACVR1C (ActRIC, ALK7) in response to Activin") "Reactome:R-HSA-2470508") -AnnotationAssertion(Annotation(rdfs:label "CK2 phosphorylates condensin I subunits") "Reactome:R-HSA-2529020") -AnnotationAssertion(Annotation(rdfs:label "PLK1 phosphorylates OPTN") "Reactome:R-HSA-2562526") -AnnotationAssertion(Annotation(rdfs:label "AJUBA facilitates AURKA autophosphorylation") "Reactome:R-HSA-2574840") -AnnotationAssertion(Annotation(rdfs:label "Autophosphorylation of PAK") "Reactome:R-HSA-2730856") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MEK7 by MEKK1") "Reactome:R-HSA-2730868") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of IKK-beta by TAK1") "Reactome:R-HSA-2730876") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MEK4 by MEKK1") "Reactome:R-HSA-2730896") -AnnotationAssertion(Annotation(rdfs:label "Activation of TAK1 complex bound to pUb-TRAF6") "Reactome:R-HSA-2730900") -AnnotationAssertion(Annotation(rdfs:label "PLK1 phosphorylates NEK9") "Reactome:R-HSA-2984226") -AnnotationAssertion(Annotation(rdfs:label "NEK9 phosphorylates NEK6/NEK7") "Reactome:R-HSA-2984258") -AnnotationAssertion(Annotation(rdfs:label "NEK6/NEK7 phosphorylates NUP98") "Reactome:R-HSA-2990880") -AnnotationAssertion(Annotation(rdfs:label "VRK1/VRK2 phosphorylate BANF1") "Reactome:R-HSA-2993898") -AnnotationAssertion(Annotation(rdfs:label "AURKA phosphorylates PLK1") "Reactome:R-HSA-3000310") -AnnotationAssertion(Annotation(rdfs:label "PLK1 phosphorylates BORA") "Reactome:R-HSA-3000327") -AnnotationAssertion(Annotation(rdfs:label "MAPKs phosphorylate ETS1 and ETS2") "Reactome:R-HSA-3132737") -AnnotationAssertion(Annotation(rdfs:label "Activated ERKs phosphorylate ERF") "Reactome:R-HSA-3209160") -AnnotationAssertion(Annotation(rdfs:label "STK11 (LKB1) phosphorylates NUAK1") "Reactome:R-HSA-3222006") -AnnotationAssertion(Annotation(rdfs:label "NUAK1 phosphorylates TP53") "Reactome:R-HSA-3222020") -AnnotationAssertion(Annotation(rdfs:label "MAP3K5 phosphorylates MKK3 and MKK6") "Reactome:R-HSA-3228469") -AnnotationAssertion(Annotation(rdfs:label "p-MAPKAPK3 phosphorylates BMI1") "Reactome:R-HSA-3229102") -AnnotationAssertion(Annotation(rdfs:label "MAP3K5 (ASK1) phosphorylates MAP2K4 (SEK1)") "Reactome:R-HSA-3229152") -AnnotationAssertion(Annotation(rdfs:label "MAPKAPK5 phosphorylates TP53") "Reactome:R-HSA-3239014") -AnnotationAssertion(Annotation(rdfs:label "Active p38 MAPK phosphorylates MAPKAPK5") "Reactome:R-HSA-3239019") -AnnotationAssertion(Annotation(rdfs:label "TBK1 phosphorylates STAT6 at Ser407") "Reactome:R-HSA-3249371") -AnnotationAssertion(Annotation(rdfs:label "Constitutive phosphorylation by GSK3") "Reactome:R-HSA-3371435") -AnnotationAssertion(Annotation(rdfs:label "Constitutive phosphorylation by pERK1/2") "Reactome:R-HSA-3371531") -AnnotationAssertion(Annotation(rdfs:label "DBC1 is phosphorylated by ATM/ART") "Reactome:R-HSA-3371567") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MDM4 by CHEK2") "Reactome:R-HSA-349426") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of COP1 at Ser-387 by ATM") "Reactome:R-HSA-349444") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MDM4 by ATM") "Reactome:R-HSA-349455") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of L1 by p90rsk") "Reactome:R-HSA-374696") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates CBY1") "Reactome:R-HSA-3769394") -AnnotationAssertion(Annotation(rdfs:label "Activated Akt1 phosphorylates AKT1S1 (PRAS40)") "Reactome:R-HSA-377186") -AnnotationAssertion(Annotation(rdfs:label "WNT signaling stimulates CSNK1-dependent phosphorylation of DVL") "Reactome:R-HSA-3772435") -AnnotationAssertion(Annotation(rdfs:label "Plk1-mediated phosphorylation of Nlp") "Reactome:R-HSA-380272") -AnnotationAssertion(Annotation(rdfs:label "IRE1 dimer autophosphorylates") "Reactome:R-HSA-381091") -AnnotationAssertion(Annotation(rdfs:label "EIF2AK3 (PERK) phosphorylates EIF2S1 (eIF2-alpha)Phosphorylation of eIF2-alpha by PERK") "Reactome:R-HSA-381111") -AnnotationAssertion(Annotation(rdfs:label "RPS6KA1/2/3 phosphorylates CEBPB on S321") "Reactome:R-HSA-3857328") -AnnotationAssertion(Annotation(rdfs:label "MAPK3 (ERK1) and MAPK1 (ERK2) phosphorylate CEBPB") "Reactome:R-HSA-3857329") -AnnotationAssertion(Annotation(rdfs:label "WNT-dependent phosphorylation of DVL") "Reactome:R-HSA-3858480") -AnnotationAssertion(Annotation(rdfs:label "AKT interacts and phosphorylates Cot") "Reactome:R-HSA-389756") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of L1 by CK-II") "Reactome:R-HSA-392752") -AnnotationAssertion(Annotation(rdfs:label "ROCK phosphorylates LIMK1,2") "Reactome:R-HSA-3928577") -AnnotationAssertion(Annotation(rdfs:label "LIMK phosphorylates CFL1, inactivating it") "Reactome:R-HSA-3928608") -AnnotationAssertion(Annotation(rdfs:label "Activated ROCK phosphorylates MRLCs") "Reactome:R-HSA-3928616") -AnnotationAssertion(Annotation(rdfs:label "PAK1 autophosphorylates") "Reactome:R-HSA-3928620") -AnnotationAssertion(Annotation(rdfs:label "PAKs autophosphorylate") "Reactome:R-HSA-3928625") -AnnotationAssertion(Annotation(rdfs:label "PAKs phosphorylate MLC") "Reactome:R-HSA-3928640") -AnnotationAssertion(Annotation(rdfs:label "Autophosphorylation of PAK") "Reactome:R-HSA-399939") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of CRMPs by Cdk5") "Reactome:R-HSA-399944") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of cofilin by LIMK-1") "Reactome:R-HSA-399950") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of CRMPs by GSK3beta") "Reactome:R-HSA-399951") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of LIMK-1 by PAK") "Reactome:R-HSA-399952") -AnnotationAssertion(Annotation(rdfs:label "Protein kinase C, alpha type phosphorylates MARCKS") "Reactome:R-HSA-399978") -AnnotationAssertion(Annotation(rdfs:label "CSNK1E,CSNK1D phosphorylate CRY and PER proteins") "Reactome:R-HSA-400382") -AnnotationAssertion(Annotation(rdfs:label "PLK1 phosphorylates FOXM1") "Reactome:R-HSA-4088134") -AnnotationAssertion(Annotation(rdfs:label "Myosin phosphatase inactivation by ROCK") "Reactome:R-HSA-419083") -AnnotationAssertion(Annotation(rdfs:label "LIM kinase phosphorylation by ROCK") "Reactome:R-HSA-419087") -AnnotationAssertion(Annotation(rdfs:label "Myosin regulatory light chain phosphorylation by ROCK") "Reactome:R-HSA-419197") -AnnotationAssertion(Annotation(rdfs:label "Transphosphorylation of pLIMK1") "Reactome:R-HSA-419644") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of cPLA2 by MAPK p38 alpha") "Reactome:R-HSA-428961") -AnnotationAssertion(Annotation(rdfs:label "ALOX5 is phosphorylated by MAPKAP2") "Reactome:R-HSA-429016") -AnnotationAssertion(Annotation(rdfs:label "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP") "Reactome:R-HSA-429714") -AnnotationAssertion(Annotation(rdfs:label "Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding") "Reactome:R-HSA-432110") -AnnotationAssertion(Annotation(rdfs:label "Dissociation of CaM and CAMK2 autophosphorylation") "Reactome:R-HSA-4332358") -AnnotationAssertion(Annotation(rdfs:label "Autophosphorylation and activation of CAMK2") "Reactome:R-HSA-4332363") -AnnotationAssertion(Annotation(rdfs:label "Activation of MAP3K7 in response to WNT") "Reactome:R-HSA-4332388") -AnnotationAssertion(Annotation(rdfs:label "NLK phosphorylates TCF/LEF") "Reactome:R-HSA-4411383") -AnnotationAssertion(Annotation(rdfs:label "Activation of NLK") "Reactome:R-HSA-4411402") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of CREB1 by ribosomal protein S6 kinases (RSKs)") "Reactome:R-HSA-442724") -AnnotationAssertion(Annotation(rdfs:label "PDPK1 phosphorylates RSKs") "Reactome:R-HSA-442739") -AnnotationAssertion(Annotation(rdfs:label "PAK phosphorylates cortactin") "Reactome:R-HSA-442832") -AnnotationAssertion(Annotation(rdfs:label "Interaction of PAK1 with Rac1-GTP") "Reactome:R-HSA-445072") -AnnotationAssertion(Annotation(rdfs:label "IRAK4 phosphorylates IRAK1") "Reactome:R-HSA-446694") -AnnotationAssertion(Annotation(rdfs:label "IRAK4-activated IRAK1 autophosphorylates") "Reactome:R-HSA-446701") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of E proteins by p38 MAPK") "Reactome:R-HSA-448948") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of MEF2 proteins by p38") "Reactome:R-HSA-448955") -AnnotationAssertion(Annotation(rdfs:label "Active p38 MAPK phosphorylates MAPKAPK2 or 3") "Reactome:R-HSA-450222") -AnnotationAssertion(Annotation(rdfs:label "c-FOS activation by phospho ERK1/2") "Reactome:R-HSA-450325") -AnnotationAssertion(Annotation(rdfs:label "Activated TAK1 phosphorylates MKK4/MKK7") "Reactome:R-HSA-450337") -AnnotationAssertion(Annotation(rdfs:label "activated human TAK1 phosphorylates MKK3/MKK6") "Reactome:R-HSA-450346") -AnnotationAssertion(Annotation(rdfs:label "MK2 phosphorylates ZFP36 (Tristetraproline, TTP)") "Reactome:R-HSA-450463") -AnnotationAssertion(Annotation(rdfs:label "MK2 phosphorylates BRF1") "Reactome:R-HSA-450474") -AnnotationAssertion(Annotation(rdfs:label "Protein Kinase B/Akt phosphorylates BRF1") "Reactome:R-HSA-450490") -AnnotationAssertion(Annotation(rdfs:label "Protein Kinase B (AKT) phosphorylates KSRP") "Reactome:R-HSA-450499") -AnnotationAssertion(Annotation(rdfs:label "hp-IRAK1, hp-IRAK4 4 phosphorylate Pellino-1 and 2.") "Reactome:R-HSA-450827") -AnnotationAssertion(Annotation(rdfs:label "MAP kinase p38 phosphorylates KSRP") "Reactome:R-HSA-451152") -AnnotationAssertion(Annotation(rdfs:label "Activation of JNK by DSCAM") "Reactome:R-HSA-451347") -AnnotationAssertion(Annotation(rdfs:label "VANGL2 is phosphorylated in response to WNT5A") "Reactome:R-HSA-4551570") -AnnotationAssertion(Annotation(rdfs:label "DVL2 is phosphorylated after WNT5A binding to FZD") "Reactome:R-HSA-4608825") -AnnotationAssertion(Annotation(rdfs:label "MAPKAPK2 phosphorylates HSF1") "Reactome:R-HSA-4793911") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of HSF1 at Ser230 induces transactivation") "Reactome:R-HSA-5082387") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of HSF1 at Ser326 induces transactivation") "Reactome:R-HSA-5082405") -AnnotationAssertion(Annotation(rdfs:label "RIPK1 is phosphorylated") "Reactome:R-HSA-5213464") -AnnotationAssertion(Annotation(rdfs:label "RIPK3 is phosphorylated") "Reactome:R-HSA-5213466") -AnnotationAssertion(Annotation(rdfs:label "PAK2 autophorylates") "Reactome:R-HSA-5218814") -AnnotationAssertion(Annotation(rdfs:label "PDK1 phosphorylates PKC") "Reactome:R-HSA-5218821") -AnnotationAssertion(Annotation(rdfs:label "Active ROCK1,ROCK2 phosphorylates p-5Y-PTK2 on S732") "Reactome:R-HSA-5218826") -AnnotationAssertion(Annotation(rdfs:label "p-Y420-FYN is phosphorylated on S21") "Reactome:R-HSA-5218854") -AnnotationAssertion(Annotation(rdfs:label "RIPK3 phosphorylates MLKL") "Reactome:R-HSA-5218906") -AnnotationAssertion(Annotation(rdfs:label "p-MAPK2/3 phosphorylates HSP27") "Reactome:R-HSA-5218916") -AnnotationAssertion(Annotation(rdfs:label "NFKBIA variant is not phosphorylated within IkBA:NF-kappaB") "Reactome:R-HSA-5228811") -AnnotationAssertion(Annotation(rdfs:label "AXIN is phosphorylated in the destruction complex") "Reactome:R-HSA-5229343") -AnnotationAssertion(Annotation(rdfs:label "p-AKT2 phosphorylates C2CD5") "Reactome:R-HSA-5260201") -AnnotationAssertion(Annotation(rdfs:label "PAK1-3 autophosphorylates") "Reactome:R-HSA-5357472") -AnnotationAssertion(Annotation(rdfs:label "PAK1-3 phosphorylates VE-cadherin") "Reactome:R-HSA-5357477") -AnnotationAssertion(Annotation(rdfs:label "CHUK, IKBKB phosphorylate CYLD at S418") "Reactome:R-HSA-5357831") -AnnotationAssertion(Annotation(rdfs:label "DMPK phosphorylates PLN") "Reactome:R-HSA-5578777") -AnnotationAssertion(Annotation(rdfs:label "Active NIK phosphorylates IKKA dimer") "Reactome:R-HSA-5607722") -AnnotationAssertion(Annotation(rdfs:label "Active NIK:p-S176,180-IKKA dimer phosphorylates p100:RELB") "Reactome:R-HSA-5607726") -AnnotationAssertion(Annotation(rdfs:label "K63polyUb-TAK1 autophosphorylates") "Reactome:R-HSA-5607732") -AnnotationAssertion(Annotation(rdfs:label "K63polyUb-p-3T,1S-TAK1 phosphorylates IKK-beta") "Reactome:R-HSA-5607742") -AnnotationAssertion(Annotation(rdfs:label "CK1 phosphorylates p-GLI2") "Reactome:R-HSA-5610718") -AnnotationAssertion(Annotation(rdfs:label "CK1 phosphorylates p-GLI3") "Reactome:R-HSA-5610722") -AnnotationAssertion(Annotation(rdfs:label "GSK3 phosphorylates p-GLI2") "Reactome:R-HSA-5610730") -AnnotationAssertion(Annotation(rdfs:label "GSK3 phosphorylates p-GLI3") "Reactome:R-HSA-5610732") -AnnotationAssertion(Annotation(rdfs:label "Protein kinase A (PKA) and RPS6KA5 (MSK1) phosphorylates p65 (RELA) subunit") "Reactome:R-HSA-5624473") -AnnotationAssertion(Annotation(rdfs:label "PAK phosphorylates p21 RAF1 on S338") "Reactome:R-HSA-5624492") -AnnotationAssertion(Annotation(rdfs:label "Autophosphorylation of PAK1,2,3") "Reactome:R-HSA-5627775") -AnnotationAssertion(Annotation(rdfs:label "CSNK1A1 phosphorylates SMO dimer") "Reactome:R-HSA-5632670") -AnnotationAssertion(Annotation(rdfs:label "ADRBK1 phosphorylates SMO dimer") "Reactome:R-HSA-5632672") -AnnotationAssertion(Annotation(rdfs:label "GLI proteins are phosphorylated") "Reactome:R-HSA-5635841") -AnnotationAssertion(Annotation(rdfs:label "ULK3 phosphorylates GLI") "Reactome:R-HSA-5635842") -AnnotationAssertion(Annotation(rdfs:label "AMPK (complex) phosphorylates ULK1 (complex)") "Reactome:R-HSA-5665868") -AnnotationAssertion(Annotation(rdfs:label "AURKB phosphorylates DIAPH2-2 at kinetochores") "Reactome:R-HSA-5666160") -AnnotationAssertion(Annotation(rdfs:label "NIK autophosphorylates on T559") "Reactome:R-HSA-5668545") -AnnotationAssertion(Annotation(rdfs:label "PAK2 phosphorylates myosin regulatory light chain (MRLC)") "Reactome:R-HSA-5668932") -AnnotationAssertion(Annotation(rdfs:label "PAK1 phosphorylates myosin phosphatase") "Reactome:R-HSA-5668947") -AnnotationAssertion(Annotation(rdfs:label "PAK1 or PAK2 phosphorylates MYLK") "Reactome:R-HSA-5668984") -AnnotationAssertion(Annotation(rdfs:label "PAK1 phosphorylates FLNA") "Reactome:R-HSA-5669250") -AnnotationAssertion(Annotation(rdfs:label "p-T774-PKN1 phosphorylates PPP1R14A") "Reactome:R-HSA-5671763") -AnnotationAssertion(Annotation(rdfs:label "Activated CIT phosphorylates MRLCs") "Reactome:R-HSA-5671919") -AnnotationAssertion(Annotation(rdfs:label "Thr-180 of ULK1 is phosphorylated") "Reactome:R-HSA-5672008") -AnnotationAssertion(Annotation(rdfs:label "Active MTORC1 phosphorylates ULK1") "Reactome:R-HSA-5672010") -AnnotationAssertion(Annotation(rdfs:label "mTORC1 phosphorylates AKT1S1") "Reactome:R-HSA-5672828") -AnnotationAssertion(Annotation(rdfs:label "MARK3 phosphorylates KSR1") "Reactome:R-HSA-5672948") -AnnotationAssertion(Annotation(rdfs:label "MAP2Ks phosphorylate MAPKs") "Reactome:R-HSA-5672973") -AnnotationAssertion(Annotation(rdfs:label "RAF phosphorylates MAP2K dimer") "Reactome:R-HSA-5672978") -AnnotationAssertion(Annotation(rdfs:label "Activated MAPKs phosphorylate MAP2K1") "Reactome:R-HSA-5674496") -AnnotationAssertion(Annotation(rdfs:label "Activated MAPK phosphorylates RAF1") "Reactome:R-HSA-5675194") -AnnotationAssertion(Annotation(rdfs:label "Activated MAPKs phosphorylate BRAF") "Reactome:R-HSA-5675198") -AnnotationAssertion(Annotation(rdfs:label "ULK1 phosphorylates ATG13 and RB1CC1") "Reactome:R-HSA-5675868") -AnnotationAssertion(Annotation(rdfs:label "ULK1 phosphorylates Beclin-1") "Reactome:R-HSA-5679205") -AnnotationAssertion(Annotation(rdfs:label "MRN bound to shortened telomeres activates ATM") "Reactome:R-HSA-5682026") -AnnotationAssertion(Annotation(rdfs:label "PKA phosphorylates 4xPALM-C-p-2S-ABCA1 tetramer") "Reactome:R-HSA-5682101") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates HERC2") "Reactome:R-HSA-5682598") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates WHSC1") "Reactome:R-HSA-5682983") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates TP53BP1 at DNA DSBs") "Reactome:R-HSA-5683425") -AnnotationAssertion(Annotation(rdfs:label "p-T68-CHEK2 autophosphorylates") "Reactome:R-HSA-5683792") -AnnotationAssertion(Annotation(rdfs:label "CHEK2 phosphorylates BRCA1") "Reactome:R-HSA-5683801") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates EYA1-4") "Reactome:R-HSA-5683964") -AnnotationAssertion(Annotation(rdfs:label "CDK2 phosphorylates RBBP8") "Reactome:R-HSA-5684096") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates RBBP8") "Reactome:R-HSA-5684140") -AnnotationAssertion(Annotation(rdfs:label "Activation of CHEK1 at resected DNA DSBs") "Reactome:R-HSA-5684887") -AnnotationAssertion(Annotation(rdfs:label "ATR phosphorylates RPA2") "Reactome:R-HSA-5685156") -AnnotationAssertion(Annotation(rdfs:label "CHEK1 phosphorylates RAD51") "Reactome:R-HSA-5685230") -AnnotationAssertion(Annotation(rdfs:label "CHEK1 phosphorylates BRCA2") "Reactome:R-HSA-5685242") -AnnotationAssertion(Annotation(rdfs:label "Activated ATM phosphorylates ABL1") "Reactome:R-HSA-5686578") -AnnotationAssertion(Annotation(rdfs:label "Activated ATM phosphorylates DCLRE1C") "Reactome:R-HSA-5686704") -AnnotationAssertion(Annotation(rdfs:label "PAK1,2,3 phosphorylates MAPK6,4") "Reactome:R-HSA-5687086") -AnnotationAssertion(Annotation(rdfs:label "p-S MAPK6 phosphorylates NCOA3") "Reactome:R-HSA-5687090") -AnnotationAssertion(Annotation(rdfs:label "p-S MAPK6,4 phosphorylate MAPKAPK5") "Reactome:R-HSA-5687094") -AnnotationAssertion(Annotation(rdfs:label "p-T182 MAPKAPK5 phosphorylates FOXO3") "Reactome:R-HSA-5687101") -AnnotationAssertion(Annotation(rdfs:label "p-S MAPKAPK5 phosphorylates HSPB1") "Reactome:R-HSA-5687121") -AnnotationAssertion(Annotation(rdfs:label "PRKDC phosphorylates DCLRE1C at DNA DSBs") "Reactome:R-HSA-5687183") -AnnotationAssertion(Annotation(rdfs:label "p-T182-MAPKAPK5 phoshphorylates DNAJB1") "Reactome:R-HSA-5690250") -AnnotationAssertion(Annotation(rdfs:label "MAPKAPK5 phosphorylates KALRN") "Reactome:R-HSA-5692768") -AnnotationAssertion(Annotation(rdfs:label "SEPT7:p-S189 MAPK6:p-T182 MAPKAPK5 phosphorylates CDC42EPs") "Reactome:R-HSA-5692775") -AnnotationAssertion(Annotation(rdfs:label "p-S182 MAPKAPK5 phosphorylates FOXO1") "Reactome:R-HSA-5692779") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates MDC1") "Reactome:R-HSA-5693536") -AnnotationAssertion(Annotation(rdfs:label "MRN activates ATM") "Reactome:R-HSA-5693540") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates histone H2AFX on S139 at DNA DSBs") "Reactome:R-HSA-5693549") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of BRCA1-A complex at multiple sites by ATM") "Reactome:R-HSA-5693551") -AnnotationAssertion(Annotation(rdfs:label "DNA-PKcs autophosphorylates") "Reactome:R-HSA-5693575") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates NBN") "Reactome:R-HSA-5693598") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates TP53 at S15") "Reactome:R-HSA-5693609") -AnnotationAssertion(Annotation(rdfs:label "CSNK1D phosphorylates SEC23") "Reactome:R-HSA-5694441") -AnnotationAssertion(Annotation(rdfs:label "ATR phosphorylates RPA2, FANCI, FANCD2 and FANCM at ICL-DNA") "Reactome:R-HSA-6788392") -AnnotationAssertion(Annotation(rdfs:label "TORC2 complex phosphorylates SGK1") "Reactome:R-HSA-6795290") -AnnotationAssertion(Annotation(rdfs:label "SGK1 phosphorylates MDM2") "Reactome:R-HSA-6795460") -AnnotationAssertion(Annotation(rdfs:label "PDPK1 phosphorylates SGK1") "Reactome:R-HSA-6795473") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates DYRK2") "Reactome:R-HSA-6798372") -AnnotationAssertion(Annotation(rdfs:label "DYRK2 phosphorylates TP53") "Reactome:R-HSA-6798374") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates ZNF420") "Reactome:R-HSA-6799097") -AnnotationAssertion(Annotation(rdfs:label "CHEK1 phosphorylates TP53") "Reactome:R-HSA-6799246") -AnnotationAssertion(Annotation(rdfs:label "ATR phosphorylates TP53") "Reactome:R-HSA-6799332") -AnnotationAssertion(Annotation(rdfs:label "HIPK2 phosphorylates TP53") "Reactome:R-HSA-6799409") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates PIDD1") "Reactome:R-HSA-6800490") -AnnotationAssertion(Annotation(rdfs:label "PLK2 phosphorylates CENPJ") "Reactome:R-HSA-6801666") -AnnotationAssertion(Annotation(rdfs:label "PLK2 phosphorylates NPM1") "Reactome:R-HSA-6801675") -AnnotationAssertion(Annotation(rdfs:label "High kinase activity BRAF complexes phosphorylate MAP2Ks") "Reactome:R-HSA-6802911") -AnnotationAssertion(Annotation(rdfs:label "RAS:GTP:moderate kinase activity p-RAF complexes phosphorylate MAP2Ks") "Reactome:R-HSA-6802919") -AnnotationAssertion(Annotation(rdfs:label "Mutant RAS:p-RAF complexes phosphorylate MAP2Ks") "Reactome:R-HSA-6802926") -AnnotationAssertion(Annotation(rdfs:label "p-BRAF and RAF fusion dimers phosphorylate MAP2Ks") "Reactome:R-HSA-6802933") -AnnotationAssertion(Annotation(rdfs:label "MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers") "Reactome:R-HSA-6802935") -AnnotationAssertion(Annotation(rdfs:label "RAS:GTP:inactive p-RAF complexes phosphorylate MAP2Ks") "Reactome:R-HSA-6802943") -AnnotationAssertion(Annotation(rdfs:label "PLK3 phosphorylates CDC25C") "Reactome:R-HSA-6802973") -AnnotationAssertion(Annotation(rdfs:label "CHEK2 phosphorylates TTC5") "Reactome:R-HSA-6804266") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates TTC5") "Reactome:R-HSA-6804276") -AnnotationAssertion(Annotation(rdfs:label "ATM phosphorylates MDM2") "Reactome:R-HSA-6804955") -AnnotationAssertion(Annotation(rdfs:label "CK2:FACT phosphorylates TP53") "Reactome:R-HSA-6805059") -AnnotationAssertion(Annotation(rdfs:label "AURKA phosphorylates TP53") "Reactome:R-HSA-6805103") -AnnotationAssertion(Annotation(rdfs:label "AURKB phosphorylates TP53") "Reactome:R-HSA-6805126") -AnnotationAssertion(Annotation(rdfs:label "CDK5 phosphorylates TP53") "Reactome:R-HSA-6805276") -AnnotationAssertion(Annotation(rdfs:label "PLK3 phosphorylates TP53") "Reactome:R-HSA-6805285") -AnnotationAssertion(Annotation(rdfs:label "TAF1 phosphorylates TP53") "Reactome:R-HSA-6805399") -AnnotationAssertion(Annotation(rdfs:label "TP53RK phosphorylates TP53") "Reactome:R-HSA-6805479") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates KAT6A") "Reactome:R-HSA-6805640") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates PHF20") "Reactome:R-HSA-6805785") -AnnotationAssertion(Annotation(rdfs:label "CDK7 phosphorylates serine-5 and serine-7 of heptad repeats in C-terminal domain of RNA polymerase II at snRNA promoter") "Reactome:R-HSA-6810233") -AnnotationAssertion(Annotation(rdfs:label "MAPKs phosphorylate PP2A") "Reactome:R-HSA-6811454") -AnnotationAssertion(Annotation(rdfs:label "CK2 phosphorylates PDCL") "Reactome:R-HSA-6814409") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Cdc25A at Ser-123 by Chk1") "Reactome:R-HSA-69604") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Cdc25A at Ser-123 by Chk2") "Reactome:R-HSA-69608") -AnnotationAssertion(Annotation(rdfs:label "CHEK2 phosphorylates TP53") "Reactome:R-HSA-69685") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation and activation of CHEK2 by ATM") "Reactome:R-HSA-69891") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Cdc25C at Ser 216 by Chk1") "Reactome:R-HSA-75010") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Wee1 kinase by Chk1") "Reactome:R-HSA-75028") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Cdc25C at Ser216 by CHEK2") "Reactome:R-HSA-75809") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta") "Reactome:R-HSA-75820") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation (Ser5) of RNA pol II CTD") "Reactome:R-HSA-77071") -AnnotationAssertion(Annotation(rdfs:label "Casein kinase II phosphorylates PTEN") "Reactome:R-HSA-8850945") -AnnotationAssertion(Annotation(rdfs:label "Mitotic phosphorylation-induced dissociation of GTSE1 from microtubule plus ends") "Reactome:R-HSA-8852306") -AnnotationAssertion(Annotation(rdfs:label "PLK1 phosphorylates GTSE1") "Reactome:R-HSA-8852317") -AnnotationAssertion(Annotation(rdfs:label "TPX2 promotes AURKA autophosphorylation") "Reactome:R-HSA-8853419") -AnnotationAssertion(Annotation(rdfs:label "AURKA phosphorylates PHLDA1") "Reactome:R-HSA-8853444") -AnnotationAssertion(Annotation(rdfs:label "PKA phosphorylates RET:GDNF:GFRA dimer") "Reactome:R-HSA-8854908") -AnnotationAssertion(Annotation(rdfs:label "AAK1 phosphorylates AP-2 mu subunit at T156") "Reactome:R-HSA-8856813") -AnnotationAssertion(Annotation(rdfs:label "p25-bound CDK5 phosphorylates CDC25B") "Reactome:R-HSA-8863007") -AnnotationAssertion(Annotation(rdfs:label "p25-bound CDK5 phosphorylates CDC25C") "Reactome:R-HSA-8863011") -AnnotationAssertion(Annotation(rdfs:label "p25-bound CDK5 phosphorylates CDC25A") "Reactome:R-HSA-8863014") -AnnotationAssertion(Annotation(rdfs:label "IKKB phosphorylates SNAP23") "Reactome:R-HSA-8863895") -AnnotationAssertion(Annotation(rdfs:label "MAPK12 phosphorylates PTPN3") "Reactome:R-HSA-8868118") -AnnotationAssertion(Annotation(rdfs:label "CDK5:p25 phosphorylates GOLGA2") "Reactome:R-HSA-8868260") -AnnotationAssertion(Annotation(rdfs:label "CDK5:p25 phosphorylates lamin B1") "Reactome:R-HSA-8868340") -AnnotationAssertion(Annotation(rdfs:label "CDK5:p25 phosphorylates lamin A") "Reactome:R-HSA-8868344") -AnnotationAssertion(Annotation(rdfs:label "CDK5:p25 phosphorylates PRDX1") "Reactome:R-HSA-8868567") -AnnotationAssertion(Annotation(rdfs:label "CDK5:p25 phosphorylates PRDX2") "Reactome:R-HSA-8868573") -AnnotationAssertion(Annotation(rdfs:label "CDK5:p25 phosphorylates JUN") "Reactome:R-HSA-8868666") -AnnotationAssertion(Annotation(rdfs:label "CDK5:p25 phosphorylates FOXO3") "Reactome:R-HSA-8870558") -AnnotationAssertion(Annotation(rdfs:label "Casein kinase II phosphorylates STARD10") "Reactome:R-HSA-8873929") -AnnotationAssertion(Annotation(rdfs:label "p-ULK1 phosphorylates DENND3") "Reactome:R-HSA-8876446") -AnnotationAssertion(Annotation(rdfs:label "MAP2K6 phosphorylates PIP4K2B") "Reactome:R-HSA-8877691") -AnnotationAssertion(Annotation(rdfs:label "HIPK2 phosphorylates RUNX1 and EP300") "Reactome:R-HSA-8878050") -AnnotationAssertion(Annotation(rdfs:label "HIPK2 phosphorylates RUNX1") "Reactome:R-HSA-8878054") -AnnotationAssertion(Annotation(rdfs:label "CK2 phosphorylates NFE2L2") "Reactome:R-HSA-8932322") -AnnotationAssertion(Annotation(rdfs:label "Active AKT phosphorylates DENND1A and DENND1B in response to insulin signaling") "Reactome:R-HSA-8933446") -AnnotationAssertion(Annotation(rdfs:label "Activated AKT phosphorylates RUNX2") "Reactome:R-HSA-8939963") -AnnotationAssertion(Annotation(rdfs:label "CDK1 phosphorylates VCPIP1") "Reactome:R-HSA-8940100") -AnnotationAssertion(Annotation(rdfs:label "CDK4/6:CCND complexes are activated by T-loop phosphorylation of CDK4/6") "Reactome:R-HSA-8942836") -AnnotationAssertion(Annotation(rdfs:label "mTORC1 phosphorylates MAF1") "Reactome:R-HSA-8944454") -AnnotationAssertion(Annotation(rdfs:label "FUNDC1 is phosphorylated by CK2") "Reactome:R-HSA-8948039") -AnnotationAssertion(Annotation(rdfs:label "FUNDC1 is phosphorylated by ULK1 at Ser17") "Reactome:R-HSA-8948146") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates MKRN1") "Reactome:R-HSA-8948757") -AnnotationAssertion(Annotation(rdfs:label "FAM20C phosphorylates FAM20C substrates") "Reactome:R-HSA-8952289") -AnnotationAssertion(Annotation(rdfs:label "CHEK1 phosphorylates E2F6") "Reactome:R-HSA-9007539") -AnnotationAssertion(Annotation(rdfs:label "GSK3B phosphorylates RUNX2") "Reactome:R-HSA-9008480") -AnnotationAssertion(Annotation(rdfs:label "PPM1D dephosphorylates RUNX2") "Reactome:R-HSA-9008822") -AnnotationAssertion(Annotation(rdfs:label "Activated ERKs phosphorylate RUNX2") "Reactome:R-HSA-9009208") -AnnotationAssertion(Annotation(rdfs:label "p-TEFb phosphorylates serine 2 in RNA polymerase II CTD") "Reactome:R-HSA-9012319") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of IRF-3/IRF7 and their release from the activated TLR3 complex") "Reactome:R-HSA-9013978") -AnnotationAssertion(Annotation(rdfs:label "HIPK2 phosphorylates MECP2") "Reactome:R-HSA-9022314") -AnnotationAssertion(Annotation(rdfs:label "AURKB phosphorylates MECP2 at S423") "Reactome:R-HSA-9023132") -AnnotationAssertion(Annotation(rdfs:label "Estrogen-independent phosphorylation of ESR1 S118 by MAPK1 and MAPK3") "Reactome:R-HSA-9032751") -AnnotationAssertion(Annotation(rdfs:label "CDK5 phosphorylates NTRK2") "Reactome:R-HSA-9032863") -AnnotationAssertion(Annotation(rdfs:label "ATR phosphorylates Histone H2A.X at unsynapsed regions") "Reactome:R-HSA-912470") -AnnotationAssertion(Annotation(rdfs:label "PKA/PKG phosphorylate Rap1GAP2") "Reactome:R-HSA-913996") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation and release of IRF3/IRF7") "Reactome:R-HSA-918229") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation and release of IRF7") "Reactome:R-HSA-933525") -AnnotationAssertion(Annotation(rdfs:label "SPRY2 is phosphorylated by phosphorylated MNK1") "Reactome:R-HSA-934559") -AnnotationAssertion(Annotation(rdfs:label "Activation of TAK1 complex bound to activated TLR4 complex") "Reactome:R-HSA-936951") -AnnotationAssertion(Annotation(rdfs:label "IRAK4 autophosphorylation in the complex with activated TLR:MyD88:TIRAP") "Reactome:R-HSA-937022") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomer:TIRAP:activated TLR complex") "Reactome:R-HSA-937059") -AnnotationAssertion(Annotation(rdfs:label "AKT1 phosphorylates NOTCH4") "Reactome:R-HSA-9604328") -AnnotationAssertion(Annotation(rdfs:label "Activated BRAF phosphorylates MAP2K dimers downstream of RAP1 and NGF") "Reactome:R-HSA-9610153") -AnnotationAssertion(Annotation(rdfs:label "MAP2Ks phosphorylate MAPKs downstream of BRAF and NGF") "Reactome:R-HSA-9610156") -AnnotationAssertion(Annotation(rdfs:label "BRAF autophosphorylates downstream of RAP1 and NGF") "Reactome:R-HSA-9610163") -AnnotationAssertion(Annotation(rdfs:label "SGK phosphorylates CREB1") "Reactome:R-HSA-9612501") -AnnotationAssertion(Annotation(rdfs:label "SGK phosphorylates SRF") "Reactome:R-HSA-9612509") -AnnotationAssertion(Annotation(rdfs:label "BRAF in Rap1-GTP complex:BRAF complex autophosphorylates") "Reactome:R-HSA-9612980") -AnnotationAssertion(Annotation(rdfs:label "PRKAA2 phosphorylates PLINs") "Reactome:R-HSA-9613530") -AnnotationAssertion(Annotation(rdfs:label "AMPK phosphorylates MAPT") "Reactome:R-HSA-9619515") -AnnotationAssertion(Annotation(rdfs:label "ERKs phosphorylate RSKs") "Reactome:R-HSA-9619843") -AnnotationAssertion(Annotation(rdfs:label "RSKs autophosphorylate") "Reactome:R-HSA-9620004") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates FOXO3 downstream of ESR1 and EGFR") "Reactome:R-HSA-9624526") -AnnotationAssertion(Annotation(rdfs:label "MAPK11 or MAPK14 phosphorylates NCF1 at Ser345") "Reactome:R-HSA-9626880") -AnnotationAssertion(Annotation(rdfs:label "CASP9 is phosphorylated at T125") "Reactome:R-HSA-9627089") -AnnotationAssertion(Annotation(rdfs:label "CDKN1B is phosphorylated in response to estrogen") "Reactome:R-HSA-9632868") -AnnotationAssertion(Annotation(rdfs:label "p-T899-EIF2AK4 (GCN2) phosphorylates EIF2AS1") "Reactome:R-HSA-9633008") -AnnotationAssertion(Annotation(rdfs:label "EIF2AK4 (GCN2) dimer autophosphorylates") "Reactome:R-HSA-9633742") -AnnotationAssertion(Annotation(rdfs:label "LINC01139 promotes phosphorylation of HIF1A by LRRK2") "Reactome:R-HSA-9634702") -AnnotationAssertion(Annotation(rdfs:label "ALPK1 phosphorylates TIFA") "Reactome:R-HSA-9645535") -AnnotationAssertion(Annotation(rdfs:label "NEK6 and NEK7 phosphorylate EML4") "Reactome:R-HSA-9648089") -AnnotationAssertion(Annotation(rdfs:label "p-T-EIF2AK1:ferriheme dimer autophosphorylates") "Reactome:R-HSA-9648883") -AnnotationAssertion(Annotation(rdfs:label "p-T,T486,T488-EIF2AK1 phosphorylates EIF2S1 (eIF2-alpha)") "Reactome:R-HSA-9648888") -AnnotationAssertion(Annotation(rdfs:label "MAP2K mutants constitutively phosphorylate MAPKs") "Reactome:R-HSA-9652165") -AnnotationAssertion(Annotation(rdfs:label "KRAS4B is phosphorylated on serine 181") "Reactome:R-HSA-9653503") -AnnotationAssertion(Annotation(rdfs:label "MAP2Ks phosphorylate MAPKs downstream of RAF1 mutants") "Reactome:R-HSA-9656214") -AnnotationAssertion(Annotation(rdfs:label "RAF1 mutant complexes phosphorylate MAP2K dimer") "Reactome:R-HSA-9656215") -AnnotationAssertion(Annotation(rdfs:label "PLK2, MAPK14 phosphorylate ADAM17") "Reactome:R-HSA-9662823") -AnnotationAssertion(Annotation(rdfs:label "Unknown kinase phosphorylates p-DVL") "Reactome:R-HSA-9673346") -AnnotationAssertion(Annotation(rdfs:label "GSK3 phosphorylates Nucleoprotein") "Reactome:R-HSA-9683664") -AnnotationAssertion(Annotation(rdfs:label "AKT phosphorylates FOXO3 downstream of FLT3") "Reactome:R-HSA-9699579") -AnnotationAssertion(Annotation(rdfs:label "TBK1, IKBKE are autophosphorylated at Ser172") "Reactome:R-HSA-9705320") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of TBK1/IKBKE") "Reactome:R-HSA-9705323") -AnnotationAssertion(Annotation(rdfs:label "MAPK1 phsophorylates ZC3HCF1 in a NPM-ALK-dependent manner") "Reactome:R-HSA-9725030") -AnnotationAssertion(Annotation(rdfs:label "GSK3 phosphorylates nucleoprotein") "Reactome:R-HSA-9729260") -AnnotationAssertion(Annotation(rdfs:label "Unknown kinase phosphorylates nucleoprotein") "Reactome:R-HSA-9729300") -AnnotationAssertion(Annotation(rdfs:label "CSNK1A1 phosphorylates nucleoprotein") "Reactome:R-HSA-9729318") -AnnotationAssertion(Annotation(rdfs:label "MAPK1 and MAPK3 phosphorylate SMAD2 and SMAD3") "Reactome:R-HSA-9731111") -AnnotationAssertion(Annotation(rdfs:label "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9") "Reactome:R-HSA-975125") -AnnotationAssertion(Annotation(rdfs:label "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9") "Reactome:R-HSA-975134") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomer:activated TLR 7/8 or 9") "Reactome:R-HSA-975160") -AnnotationAssertion(Annotation(rdfs:label "IRAK4 autophosphorylation in the complex with MyD88:activated TLR 7/8 or 9") "Reactome:R-HSA-975170") -AnnotationAssertion(Annotation(rdfs:label "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9") "Reactome:R-HSA-975180") -AnnotationAssertion(Annotation(rdfs:label "Unknown kinase phosphorylates 9b") "Reactome:R-HSA-9758486") -AnnotationAssertion(Annotation(rdfs:label "Multiple IRAK1 autophosphorylation within the complex p-IRAK4:oligo MyD88:activated TLR") "Reactome:R-HSA-975853") -AnnotationAssertion(Annotation(rdfs:label "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomerl:activated TLR5 or 10 complex") "Reactome:R-HSA-975861") -AnnotationAssertion(Annotation(rdfs:label "IRAK4 autophosphorylation within the complex activated TLR:MyD88") "Reactome:R-HSA-975865") -AnnotationAssertion(Annotation(rdfs:label "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR complex") "Reactome:R-HSA-975874") -AnnotationAssertion(Annotation(rdfs:label "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR") "Reactome:R-HSA-975878") -AnnotationAssertion(Annotation(rdfs:label "GSK3B phosphorylates p-NFE2L2") "Reactome:R-HSA-9762094") -AnnotationAssertion(Annotation(rdfs:label "SQSTM1 oligomer is phosphorylated") "Reactome:R-HSA-9766532") -AnnotationAssertion(Annotation(rdfs:label "MAPK1,(MAPK3) phosphorylates NPAS4") "Reactome:R-HSA-9769115") -AnnotationAssertion(Annotation(rdfs:label "Active IKBKB phosphorylates NF-kappa-B inhibitor") "Reactome:R-HSA-9773803") -AnnotationAssertion(Annotation(rdfs:label "MAPKAPK2 phosphorylates RIPK1 at S320") "Reactome:R-HSA-9815501") -AnnotationAssertion(Annotation(rdfs:label "TBK1, IKBKE phosphorylate RIPK1 at T189") "Reactome:R-HSA-9817397") -AnnotationAssertion(Annotation(rdfs:label "CHUK, IKBKB phosphorylate RIPK1 at S25") "Reactome:R-HSA-9818789") -AnnotationAssertion(Annotation(rdfs:label "ULK1 phosphorylates RIPK1 at S357") "Reactome:R-HSA-9819106") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "protein serine kinase activity") -AnnotationAssertion( "protein threonine kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "protein-serine kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "serine kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "serine protein kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "serine-specific protein kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "threonine-specific protein kinase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "protein serine-threonine kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "serine(threonine) protein kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "serine/threonine protein kinase activity") -AnnotationAssertion( "GO:0004674") -AnnotationAssertion(rdfs:label "protein serine/threonine kinase activity") -SubClassOf( ) - # Class: (protein tyrosine kinase activity) AnnotationAssertion(Annotation( "RHEA:10596") "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.") @@ -54688,7 +53858,9 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) +DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (nuclear envelope) @@ -54861,18 +54033,6 @@ AnnotationAssertion(rdfs:label "vacu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (autophagosome) - -AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "ISBN:0198547684") Annotation( "PMID:11099404") "A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the lytic vacuole/lysosome for degradation as part of macroautophagy.") -AnnotationAssertion( "NIF_Subcellular:sao8663416959") -AnnotationAssertion(Annotation( "NIF_Subcellular:sao8663416959") "autophagic vacuole") -AnnotationAssertion( "cellular_component") -AnnotationAssertion(Annotation( "NIF_Subcellular:sao8663416959") "initial autophagic vacuole") -AnnotationAssertion( "GO:0005776") -AnnotationAssertion(rdfs:label "autophagosome") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (Golgi apparatus) AnnotationAssertion(Annotation( "ISBN:0198506732") "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.") @@ -54912,6 +54072,26 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "Golgi-associated vesicle") SubClassOf( ) +# Class: (cytosol) + +AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "GOC:jl") "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.") +AnnotationAssertion( "NIF_Subcellular:sao101633890") +AnnotationAssertion( "Wikipedia:Cytosol") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005829") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cytosol") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) + # Class: (ribosome) AnnotationAssertion(Annotation( "ISBN:0198506732") "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.") @@ -55859,6 +55039,29 @@ AnnotationAssertion( "RNA localization") SubClassOf( ) +# Class: (RNA import into nucleus) + +AnnotationAssertion(Annotation( "GOC:ma") "The import of RNA from the cytoplasm to the nucleus.") +AnnotationAssertion( "RNA import into cell nucleus") +AnnotationAssertion( "RNA transport from cytoplasm to nucleus") +AnnotationAssertion( "RNA-nucleus import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006404") +AnnotationAssertion(rdfs:label "RNA import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (RNA export from nucleus) + +AnnotationAssertion(Annotation( "GOC:ma") "The directed movement of RNA from the nucleus to the cytoplasm.") +AnnotationAssertion( "RNA export from cell nucleus") +AnnotationAssertion( "RNA export out of nucleus") +AnnotationAssertion( "RNA transport from nucleus to cytoplasm") +AnnotationAssertion( "RNA-nucleus export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006405") +AnnotationAssertion(rdfs:label "RNA export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (translation) AnnotationAssertion(Annotation( "GOC:go_curators") "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.") @@ -56198,6 +55401,32 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "thyroid hormone generation") SubClassOf( ) +# Class: (protein import into nucleus) + +AnnotationAssertion(Annotation( "GOC:jl") "The directed movement of a protein from the cytoplasm to the nucleus.") +AnnotationAssertion(Annotation( "GOC:mah") "establishment of protein localization to nucleus") +AnnotationAssertion( "protein import into cell nucleus") +AnnotationAssertion( "protein nucleus import") +AnnotationAssertion( "protein transport from cytoplasm to nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006606") +AnnotationAssertion(rdfs:label "protein import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (protein export from nucleus) + +AnnotationAssertion(Annotation( "GOC:jl") "The directed movement of a protein from the nucleus into the cytoplasm.") +AnnotationAssertion( "GO:0097349") +AnnotationAssertion( "protein export from cell nucleus") +AnnotationAssertion( "protein export out of nucleus") +AnnotationAssertion( "protein transport from nucleus to cytoplasm") +AnnotationAssertion( "protein-nucleus export") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:al") "copper-induced protein export from nucleus") +AnnotationAssertion( "GO:0006611") +AnnotationAssertion(rdfs:label "protein export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (vacuolar protein processing) AnnotationAssertion(Annotation( "GOC:mah") "Protein processing that takes place in the vacuole. Most protein processing in the vacuole represents proteolytic cleavage of precursors to form active enzymes.") @@ -57135,24 +56364,21 @@ SubClassOf( ObjectComplementOf(Object SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (autophagy) - -AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "ISBN:0198547684") Annotation( "PMID:11099404") Annotation( "PMID:9412464") "The cellular catabolic process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.") -AnnotationAssertion( "GO:0016238") -AnnotationAssertion( "Wikipedia:Autophagy_(cellular)") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006914") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "autophagy") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) +# Class: (nucleocytoplasmic transport) + +AnnotationAssertion(Annotation( "GOC:go_curators") "The directed movement of molecules between the nucleus and the cytoplasm.") +AnnotationAssertion( "GO:0000063") +AnnotationAssertion( "nucleocytoplasmic shuttling") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006913") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed.") +AnnotationAssertion(rdfs:label "nucleocytoplasmic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (apoptotic process) @@ -59490,24 +58716,6 @@ AnnotationAssertion( "cytoskeletal protein binding") SubClassOf( ) -# Class: (ATP-dependent activity, acting on DNA) - -AnnotationAssertion(Annotation( "GOC:pdt") "Catalytic activity that acts to modify DNA, driven by ATP hydrolysis.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20876"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21775"^^xsd:anyURI) -AnnotationAssertion( "GO:0004011") -AnnotationAssertion( "ATPase activity, acting on DNA") -AnnotationAssertion( "ATPase, acting on DNA") -AnnotationAssertion( "DNA dependent ATPase activity") -AnnotationAssertion( "DNA-dependent ATPase activity") -AnnotationAssertion( "DNA-dependent adenosinetriphosphatase activity") -AnnotationAssertion( "adenosinetriphosphatase (DNA-dependent)") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0008094") -AnnotationAssertion(rdfs:label "ATP-dependent activity, acting on DNA") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (protein localization) AnnotationAssertion(Annotation( "GOC:ai") "Any process in which a protein is transported to, or maintained in, a specific location.") @@ -59602,23 +58810,6 @@ SubClassOf( ) DisjointClasses( ) -# Class: (ATP-dependent activity, acting on RNA) - -AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20876"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21775"^^xsd:anyURI) -AnnotationAssertion( "GO:0004010") -AnnotationAssertion(Annotation(rdfs:label "Spliceosomal P complex dissociates yielding the intron-containing complex (ILS) and the spliced mRNP (new)") "Reactome:R-HSA-9770847") -AnnotationAssertion(Annotation(rdfs:label "Disassembly of the Intron Lariat Spliceosome (new)") "Reactome:R-HSA-9772351") -AnnotationAssertion( "ATPase activity, acting on RNA") -AnnotationAssertion( "ATPase, acting on RNA") -AnnotationAssertion( "RNA-dependent ATPase activity") -AnnotationAssertion( "RNA-dependent adenosinetriphosphatase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0008186") -AnnotationAssertion(rdfs:label "ATP-dependent activity, acting on RNA") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (neuropeptide receptor activity) AnnotationAssertion(Annotation( "GOC:ai") "Combining with a neuropeptide to initiate a change in cell activity.") @@ -59722,11 +58913,13 @@ SubClassOf( ObjectSomeValuesFrom( (cell death) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:25236395") "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).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24680"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "accidental cell death") AnnotationAssertion( "necrosis") AnnotationAssertion( "GO:0008219") -AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms.") AnnotationAssertion(rdfs:label "cell death") SubClassOf( ) @@ -60218,20 +59411,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (ubiquitin-like modifier activating enzyme activity) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") "Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14208"^^xsd:anyURI) -AnnotationAssertion( "GO:0008642") -AnnotationAssertion( "small protein activating enzyme activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0008641") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ubiquitin-like modifier activating enzyme activity") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (carbohydrate transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.") @@ -60359,7 +59538,8 @@ SubClassOf( (macromolecule biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") -AnnotationAssertion( "http://amigo.geneontology.org/amigo/term/GO:0070589"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15249"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25418"^^xsd:anyURI) AnnotationAssertion( "GO:0043284") AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer biosynthetic process") AnnotationAssertion( "macromolecule anabolism") @@ -60372,6 +59552,7 @@ AnnotationAssertion( "macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (fatty acid catabolic process) @@ -62060,14 +61241,15 @@ SubClassOf( (gene expression) -AnnotationAssertion(Annotation( "GOC:txnOH-2018") Annotation( "PMID:25934543") Annotation( "PMID:31580950") "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.") +AnnotationAssertion(Annotation( "GOC:txnOH-2018") Annotation( "PMID:25934543") Annotation( "PMID:31580950") "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22557"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25419"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Gene_expression") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010467") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gene expression") -SubClassOf( ) +SubClassOf( ) # Class: (regulation of gene expression) @@ -62139,30 +61321,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (regulation of autophagy) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010506") -AnnotationAssertion(rdfs:label "regulation of autophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of autophagy) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010507") -AnnotationAssertion(rdfs:label "negative regulation of autophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of autophagy) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010508") -AnnotationAssertion(rdfs:label "positive regulation of autophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of platelet activation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue.") @@ -62903,30 +62061,24 @@ AnnotationAssertion( "negative regulation of sodium ion transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of cell morphogenesis involved in differentiation) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010769") -AnnotationAssertion(rdfs:label "regulation of cell morphogenesis involved in differentiation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of cell morphogenesis involved in differentiation) +# Class: (positive regulation of cell morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24299"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010770") -AnnotationAssertion(rdfs:label "positive regulation of cell morphogenesis involved in differentiation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +AnnotationAssertion(rdfs:label "positive regulation of cell morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (negative regulation of cell morphogenesis involved in differentiation) +# Class: (negative regulation of cell morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24299"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010771") -AnnotationAssertion(rdfs:label "negative regulation of cell morphogenesis involved in differentiation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +AnnotationAssertion(rdfs:label "negative regulation of cell morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (calcitonin catabolic process) @@ -63210,6 +62362,17 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (regulation of amino acid import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of amino acid import into a cell.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2009-05-06T11:33:12Z") +AnnotationAssertion( "regulation of amino acid import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0010958") +AnnotationAssertion(rdfs:label "regulation of amino acid import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of metal ion transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate, or extent of metal ion transport. Metal ion transport is the directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -65812,54 +64975,6 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (macroautophagy) - -AnnotationAssertion(Annotation( "PMID:11099404") Annotation( "PMID:12914914") Annotation( "PMID:15798367") Annotation( "PMID:16973210") Annotation( "PMID:20159618") Annotation( "PMID:9412464") "The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Some types of macroautophagy, e.g. pexophagy, mitophagy, involve selective targeting of the targets to be degraded.") -AnnotationAssertion( "GO:0034262") -AnnotationAssertion( "autophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0016236") -AnnotationAssertion(rdfs:comment "Targeted macroautophagy sometimes targets regions of cytoplasm containing non-self, such as virus particles or components (e.g. see PMID:20159618). As this is essentially the same process as macroautophagy that encloses and digests only self, the term autophagy is still used despite the enclosure of some non-self (non-auto) entities.") -AnnotationAssertion(rdfs:label "macroautophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (positive regulation of macroautophagy) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "PMID:9412464") "Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.") -AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "positive regulation of starvation-induced autophagy") -AnnotationAssertion( "up regulation of macroautophagy") -AnnotationAssertion( "up-regulation of macroautophagy") -AnnotationAssertion( "upregulation of macroautophagy") -AnnotationAssertion( "activation of macroautophagy") -AnnotationAssertion( "stimulation of macroautophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0016239") -AnnotationAssertion(rdfs:label "positive regulation of macroautophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (regulation of macroautophagy) - -AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the frequency, rate or extent of macroautophagy.") -AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "regulation of starvation-induced autophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0016241") -AnnotationAssertion(rdfs:label "regulation of macroautophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of macroautophagy) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of macroautophagy.") -AnnotationAssertion( "down regulation of macroautophagy") -AnnotationAssertion( "down-regulation of macroautophagy") -AnnotationAssertion( "downregulation of macroautophagy") -AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "negative regulation of starvation-induced autophagy") -AnnotationAssertion( "inhibition of macroautophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0016242") -AnnotationAssertion(rdfs:label "negative regulation of macroautophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (kinase activity) AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") @@ -65875,7 +64990,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectHasSelf()) @@ -65977,15 +65091,6 @@ AnnotationAssertion(rdfs:label "soma SubClassOf( ) SubClassOf( ) -# Class: (pyrophosphatase activity) - -AnnotationAssertion(Annotation( "GOC:curators") Annotation( "https://en.wikipedia.org/wiki/Pyrophosphatase") "Catalysis of the hydrolysis of a pyrophosphate bond (diphosphate bond) between two phosphate groups.") -AnnotationAssertion(Annotation(rdfs:label "NUDT13 hydrolyses AP6A to AP4 and ADP") "Reactome:R-HSA-6810472") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016462") -AnnotationAssertion(rdfs:label "pyrophosphatase activity") -SubClassOf( ) - # Class: (cell migration) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:ems") Annotation( "GOC:pf") Annotation( "Wikipedia:Cell_migration") "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.") @@ -66000,6 +65105,14 @@ SubClassOf( ObjectComplementOf(Object SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) +# Class: (cytosolic transport) + +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of substances or organelles within the cytosol.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0016482") +AnnotationAssertion(rdfs:label "cytosolic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (protein processing) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:jl") Annotation( "GOC:jsg") "Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.") @@ -66113,35 +65226,6 @@ AnnotationAssertion( "transferase activity") SubClassOf( ) -# Class: (acyltransferase activity) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20486"^^xsd:anyURI) -AnnotationAssertion( "GO:0008415") -AnnotationAssertion( "EC:2.3.-.-") -AnnotationAssertion(Annotation(rdfs:label "Cytosolic chenodeoxycholoyl-CoA or choloyl-CoA are conjugated with glycine or taurine") "Reactome:R-HSA-159431") -AnnotationAssertion(Annotation(rdfs:label "Choloyl CoA reacts with glycine or taurine to form glycocholate or taurocholate") "Reactome:R-HSA-192312") -AnnotationAssertion(Annotation(rdfs:label "Chenodeoxycholoyl CoA reacts with glycine or taurine to form glycochenodeoxycholate or taurochenodeoxycholate") "Reactome:R-HSA-193491") -AnnotationAssertion(Annotation(rdfs:label "LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs") "Reactome:R-HSA-6792572") -AnnotationAssertion(Annotation(rdfs:label "HRASLS transfer acyl group from PC to PE to form NAPE") "Reactome:R-HSA-8858298") -AnnotationAssertion( "transferase activity, transferring acyl groups") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016746") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acyltransferase activity") -SubClassOf( ) - -# Class: (aminoacyltransferase activity) - -AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "EC:2.3.2.-") -AnnotationAssertion( "transferase activity, transferring amino-acyl groups") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016755") -AnnotationAssertion(rdfs:label "aminoacyltransferase activity") -SubClassOf( ) - # Class: (transferase activity, transferring phosphorus-containing groups) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") @@ -66206,106 +65290,6 @@ AnnotationAssertion( "hydrolase activity, acting on ester bonds") SubClassOf( ) -# Class: (hydrolase activity, acting on acid anhydrides) - -AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of the hydrolysis of any acid anhydride.") -AnnotationAssertion( "EC:3.6.-.-") -AnnotationAssertion( "hydrolase activity, acting on acid anhydrides, involved in cellular and subcellular movement") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016817") -AnnotationAssertion(rdfs:label "hydrolase activity, acting on acid anhydrides") -SubClassOf( ) - -# Class: (hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides) - -AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.") -AnnotationAssertion( "EC:3.6.1.-") -AnnotationAssertion(Annotation(rdfs:label "NUDT1 hydrolyzes O6-methyl-dGTP to O6-methyl-dGMP") "Reactome:R-HSA-9731590") -AnnotationAssertion(Annotation(rdfs:label "NUDT1 hydrolyzes N6-methyl-dATP to N6-methyl-dAMP") "Reactome:R-HSA-9731613") -AnnotationAssertion(Annotation(rdfs:label "NUDT1 hydrolyzes N6-methyl-ATP to N6-methyl-AMP") "Reactome:R-HSA-9731632") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016818") -AnnotationAssertion(rdfs:label "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides") -SubClassOf( ) - -# Class: (ligase activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19380"^^xsd:anyURI) -AnnotationAssertion( "EC:6.-.-.-") -AnnotationAssertion(Annotation( "GOC:jh2") "synthetase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016874") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ligase activity") -SubClassOf( ) - -# Class: (ligase activity, forming carbon-sulfur bonds) - -AnnotationAssertion(Annotation( "EC:6.2.-.-") Annotation( "GOC:mah") "Catalysis of the joining of two molecules via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.") -AnnotationAssertion( "EC:6.2.-.-") -AnnotationAssertion( "ligase activity, forming carbon-sulphur bonds") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016877") -AnnotationAssertion(rdfs:label "ligase activity, forming carbon-sulfur bonds") -SubClassOf( ) - -# Class: (ATP hydrolysis activity) - -AnnotationAssertion(Annotation( "RHEA:13065") "Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19078"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20498"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22371"^^xsd:anyURI) -AnnotationAssertion( "GO:0004002") -AnnotationAssertion( "GO:0042623") -AnnotationAssertion( "RHEA:13065") -AnnotationAssertion(Annotation(rdfs:label "NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)") "Reactome:R-HSA-159101") -AnnotationAssertion(Annotation(rdfs:label "ATP hydrolysis by HSP70") "Reactome:R-HSA-3371422") -AnnotationAssertion(Annotation(rdfs:label "Trafficking of GluR2-containing AMPA receptors to synapse") "Reactome:R-HSA-416985") -AnnotationAssertion(Annotation(rdfs:label "ATP hydrolysis by HSP90") "Reactome:R-HSA-5618093") -AnnotationAssertion(Annotation(rdfs:label "SPRTN:VCP-mediated release of POLH from monoUb:K164-PCNA") "Reactome:R-HSA-5654989") -AnnotationAssertion(Annotation(rdfs:label "NSF ATPase activity dissociates cis-SNARE") "Reactome:R-HSA-5694425") -AnnotationAssertion(Annotation(rdfs:label "NSF ATPase activity dissociates cis-SNARE at cis-Golgi") "Reactome:R-HSA-6809015") -AnnotationAssertion(Annotation(rdfs:label "NSF ATPase activity dissociates cis-SNARE at the ER") "Reactome:R-HSA-6811422") -AnnotationAssertion(Annotation(rdfs:label "ATP hydrolysis by RHOBTB3 promotes PLIN3 dissociation") "Reactome:R-HSA-6814670") -AnnotationAssertion(Annotation(rdfs:label "ATP hydrolysis by NSF disassembles the cis-SNARE at the TGN") "Reactome:R-HSA-6814678") -AnnotationAssertion(Annotation(rdfs:label "NSF-dependent ATP hydrolysis disassembles the cis-SNARE at the TGN") "Reactome:R-HSA-6814683") -AnnotationAssertion(Annotation(rdfs:label "ATP hydrolysis by NSF disassembles the cis-SNARE at the Golgi membrane") "Reactome:R-HSA-8847638") -AnnotationAssertion(Annotation(rdfs:label "HSPA8-mediated ATP hydrolysis promotes vesicle uncoating") "Reactome:R-HSA-8868658") -AnnotationAssertion(Annotation(rdfs:label "HSP90-dependent ATP hydrolysis promotes release of ESR:ESTG from chaperone complex") "Reactome:R-HSA-8939203") -AnnotationAssertion(Annotation(rdfs:label "Progesterone stimulation promotes PGR:P4 binding to ESR1:ESTG") "Reactome:R-HSA-9038161") -AnnotationAssertion(Annotation(rdfs:label "ESCRT Disassembly") "Reactome:R-HSA-917693") -AnnotationAssertion(Annotation(rdfs:label "Tail-anchored protein:SGTA:BAG6:GET4:UBL4A:ASNA1:ATP dissociates and ASNA1 hydrolyzes ATP yielding Tail-anchored protein:ASNA1:ADP") "Reactome:R-HSA-9609860") -AnnotationAssertion(Annotation(rdfs:label "VPS4 mediates disassembly of ESCRTIII subunits to promote sealing of holes in the nuclear envelope") "Reactome:R-HSA-9668415") -AnnotationAssertion(Annotation(rdfs:label "RHOBTB3 hydrolyzes ATP") "Reactome:R-HSA-9706399") -AnnotationAssertion(Annotation(rdfs:label "ATP-dependent release of CDT1 from the OCCM complex") "Reactome:R-HSA-9749350") -AnnotationAssertion( "ATP hydrolase activity") -AnnotationAssertion( "ATP phosphohydrolase activity") -AnnotationAssertion( "adenosine 5'-triphosphatase activity") -AnnotationAssertion( "adenosine triphosphatase activity") -AnnotationAssertion( "adenosinetriphosphatase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "ATP monophosphatase activity") -AnnotationAssertion( "GO:0016887") -AnnotationAssertion(rdfs:comment "Note that this term is meant to specifically represent the ATPase activity of proteins using ATP as a source of energy to drive a reaction. If possible, gene products should also be annotated to a child of 'ATP-dependent activity ; GO:0140657', to capture their overall function.") -AnnotationAssertion(rdfs:label "ATP hydrolysis activity") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (G protein-coupled acetylcholine receptor activity) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:fj") Annotation( "GOC:mah") "Combining with acetylcholine and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.") @@ -66368,41 +65352,6 @@ AnnotationAssertion( "response to insecticide") SubClassOf( ) -# Class: (ribonucleoside triphosphate phosphatase activity) - -AnnotationAssertion(Annotation( "RHEA:23680") "Catalysis of the reaction: a ribonucleoside triphosphate + H2O = a ribonucleoside diphosphate + H+ + phosphate.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21232"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23401"^^xsd:anyURI) -AnnotationAssertion( "apyrase activity") -AnnotationAssertion(Annotation( "EC:3.6.1.15") "nucleoside 5-triphosphatase activity") -AnnotationAssertion( "nucleoside triphosphatase activity") -AnnotationAssertion( "nucleoside triphosphate hydrolase activity") -AnnotationAssertion( "nucleoside triphosphate phosphatase activity") -AnnotationAssertion( "nucleoside-triphosphatase activity") -AnnotationAssertion( "EC:3.6.1.15") -AnnotationAssertion( "MetaCyc:NUCLEOSIDE-TRIPHOSPHATASE-RXN") -AnnotationAssertion( "RHEA:23680") -AnnotationAssertion(Annotation(rdfs:label "NTPDase1 hydrolyzes nucleoside triphosphates") "Reactome:R-HSA-8850846") -AnnotationAssertion(Annotation(rdfs:label "NTPDase2 hydrolyzes nucleoside triphosphates") "Reactome:R-HSA-8851089") -AnnotationAssertion(Annotation(rdfs:label "NTPDase3 hydrolyzes nucleoside triphosphates") "Reactome:R-HSA-8851110") -AnnotationAssertion(Annotation(rdfs:label "NTPDase4 hydrolyzes nucleoside triphosphates") "Reactome:R-HSA-8851234") -AnnotationAssertion(Annotation(rdfs:label "NTPDase7 hydrolyzes nucleoside triphosphates") "Reactome:R-HSA-8851494") -AnnotationAssertion(Annotation(rdfs:label "NTPDase8 hydrolyzes nucleoside triphosphates") "Reactome:R-HSA-8851538") -AnnotationAssertion( "NTPase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "nucleoside triphosphate phosphohydrolase activity") -AnnotationAssertion( "nucleoside-5-triphosphate phosphohydrolase activity") -AnnotationAssertion( "GO:0017111") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ribonucleoside triphosphate phosphatase activity") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nucleologenesis) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells.") @@ -67128,67 +66077,6 @@ AnnotationAssertion(rdfs:label "one- EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (Atg12 transferase activity) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:12826404") "Catalysis of the transfer of ATG12 from one protein to another via the reaction X-ATG12 + Y = Y-ATG12 + X, where both X-ATG12 and Y-ATG12 are covalent linkages.") -AnnotationAssertion(Annotation(rdfs:label "ATG10 transfers ATG12 from ATG7 to ATG10") "Reactome:R-HSA-5681999") -AnnotationAssertion( "APG12 conjugating enzyme activity") -AnnotationAssertion( "APG12 ligase activity") -AnnotationAssertion( "Atg12 conjugating enzyme activity") -AnnotationAssertion( "Atg12 ligase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0019777") -AnnotationAssertion(rdfs:label "Atg12 transferase activity") -SubClassOf( ) - -# Class: (Atg12 activating enzyme activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Catalysis of the activation of the small ubiquitin-related modifier APG12, through the formation of an ATP-dependent high-energy thiolester bond.") -AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "GOC:vw") "APG12 activating enzyme activity") -AnnotationAssertion( "GO:0019778") -AnnotationAssertion(rdfs:label "Atg12 activating enzyme activity") -SubClassOf( ) - -# Class: (protein-phosphatidylethanolamide deconjugating activity) - -AnnotationAssertion(Annotation( "PMID:22240591") Annotation( "PMID:22652539") Annotation( "PMID:28330855") Annotation( "PMID:2882172") Annotation( "PMID:28901328") "Catalysis of the reaction: [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine. An example of this reaction is the removal of ATG8 from membranes to which it is covalently linked to a phosphatidylethanolamid via its terminal glycine residue.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25472"^^xsd:anyURI) -AnnotationAssertion(Annotation( "skos:narrowMatch") "Atg8-specific protease activity") -AnnotationAssertion(Annotation( "GOC:vw") "APG8-specific protease activity") -AnnotationAssertion(Annotation( "skos:narrowMatch") "ATG8-PE deconjugation activity") -AnnotationAssertion(Annotation( "skos:narrowMatch") "ATG8-PE hydrolase activity") -AnnotationAssertion(Annotation( "skos:narrowMatch") "Atg8-specific peptidase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "skos:narrowMatch") "APG8-PE hydrolase") -AnnotationAssertion( "GO:0019786") -AnnotationAssertion(rdfs:label "protein-phosphatidylethanolamide deconjugating activity") -SubClassOf( ) -SubClassOf( ) - -# Class: (ubiquitin-like protein transferase activity) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:rn") Annotation( "PMID:10806345") Annotation( "PMID:10884686") "Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y = Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24697"^^xsd:anyURI) -AnnotationAssertion( "GO:0008639") -AnnotationAssertion( "GO:0008640") -AnnotationAssertion( "E2") -AnnotationAssertion(Annotation(rdfs:label "ATG16L1 complex transfers LC3 from ATG3 to PE") "Reactome:R-HSA-5678490") -AnnotationAssertion(Annotation(rdfs:label "RIP2 is K63 polyubiquitinated") "Reactome:R-HSA-688137") -AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein transferase activity") -AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein ligase activity") -AnnotationAssertion( "small protein conjugating enzyme activity") -AnnotationAssertion( "ubiquitin-like conjugating enzyme activity") -AnnotationAssertion( "ubiquitin-like-protein ligase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "GOC:dph") "E3") -AnnotationAssertion( "GO:0019787") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ubiquitin-like protein transferase activity") -SubClassOf( ) -SubClassOf( ) - # Class: (immunoglobulin complex) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:jl") Annotation( "ISBN:0781765196") "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") @@ -70747,6 +69635,21 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (cytosolic ribosome) + +AnnotationAssertion(Annotation( "GOC:mtg_sensu") "A ribosome located in the cytosol.") +AnnotationAssertion( "GO:0005830") +AnnotationAssertion( "GO:0009281") +AnnotationAssertion( "GO:0030871") +AnnotationAssertion( "70S ribosome") +AnnotationAssertion( "80S ribosome") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0022626") +AnnotationAssertion(rdfs:label "cytosolic ribosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + # Class: (active transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:mtg_transport") Annotation( "ISBN:0815340729") "Enables the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction.") @@ -71017,7 +69920,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell projection organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) # Class: (cell projection assembly) @@ -71982,20 +70885,6 @@ AnnotationAssertion(rdfs:label "memb EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (autophagosome membrane disassembly) - -AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "GOC:mah") "The controlled breakdown of the membranes of autophagosomes.") -AnnotationAssertion( "autophagic membrane breakdown") -AnnotationAssertion(Annotation( "GOC:autophagy") "autophagic vacuole membrane disassembly") -AnnotationAssertion(Annotation( "GOC:autophagy") "autophagic membrane catabolism") -AnnotationAssertion(Annotation( "GOC:autophagy") "autophagic membrane degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0030399") -AnnotationAssertion(rdfs:label "autophagosome membrane disassembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (defecation) AnnotationAssertion(Annotation( "GOC:mah") "The expulsion of feces from the rectum.") @@ -72895,6 +71784,16 @@ AnnotationAssertion(rdfs:label "acto EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (dense core granule) + +AnnotationAssertion(Annotation( "NIF_Subcellular:sao772007592") Annotation( "PMID:14690495") "Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted.") +AnnotationAssertion( "NIF_Subcellular:sao772007592") +AnnotationAssertion(Annotation( "GOC:kmv") Annotation( ) "dense core vesicle") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031045") +AnnotationAssertion(rdfs:label "dense core granule") +SubClassOf( ) + # Class: (hair follicle morphogenesis) AnnotationAssertion(Annotation( "GOC:ln") "The process in which the anatomical structures of the hair follicle are generated and organized.") @@ -74079,6 +72978,15 @@ AnnotationAssertion( "bleb assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (maintenance of protein location in cell cortex) + +AnnotationAssertion(Annotation( "GOC:vw") "A process in which a protein or protein complex is maintained in a specific location in the cell cortex.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "cortical protein anchoring") +AnnotationAssertion( "GO:0032065") +AnnotationAssertion(rdfs:label "maintenance of protein location in cell cortex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of nuclease activity) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids.") @@ -74237,6 +73145,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (dense core granule membrane) + +AnnotationAssertion(Annotation( "GOC:mah") "The lipid bilayer surrounding a dense core granule.") +AnnotationAssertion(Annotation( "GOC:kmv") "dense core vesicle membrane") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0032127") +AnnotationAssertion(rdfs:label "dense core granule membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of synaptic transmission, cholinergic) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine.") @@ -74533,6 +73451,17 @@ AnnotationAssertion( "secretory granule localization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (dense core granule localization) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a dense core granule is transported to, and/or maintained in, a specific location within the cell.") +AnnotationAssertion(Annotation( "GOC:mah") "dense core granule localisation") +AnnotationAssertion(Annotation( "GOC:kmv") "dense core vesicle localization") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "dense core granule clustering") +AnnotationAssertion( "GO:0032253") +AnnotationAssertion(rdfs:label "dense core granule localization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of protein polymerization) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the process of creating protein polymers.") @@ -75281,6 +74210,19 @@ AnnotationAssertion(rdfs:label "mult SubClassOf( ) SubClassOf( ) +# Class: (maintenance of protein location in cell) + +AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:mah") "Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of protein localization in cell") +AnnotationAssertion( "GO:0032507") +AnnotationAssertion(rdfs:label "maintenance of protein location in cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + # Class: (microvillus organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.") @@ -75434,40 +74376,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.") AnnotationAssertion(rdfs:label "RNA biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of ATP-dependent activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops or reduces the rate of an ATP-dependent activity.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22371"^^xsd:anyURI) -AnnotationAssertion( "down regulation of ATPase activity") -AnnotationAssertion( "down-regulation of ATPase activity") -AnnotationAssertion( "downregulation of ATPase activity") -AnnotationAssertion( "negative regulation of ATPase activity") -AnnotationAssertion( "negative regulation of adenosinetriphosphatase activity") -AnnotationAssertion( "inhibition of ATPase activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032780") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of ATP-dependent activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of ATP-dependent activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the rate of an ATP-dependent activity.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22371"^^xsd:anyURI) -AnnotationAssertion( "positive regulation of ATPase activity") -AnnotationAssertion( "positive regulation of adenosinetriphosphatase activity") -AnnotationAssertion( "up regulation of ATPase activity") -AnnotationAssertion( "up-regulation of ATPase activity") -AnnotationAssertion( "upregulation of ATPase activity") -AnnotationAssertion( "activation of ATPase activity") -AnnotationAssertion( "stimulation of ATPase activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032781") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of ATP-dependent activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (bile acid secretion) @@ -75898,6 +74807,39 @@ AnnotationAssertion( "regulation of actin filament-based process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (amino acid export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:jl") "The directed movement of amino acids from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-11-14T14:27:40Z") +AnnotationAssertion( "GO:0044746") +AnnotationAssertion( "amino acid export") +AnnotationAssertion( "amino acid transmembrane export") +AnnotationAssertion( "amino acid efflux") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032973") +AnnotationAssertion(rdfs:label "amino acid export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (amino acid transmembrane export from vacuole) + +AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of amino acids out of the vacuole, across the vacuolar membrane.") +AnnotationAssertion( "amino acid efflux from vacuole") +AnnotationAssertion( "vacuolar amino acid export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032974") +AnnotationAssertion(rdfs:label "amino acid transmembrane export from vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (amino acid transmembrane import into vacuole) + +AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of amino acids into the vacuole across the vacuolar membrane.") +AnnotationAssertion( "vacuolar amino acid import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032975") +AnnotationAssertion(rdfs:label "amino acid transmembrane import into vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (keratinocyte activation) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:15737202") "A change in the morphology or behavior of a keratinocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. Upon activation, keratinocytes become migratory and hyperproliferative, and produce growth factors and cytokines.") @@ -77841,35 +76783,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (salivary gland histolysis) - -AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dph") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:9409683") "The stage-specific break down of the larval salivary glands during Drosophila metamorphosis, to allow replacement of larval structures by tissues and structures that form the adult fly.") -AnnotationAssertion( "salivary gland regression") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0035070") -AnnotationAssertion(rdfs:label "salivary gland histolysis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (salivary gland cell autophagic cell death) - -AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:10882130") "The stage-specific programmed cell death of salivary gland cells during salivary gland histolysis.") -AnnotationAssertion( "autophagic cell death of salivary gland cells") -AnnotationAssertion( "programmed cell death of salivary gland cells by autophagy") -AnnotationAssertion( "salivary gland cell death") -AnnotationAssertion( "salivary gland cell programmed cell death by autophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0035071") -AnnotationAssertion(rdfs:label "salivary gland cell autophagic cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (axoneme assembly) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:cilia") Annotation( "GOC:jl") Annotation( "ISBN:0815316194") "The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.") @@ -79911,7 +78824,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036344") AnnotationAssertion(rdfs:label "platelet morphogenesis") -SubClassOf( ) +SubClassOf( ) # Class: (platelet maturation) @@ -79924,6 +78837,21 @@ AnnotationAssertion(rdfs:label "plat EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (sodium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:14674689") "The directed movement of sodium ions from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2009-12-16T11:13:55Z") +AnnotationAssertion( "GO:0071436") +AnnotationAssertion( "GO:0098667") +AnnotationAssertion( "sodium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:mah") "sodium export") +AnnotationAssertion( "sodium ion export") +AnnotationAssertion( "GO:0036376") +AnnotationAssertion(rdfs:label "sodium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (myofilament) AnnotationAssertion(Annotation( "Wikipedia:Myofilament") "Any of the smallest contractile units of a myofibril (striated muscle fiber).") @@ -80796,7 +79724,6 @@ AnnotationAssertion( "GO:0042133") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neurotransmitter metabolic process") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) @@ -81158,6 +80085,48 @@ AnnotationAssertion( "regulation of fatty acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of protein import into nucleus) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus.") +AnnotationAssertion( "regulation of protein import into cell nucleus") +AnnotationAssertion( "regulation of protein transport from cytoplasm to nucleus") +AnnotationAssertion( "regulation of protein-nucleus import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0042306") +AnnotationAssertion(rdfs:label "regulation of protein import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of protein import into nucleus) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus.") +AnnotationAssertion( "positive regulation of protein import into cell nucleus") +AnnotationAssertion( "positive regulation of protein transport from cytoplasm to nucleus") +AnnotationAssertion( "positive regulation of protein-nucleus import") +AnnotationAssertion( "up regulation of protein import into nucleus") +AnnotationAssertion( "up-regulation of protein import into nucleus") +AnnotationAssertion( "upregulation of protein import into nucleus") +AnnotationAssertion( "activation of protein import into nucleus") +AnnotationAssertion( "stimulation of protein import into nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0042307") +AnnotationAssertion(rdfs:label "positive regulation of protein import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of protein import into nucleus) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus.") +AnnotationAssertion( "down regulation of protein import into nucleus") +AnnotationAssertion( "down-regulation of protein import into nucleus") +AnnotationAssertion( "downregulation of protein import into nucleus") +AnnotationAssertion( "negative regulation of protein import into cell nucleus") +AnnotationAssertion( "negative regulation of protein transport from cytoplasm to nucleus") +AnnotationAssertion( "negative regulation of protein-nucleus import") +AnnotationAssertion( "inhibition of protein import into nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0042308") +AnnotationAssertion(rdfs:label "negative regulation of protein import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (negative regulation of circadian sleep/wake cycle, sleep) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:jl") Annotation( "ISBN:0192800981") "Any process that stops, prevents or reduces the duration or quality of sleep, a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.") @@ -83672,18 +82641,6 @@ AnnotationAssertion( "regulation of secondary metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of ATP-dependent activity) - -AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the rate of an ATP-dependent activity.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22371"^^xsd:anyURI) -AnnotationAssertion( "regulation of ATPase activity") -AnnotationAssertion( "regulation of adenosinetriphosphatase activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043462") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of ATP-dependent activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of fermentation) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of fermentation, the anaerobic enzymatic conversion of organic compounds, especially carbohydrates, to other compounds, especially to ethyl alcohol, resulting in energy in the form of adenosine triphosphate (ATP).") @@ -84478,17 +83435,17 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (dentate gyrus mossy fiber) -AnnotationAssertion(Annotation( "NIF_Subcellular:nlx_subcell_20090601") Annotation( "PMID:17765709") "Distinctive, unmyelinated axons produced by granule cells.") +AnnotationAssertion(Annotation( "NIF_Subcellular:nlx_subcell_20090601") Annotation( "PMID:17765709") "Distinctive, unmyelinated axons produced by dentate gyrus granule cells.") AnnotationAssertion( "jl") AnnotationAssertion( "2010-02-05T11:23:55Z") +AnnotationAssertion( "granule cell axon") AnnotationAssertion( "NIF_Subcellular:nlx_subcell_20090601") AnnotationAssertion( "dentate gyrus mossy fibre") -AnnotationAssertion( "granule cell axon") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0044302") AnnotationAssertion(rdfs:label "dentate gyrus mossy fiber") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (type B pancreatic cell proliferation) @@ -84619,6 +83576,16 @@ AnnotationAssertion( "multi-multicellular organism process") SubClassOf( ) +# Class: (protein transmembrane import into intracellular organelle) + +AnnotationAssertion(Annotation( "GOC:jl") "The directed movement of proteins into an intracellular organelle, across a membrane.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-11-07T15:37:36Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044743") +AnnotationAssertion(rdfs:label "protein transmembrane import into intracellular organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (cilium organization) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:jl") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.") @@ -84636,19 +83603,6 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) -# Class: (nucleophagy) - -AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "GOC:jl") Annotation( "PMID:24013549") "A form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2013-09-10T15:50:25Z") -AnnotationAssertion( "autophagy of nucleus") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "nucleus degradation") -AnnotationAssertion( "GO:0044804") -AnnotationAssertion(rdfs:label "nucleophagy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (biological phase) AnnotationAssertion(Annotation( "GOC:jl") "A distinct period or stage in a biological process or cycle.") @@ -84933,6 +83887,19 @@ AnnotationAssertion(rdfs:label "esta EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (maintenance of protein location) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away.") +AnnotationAssertion( "active protein retrieval") +AnnotationAssertion( "protein retention") +AnnotationAssertion( "protein sequestering") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of protein localization") +AnnotationAssertion( "GO:0045185") +AnnotationAssertion(rdfs:label "maintenance of protein location") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of circadian sleep/wake cycle, sleep) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0192800981") "Any process that modulates the frequency, rate or extent of sleep; a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.") @@ -88785,6 +87752,172 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of nucleocytoplasmic transport) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046822") +AnnotationAssertion(rdfs:label "regulation of nucleocytoplasmic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of nucleocytoplasmic transport) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus.") +AnnotationAssertion( "down regulation of nucleocytoplasmic transport") +AnnotationAssertion( "down-regulation of nucleocytoplasmic transport") +AnnotationAssertion( "downregulation of nucleocytoplasmic transport") +AnnotationAssertion( "inhibition of nucleocytoplasmic transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046823") +AnnotationAssertion(rdfs:label "negative regulation of nucleocytoplasmic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of nucleocytoplasmic transport) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm.") +AnnotationAssertion( "up regulation of nucleocytoplasmic transport") +AnnotationAssertion( "up-regulation of nucleocytoplasmic transport") +AnnotationAssertion( "upregulation of nucleocytoplasmic transport") +AnnotationAssertion( "activation of nucleocytoplasmic transport") +AnnotationAssertion( "stimulation of nucleocytoplasmic transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046824") +AnnotationAssertion(rdfs:label "positive regulation of nucleocytoplasmic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (regulation of protein export from nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that modulates the frequency, rate or extent of the directed movement of proteins from the nucleus to the cytoplasm.") +AnnotationAssertion( "regulation of protein export from cell nucleus") +AnnotationAssertion( "regulation of protein export out of nucleus") +AnnotationAssertion( "regulation of protein transport from nucleus to cytoplasm") +AnnotationAssertion( "regulation of protein-nucleus export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046825") +AnnotationAssertion(rdfs:label "regulation of protein export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of protein export from nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm.") +AnnotationAssertion( "down regulation of protein export from nucleus") +AnnotationAssertion( "down-regulation of protein export from nucleus") +AnnotationAssertion( "downregulation of protein export from nucleus") +AnnotationAssertion( "negative regulation of protein export from cell nucleus") +AnnotationAssertion( "negative regulation of protein export out of nucleus") +AnnotationAssertion( "negative regulation of protein transport from nucleus to cytoplasm") +AnnotationAssertion( "negative regulation of protein-nucleus export") +AnnotationAssertion( "inhibition of protein export from nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046826") +AnnotationAssertion(rdfs:label "negative regulation of protein export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (positive regulation of protein export from nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.") +AnnotationAssertion( "positive regulation of protein export from cell nucleus") +AnnotationAssertion( "positive regulation of protein export out of nucleus") +AnnotationAssertion( "positive regulation of protein transport from nucleus to cytoplasm") +AnnotationAssertion( "positive regulation of protein-nucleus export") +AnnotationAssertion( "up regulation of protein export from nucleus") +AnnotationAssertion( "up-regulation of protein export from nucleus") +AnnotationAssertion( "upregulation of protein export from nucleus") +AnnotationAssertion( "activation of protein export from nucleus") +AnnotationAssertion( "stimulation of protein export from nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046827") +AnnotationAssertion(rdfs:label "positive regulation of protein export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (regulation of RNA import into nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that modulates the frequency, rate or extent of movement of RNA from the cytoplasm to the nucleus.") +AnnotationAssertion( "regulation of RNA import into cell nucleus") +AnnotationAssertion( "regulation of RNA transport from cytoplasm to nucleus") +AnnotationAssertion( "regulation of RNA-nucleus import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046828") +AnnotationAssertion(rdfs:label "regulation of RNA import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of RNA import into nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of RNA from the cytoplasm into the nucleus.") +AnnotationAssertion( "down regulation of RNA import into nucleus") +AnnotationAssertion( "down-regulation of RNA import into nucleus") +AnnotationAssertion( "downregulation of RNA import into nucleus") +AnnotationAssertion( "negative regulation of RNA import into cell nucleus") +AnnotationAssertion( "negative regulation of RNA transport from cytoplasm to nucleus") +AnnotationAssertion( "negative regulation of RNA-nucleus import") +AnnotationAssertion( "inhibition of RNA import into nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046829") +AnnotationAssertion(rdfs:label "negative regulation of RNA import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of RNA import into nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that activates or increases the frequency, rate or extent of movement of RNA from the cytoplasm into the nucleus.") +AnnotationAssertion( "positive regulation of RNA import into cell nucleus") +AnnotationAssertion( "positive regulation of RNA transport from cytoplasm to nucleus") +AnnotationAssertion( "positive regulation of RNA-nucleus import") +AnnotationAssertion( "up regulation of RNA import into nucleus") +AnnotationAssertion( "up-regulation of RNA import into nucleus") +AnnotationAssertion( "upregulation of RNA import into nucleus") +AnnotationAssertion( "activation of RNA import into nucleus") +AnnotationAssertion( "stimulation of RNA import into nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046830") +AnnotationAssertion(rdfs:label "positive regulation of RNA import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (regulation of RNA export from nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that modulates the frequency, rate or extent of the directed movement of RNA from the nucleus to the cytoplasm.") +AnnotationAssertion( "regulation of RNA export from cell nucleus") +AnnotationAssertion( "regulation of RNA export out of nucleus") +AnnotationAssertion( "regulation of RNA transport from nucleus to cytoplasm") +AnnotationAssertion( "regulation of RNA-nucleus export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046831") +AnnotationAssertion(rdfs:label "regulation of RNA export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of RNA export from nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of RNA from the nucleus into the cytoplasm.") +AnnotationAssertion( "down regulation of RNA export from nucleus") +AnnotationAssertion( "down-regulation of RNA export from nucleus") +AnnotationAssertion( "downregulation of RNA export from nucleus") +AnnotationAssertion( "negative regulation of RNA export from cell nucleus") +AnnotationAssertion( "negative regulation of RNA export out of nucleus") +AnnotationAssertion( "negative regulation of RNA transport from nucleus to cytoplasm") +AnnotationAssertion( "negative regulation of RNA-nucleus export") +AnnotationAssertion( "inhibition of RNA export from nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046832") +AnnotationAssertion(rdfs:label "negative regulation of RNA export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of RNA export from nucleus) + +AnnotationAssertion(Annotation( "GOC:bf") "Any process that activates or increases the frequency, rate or extent of directed movement of RNA from the nucleus into the cytoplasm.") +AnnotationAssertion( "positive regulation of RNA export from cell nucleus") +AnnotationAssertion( "positive regulation of RNA export out of nucleus") +AnnotationAssertion( "positive regulation of RNA transport from nucleus to cytoplasm") +AnnotationAssertion( "positive regulation of RNA-nucleus export") +AnnotationAssertion( "up regulation of RNA export from nucleus") +AnnotationAssertion( "up-regulation of RNA export from nucleus") +AnnotationAssertion( "upregulation of RNA export from nucleus") +AnnotationAssertion( "activation of RNA export from nucleus") +AnnotationAssertion( "stimulation of RNA export from nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046833") +AnnotationAssertion(rdfs:label "positive regulation of RNA export from nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (glycolipid transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of glycolipids, compounds containing (usually) 1-4 linked monosaccharide residues joined by a glycosyl linkage to a lipid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -89254,23 +88387,6 @@ AnnotationAssertion( "positive regulation of developmental pigmentation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (autophagic cell death) - -AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:18846107") Annotation( "PMID:23347517") "A form of programmed cell death that is accompanied by the formation of autophagosomes. Autophagic cell death is characterized by lack of chromatin condensation and massive vacuolization of the cytoplasm, with little or no uptake by phagocytic cells.") -AnnotationAssertion( "autophagic death") -AnnotationAssertion(Annotation( "GOC:pr") "programmed cell death by autophagy") -AnnotationAssertion(Annotation( "GOC:cjm") "programmed cell death by macroautophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "PMID:25236395") "autosis") -AnnotationAssertion(Annotation( "GOC:sl") "type II programmed cell death") -AnnotationAssertion( "GO:0048102") -AnnotationAssertion(rdfs:comment "The precise nature of autophagic cell death is still being debated, and the link between autophagy and cell death unclear. As autophagy is often induced under conditions of stress that could also lead to cell death, there has been a propagation of the idea that autophagy can act as a cell death mechanism; but others suggest that autophagy may simply be an attempt of dying cells to adapt to lethal stress rather than a mechanism to execute a cell death program. Further studies are required to resolve this controversy (see e.g. PMID:22082964, PMID:22052193, PMID:25236395). In the meantime, curators should carefully examine the experimental evidence presented in papers concerning autophagic cell death, and annotate accordingly. Recently, an instance of autophagic cell death, termed autosis, was discovered that relies on the plasma membrane Na+/K+-ATPase. Autosis was observed in vivo in the brain of rats subjected to an ischemic insult. It's still unclear if all cases of autophagic cell death require the Na+/K+-ATPase or not.") -AnnotationAssertion(rdfs:label "autophagic cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) - # Class: (somatic stem cell division) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "ISBN:0582227089") "The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line.") @@ -90340,7 +89456,7 @@ AnnotationAssertion( "GO:0048601") AnnotationAssertion(rdfs:label "oocyte morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -91888,7 +91004,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0048938") AnnotationAssertion(rdfs:label "lateral line nerve glial cell morphogenesis involved in differentiation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior lateral line nerve glial cell development) @@ -91907,7 +91023,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0048940") AnnotationAssertion(rdfs:label "anterior lateral line nerve glial cell morphogenesis involved in differentiation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (posterior lateral line nerve glial cell development) @@ -91925,7 +91041,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0048942") AnnotationAssertion(rdfs:label "posterior lateral line nerve glial cell morphogenesis involved in differentiation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (chromosome localization) @@ -92437,7 +91553,7 @@ AnnotationAssertion( "positive regulation of dendrite morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) # Class: (regulation of immune response) @@ -94106,6 +93222,17 @@ AnnotationAssertion( "positive regulation of striated muscle cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (nuclear export) + +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of substances out of the nucleus.") +AnnotationAssertion( "export from nucleus") +AnnotationAssertion( "nucleus export") +AnnotationAssertion( "substance nuclear export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051168") +AnnotationAssertion(rdfs:label "nuclear export") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (nuclear transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of substances into, out of, or within the nucleus.") @@ -94117,6 +93244,19 @@ AnnotationAssertion( "nuclear transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +# Class: (import into nucleus) + +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of substances into the nucleus.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2013-12-19T15:26:34Z") +AnnotationAssertion( "GO:1902593") +AnnotationAssertion( "nuclear import") +AnnotationAssertion( "nuclear translocation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051170") +AnnotationAssertion(rdfs:label "import into nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (regulation of nitrogen compound metabolic process) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") @@ -94221,6 +93361,45 @@ AnnotationAssertion( "localization") SubClassOf( ) +# Class: (sequestering of calcium ion) + +AnnotationAssertion(Annotation( "GOC:ai") "The process of binding or confining calcium ions such that they are separated from other components of a biological system.") +AnnotationAssertion( "calcium ion (Ca2+) retention") +AnnotationAssertion( "calcium ion (Ca2+) sequestering") +AnnotationAssertion( "calcium ion (Ca2+) sequestration") +AnnotationAssertion( "calcium ion (Ca2+) storage") +AnnotationAssertion( "retention of calcium ion (Ca2+)") +AnnotationAssertion( "sequestering of calcium ion (Ca2+)") +AnnotationAssertion( "sequestration of calcium ion (Ca2+)") +AnnotationAssertion( "storage of calcium ion (Ca2+)") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "calcium ion storage activity") +AnnotationAssertion( "negative regulation of calcium ion (Ca2+) transport") +AnnotationAssertion( "GO:0051208") +AnnotationAssertion(rdfs:label "sequestering of calcium ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (release of sequestered calcium ion into cytosol) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:hjd") Annotation( "GOC:mtg_lung") Annotation( "PMID:1814929") "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment.") +AnnotationAssertion( "calcium ion (Ca2+) mobilization") +AnnotationAssertion( "calcium mobilization") +AnnotationAssertion( "cytoplasmic release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "cytoplasmic release of stored calcium ion (Ca2+)") +AnnotationAssertion( "release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "release of sequestered calcium ion into cytoplasm") +AnnotationAssertion( "release of stored calcium ion (Ca2+)") +AnnotationAssertion( "release of stored calcium ion (Ca2+) into cytoplasm") +AnnotationAssertion( "cytosolic release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "cytosolic release of stored calcium ion (Ca2+)") +AnnotationAssertion( "release of stored calcium ion (Ca2+) into cytosol") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051209") +AnnotationAssertion(rdfs:label "release of sequestered calcium ion into cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (cartilage development) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "PMID:23251424") "The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.") @@ -94293,6 +93472,18 @@ AnnotationAssertion( "establishment of localization") SubClassOf( ) +# Class: (maintenance of location) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere.") +AnnotationAssertion( "maintenance of localization") +AnnotationAssertion( "retention") +AnnotationAssertion( "sequestering") +AnnotationAssertion( "storage") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051235") +AnnotationAssertion(rdfs:label "maintenance of location") +SubClassOf( ) + # Class: (establishment of RNA localization) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of RNA to a specific location.") @@ -94523,6 +93714,129 @@ AnnotationAssertion( "chromosome organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of release of sequestered calcium ion into cytosol) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.") +AnnotationAssertion( "regulation of release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "regulation of release of stored calcium ion (Ca2+)") +AnnotationAssertion( "regulation of calcium ion (Ca2+) mobilization") +AnnotationAssertion( "regulation of calcium mobilization") +AnnotationAssertion( "regulation of cytoplasmic release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "regulation of cytoplasmic release of stored calcium ion (Ca2+)") +AnnotationAssertion( "regulation of release of stored calcium ion (Ca2+) into cytoplasm") +AnnotationAssertion( "regulation of release of stored calcium ion (Ca2+) into cytosol") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051279") +AnnotationAssertion(rdfs:label "regulation of release of sequestered calcium ion into cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of release of sequestered calcium ion into cytosol) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.") +AnnotationAssertion( "negative regulation of calcium ion (Ca2+) mobilization") +AnnotationAssertion( "negative regulation of calcium mobilization") +AnnotationAssertion( "negative regulation of cytoplasmic release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of cytoplasmic release of stored calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of release of sequestered calcium ion into cytoplasm") +AnnotationAssertion( "negative regulation of release of stored calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of release of stored calcium ion (Ca2+) into cytoplasm") +AnnotationAssertion( "down regulation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "down-regulation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "downregulation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "negative regulation of cytosolic release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of cytosolic release of stored calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of release of stored calcium ion (Ca2+) into cytosol") +AnnotationAssertion( "inhibition of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051280") +AnnotationAssertion(rdfs:label "negative regulation of release of sequestered calcium ion into cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of release of sequestered calcium ion into cytosol) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.") +AnnotationAssertion( "positive regulation of calcium ion (Ca2+) mobilization") +AnnotationAssertion( "positive regulation of calcium mobilization") +AnnotationAssertion( "positive regulation of cytoplasmic release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of cytoplasmic release of stored calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of release of sequestered calcium ion into cytoplasm") +AnnotationAssertion( "positive regulation of release of stored calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of release of stored calcium ion (Ca2+) into cytoplasm") +AnnotationAssertion( "positive regulation of cytosolic release of sequestered calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of cytosolic release of stored calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of release of stored calcium ion (Ca2+) into cytosol") +AnnotationAssertion( "up regulation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "up-regulation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "upregulation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "activation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "stimulation of release of sequestered calcium ion into cytosol") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051281") +AnnotationAssertion(rdfs:label "positive regulation of release of sequestered calcium ion into cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (regulation of sequestering of calcium ion) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the binding or confining calcium ions such that they are separated from other components of a biological system.") +AnnotationAssertion( "regulation of calcium ion (Ca2+) retention") +AnnotationAssertion( "regulation of calcium ion (Ca2+) sequestering") +AnnotationAssertion( "regulation of calcium ion (Ca2+) sequestration") +AnnotationAssertion( "regulation of calcium ion (Ca2+) storage") +AnnotationAssertion( "regulation of retention of calcium ion (Ca2+)") +AnnotationAssertion( "regulation of sequestering of calcium ion (Ca2+)") +AnnotationAssertion( "regulation of sequestration of calcium ion (Ca2+)") +AnnotationAssertion( "regulation of storage of calcium ion (Ca2+)") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051282") +AnnotationAssertion(rdfs:label "regulation of sequestering of calcium ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + +# Class: (negative regulation of sequestering of calcium ion) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the binding or confining calcium ions such that they are separated from other components of a biological system.") +AnnotationAssertion( "down regulation of sequestering of calcium ion") +AnnotationAssertion( "down-regulation of sequestering of calcium ion") +AnnotationAssertion( "downregulation of sequestering of calcium ion") +AnnotationAssertion( "negative regulation of calcium ion (Ca2+) retention") +AnnotationAssertion( "negative regulation of calcium ion (Ca2+) sequestering") +AnnotationAssertion( "negative regulation of calcium ion (Ca2+) sequestration") +AnnotationAssertion( "negative regulation of calcium ion (Ca2+) storage") +AnnotationAssertion( "negative regulation of retention of calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of sequestering of calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of sequestration of calcium ion (Ca2+)") +AnnotationAssertion( "negative regulation of storage of calcium ion (Ca2+)") +AnnotationAssertion( "inhibition of sequestering of calcium ion") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051283") +AnnotationAssertion(rdfs:label "negative regulation of sequestering of calcium ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + +# Class: (positive regulation of sequestering of calcium ion) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of the binding or confining calcium ions such that they are separated from other components of a biological system.") +AnnotationAssertion( "positive regulation of calcium ion (Ca2+) retention") +AnnotationAssertion( "positive regulation of calcium ion (Ca2+) sequestering") +AnnotationAssertion( "positive regulation of calcium ion (Ca2+) sequestration") +AnnotationAssertion( "positive regulation of calcium ion (Ca2+) storage") +AnnotationAssertion( "positive regulation of retention of calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of sequestering of calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of sequestration of calcium ion (Ca2+)") +AnnotationAssertion( "positive regulation of storage of calcium ion (Ca2+)") +AnnotationAssertion( "up regulation of sequestering of calcium ion") +AnnotationAssertion( "up-regulation of sequestering of calcium ion") +AnnotationAssertion( "upregulation of sequestering of calcium ion") +AnnotationAssertion( "activation of sequestering of calcium ion") +AnnotationAssertion( "stimulation of sequestering of calcium ion") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051284") +AnnotationAssertion(rdfs:label "positive regulation of sequestering of calcium ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + # Class: (cell division) AnnotationAssertion(Annotation( "GOC:di") Annotation( "GOC:go_curators") Annotation( "GOC:pr") "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.") @@ -94598,16 +93912,6 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of ligase activity) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6.") -AnnotationAssertion( "ligase regulator") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051340") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of ligase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (positive regulation of hydrolase activity) AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.") @@ -94670,35 +93974,6 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "negative regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (positive regulation of ligase activity) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate.") -AnnotationAssertion( "ligase activator") -AnnotationAssertion( "up regulation of ligase activity") -AnnotationAssertion( "up-regulation of ligase activity") -AnnotationAssertion( "upregulation of ligase activity") -AnnotationAssertion( "activation of ligase activity") -AnnotationAssertion( "stimulation of ligase activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051351") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of ligase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of ligase activity) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops or reduces the rate of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate.") -AnnotationAssertion( "down regulation of ligase activity") -AnnotationAssertion( "down-regulation of ligase activity") -AnnotationAssertion( "downregulation of ligase activity") -AnnotationAssertion( "ligase inhibitor") -AnnotationAssertion( "inhibition of ligase activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051352") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of ligase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (proprioception involved in equilibrioception) AnnotationAssertion(Annotation( "GOC:ai") "The series of events contributing to equilibrioception by which an organism senses the position, location, orientation, and movement of the body and its parts. Proprioception plays an important role in the ability of an organism to perceive its orientation with respect to gravity.") @@ -94795,7 +94070,6 @@ AnnotationAssertion( "neuron apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (detoxification of nitrogen compound) @@ -94878,6 +94152,30 @@ AnnotationAssertion(rdfs:label "myob EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (maintenance of protein location in nucleus) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus.") +AnnotationAssertion( "maintenance of nuclear protein localization") +AnnotationAssertion( "maintenance of protein location in cell nucleus") +AnnotationAssertion( "nuclear protein retention") +AnnotationAssertion( "nuclear protein sequestering") +AnnotationAssertion( "nuclear protein sequestration") +AnnotationAssertion( "protein retention in nucleus") +AnnotationAssertion( "protein sequestration in nucleus") +AnnotationAssertion( "protein storage in nucleus") +AnnotationAssertion( "protein-nuclear retention") +AnnotationAssertion( "sequestration of protein in nucleus") +AnnotationAssertion( "storage of protein in nucleus") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of protein localization in nucleus") +AnnotationAssertion( "GO:0051457") +AnnotationAssertion(rdfs:label "maintenance of protein location in nucleus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + # Class: (corticotropin secretion) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "PMID:11027914") "The regulated release of corticotropin by a cell. Corticotropin hormone is a polypeptide hormone synthesized and secreted from corticotropes in the anterior lobe of the pituitary gland in response to corticotropin-releasing hormone (CRH) released by the hypothalamus.") @@ -95053,6 +94351,43 @@ AnnotationAssertion( "positive regulation of keratinocyte migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of neurotransmitter uptake) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into a neuron or glial cell.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "regulation of neurotransmitter import") +AnnotationAssertion( "regulation of neurotransmitter reuptake") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051580") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulation of neurotransmitter uptake") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of neurotransmitter uptake) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into a neuron or glial cell.") +AnnotationAssertion( "down regulation of neurotransmitter uptake") +AnnotationAssertion( "down-regulation of neurotransmitter uptake") +AnnotationAssertion( "downregulation of neurotransmitter uptake") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "negative regulation of neurotransmitter import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051581") +AnnotationAssertion(rdfs:label "negative regulation of neurotransmitter uptake") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of neurotransmitter uptake) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into a neuron or glial cell.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "positive regulation of neurotransmitter import") +AnnotationAssertion( "up regulation of neurotransmitter uptake") +AnnotationAssertion( "up-regulation of neurotransmitter uptake") +AnnotationAssertion( "upregulation of neurotransmitter uptake") +AnnotationAssertion( "activation of neurotransmitter uptake") +AnnotationAssertion( "stimulation of neurotransmitter uptake") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051582") +AnnotationAssertion(rdfs:label "positive regulation of neurotransmitter uptake") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of neurotransmitter transport) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -95157,6 +94492,51 @@ AnnotationAssertion( "histamine transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (histamine uptake) + +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of histamine into a cell, typically presynaptic neurons or glial cells. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "histamine import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051615") +AnnotationAssertion(rdfs:label "histamine uptake") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (regulation of histamine uptake) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter histamine into a cell.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "regulation of histamine import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051616") +AnnotationAssertion(rdfs:label "regulation of histamine uptake") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of histamine uptake) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of histamine into a cell.") +AnnotationAssertion( "down regulation of histamine uptake") +AnnotationAssertion( "down-regulation of histamine uptake") +AnnotationAssertion( "downregulation of histamine uptake") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "negative regulation of histamine import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051617") +AnnotationAssertion(rdfs:label "negative regulation of histamine uptake") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of histamine uptake) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of the directed movement of histamine into a cell.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "positive regulation of histamine import") +AnnotationAssertion( "up regulation of histamine uptake") +AnnotationAssertion( "up-regulation of histamine uptake") +AnnotationAssertion( "upregulation of histamine uptake") +AnnotationAssertion( "activation of histamine uptake") +AnnotationAssertion( "stimulation of histamine uptake") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051618") +AnnotationAssertion(rdfs:label "positive regulation of histamine uptake") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (norepinephrine uptake) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of norepinephrine into a cell, typically presynaptic neurons or glial cells. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine.") @@ -95405,6 +94785,50 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (maintenance of location in cell) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.") +AnnotationAssertion( "cellular retention") +AnnotationAssertion( "cellular sequestering") +AnnotationAssertion( "cellular storage") +AnnotationAssertion( "intracellular retention") +AnnotationAssertion( "intracellular sequestering") +AnnotationAssertion( "intracellular storage") +AnnotationAssertion( "maintenance of intracellular localization") +AnnotationAssertion( "maintenance of localization within cell") +AnnotationAssertion( "retention within cell") +AnnotationAssertion( "sequestering within cell") +AnnotationAssertion( "storage within cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of cellular localization") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of localization in cell") +AnnotationAssertion( "GO:0051651") +AnnotationAssertion(rdfs:label "maintenance of location in cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (maintenance of chromosome location) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which a chromosome is maintained in a specific location within a cell and prevented from moving elsewhere.") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of chromosome localization") +AnnotationAssertion( "GO:0051652") +AnnotationAssertion(rdfs:label "maintenance of chromosome location") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (maintenance of vesicle location) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which a vesicle is maintained in a specific location within a cell and prevented from moving elsewhere.") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of vesicle localization") +AnnotationAssertion( "GO:0051655") +AnnotationAssertion(rdfs:label "maintenance of vesicle location") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (establishment of organelle localization) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of an organelle to a specific location.") @@ -95415,6 +94839,27 @@ AnnotationAssertion(rdfs:label "esta EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (maintenance of organelle location) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which an organelle is maintained in a specific location within a cell and prevented from moving elsewhere.") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of organelle localization") +AnnotationAssertion( "GO:0051657") +AnnotationAssertion(rdfs:label "maintenance of organelle location") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (maintenance of nucleus location) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which the nucleus is maintained in a specific location within a cell and prevented from moving elsewhere.") +AnnotationAssertion( "maintenance of cell nucleus location") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of nucleus localization") +AnnotationAssertion( "GO:0051658") +AnnotationAssertion(rdfs:label "maintenance of nucleus location") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (localization within membrane) AnnotationAssertion(Annotation( "GOC:ai") "Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane.") @@ -95455,6 +94900,18 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (maintenance of Golgi location) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which the Golgi is maintained in a specific location within a cell and prevented from moving elsewhere.") +AnnotationAssertion( "maintenance of Golgi apparatus localization") +AnnotationAssertion( "maintenance of Golgi body localization") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "maintenance of Golgi localization") +AnnotationAssertion( "GO:0051684") +AnnotationAssertion(rdfs:label "maintenance of Golgi location") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (response to other organism) AnnotationAssertion(Annotation( "GOC:ai") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism.") @@ -96711,29 +96168,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (notochord regression) - -AnnotationAssertion(Annotation( "GOC:dph") "The developmental process in which the stucture of the notochord is destroyed in an embryo.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0060032") -AnnotationAssertion(rdfs:label "notochord regression") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (anatomical structure regression) - -AnnotationAssertion(Annotation( "GOC:dph") "The developmental process in which an anatomical stucture is destroyed as a part of its normal progression.") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "histolysis") -AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "tissue death") -AnnotationAssertion( "GO:0060033") -AnnotationAssertion(rdfs:label "anatomical structure regression") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) - # Class: (pharyngeal system development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear.") @@ -99223,18 +98657,6 @@ AnnotationAssertion( "regulation of microtubule-based movement") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (mammary gland duct regression in males) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which the epithelium of the mammary duct is destroyed in males.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2009-05-20T04:50:57Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0060641") -AnnotationAssertion(rdfs:label "mammary gland duct regression in males") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (white fat cell differentiation involved in mammary gland fat development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which a preadipocyte acquires specialized features of a white adipocyte of the mammary gland. White adipocytes have cytoplasmic lipids arranged in a unique vacuole.") @@ -100324,7 +99746,7 @@ AnnotationAssertion( "GO:0060880") AnnotationAssertion(rdfs:label "cell morphogenesis involved in semicircular canal fusion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (basement membrane disassembly involved in semicircular canal fusion) @@ -101558,6 +100980,18 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (dense core granule organization) + +AnnotationAssertion(Annotation( "GOC:dph") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dense core granule. A dense core granule is a secretory organelle found in endocrine cells.") +AnnotationAssertion( "dph") +AnnotationAssertion( "2010-05-01T09:34:37Z") +AnnotationAssertion(Annotation( "GOC:mah") "dense core granule organisation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0061109") +AnnotationAssertion(rdfs:label "dense core granule organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (pancreas morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized.") @@ -102861,7 +102295,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061336") AnnotationAssertion(rdfs:label "cell morphogenesis involved in Malpighian tubule morphogenesis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (cardiac conduction) @@ -103155,6 +102589,18 @@ AnnotationAssertion(rdfs:label "conn EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (olfactory bulb tufted cell development) + +AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of an olfactory bulb tufted cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.") +AnnotationAssertion( "dph") +AnnotationAssertion( "2012-05-15T12:30:21Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0061449") +AnnotationAssertion(rdfs:label "olfactory bulb tufted cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (trophoblast cell migration) AnnotationAssertion(Annotation( "GOC:dph") "Trophoblast cell migration that is accomplished by extension and retraction of a pseudopodium. Trophoblast cells line the outside of the blastocyst.") @@ -103203,6 +102649,17 @@ AnnotationAssertion(rdfs:label "inte EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (release of sequestered calcium ion into cytosol by Golgi) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The directed movement of calcium ions (Ca2+) out of the Golgi apparatus into the cytosol.") +AnnotationAssertion( "dph") +AnnotationAssertion( "2012-07-27T02:29:43Z") +AnnotationAssertion( "Golgi calcium ion export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0061454") +AnnotationAssertion(rdfs:label "release of sequestered calcium ion into cytosol by Golgi") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (reproductive system development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction.") @@ -103699,55 +103156,6 @@ AnnotationAssertion( "RNA polymerase II-specific DNA-binding transcription factor binding") SubClassOf( ) -# Class: (ubiquitin-like protein conjugating enzyme activity) - -AnnotationAssertion(Annotation( "GOC:dph") "Isoenergetic transfer of a ubiquitin-like protein (ULP) from one protein to another via the reaction X-SCP + Y = Y-SCP + X, where both the X-SCP and Y-SCP linkages are thioester bonds between the C-terminal amino acid of SCP and a sulfhydryl side group of a cysteine residue.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2014-11-06T13:15:27Z") -AnnotationAssertion( "E2") -AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein conjugating enzyme activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0061650") -AnnotationAssertion(rdfs:label "ubiquitin-like protein conjugating enzyme activity") -SubClassOf( ) - -# Class: (Atg12 conjugating enzyme activity) - -AnnotationAssertion(Annotation( "GOC:dph") "Isoenergetic transfer of Atg12 from one protein to another via the reaction X-Atg12 + Y = Y-Atg12 + X, where both the X-Atg12 and Y-Atg12 linkages are thioester bonds between the C-terminal amino acid of Atg12 and a sulfhydryl side group of a cysteine residue.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2014-11-06T13:17:36Z") -AnnotationAssertion(Annotation( "GOC:dph") "E2") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0061651") -AnnotationAssertion(rdfs:label "Atg12 conjugating enzyme activity") -SubClassOf( ) -SubClassOf( ) - -# Class: (ubiquitin-like protein ligase activity) - -AnnotationAssertion(Annotation( "GOC:dph") "Catalysis of the transfer of a ubiquitin-like protein (ULP) to a substrate protein via the reaction X-ULP + S = X + S-ULP, where X is either an E2 or E3 enzyme, the X-ULP linkage is a thioester bond, and the S-ULP linkage is an isopeptide bond between the C-terminal glycine of ULP and the epsilon-amino group of lysine residues in the substrate.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2014-11-06T13:46:23Z") -AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein ligase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "GOC:dph") "E3") -AnnotationAssertion( "GO:0061659") -AnnotationAssertion(rdfs:label "ubiquitin-like protein ligase activity") -SubClassOf( ) -SubClassOf( ) - -# Class: (Atg12 ligase activity) - -AnnotationAssertion(Annotation( "GOC:dph") "Catalysis of the transfer of Atg12 to a substrate protein via the reaction X-Atg12 + S = X + S-Atg12, where X is either an E2 or E3 enzyme, the X-Atg12 linkage is a thioester bond, and the S-Atg12 linkage is an isopeptide bond between the C-terminal amino acid of Atg12 and the epsilon-amino group of lysine residues in the substrate.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2014-11-06T13:50:42Z") -AnnotationAssertion(Annotation( "GOC:dph") "E3") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0061660") -AnnotationAssertion(rdfs:label "Atg12 ligase activity") -SubClassOf( ) -SubClassOf( ) - # Class: (seminal vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of a seminal vesicle are generated and organized.") @@ -103811,16 +103219,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (engulfment of target by autophagosome) +# Class: (cytosolic lipolysis) -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:autophagy") Annotation( "GOC:dph") Annotation( "GOC:pad") "The membrane invagination process by which an autophagosomal membrane surrounds an object that will be degraded by macroautophagy.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2015-09-14T14:10:24Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0061736") -AnnotationAssertion(rdfs:label "engulfment of target by autophagosome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +AnnotationAssertion(Annotation( "GOC:autophagy") "The chemical reactions and pathways resulting in the breakdown of lipid droplets and hydrolysis of stored triglycerides occurring through the orchestrated activation of cytosolic lipases.") +AnnotationAssertion( "dph") +AnnotationAssertion( "2015-07-08T13:42:15Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0061725") +AnnotationAssertion(rdfs:label "cytosolic lipolysis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (secretory granule maturation) @@ -103969,27 +103377,6 @@ AnnotationAssertion(rdfs:label "glia EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (autophagosome localization) - -AnnotationAssertion(Annotation( "PMID:26763909") "Any process in which an autophagosome is transported to, and/or maintained in, a specific location within the cell.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2017-06-28T17:27:57Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0061906") -AnnotationAssertion(rdfs:label "autophagosome localization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (process utilizing autophagic mechanism) - -AnnotationAssertion(Annotation( "PMID:21997368") Annotation( "PMID:22966490") Annotation( "PMID:28596378") "A cellular process involving delivery of a portion of the cytoplasm to lysosomes or to the plant or fungal vacuole that does not involve direct transport through the endocytic or vacuolar protein sorting (Vps) pathways. This process typically leads to degradation of the cargo; however, it can also be used to deliver resident proteins, such as in the cytoplasm-to-vacuole targeting (Cvt) pathway.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2017-07-13T19:42:14Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0061919") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "process utilizing autophagic mechanism") -SubClassOf( ) - # Class: (regulation of adenine biosynthetic process) AnnotationAssertion(Annotation( "PMID:19933844") "Any process that modulates the frequency, rate or extent of an adenine biosynthetic process.") @@ -105472,20 +104859,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (neuron death) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "The process of cell death in a neuron.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2009-11-03T02:37:17Z") -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:rl") "neuron cell death") -AnnotationAssertion(Annotation( "GOC:mah") "neuronal cell death") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0070997") -AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide or use of neuron-specific markers) show that neuron death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the neuron death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'), and the cell type captured as an annotation extension; or the term GO:0051402 'neuron apoptotic process' may be considered, if appropriate.") -AnnotationAssertion(rdfs:label "neuron death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (regulation of phospholipid biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phospholipids.") @@ -106199,7 +105572,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071695") AnnotationAssertion(rdfs:label "anatomical structure maturation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -106706,39 +106079,6 @@ AnnotationAssertion( "DNA biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of protein serine/threonine kinase activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the rate, frequency, or extent of protein serine/threonine kinase activity.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2010-09-15T03:08:35Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071900") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of protein serine/threonine kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of protein serine/threonine kinase activity) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2010-09-15T03:09:43Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071901") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of protein serine/threonine kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of protein serine/threonine kinase activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2010-09-15T03:09:57Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071902") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of protein serine/threonine kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (cell periphery) AnnotationAssertion(Annotation( "GOC:pdt") "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.") @@ -109658,6 +108998,20 @@ AnnotationAssertion(rdfs:label "esta EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (maintenance of protein localization in organelle) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is maintained in a specific location a specific location on or in an organelle, and is prevented from moving elsewhere. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2011-02-14T02:09:13Z") +AnnotationAssertion(Annotation( "GOC:mah") "maintenance of protein localisation to organelle") +AnnotationAssertion( "maintenance of protein localization to organelle") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0072595") +AnnotationAssertion(rdfs:label "maintenance of protein localization in organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (protein localization to membrane) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a protein is transported to, or maintained in, a specific location in a membrane.") @@ -109713,6 +109067,18 @@ AnnotationAssertion(rdfs:label "esta EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (maintenance of protein location in vacuole) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is maintained in a specific location in a vacuole, and is prevented from moving elsewhere.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2011-02-14T02:56:57Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0072667") +AnnotationAssertion(rdfs:label "maintenance of protein location in vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (multinuclear osteoclast differentiation) AnnotationAssertion(Annotation( "CL:0000779") Annotation( "GOC:mah") Annotation( "PMID:12713016") "The process in which a relatively unspecialized monocyte acquires the specialized features of a multinuclear osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.") @@ -110084,6 +109450,31 @@ AnnotationAssertion( "G protein-coupled receptor signaling pathway involved in heart process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (L-glutamate transmembrane export from vacuole) + +AnnotationAssertion(Annotation( "PMID:21307582") "The directed movement of L-glutamate out of the vacuole, across the vacuolar membrane.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0089704") +AnnotationAssertion(rdfs:label "L-glutamate transmembrane export from vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (amino acid import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:8195186") "The directed movement of an amino acid from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-11-14T14:21:41Z") +AnnotationAssertion( "GO:0043092") +AnnotationAssertion( "GO:0044745") +AnnotationAssertion( "GO:1902837") +AnnotationAssertion( "L-amino acid import") +AnnotationAssertion( "amino acid transmembrane import") +AnnotationAssertion( "amino acid import into cell") +AnnotationAssertion( "L-amino acid uptake") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0089718") +AnnotationAssertion(rdfs:label "amino acid import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (hypoblast development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The process whose specific outcome is the progression of the hypoblast over time, from its formation to the mature structure. The hypoblast is a tissue formed from the inner cell mass that lies beneath the epiblast.") @@ -110405,6 +109796,16 @@ AnnotationAssertion( "intracellular sphingolipid homeostasis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (Golgi to lysosome transport) + +AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The directed movement of substances from the Golgi to lysosomes.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2009-12-08T08:35:13Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090160") +AnnotationAssertion(rdfs:label "Golgi to lysosome transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (establishment of epithelial cell polarity) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The specification and formation of anisotropic intracellular organization of an epithelial cell.") @@ -110461,7 +109862,7 @@ AnnotationAssertion( "GO:0090171") AnnotationAssertion(rdfs:label "chondrocyte morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (organelle membrane fusion) @@ -110925,6 +110326,17 @@ AnnotationAssertion(rdfs:label "prot EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (glutamate transmembrane import into vacuole) + +AnnotationAssertion(Annotation( "GOC:tb") "The directed movement of glutamate into the vacuole across the vacuolar membrane.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2012-09-24T14:12:46Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:tb") "vacuolar glutamate import") +AnnotationAssertion( "GO:0090454") +AnnotationAssertion(rdfs:label "glutamate transmembrane import into vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (intracellular glutamate homeostasis) AnnotationAssertion(Annotation( "GOC:tb") "A homeostatic process involved in the maintenance of a steady state level of glutamate within a cell.") @@ -110981,6 +110393,16 @@ AnnotationAssertion(rdfs:label "mese EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (L-glutamate transmembrane import into vacuole) + +AnnotationAssertion(Annotation( "GOC:al") "The directed movement of L-glutamate into the vacuole across the vacuolar membrane.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2012-12-14T11:25:52Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090515") +AnnotationAssertion(rdfs:label "L-glutamate transmembrane import into vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (podocyte cell migration) AnnotationAssertion(Annotation( "GOC:pm") Annotation( "PMID:21402783") "The orderly movement of a podocyte from one site to another, often during the development of a multicellular organism or multicellular structure. A podocyte is a specialized kidney epithelial cell.") @@ -111842,6 +111264,20 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (calcium ion transmembrane import into cytosol) + +AnnotationAssertion(Annotation( "GOC:vw") "A process in which a calcium ion is transported from one side of a membrane to the other into the cytosol by means of some agent such as a transporter or pore.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23015"^^xsd:anyURI) +AnnotationAssertion( "pr") +AnnotationAssertion( "2014-01-23T11:05:13Z") +AnnotationAssertion( "GO:0060401") +AnnotationAssertion( "calcium transmembrane import into cytosol") +AnnotationAssertion( "cytosolic calcium ion transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0097553") +AnnotationAssertion(rdfs:label "calcium ion transmembrane import into cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (vacuole fusion) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "GOC:vw") Annotation( "Wikipedia:Vacuole") "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole.") @@ -112111,6 +111547,27 @@ AnnotationAssertion(rdfs:label "defe EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (maintenance of protein complex location) + +AnnotationAssertion(Annotation( "GOC:dos") "Any process in which a protein complex is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of protein complexes that move away.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2013-11-15T18:20:16Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098544") +AnnotationAssertion(rdfs:label "maintenance of protein complex location") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (maintenance of protein complex location in cytoplasm) + +AnnotationAssertion(Annotation( "GOC:dos") "Any process in which a protein complex is maintained in a specific location within the cytoplasm and is prevented from moving elsewhere.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2013-11-15T20:49:15Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098545") +AnnotationAssertion(rdfs:label "maintenance of protein complex location in cytoplasm") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (learned vocalization behavior) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dos") Annotation( "GOC:rl") Annotation( "PMID:16418265") Annotation( "PMID:17035521") "A vocalization behavior that is the result of learning.") @@ -112303,6 +111760,24 @@ AnnotationAssertion( "import into cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +# Class: (inorganic anion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of inorganic anions from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "inorganic anion import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098658") +AnnotationAssertion(rdfs:label "inorganic anion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (inorganic cation import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of inorganic cations from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "inorganic cation import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098659") +AnnotationAssertion(rdfs:label "inorganic cation import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (inorganic ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:mah") "The process in which an inorganic ion is transported across a membrane.") @@ -112400,6 +111875,105 @@ AnnotationAssertion( "regulation of synaptic vesicle cycle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (adenine import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of adenine from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "dph") +AnnotationAssertion( "2012-12-06T14:51:42Z") +AnnotationAssertion( "GO:0061488") +AnnotationAssertion( "adenine import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098702") +AnnotationAssertion(rdfs:label "adenine import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (calcium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of calcium ions from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2013-02-07T13:07:59Z") +AnnotationAssertion( "GO:1990035") +AnnotationAssertion( "calcium ion import into cell") +AnnotationAssertion(Annotation( "GOC:vw") "calcium ion uptake into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098703") +AnnotationAssertion(rdfs:label "calcium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (carbohydrate import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of a carbohydrate from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-05-31T02:45:02Z") +AnnotationAssertion( "GO:0097319") +AnnotationAssertion( "carbohydrate import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098704") +AnnotationAssertion(rdfs:label "carbohydrate import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (glucose import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of glucose from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "al") +AnnotationAssertion( "2012-12-06T14:54:07Z") +AnnotationAssertion( "GO:0061490") +AnnotationAssertion( "GO:1990821") +AnnotationAssertion( "glucose import into cell") +AnnotationAssertion( "high affinity glucose import") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098708") +AnnotationAssertion(rdfs:label "glucose import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (iron ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:8321236") "The directed movement of iron ions from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-12-20T08:29:00Z") +AnnotationAssertion( "GO:0097459") +AnnotationAssertion( "GO:0097460") +AnnotationAssertion( "GO:0098707") +AnnotationAssertion( "iron ion import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:mah") "ferrous ion import into cell") +AnnotationAssertion( "ferrous iron import across plasma membrane") +AnnotationAssertion( "ferrous iron import into cell") +AnnotationAssertion(Annotation( "GOC:mah") "iron import into cell") +AnnotationAssertion( "GO:0098711") +AnnotationAssertion(rdfs:label "iron ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (L-glutamate import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of L-glutamate from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2013-06-12T12:32:47Z") +AnnotationAssertion( "GO:1903802") +AnnotationAssertion( "GO:1990123") +AnnotationAssertion( "L-glutamate(1-) import across plasma membrane") +AnnotationAssertion( "L-glutamate import into cell") +AnnotationAssertion( "L-glutamate(1-) import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098712") +AnnotationAssertion(rdfs:label "L-glutamate import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (sodium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of sodium ions from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-08-03T16:55:52Z") +AnnotationAssertion( "GO:0097369") +AnnotationAssertion( "GO:1990118") +AnnotationAssertion( "sodium import") +AnnotationAssertion( "sodium ion import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "sodium ion import") +AnnotationAssertion( "GO:0098719") +AnnotationAssertion(rdfs:label "sodium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (asymmetric stem cell division) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "PMID:18513950") "Division of a stem cell during which it retains its identity and buds off a daughter cell with a new identity.") @@ -112433,6 +112007,15 @@ AnnotationAssertion( "germline stem cell asymmetric division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of some substance from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "uptake") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098739") +AnnotationAssertion(rdfs:label "import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (cerebellar neuron development) AnnotationAssertion(Annotation( "GOC:dos") "The process whose specific outcome is the progression of a cerebellar neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.") @@ -112984,6 +112567,16 @@ AnnotationAssertion(rdfs:label "G pr EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (neuronal dense core vesicle) + +AnnotationAssertion(Annotation( "GOC:dos") Annotation( "ISBN:978-0-07-181001-2") Annotation( "Wikipedia:Neuropeptide&oldid=713905176") "A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0098992") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "neuronal dense core vesicle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (vesicle-mediated transport in synapse) AnnotationAssertion(Annotation( "GOC:dos") "Any vesicle-mediated transport that occurs in a synapse.") @@ -112995,6 +112588,24 @@ EquivalentClasses( ObjectIntersection SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) +# Class: (neuronal dense core vesicle membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The lipid bilayer surrounding a neuronal dense core vesicle.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0099012") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "neuronal dense core vesicle membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (neuronal dense core vesicle organization) + +AnnotationAssertion(Annotation( "GOC:dos") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuronal dense core vesicle.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0099014") +AnnotationAssertion(rdfs:label "neuronal dense core vesicle organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (presynapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "GOC:dos") Annotation( "PMID:24449494") "The aggregation, arrangement and bonding together of a set of components to form a presynapse.") @@ -113163,16 +112774,17 @@ AnnotationAssertion( "cell-cell signaling via exosome") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (trans-synaptic signalling via exosome) +# Class: (trans-synaptic signaling via exosome) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "PMID:19837038") "Transynaptic signaling in which the ligand is carried across the synapse by an exosome.") AnnotationAssertion( "dos") AnnotationAssertion( "2017-07-05T16:49:44Z") AnnotationAssertion( "exosome mediated transynaptic signalling") +AnnotationAssertion( "trans-synaptic signalling via exosome") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099157") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "trans-synaptic signalling via exosome") +AnnotationAssertion(rdfs:label "trans-synaptic signaling via exosome") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (postsynaptic intermediate filament cytoskeleton) @@ -113397,6 +113009,46 @@ AnnotationAssertion( "vesicle cytoskeletal trafficking") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +# Class: (dense core granule cytoskeletal transport) + +AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "PMID:23358451") "The directed movement of dense core granules along cytoskeletal fibers, such as microtubules or actin filaments.") +AnnotationAssertion( "dense core vesicle cytoskeletal trafficking") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0099519") +AnnotationAssertion(rdfs:label "dense core granule cytoskeletal transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (cytosolic region) + +AnnotationAssertion(Annotation( "GOC:dos") "Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol.") +AnnotationAssertion( "region of cytosol") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0099522") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cytosolic region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (presynaptic cytosol) + +AnnotationAssertion(Annotation( "GOC:dos") "The region of the cytosol consisting of all cytosol that is part of the presynapse.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0099523") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "presynaptic cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (postsynaptic cytosol) + +AnnotationAssertion(Annotation( "GOC:dos") "The region of the cytosol consisting of all cytosol that is part of the postsynapse.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0099524") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "postsynaptic cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (G protein-coupled neurotransmitter receptor activity) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:fj") Annotation( "GOC:mah") "Combining with a neurotransmitter and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.") @@ -113548,8 +113200,8 @@ EquivalentClasses( ObjectIntersection # Class: (chemical synaptic transmission, postsynaptic) AnnotationAssertion(Annotation( "GOC:dos") "The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol.") +AnnotationAssertion(Annotation( ) "postsynaptic process involved in chemical synaptic transmission") AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( ) "postsynaptic process involved in chemical synaptic transmission") AnnotationAssertion( "GO:0099565") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chemical synaptic transmission, postsynaptic") @@ -113651,6 +113303,35 @@ AnnotationAssertion(rdfs:label "G pr EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (release of sequestered calcium ion into presynaptic cytosol) + +AnnotationAssertion(Annotation( "GOC:dos") "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the presynaptic cytosol.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0099585") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "release of sequestered calcium ion into presynaptic cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (release of sequestered calcium ion into postsynaptic cytosol) + +AnnotationAssertion(Annotation( "GOC:dos") "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the postsynaptic cytosol.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0099586") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "release of sequestered calcium ion into postsynaptic cytosol") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (inorganic ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of inorganic ions from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "inorganic ion import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0099587") +AnnotationAssertion(rdfs:label "inorganic ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (serotonin receptor activity) AnnotationAssertion(Annotation( "GOC:dos") "Combining with the biogenic amine serotonin and transmitting a signal across a membrane by activating some effector activity. Serotonin (5-hydroxytryptamine) is a neurotransmitter and hormone found in vertebrates and invertebrates.") @@ -114291,6 +113972,7 @@ AnnotationAssertion( "cellular anatomical entity") SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (regulation of glutamatergic neuron differentiation) @@ -114967,6 +114649,17 @@ AnnotationAssertion( "extracellular vesicle biogenesis") SubClassOf( ) +# Class: (export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of some substance from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2017-10-24T14:38:16Z") +AnnotationAssertion( "efflux") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0140115") +AnnotationAssertion(rdfs:label "export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (positive regulation of lymphocyte chemotaxis) AnnotationAssertion(Annotation( "PMID:19255442") "Any process that activates or increases the frequency, rate or extent of lymphocyte chemotaxis.") @@ -114977,6 +114670,26 @@ AnnotationAssertion( "positive regulation of lymphocyte chemotaxis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (calcium ion import into vacuole) + +AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:8628289") "The directed movement of calcium cations into the vacuole across the vacuolar membrane.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2017-12-13T15:15:29Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0140146") +AnnotationAssertion(rdfs:label "calcium ion import into vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (ammonium import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:16999738") "The directed movement of an ammonium ion from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2018-01-26T12:39:56Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0140157") +AnnotationAssertion(rdfs:label "ammonium import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (anterograde axonal transport of neurotransmitter receptor complex) AnnotationAssertion(Annotation( "PMID:28680963") "The directed movement of a neurotransmitter receptor complex along microtubules from the cell body toward the cell periphery in nerve cell axons.") @@ -115206,6 +114919,16 @@ AnnotationAssertion(rdfs:label "cell SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (hexose import across plasma membrane) + +AnnotationAssertion(Annotation( "PMID:10735857") "The directed movement of hexose from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2018-10-01T08:49:49Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0140271") +AnnotationAssertion(rdfs:label "hexose import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (DNA-binding transcription factor binding) AnnotationAssertion(Annotation( "GOC:txnOH-2018") "Binding to a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription.") @@ -115346,29 +115069,6 @@ AnnotationAssertion(rdfs:label "radi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (ATP-dependent activity) - -AnnotationAssertion(Annotation( "PMID:24878343") Annotation( "PMID:25750732") Annotation( "PMID:32933017") Annotation( "PMID:33818025") Annotation( "PMID:33873056") Annotation( "PMID:33988324") "A molecular function characterized by the coupling of ATP hydrolysis to other steps of a reaction mechanism to make the reaction energetically favorable, for example to catalyze a reaction or drive transport against a concentration gradient.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22371"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2021-06-15T07:35:06Z") -AnnotationAssertion( "ATP hydrolysis-dependent activity") -AnnotationAssertion( "ATPase activity") -AnnotationAssertion( "ATPase activity, coupled") -AnnotationAssertion( "ATPase-dependent activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0140657") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term represents a grouping class that includes all proteins that use ATP hydrolysis to drive a reaction; it is not meant to capture the ATP hydrolysis reaction itself. To annotate ATP hydrolysis, please use 'ATP hydrolysis activity ; GO:0016887'.") -AnnotationAssertion(rdfs:label "ATP-dependent activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (non-membrane-bounded organelle assembly) AnnotationAssertion(Annotation( "PMID:28225081") "The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle.") @@ -115395,6 +115095,17 @@ AnnotationAssertion( "ammonium excretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (cytosol to Golgi apparatus transport) + +AnnotationAssertion(Annotation( "PMID:28373556") "The directed movement of substances from the cytosol into the Golgi apparatus of a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21524"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2022-05-16T06:59:22Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0140820") +AnnotationAssertion(rdfs:label "cytosol to Golgi apparatus transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (cellular detoxification of metal ion) AnnotationAssertion(Annotation( "PMID:26729300") Annotation( "PMID:33046888") Annotation( "PMID:34442707") "Any process carried out at the cellular level that reduces or removes the toxicity of a metal ion.") @@ -115441,6 +115152,19 @@ AnnotationAssertion( "intracellular nucleoside homeostasis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (intracellular nitrogen homeostasis) + +AnnotationAssertion(Annotation( "GOC:tb") "A homeostatic process involved in the maintenance of a steady state level of nitrogen within a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25558"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2023-06-15T08:56:16Z") +AnnotationAssertion( "cellular nitrogen homeostasis") +AnnotationAssertion( "nitrogen homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0141067") +AnnotationAssertion(rdfs:label "intracellular nitrogen homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of protein localization to lysosome) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:24305806") "Any process that modulates the frequency, rate or extent of protein localization to lysosome.") @@ -115542,7 +115266,7 @@ EquivalentClasses( ObjectIntersection # Class: (glial cell-neuron signaling) -AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:14980203") Annotation( "PMID:16144764") Annotation( "PMID:16547515") Annotation( "PMID:18685038") Annotation( "PMID:27788368") Annotation( "PMID:9459440") "Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signalling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum.") +AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:14980203") Annotation( "PMID:16144764") Annotation( "PMID:16547515") Annotation( "PMID:18685038") Annotation( "PMID:27788368") Annotation( "PMID:9459440") "Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signaling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum.") AnnotationAssertion( "bc") AnnotationAssertion( "2018-12-17T12:28:09Z") AnnotationAssertion( "glia-neuron signaling") @@ -115559,7 +115283,7 @@ EquivalentClasses( ObjectIntersection # Class: (neuron-glial cell signaling) -AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:10195197") Annotation( "PMID:10196584") Annotation( "PMID:10377338") Annotation( "PMID:10493741") Annotation( "PMID:11356870") Annotation( "PMID:11399439") Annotation( "PMID:15252819") Annotation( "PMID:27788368") "Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signalling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine.") +AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:10195197") Annotation( "PMID:10196584") Annotation( "PMID:10377338") Annotation( "PMID:10493741") Annotation( "PMID:11356870") Annotation( "PMID:11399439") Annotation( "PMID:15252819") Annotation( "PMID:27788368") "Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine.") AnnotationAssertion( "bc") AnnotationAssertion( "2018-12-17T12:30:12Z") AnnotationAssertion( "neuron-glia signaling") @@ -117074,6 +116798,45 @@ AnnotationAssertion( "positive regulation of apoptotic process involved in metanephric nephron tubule development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of cytoplasmic translational elongation) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of cytoplasmic translational elongation.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2012-04-03T05:07:02Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1900247") +AnnotationAssertion(rdfs:label "regulation of cytoplasmic translational elongation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of cytoplasmic translational elongation) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational elongation.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2012-04-03T05:07:14Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cytoplasmic translational elongation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cytoplasmic translational elongation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cytoplasmic translational elongation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cytoplasmic translational elongation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1900248") +AnnotationAssertion(rdfs:label "negative regulation of cytoplasmic translational elongation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cytoplasmic translational elongation) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of cytoplasmic translational elongation.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2012-04-03T05:07:24Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cytoplasmic translational elongation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cytoplasmic translational elongation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cytoplasmic translational elongation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cytoplasmic translational elongation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1900249") +AnnotationAssertion(rdfs:label "positive regulation of cytoplasmic translational elongation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (negative regulation of defense response to insect) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22474183") "Any process that stops, prevents or reduces the frequency, rate or extent of defense response to insect.") @@ -118014,68 +117777,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -# Class: (regulation of neuron death) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:rph") "Any process that modulates the frequency, rate or extent of neuron death.") -AnnotationAssertion( "rph") -AnnotationAssertion( "2012-08-02T09:57:41Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of neuronal cell death") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901214") -AnnotationAssertion(rdfs:label "regulation of neuron death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (negative regulation of neuron death) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:rph") "Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.") -AnnotationAssertion( "rph") -AnnotationAssertion( "2012-08-02T09:58:07Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of neuronal cell death") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901215") -AnnotationAssertion(rdfs:label "negative regulation of neuron death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of neuron death) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:rph") "Any process that activates or increases the frequency, rate or extent of neuron death.") -AnnotationAssertion( "rph") -AnnotationAssertion( "2012-08-02T09:58:15Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of neuronal cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of neuron cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of neuron death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of neuronal cell death") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901216") -AnnotationAssertion(rdfs:label "positive regulation of neuron death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of cardiac chamber morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis.") @@ -118900,6 +118601,16 @@ AnnotationAssertion( "positive regulation of tetrapyrrole biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of Golgi calcium ion export) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of Golgi calcium ion export.") +AnnotationAssertion( "al") +AnnotationAssertion( "2012-10-03T07:26:03Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901472") +AnnotationAssertion(rdfs:label "regulation of Golgi calcium ion export") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (azole transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:3527307206") Annotation( "Wikipedia:Azole") "Enables the directed movement of azoles, heterocyclic compound found in many biologically important substances, from one side of a membrane to the other.") @@ -120240,6 +119951,95 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +# Class: (dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "The directed movement a dense core granule within a cell.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:00:52Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "dense core vesicle transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901950") +AnnotationAssertion(rdfs:comment "goslim_synapse") +AnnotationAssertion(rdfs:label "dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (regulation of anterograde dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that modulates the frequency, rate or extent of anterograde dense core granule transport.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:36:21Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901951") +AnnotationAssertion(rdfs:label "regulation of anterograde dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of anterograde dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that stops, prevents or reduces the frequency, rate or extent of anterograde dense core granule transport.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:36:30Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of anterograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of anterograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of anterograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of anterograde dense core granule transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901952") +AnnotationAssertion(rdfs:label "negative regulation of anterograde dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of anterograde dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that activates or increases the frequency, rate or extent of anterograde dense core granule transport.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:36:35Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of anterograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of anterograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of anterograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of anterograde dense core granule transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901953") +AnnotationAssertion(rdfs:label "positive regulation of anterograde dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (regulation of retrograde dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that modulates the frequency, rate or extent of retrograde dense core granule transport.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:36:43Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901954") +AnnotationAssertion(rdfs:label "regulation of retrograde dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of retrograde dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde dense core granule transport.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:36:47Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of retrograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of retrograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of retrograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of retrograde dense core granule transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901955") +AnnotationAssertion(rdfs:label "negative regulation of retrograde dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of retrograde dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that activates or increases the frequency, rate or extent of retrograde dense core granule transport.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:36:52Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of retrograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of retrograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of retrograde dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of retrograde dense core granule transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901956") +AnnotationAssertion(rdfs:label "positive regulation of retrograde dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of cell proliferation involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "PMID:21419760") "Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis.") @@ -121156,6 +120956,18 @@ AnnotationAssertion( "protein localization to cell junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (sulfate import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:14723223") "The directed movement of sulfate from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2013-10-07T14:12:38Z") +AnnotationAssertion( "sulfate import into cell") +AnnotationAssertion( "sulphate import into cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1902434") +AnnotationAssertion(rdfs:label "sulfate import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (negative regulation of stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:22969033") "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell population maintenance.") @@ -121575,19 +121387,6 @@ AnnotationAssertion( "positive regulation of intracellular signal transduction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (serine/threonine protein kinase complex) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "PMID:18191223") "A protein complex which is capable of protein serine/threonine kinase activity.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2013-12-06T16:06:12Z") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "PDR16 complex dimer") -AnnotationAssertion( "PDR16 complex homodimer") -AnnotationAssertion( "GO:1902554") -AnnotationAssertion(rdfs:comment "An example is IRE1 in S. cerevisiae (UniProt ID P32361) in PMID:18191223 (inferred from direct assay).") -AnnotationAssertion(rdfs:label "serine/threonine protein kinase complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of neutrophil activation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:17588661") "Any process that modulates the frequency, rate or extent of neutrophil activation.") @@ -122690,42 +122489,6 @@ AnnotationAssertion( "positive regulation of embryonic pattern specification") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (negative regulation of autophagosome assembly) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GOC:autophagy") Annotation( "GO_REF:0000058") Annotation( "PMID:21975012") "Any process that stops, prevents or reduces the frequency, rate or extent of autophagosome assembly.") -AnnotationAssertion( "als") -AnnotationAssertion( "2014-04-15T10:37:40Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of autophagic vacuole assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of autophagosome biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of autophagosome formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of autophagic vacuole assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of autophagosome biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of autophagosome formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of autophagic vacuole assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of autophagosome biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of autophagosome formation") -AnnotationAssertion(Annotation( "GOC:autophagy") "negative regulation of autophagic vacuole assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of autophagosome biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of autophagosome formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of PAS formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of PAS formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of PAS formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of PAS formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of autophagic vacuole assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of autophagosome biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of autophagosome formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of PAS formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of autophagic vacuole formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of autophagic vacuole formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of autophagic vacuole formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of autophagic vacuole formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of autophagic vacuole formation") -AnnotationAssertion( "GO:1902902") -AnnotationAssertion(rdfs:label "negative regulation of autophagosome assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) - # Class: (regulation of supramolecular fiber organization) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:23921388") "Any process that modulates the frequency, rate or extent of supramolecular fiber organization.") @@ -123894,6 +123657,72 @@ AnnotationAssertion( "multi-ciliated epithelial cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of sodium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17095720") "Any process that modulates the frequency, rate or extent of sodium ion export across the plasma membrane.") +AnnotationAssertion( "rl") +AnnotationAssertion( "2014-08-08T17:06:46Z") +AnnotationAssertion( "GO:1903273") +AnnotationAssertion( "regulation of sodium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of sodium export") +AnnotationAssertion( "regulation of sodium ion export") +AnnotationAssertion( "GO:1903276") +AnnotationAssertion(rdfs:label "regulation of sodium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of sodium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17095720") "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion export across the plasma membrane.") +AnnotationAssertion( "rl") +AnnotationAssertion( "2014-08-08T17:10:22Z") +AnnotationAssertion( "GO:1903274") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sodium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of sodium ion export from cell") +AnnotationAssertion( "negative regulation of sodium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of sodium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of sodium export") +AnnotationAssertion( "negative regulation of sodium ion export") +AnnotationAssertion( "GO:1903277") +AnnotationAssertion(rdfs:label "negative regulation of sodium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of sodium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17095720") "Any process that activates or increases the frequency, rate or extent of sodium ion export across the plasma membrane.") +AnnotationAssertion( "rl") +AnnotationAssertion( "2014-08-08T17:10:30Z") +AnnotationAssertion( "GO:1903275") +AnnotationAssertion( "positive regulation of sodium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sodium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of sodium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of sodium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of sodium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of sodium export") +AnnotationAssertion( "positive regulation of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of sodium ion export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of sodium export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of sodium ion export") +AnnotationAssertion( "GO:1903278") +AnnotationAssertion(rdfs:label "positive regulation of sodium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (protein localization to Golgi membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:11378902") "A process in which a protein is transported to, or maintained in, a location within a Golgi membrane.") @@ -124946,6 +124775,55 @@ AnnotationAssertion( "positive regulation of DNA catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of cytoplasmic transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25049409") "Any process that modulates the frequency, rate or extent of cytoplasmic transport.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2014-11-24T13:38:17Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cytoplasmic streaming") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903649") +AnnotationAssertion(rdfs:label "regulation of cytoplasmic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of cytoplasmic transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25049409") "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic transport.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2014-11-24T13:38:26Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of cytoplasmic streaming") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903650") +AnnotationAssertion(rdfs:label "negative regulation of cytoplasmic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of cytoplasmic transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25049409") "Any process that activates or increases the frequency, rate or extent of cytoplasmic transport.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2014-11-24T13:38:34Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cytoplasmic transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cytoplasmic streaming") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cytoplasmic streaming") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903651") +AnnotationAssertion(rdfs:label "positive regulation of cytoplasmic transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (acinar cell of sebaceous gland differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:17018284") Annotation( "PMID:18334552") Annotation( "PMID:19944183") "The process in which a relatively unspecialized cell acquires the specialized features of an acinar cell of sebaceous gland.") @@ -125288,6 +125166,44 @@ AnnotationAssertion( "positive regulation of cardiac conduction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of sodium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19376779") "Any process that modulates the frequency, rate or extent of sodium ion import across the plasma membrane.") +AnnotationAssertion( "nc") +AnnotationAssertion( "2015-01-07T16:48:43Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903782") +AnnotationAssertion(rdfs:label "regulation of sodium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of sodium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19376779") "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion import across the plasma membrane.") +AnnotationAssertion( "nc") +AnnotationAssertion( "2015-01-07T16:48:51Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sodium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of sodium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of sodium ion import across plasma membrane") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903783") +AnnotationAssertion(rdfs:label "negative regulation of sodium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of sodium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19376779") "Any process that activates or increases the frequency, rate or extent of sodium ion import across the plasma membrane.") +AnnotationAssertion( "nc") +AnnotationAssertion( "2015-01-07T16:49:00Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sodium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of sodium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of sodium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of sodium ion import across plasma membrane") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903784") +AnnotationAssertion(rdfs:label "positive regulation of sodium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of amino acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16115814") "Any process that modulates the frequency, rate or extent of amino acid transmembrane transport.") @@ -125769,6 +125685,22 @@ AnnotationAssertion( "positive regulation of glial cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (iron ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GOC:rl") Annotation( "GO_REF:0000074") Annotation( "PMID:15514116") "The directed movement of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "rl") +AnnotationAssertion( "2014-09-03T13:01:37Z") +AnnotationAssertion( "GO:1903414") +AnnotationAssertion( "ferrous iron export") +AnnotationAssertion( "ferrous iron export across plasma membrane") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "iron cation export") +AnnotationAssertion( "iron(2+) export") +AnnotationAssertion( "GO:1903988") +AnnotationAssertion(rdfs:comment "An example of this is mouse ferroportin (symbol Slc40a1, UniProtKB identifier: Q9JHI9).") +AnnotationAssertion(rdfs:label "iron ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (regulation of sebum secreting cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "GO_REF:0000058") Annotation( "PMID:16901790") "Any process that modulates the frequency, rate or extent of sebum secreting cell proliferation.") @@ -126014,6 +125946,58 @@ AnnotationAssertion( "positive regulation of epithelial cell apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of iron export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:15514116") "Any process that modulates the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "kom") +AnnotationAssertion( "2015-03-16T15:36:37Z") +AnnotationAssertion( "regulation of ferrous iron export") +AnnotationAssertion( "regulation of iron(2+) export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904038") +AnnotationAssertion(rdfs:label "regulation of iron export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of iron export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:15514116") "Any process that stops, prevents or reduces the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "kom") +AnnotationAssertion( "2015-03-16T15:36:43Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ferrous iron export") +AnnotationAssertion( "negative regulation of iron(2+) export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904039") +AnnotationAssertion(rdfs:label "negative regulation of iron export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of iron export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:15514116") "Any process that activates or increases the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "kom") +AnnotationAssertion( "2015-03-16T15:36:49Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ferrous iron export") +AnnotationAssertion( "positive regulation of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of iron(2+) export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ferrous iron export") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of iron(2+) export") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904040") +AnnotationAssertion(rdfs:label "positive regulation of iron export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (response to aldosterone) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:17644563") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldosterone stimulus.") @@ -126252,68 +126236,6 @@ AnnotationAssertion( "positive regulation of trophectodermal cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of autophagic cell death) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25736836") "Any process that modulates the frequency, rate or extent of autophagic cell death.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2015-03-26T16:41:32Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of autophagic death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of programmed cell death by autophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of programmed cell death by macroautophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of type II programmed cell death") -AnnotationAssertion( "GO:1904092") -AnnotationAssertion(rdfs:label "regulation of autophagic cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of autophagic cell death) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25736836") "Any process that stops, prevents or reduces the frequency, rate or extent of autophagic cell death.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2015-03-26T16:41:39Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of programmed cell death by macroautophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of type II programmed cell death") -AnnotationAssertion( "GO:1904093") -AnnotationAssertion(rdfs:label "negative regulation of autophagic cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of autophagic cell death) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25736836") "Any process that activates or increases the frequency, rate or extent of autophagic cell death.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2015-03-26T16:41:45Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of programmed cell death by macroautophagy") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of autophagic cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of programmed cell death by macroautophagy") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of type II programmed cell death") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of type II programmed cell death") -AnnotationAssertion( "GO:1904094") -AnnotationAssertion(rdfs:label "positive regulation of autophagic cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (protein localization to microvillus) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000087") Annotation( "PMID:25335890") "A process in which a protein is transported to, or maintained in, a location within a microvillus.") @@ -127593,6 +127515,65 @@ AnnotationAssertion( "positive regulation of calcium ion transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of iron ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:18353247") "Any process that modulates the frequency, rate or extent of iron ions import across plasma membrane.") +AnnotationAssertion( "rl") +AnnotationAssertion( "2015-03-04T14:37:36Z") +AnnotationAssertion( "GO:1903989") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ferrous ion import into cell") +AnnotationAssertion( "regulation of ferrous iron import across plasma membrane") +AnnotationAssertion( "regulation of ferrous iron import into cell") +AnnotationAssertion( "GO:1904438") +AnnotationAssertion(rdfs:label "regulation of iron ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + +# Class: (negative regulation of iron ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:18353247") "Any process that stops, prevents or reduces the frequency, rate or extent of iron ions import across plasma membrane.") +AnnotationAssertion( "rl") +AnnotationAssertion( "2015-07-06T13:49:58Z") +AnnotationAssertion( "GO:1903990") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ferrous iron import across plasma membrane") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ferrous iron import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ferrous iron import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ferrous iron import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ferrous ion import into cell") +AnnotationAssertion( "negative regulation of ferrous iron import across plasma membrane") +AnnotationAssertion( "negative regulation of ferrous iron import into cell") +AnnotationAssertion( "GO:1904439") +AnnotationAssertion(rdfs:label "negative regulation of iron ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of iron ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:18353247") "Any process that activates or increases the frequency, rate or extent of iron ions import across plasma membrane.") +AnnotationAssertion( "rl") +AnnotationAssertion( "2015-07-06T13:50:04Z") +AnnotationAssertion( "GO:1903991") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ferrous iron import across plasma membrane") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ferrous ion import into cell") +AnnotationAssertion( "positive regulation of ferrous iron import across plasma membrane") +AnnotationAssertion( "positive regulation of ferrous iron import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ferrous iron import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ferrous iron import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ferrous ion import into cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ferrous iron import across plasma membrane") +AnnotationAssertion( "GO:1904440") +AnnotationAssertion(rdfs:label "positive regulation of iron ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (negative regulation of neuronal action potential) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25126967") "Any process that stops, prevents or reduces the frequency, rate or extent of neuronal action potential.") @@ -128141,6 +128122,46 @@ AnnotationAssertion( "peptide transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +# Class: (regulation of cytoplasmic translational initiation) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:12242291") "Any process that modulates the frequency, rate or extent of cytoplasmic translational initiation.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21560"^^xsd:anyURI) +AnnotationAssertion( "dos") +AnnotationAssertion( "2015-09-25T14:39:38Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904688") +AnnotationAssertion(rdfs:label "regulation of cytoplasmic translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cytoplasmic translational initiation) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:12242291") "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational initiation.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2015-09-25T14:39:44Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cytoplasmic translational initiation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cytoplasmic translational initiation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cytoplasmic translational initiation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cytoplasmic translational initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904689") +AnnotationAssertion(rdfs:label "negative regulation of cytoplasmic translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of cytoplasmic translational initiation) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:12242291") "Any process that activates or increases the frequency, rate or extent of cytoplasmic translational initiation.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2015-09-25T14:39:50Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cytoplasmic translational initiation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cytoplasmic translational initiation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cytoplasmic translational initiation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cytoplasmic translational initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904690") +AnnotationAssertion(rdfs:label "positive regulation of cytoplasmic translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (negative regulation of type B pancreatic cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24055447") "Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell proliferation.") @@ -128410,31 +128431,6 @@ AnnotationAssertion( "vascular associated smooth muscle cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (Atg1/ULK1 kinase complex assembly) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000079") Annotation( "PMID:25139988") "The aggregation, arrangement and bonding together of a set of components to form an Atg1/UKL1 kinase complex.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2015-10-19T12:33:08Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1904745") -AnnotationAssertion(rdfs:label "Atg1/ULK1 kinase complex assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (negative regulation of apoptotic process involved in development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22801495") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development.") @@ -129012,6 +129008,58 @@ AnnotationAssertion( "positive regulation of euchromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22699897") "Any process that modulates the frequency, rate or extent of dense core granule transport.") +AnnotationAssertion( "es") +AnnotationAssertion( "2015-11-11T10:40:10Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of dense core vesicle transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904809") +AnnotationAssertion(rdfs:comment "cdk-5 in C.elegans (G5ECH7) in PMID:22699897 (inferred from mutant phenotype).") +AnnotationAssertion(rdfs:label "regulation of dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22699897") "Any process that stops, prevents or reduces the frequency, rate or extent of dense core granule transport.") +AnnotationAssertion( "es") +AnnotationAssertion( "2015-11-11T10:40:18Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of dense core vesicle transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904810") +AnnotationAssertion(rdfs:comment "cdk-5 in C.elegans (G5ECH7) in PMID:22699897 (inferred from mutant phenotype).") +AnnotationAssertion(rdfs:label "negative regulation of dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of dense core granule transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22699897") "Any process that activates or increases the frequency, rate or extent of dense core granule transport.") +AnnotationAssertion( "es") +AnnotationAssertion( "2015-11-11T10:40:25Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of dense core vesicle transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of dense core granule transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of dense core vesicle transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904811") +AnnotationAssertion(rdfs:comment "cdk-5 in C.elegans (G5ECH7) in PMID:22699897 (inferred from mutant phenotype).") +AnnotationAssertion(rdfs:label "positive regulation of dense core granule transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (serous membrane development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000094") Annotation( "PMID:15840053") "The process whose specific outcome is the progression of a serous membrane over time, from its formation to the mature structure.") @@ -129449,18 +129497,6 @@ AnnotationAssertion(rdfs:label "midb EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (ATPase complex) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:9606181") "A protein complex which is capable of ATPase activity.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2016-02-04T22:13:32Z") -AnnotationAssertion( "VPS4 complex") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:1904949") -AnnotationAssertion(rdfs:comment "An example of this is VPS4 in Saccharomyces cerevisiae (UniProt ID P52917) in PMID:9606181 (inferred from direct assay).") -AnnotationAssertion(rdfs:label "ATPase complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (negative regulation of establishment of protein localization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22761445") "Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization.") @@ -129666,18 +129702,17 @@ AnnotationAssertion( "positive regulation of endothelial cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (autophagosome organization) +# Class: (transmembrane phosphate ion transport from cytosol to vacuole) -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "PMID:22186024") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an autophagosome.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2016-03-08T14:18:10Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "autophagic vacuole organization") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "initial autophagic vacuole organization") -AnnotationAssertion( "GO:1905037") -AnnotationAssertion(rdfs:label "autophagosome organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000078") Annotation( "PMID:26554016") "The directed movement of phosphate ions from the cytosol across the vacuolar membrane and into the vacuolar lumen.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2016-03-03T00:34:12Z") +AnnotationAssertion( "GO:0007037") +AnnotationAssertion( "vacuolar phosphate transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905011") +AnnotationAssertion(rdfs:label "transmembrane phosphate ion transport from cytosol to vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (regulation of membrane lipid metabolic process) @@ -129916,23 +129951,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -# Class: (cell surface receptor signaling pathway involved in cell-cell signaling) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000060") Annotation( "ISBN:0-7167-3051-0") "Any cell surface receptor signaling pathway that is involved in cell-cell signaling.") -AnnotationAssertion( "dos") -AnnotationAssertion( "2016-04-06T16:59:57Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "cell surface receptor linked signal transduction involved in cell-cell signaling") -AnnotationAssertion(Annotation( "GOC:TermGenie") "cell surface receptor linked signal transduction involved in cell-cell signalling") -AnnotationAssertion(Annotation( "GOC:TermGenie") "cell surface receptor linked signaling pathway involved in cell-cell signaling") -AnnotationAssertion(Annotation( "GOC:TermGenie") "cell surface receptor linked signaling pathway involved in cell-cell signalling") -AnnotationAssertion(Annotation( "GOC:TermGenie") "cell surface receptor linked signalling pathway involved in cell-cell signaling") -AnnotationAssertion(Annotation( "GOC:TermGenie") "cell surface receptor linked signalling pathway involved in cell-cell signalling") -AnnotationAssertion(Annotation( "GOC:TermGenie") "cell surface receptor signaling pathway involved in cell-cell signalling") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905114") -AnnotationAssertion(rdfs:label "cell surface receptor signaling pathway involved in cell-cell signaling") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of axo-dendritic protein transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20694152") "Any process that modulates the frequency, rate or extent of axo-dendritic protein transport.") @@ -130431,7 +130449,7 @@ AnnotationAssertion( "GO:1905219") AnnotationAssertion(rdfs:label "regulation of platelet formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) # Class: (negative regulation of platelet formation) @@ -130470,7 +130488,7 @@ AnnotationAssertion( "GO:1905221") AnnotationAssertion(rdfs:label "positive regulation of platelet formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) # Class: (atrioventricular canal morphogenesis) @@ -132140,6 +132158,32 @@ AnnotationAssertion( "positive regulation of artery morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of calcium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:17640527") "Any process that modulates the frequency, rate or extent of calcium ion import across plasma membrane.") +AnnotationAssertion( "bhm") +AnnotationAssertion( "2016-11-11T09:26:06Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905664") +AnnotationAssertion(rdfs:comment "An example of this is PPP3CA in human (Q08209) in 17640527 (inferred from direct assay).") +AnnotationAssertion(rdfs:label "regulation of calcium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of calcium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:17640527") "Any process that activates or increases the frequency, rate or extent of calcium ion import across plasma membrane.") +AnnotationAssertion( "bhm") +AnnotationAssertion( "2016-11-11T09:26:23Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of calcium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of calcium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of calcium ion import across plasma membrane") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905665") +AnnotationAssertion(rdfs:comment "An example of this is PPP3CA in human (Q08209) in 17640527 (inferred from direct assay).") +AnnotationAssertion(rdfs:label "positive regulation of calcium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of lysosome organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25561470") "Any process that modulates the frequency, rate or extent of lysosome organization.") @@ -132591,209 +132635,6 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -# Class: (regulation of Atg1/ULK1 kinase complex assembly) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:autophagy") Annotation( "GOC:mf") Annotation( "GO_REF:0000058") Annotation( "PMID:26567215") "Any process that modulates the frequency, rate or extent of Atg1/ULK1 kinase complex assembly.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2017-01-26T13:23:26Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905864") -AnnotationAssertion(rdfs:label "regulation of Atg1/ULK1 kinase complex assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of Atg1/ULK1 kinase complex assembly) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:autophagy") Annotation( "GOC:mf") Annotation( "GO_REF:0000058") Annotation( "PMID:26567215") "Any process that stops, prevents or reduces the frequency, rate or extent of Atg1/ULK1 kinase complex assembly.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2017-01-26T13:23:35Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905865") -AnnotationAssertion(rdfs:label "negative regulation of Atg1/ULK1 kinase complex assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of Atg1/ULK1 kinase complex assembly) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:autophagy") Annotation( "GOC:mf") Annotation( "GO_REF:0000058") Annotation( "PMID:26567215") "Any process that activates or increases the frequency, rate or extent of Atg1/ULK1 kinase complex assembly.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2017-01-26T13:23:44Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1-ATG13 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1-ATG13 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 kinase complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 kinase complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of Atg1p signalling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of Atg1p signalling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1 signaling complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1 signaling complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-FIP200 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-FIP200 complex formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-RB1CC1 complex assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-RB1CC1 complex formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905866") -AnnotationAssertion(rdfs:label "positive regulation of Atg1/ULK1 kinase complex assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (epididymis development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "PMID:12388089") "The process whose specific outcome is the progression of an epididymis over time, from its formation to the mature structure.") @@ -133018,6 +132859,58 @@ AnnotationAssertion( "pharyngeal gland morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of calcium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22362515") "Any process that modulates the frequency, rate or extent of calcium ion export across the plasma membrane.") +AnnotationAssertion( "rph") +AnnotationAssertion( "2017-02-07T13:20:39Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of calcium ion efflux from cell") +AnnotationAssertion( "regulation of calcium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905912") +AnnotationAssertion(rdfs:label "regulation of calcium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of calcium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22362515") "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion export across the plasma membrane.") +AnnotationAssertion( "rph") +AnnotationAssertion( "2017-02-07T13:20:48Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of calcium ion efflux from cell") +AnnotationAssertion( "negative regulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of calcium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905913") +AnnotationAssertion(rdfs:label "negative regulation of calcium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of calcium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22362515") "Any process that activates or increases the frequency, rate or extent of calcium ion export across the plasma membrane.") +AnnotationAssertion( "rph") +AnnotationAssertion( "2017-02-07T13:20:56Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of calcium ion efflux from cell") +AnnotationAssertion( "positive regulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of calcium ion export from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of calcium ion efflux from cell") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of calcium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905914") +AnnotationAssertion(rdfs:label "positive regulation of calcium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of acetylcholine biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:20164328") "Any process that modulates the frequency, rate or extent of acetylcholine biosynthetic process.") @@ -133241,6 +133134,21 @@ AnnotationAssertion( "positive regulation of response to calcium ion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (negative regulation of calcium ion import across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:17640527") "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion import across plasma membrane.") +AnnotationAssertion( "bhm") +AnnotationAssertion( "2017-02-17T09:42:30Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of calcium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of calcium ion import across plasma membrane") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of calcium ion import across plasma membrane") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905949") +AnnotationAssertion(rdfs:comment "An example of this is PPP3CA in human (Q08209) in PMID:17640527 (inferred from direct assay).") +AnnotationAssertion(rdfs:label "negative regulation of calcium ion import across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of lipid localization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17564681") "Any process that modulates the frequency, rate or extent of lipid localization.") @@ -133392,6 +133300,43 @@ AnnotationAssertion(rdfs:label "comp EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (calcium ion export across plasma membrane) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:2145281") "The directed movement of calcium ions from inside of a cell, across the plasma membrane and into the extracellular region.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2013-02-07T13:01:29Z") +AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:2145281") "calcium ion efflux from cell") +AnnotationAssertion( "calcium ion export from cell") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1990034") +AnnotationAssertion(rdfs:label "calcium ion export across plasma membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (anterograde neuronal dense core vesicle transport) + +AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "PMID:23358451") "The directed movement of substances in neuronal dense core vesicles along axonal microtubules towards the presynapse.") +AnnotationAssertion( "anterograde dense core granule trafficking") +AnnotationAssertion( "anterograde dense core granule transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1990048") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anterograde neuronal dense core vesicle transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (retrograde neuronal dense core vesicle transport) + +AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "PMID:23358451") Annotation( "PMID:24762653") "The directed movement of neuronal dense core vesicles along axonal microtubules towards the cell body.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2013-02-19T13:31:44Z") +AnnotationAssertion( "retrograde dense core granule trafficking") +AnnotationAssertion( "retrograde dense core granule transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1990049") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "retrograde neuronal dense core vesicle transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (lens fiber cell apoptotic process) AnnotationAssertion(Annotation( "CL:0011004") Annotation( "GOC:hjd") Annotation( "PMID:11095619") "Any apoptotic process in a lens fiber cell. Lens fiber cells are elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye.") @@ -133490,31 +133435,6 @@ AnnotationAssertion(rdfs:label "RNA EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (Atg1/ULK1 kinase complex) - -AnnotationAssertion(Annotation( "GOC:DOS") Annotation( "GOC:bhm") Annotation( "GOC:rb") Annotation( "PMID:15743910") Annotation( "PMID:19211835") Annotation( "PMID:19258318") Annotation( "PMID:19597335") Annotation( "PMID:22885598") "A protein complex consisting of Atg1 (or Atg1 homologs e.g. ULK1, ULK2 in mammals) and Atg13 along with other proteins that regulate its function (e.g. Atg17 in yeast or RB1CC1(FIP200) in mammals). This complex has serine/threonine protein kinase activity and is involved in autophagosome formation.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2014-03-14T10:55:11Z") -AnnotationAssertion( "GO:0034273") -AnnotationAssertion( "GO:0070969") -AnnotationAssertion( "ATG1 kinase complex") -AnnotationAssertion( "ATG1-ATG13 complex") -AnnotationAssertion( "ATG1/ULK1 signaling complex") -AnnotationAssertion( "Atg1p signalling complex") -AnnotationAssertion(Annotation( "PMID:28816597") "ULK complex") -AnnotationAssertion(Annotation( "PMID:26921696") "ULK1 complex") -AnnotationAssertion( "ULK1 signaling complex") -AnnotationAssertion( "ULK1-ATG13-FIP200 complex") -AnnotationAssertion( "ULK1-ATG13-RB1CC1 complex") -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:autophagy") Annotation( "GOC:pad") Annotation( "PMID:26754330") "autophagy-initiation complex") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:1990316") -AnnotationAssertion(rdfs:label "Atg1/ULK1 kinase complex") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (transporter complex) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:15449578") "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.") @@ -133553,18 +133473,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) -# Class: (hyaloid vascular plexus regression) - -AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "PMID:18841878") "The developmental process in which the hyaloid vascular plexus is destroyed as a part of its normal progression.") -AnnotationAssertion( "hjd") -AnnotationAssertion( "2014-05-28T18:43:21Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1990384") -AnnotationAssertion(rdfs:label "hyaloid vascular plexus regression") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (detoxification of iron ion) AnnotationAssertion(Annotation( "GOC:sart") Annotation( "PMID:23064556") "Any process that reduces or removes the toxicity of iron ion. These include transport of iron away from sensitive areas and to compartments or complexes whose purpose is sequestration of iron ion.") @@ -133577,6 +133485,30 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (dense core granule maturation) + +AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "PMID:22654674") "Steps required to transform a dense core granule generated at the trans-Golgi network into a fully formed and transmissible dense core granule. Dense core granule maturation proceeds through clathrin-mediated membrane remodeling events and is essential for efficient processing of cargo within dense core granules as well as for removing factors that might otherwise interfere with dense core granule trafficking and exocytosis.") +AnnotationAssertion( "kmv") +AnnotationAssertion( "2014-09-30T20:35:11Z") +AnnotationAssertion( "dense core vesicle maturation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1990502") +AnnotationAssertion(rdfs:label "dense core granule maturation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (regulation of cytoplasmic translational termination) + +AnnotationAssertion(Annotation( "PMID:11570975") "Any process that modulates the frequency, rate or extent of cytoplasmic translational termination.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2014-12-10T15:48:55Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1990580") +AnnotationAssertion(rdfs:label "regulation of cytoplasmic translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + # Class: (sebum secreting cell proliferation) AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "PMID:16901790") Annotation( "PMID:18474083") "The multiplication or reproduction of sebocytes by cell division, resulting in the expansion of their population. A sebocyte is an epithelial cell that makes up the sebaceous glands, and secrete sebum.") @@ -136164,6 +136096,36 @@ AnnotationAssertion( "positive regulation of stem cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of cytoplasmic translation) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of cytoplasmic translation.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2011-06-20T10:39:19Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2000765") +AnnotationAssertion(rdfs:label "regulation of cytoplasmic translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of cytoplasmic translation) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translation.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2011-06-20T10:39:23Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2000766") +AnnotationAssertion(rdfs:label "negative regulation of cytoplasmic translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of cytoplasmic translation) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of cytoplasmic translation.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2011-06-20T10:39:26Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2000767") +AnnotationAssertion(rdfs:label "positive regulation of cytoplasmic translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (positive regulation of nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of nephron tubule epithelial cell differentiation.") @@ -136174,37 +136136,6 @@ AnnotationAssertion( "positive regulation of nephron tubule epithelial cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of autophagosome assembly) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:autophagy") "Any process that modulates the frequency, rate or extent of autophagosome assembly.") -AnnotationAssertion( "rl") -AnnotationAssertion( "2011-06-24T11:19:08Z") -AnnotationAssertion(Annotation( "GOC:autophagy") "regulation of autophagic vacuole assembly") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of autophagosome biosynthesis") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of autophagosome formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of PAS formation") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of autophagic vacuole formation") -AnnotationAssertion( "GO:2000785") -AnnotationAssertion(rdfs:label "regulation of autophagosome assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of autophagosome assembly) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:autophagy") "Any process that activates or increases the frequency, rate or extent of autophagic vacuole assembly.") -AnnotationAssertion( "rl") -AnnotationAssertion( "2011-06-24T11:19:12Z") -AnnotationAssertion(Annotation( "GOC:autophagy") "positive regulation of autophagic vacuole assembly") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of autophagosome biosynthesis") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of autophagosome formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of PAS formation") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of autophagic vacuole formation") -AnnotationAssertion( "GO:2000786") -AnnotationAssertion(rdfs:label "positive regulation of autophagosome assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) - # Class: (regulation of mesenchymal cell proliferation involved in lung development) AnnotationAssertion(Annotation( "PMID:21513708") "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.") @@ -137378,18 +137309,6 @@ AnnotationAssertion( "positive regulation of chromosome organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (curation status specification) - -AnnotationAssertion( "curation status specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) -AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "OBI_0000266"@en) -AnnotationAssertion(rdfs:label "curation status specification"@en) -EquivalentClasses( ObjectOneOf( )) - # Class: (body part movement) AnnotationAssertion( "A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC]") @@ -137778,7 +137697,6 @@ AnnotationAssertion( ) "all") AnnotationAssertion( "NCBITaxon:1") AnnotationAssertion(rdfs:label "root") -SubClassOf( ) # Class: (Gerbillinae) @@ -143328,7 +143246,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "branched") -SubClassOf( ) SubClassOf( ) # Class: (coiled) @@ -143640,7 +143557,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "linear") -SubClassOf( ) SubClassOf( ) # Class: (Y-shaped) @@ -144490,7 +144406,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "laminar") -SubClassOf( ) SubClassOf( ) # Class: (high-arched) @@ -145079,7 +144994,6 @@ AnnotationAssertion(Annotation( "PR:000001006") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-M) @@ -145099,7 +145013,6 @@ AnnotationAssertion(Annotation( "PR:000001012") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-M") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-X) @@ -145117,7 +145030,6 @@ AnnotationAssertion(Annotation( "PR:000001013") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-X") -AnnotationAssertion( ) SubClassOf( ) # Class: (receptor-type tyrosine-protein phosphatase C isoform CD45RABC) @@ -145131,7 +145043,6 @@ AnnotationAssertion( "PR:000001014") AnnotationAssertion(rdfs:comment "Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exons 4(A), 5(B), and 6(C).") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C isoform CD45RABC") -AnnotationAssertion( ) SubClassOf( ) # Class: (receptor-type tyrosine-protein phosphatase C isoform CD45RA) @@ -145143,7 +145054,6 @@ AnnotationAssertion( "PR:000001015") AnnotationAssertion(rdfs:comment "Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C).") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C isoform CD45RA") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD3 subunit with immunoglobulin domain) @@ -145204,7 +145114,6 @@ AnnotationAssertion(Annotation( "PR:000001024") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "neural cell adhesion molecule 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD2 molecule) @@ -145243,7 +145152,6 @@ AnnotationAssertion(Annotation( "PR:000001084") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD8 alpha chain") -AnnotationAssertion( ) SubClassOf( ) # Class: (rhodopsin-like G-protein coupled receptor) @@ -145290,7 +145198,6 @@ AnnotationAssertion(Annotation( "PR:000001199") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (CX3C chemokine receptor 1) @@ -145313,7 +145220,6 @@ AnnotationAssertion(Annotation( "PR:000001206") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "CX3C chemokine receptor 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (ADP-ribosyl cyclase) @@ -145358,7 +145264,6 @@ AnnotationAssertion(Annotation( "PR:000001293") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-type lectin domain family 4 member K") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD44 molecule) @@ -145440,7 +145345,6 @@ AnnotationAssertion(Annotation( "PR:000001332") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "carcinoembryonic antigen-related cell adhesion molecule 8") -AnnotationAssertion( ) SubClassOf( ) # Class: (complement receptor type 2) @@ -145458,7 +145362,6 @@ AnnotationAssertion(Annotation( "PR:000001338") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "complement receptor type 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (endoglin) @@ -145475,7 +145378,6 @@ AnnotationAssertion(Annotation( "PR:000001345") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "endoglin") -AnnotationAssertion( ) SubClassOf( ) # Class: (glycophorin) @@ -145516,7 +145418,6 @@ AnnotationAssertion(Annotation( "PR:000001380") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-2 receptor subunit alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1) @@ -145538,7 +145439,6 @@ AnnotationAssertion( "PR:000001408") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (cadherin-5) @@ -145553,7 +145453,6 @@ AnnotationAssertion( "PR:000001444") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "cadherin-5") -AnnotationAssertion( ) SubClassOf( ) # Class: (glycophorin-A) @@ -145569,7 +145468,6 @@ AnnotationAssertion(Annotation( "PR:000001460") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "glycophorin-A") -AnnotationAssertion( ) SubClassOf( ) # Class: (low affinity immunoglobulin gamma Fc region receptor II) @@ -145607,7 +145505,6 @@ AnnotationAssertion(Annotation( "PR:000001481") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "low affinity immunoglobulin gamma Fc region receptor II-b") -AnnotationAssertion( ) SubClassOf( ) # Class: (low affinity immunoglobulin gamma Fc region receptor III) @@ -145661,7 +145558,6 @@ AnnotationAssertion(Annotation( "PR:000001786") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "prominin-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD59-like glycoprotein) @@ -145728,7 +145624,6 @@ AnnotationAssertion(Annotation( "PR:000001839") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD5") -AnnotationAssertion( ) SubClassOf( ) # Class: (Thy-1 membrane glycoprotein) @@ -145744,7 +145639,6 @@ AnnotationAssertion(Annotation( "PR:000001843") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "Thy-1 membrane glycoprotein") -AnnotationAssertion( ) SubClassOf( ) # Class: (cathepsin K) @@ -145761,7 +145655,6 @@ AnnotationAssertion( "PR:000001850") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "cathepsin K") -AnnotationAssertion( ) SubClassOf( ) # Class: (immunoglobulin iota chain) @@ -145779,7 +145672,6 @@ AnnotationAssertion(Annotation( "PR:000001858") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "immunoglobulin iota chain") -AnnotationAssertion( ) SubClassOf( ) # Class: (immunoglobulin lambda-like polypeptide 1) @@ -145797,7 +145689,6 @@ AnnotationAssertion( "PR:000001859") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "immunoglobulin lambda-like polypeptide 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (interleukin-3 receptor class 2 alpha chain) @@ -145836,7 +145727,6 @@ AnnotationAssertion(Annotation( "PR:000001867") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-5 receptor subunit alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (interleukin-7 receptor subunit alpha) @@ -145855,7 +145745,6 @@ AnnotationAssertion( "PR:000001869") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-7 receptor subunit alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (KLRB1-like protein) @@ -145885,7 +145774,6 @@ AnnotationAssertion(Annotation( "PR:000001879") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "leukosialin") -AnnotationAssertion( ) SubClassOf( ) # Class: (low affinity immunoglobulin epsilon Fc receptor) @@ -145909,7 +145797,6 @@ AnnotationAssertion(Annotation( "PR:000001880") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "low affinity immunoglobulin epsilon Fc receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (membrane alanyl aminopeptidase-like metallopeptidase) @@ -145969,7 +145856,6 @@ AnnotationAssertion(Annotation( "PR:000001896") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "natural killer cell receptor 2B4") -AnnotationAssertion( ) SubClassOf( ) # Class: (neprilysin) @@ -145993,7 +145879,6 @@ AnnotationAssertion(Annotation( "PR:000001898") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "neprilysin") -AnnotationAssertion( ) SubClassOf( ) # Class: (paired box protein PAX-5) @@ -146007,7 +145892,6 @@ AnnotationAssertion(Annotation( "PR:000001903") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "paired box protein PAX-5") -AnnotationAssertion( ) SubClassOf( ) # Class: (scavenger receptor cysteine-rich type 1 protein M130) @@ -146020,7 +145904,6 @@ AnnotationAssertion(Annotation( "PR:000001925") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "scavenger receptor cysteine-rich type 1 protein M130") -AnnotationAssertion( ) SubClassOf( ) # Class: (signal transducer CD24) @@ -146040,7 +145923,6 @@ AnnotationAssertion(Annotation( "PR:000001932") AnnotationAssertion(rdfs:comment "Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. Requested by=CL.") AnnotationAssertion(rdfs:label "signal transducer CD24") -AnnotationAssertion( ) SubClassOf( ) # Class: (syndecan-1) @@ -146056,7 +145938,6 @@ AnnotationAssertion(Annotation( "PR:000001935") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "syndecan-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (tartrate-resistant acid phosphatase type 5) @@ -146074,7 +145955,6 @@ AnnotationAssertion(Annotation( "PR:000001937") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "tartrate-resistant acid phosphatase type 5") -AnnotationAssertion( ) SubClassOf( ) # Class: (thrombomodulin-like receptor) @@ -146099,7 +145979,6 @@ AnnotationAssertion(Annotation( "PR:000001944") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "transcription factor PU.1") -AnnotationAssertion( ) SubClassOf( ) # Class: (transferrin receptor protein 1) @@ -146117,7 +145996,6 @@ AnnotationAssertion(Annotation( "PR:000001945") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "transferrin receptor protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (tumor necrosis factor receptor superfamily member 11A) @@ -146135,7 +146013,6 @@ AnnotationAssertion(Annotation( "PR:000001954") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "tumor necrosis factor receptor superfamily member 11A") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD27 molecule) @@ -146170,7 +146047,6 @@ AnnotationAssertion(Annotation( "PR:000001969") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "urokinase plasminogen activator surface receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (vascular endothelial growth factor receptor) @@ -146206,7 +146082,6 @@ AnnotationAssertion(Annotation( "PR:000002001") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein kinase FLT3") -AnnotationAssertion( ) SubClassOf( ) # Class: (complement component C1q receptor) @@ -146231,7 +146106,6 @@ AnnotationAssertion(Annotation( "PR:000002037") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "complement component C1q receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (glutamyl aminopeptidase) @@ -146249,7 +146123,6 @@ AnnotationAssertion( "PR:000002039") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "glutamyl aminopeptidase") -AnnotationAssertion( ) SubClassOf( ) # Class: (macrophage colony-stimulating factor 1 receptor) @@ -146270,7 +146143,6 @@ AnnotationAssertion(Annotation( "PR:000002062") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "macrophage colony-stimulating factor 1 receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (mast/stem cell growth factor receptor) @@ -146308,7 +146180,6 @@ AnnotationAssertion(Annotation( "PR:000002112") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (Ly-6-like protein) @@ -146406,7 +146277,6 @@ AnnotationAssertion(Annotation( "PR:000003457") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "V(D)J recombination-activating protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (V(D)J recombination-activating protein 2) @@ -146418,7 +146288,6 @@ AnnotationAssertion( "PR:000003460") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "V(D)J recombination-activating protein 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (lactosylceramide 4-alpha-galactosyltransferase) @@ -146439,7 +146308,6 @@ AnnotationAssertion(Annotation( "PR:000003516") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "lactosylceramide 4-alpha-galactosyltransferase") -AnnotationAssertion( ) SubClassOf( ) # Class: (CCAAT/enhancer-binding protein alpha) @@ -146452,7 +146320,6 @@ AnnotationAssertion(Annotation( "PR:000005307") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "CCAAT/enhancer-binding protein alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (DNA nucleotidylexotransferase) @@ -146467,7 +146334,6 @@ AnnotationAssertion(Annotation( "PR:000006611") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "DNA nucleotidylexotransferase") -AnnotationAssertion( ) SubClassOf( ) # Class: (fibroblast growth factor 8) @@ -146483,7 +146349,6 @@ AnnotationAssertion( "PR:000007499") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "fibroblast growth factor 8") -AnnotationAssertion( ) SubClassOf( ) # Class: (protein c-Fos) @@ -146499,7 +146364,6 @@ AnnotationAssertion(Annotation( "PR:000007597") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "protein c-Fos") -AnnotationAssertion( ) SubClassOf( ) # Class: (forkhead box protein N1) @@ -146519,7 +146383,6 @@ AnnotationAssertion( "PR:000007636") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "forkhead box protein N1") -AnnotationAssertion( ) SubClassOf( ) # Class: (erythroid transcription factor) @@ -146537,7 +146400,6 @@ AnnotationAssertion(Annotation( "PR:000007857") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "erythroid transcription factor") -AnnotationAssertion( ) SubClassOf( ) # Class: (endothelial transcription factor GATA-2) @@ -146549,7 +146411,6 @@ AnnotationAssertion( "PR:000007858") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "endothelial transcription factor GATA-2") -AnnotationAssertion( ) SubClassOf( ) # Class: (glial fibrillary acidic protein) @@ -146560,7 +146421,6 @@ AnnotationAssertion( "PR:000007939") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "glial fibrillary acidic protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (insulin gene translation product) @@ -146572,7 +146432,6 @@ AnnotationAssertion( "PR:000009054") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "insulin gene translation product") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-IIb) @@ -146590,7 +146449,6 @@ AnnotationAssertion(Annotation( "PR:000009127") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-IIb") -AnnotationAssertion( ) SubClassOf( ) # Class: (lactotransferrin) @@ -146605,7 +146463,6 @@ AnnotationAssertion(Annotation( "PR:000009978") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "lactotransferrin") -AnnotationAssertion( ) SubClassOf( ) # Class: (myelin basic protein) @@ -146619,7 +146476,6 @@ AnnotationAssertion(Annotation( "PR:000010228") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "myelin basic protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (nuclear factor NF-kappa-B p100 subunit) @@ -146637,7 +146493,6 @@ AnnotationAssertion(Annotation( "PR:000011178") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "nuclear factor NF-kappa-B p100 subunit") -AnnotationAssertion( ) SubClassOf( ) # Class: (prolactin) @@ -146648,7 +146503,6 @@ AnnotationAssertion( "PR:000013246") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "prolactin") -AnnotationAssertion( ) SubClassOf( ) # Class: (renin) @@ -146661,7 +146515,6 @@ AnnotationAssertion( "PR:000013883") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "renin") -AnnotationAssertion( ) SubClassOf( ) # Class: (sonic hedgehog protein) @@ -146676,7 +146529,6 @@ AnnotationAssertion(Annotation( "PR:000014841") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "sonic hedgehog protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (spondin-1) @@ -146691,7 +146543,6 @@ AnnotationAssertion(Annotation( "PR:000015557") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "spondin-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (SCO-spondin) @@ -146704,7 +146555,6 @@ AnnotationAssertion(Annotation( "PR:000015658") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "SCO-spondin") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell acute lymphocytic leukemia protein 1) @@ -146723,7 +146573,6 @@ AnnotationAssertion(Annotation( "PR:000016043") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell acute lymphocytic leukemia protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (thyroglobulin) @@ -146736,7 +146585,6 @@ AnnotationAssertion(Annotation( "PR:000016283") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "thyroglobulin") -AnnotationAssertion( ) SubClassOf( ) # Class: (amino acid chain) @@ -146949,7 +146797,6 @@ AnnotationAssertion( "PR:000027222") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "CALCA gene translation product") -AnnotationAssertion( ) SubClassOf( ) # Class: (CALCA gene translation product (mouse)) @@ -150737,207 +150584,6 @@ AnnotationAssertion( "system") SubClassOf( ) -# Class: (anatomical structure) - -AnnotationAssertion(Annotation( "CARO:0000003") "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010825") -AnnotationAssertion( "AEO:0000003") -AnnotationAssertion( "BILA:0000003") -AnnotationAssertion( "CARO:0000003") -AnnotationAssertion( "EHDAA2:0003003") -AnnotationAssertion( "EMAPA:0") -AnnotationAssertion( "FBbt:00007001") -AnnotationAssertion( "FMA:305751") -AnnotationAssertion( "FMA:67135") -AnnotationAssertion( "GAID:781") -AnnotationAssertion( "HAO:0000003") -AnnotationAssertion( "MA:0003000") -AnnotationAssertion( "MESH:D000825") -AnnotationAssertion( "SCTID:362889002") -AnnotationAssertion( "TAO:0000037") -AnnotationAssertion( "TGMA:0001823") -AnnotationAssertion( "VHOG:0001759") -AnnotationAssertion( "XAO:0003000") -AnnotationAssertion( "ZFA:0000037") -AnnotationAssertion( "http://dbpedia.org/ontology/AnatomicalStructure") -AnnotationAssertion( "biological structure") -AnnotationAssertion(Annotation( "CARO:0000003") "connected biological structure") -AnnotationAssertion( "UBERON:0000061") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical structure") -SubClassOf( ) - -# Class: (neuron projection bundle) - -AnnotationAssertion(Annotation( "CARO:0001001") Annotation( "FBC:DOS") Annotation( "FBbt:00005099") "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.") -AnnotationAssertion( "CARO:0001001") -AnnotationAssertion( "FBbt:00005099") -AnnotationAssertion( "NLX:147821") -AnnotationAssertion( "funiculus") -AnnotationAssertion(Annotation( "FBbt:00005099") "nerve fiber bundle") -AnnotationAssertion( "neural fiber bundle") -AnnotationAssertion( "UBERON:0000122") -AnnotationAssertion(rdfs:label "neuron projection bundle") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Anatomical entity that has mass.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010264") -AnnotationAssertion( "AEO:0000006") -AnnotationAssertion( "BILA:0000006") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion( "FBbt:00007016") -AnnotationAssertion( "FMA:67165") -AnnotationAssertion( "HAO:0000006") -AnnotationAssertion( "TAO:0001836") -AnnotationAssertion( "TGMA:0001826") -AnnotationAssertion( "VHOG:0001721") -AnnotationAssertion( "UBERON:0000465") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) -SubClassOf( ) -DisjointClasses( ) - -# Class: (immaterial anatomical entity) - -AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Anatomical entity that has no mass.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010265") -AnnotationAssertion( "AEO:0000007") -AnnotationAssertion( "BILA:0000007") -AnnotationAssertion( "CARO:0000007") -AnnotationAssertion( "EHDAA2:0003007") -AnnotationAssertion( "FBbt:00007015") -AnnotationAssertion( "FMA:67112") -AnnotationAssertion( "HAO:0000007") -AnnotationAssertion( "TAO:0001835") -AnnotationAssertion( "TGMA:0001827") -AnnotationAssertion( "VHOG:0001727") -AnnotationAssertion(Annotation( "FMA:67112") "immaterial physical anatomical entity") -AnnotationAssertion( "UBERON:0000466") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immaterial anatomical entity") -SubClassOf( ) -SubClassOf( ) - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "FMA:62955") Annotation( "http://orcid.org/0000-0001-9114-8737") "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010841") -AnnotationAssertion( "AEO:0000000") -AnnotationAssertion( "BILA:0000000") -AnnotationAssertion( "BIRNLEX:6") -AnnotationAssertion( "CARO:0000000") -AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion( "FBbt:10000000") -AnnotationAssertion( "FMA:62955") -AnnotationAssertion( "HAO:0000000") -AnnotationAssertion( "MA:0000001") -AnnotationAssertion( "NCIT:C12219") -AnnotationAssertion( "TAO:0100000") -AnnotationAssertion( "TGMA:0001822") -AnnotationAssertion(Annotation( "ncithesaurus:Anatomic_Structure_System_or_Substance") "UMLS:C1515976") -AnnotationAssertion( "WBbt:0000100") -AnnotationAssertion( "XAO:0000000") -AnnotationAssertion( "ZFA:0100000") -AnnotationAssertion( "UBERON:0001062") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) - -# Class: (multicellular anatomical structure) - -AnnotationAssertion(Annotation( "CARO:0010000") "An anatomical structure that has more than one cell as a part.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "CARO:0010000") -AnnotationAssertion( "FBbt:00100313") -AnnotationAssertion(Annotation( "FBbt:00100313") "multicellular structure") -AnnotationAssertion( "UBERON:0010000") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "multicellular anatomical structure") -SubClassOf( ) - - -############################ -# Named Individuals -############################ - -# Individual: (example to be eventually removed) - -AnnotationAssertion( "example to be eventually removed"@en) -AnnotationAssertion(rdfs:label "example to be eventually removed"@en) - -# Individual: (metadata complete) - -AnnotationAssertion( "metadata complete"@en) -AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) -AnnotationAssertion(rdfs:label "metadata complete"@en) - -# Individual: (organizational term) - -AnnotationAssertion( "organizational term"@en) -AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) -AnnotationAssertion(rdfs:label "organizational term"@en) - -# Individual: (ready for release) - -AnnotationAssertion( "ready for release"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) -AnnotationAssertion(rdfs:label "ready for release"@en) - -# Individual: (metadata incomplete) - -AnnotationAssertion( "metadata incomplete"@en) -AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) -AnnotationAssertion(rdfs:label "metadata incomplete"@en) - -# Individual: (uncurated) - -AnnotationAssertion( "uncurated"@en) -AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) -AnnotationAssertion(rdfs:label "uncurated"@en) - -# Individual: (pending final vetting) - -AnnotationAssertion( "pending final vetting"@en) -AnnotationAssertion( ) -AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) -AnnotationAssertion(rdfs:label "pending final vetting"@en) - -# Individual: (to be replaced with external ontology term) - -AnnotationAssertion( "to be replaced with external ontology term"@en) -AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) - -# Individual: (requires discussion) - -AnnotationAssertion( "requires discussion"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "requires discussion"@en) - EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectMinCardinality(2 ))) EquivalentClasses(ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -150955,6 +150601,7 @@ SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -150974,7 +150621,6 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -151089,14 +150735,4 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -AnnotationAssertion(Annotation( ) "researcher") -AnnotationAssertion(Annotation( ) rdfs:label "Shawn Zheng Kai Tan") -AnnotationAssertion(Annotation( ) "data scientist") -AnnotationAssertion(Annotation( ) rdfs:label "Anne Thessen") -AnnotationAssertion(Annotation( ) "bioinformatics researcher") -AnnotationAssertion(Annotation( ) rdfs:label "Christopher J. Mungall") -AnnotationAssertion(Annotation( ) "researcher") -AnnotationAssertion(Annotation( ) rdfs:label "David Osumi-Sutherland") -AnnotationAssertion(Annotation( ) "researcher") -AnnotationAssertion(Annotation( ) rdfs:label "James P. Balhoff") ) \ No newline at end of file diff --git a/src/ontology/mappings/fbbt-mappings.sssom.tsv b/src/ontology/mappings/fbbt-mappings.sssom.tsv index b92cde7a1e..2b4fff2216 100644 --- a/src/ontology/mappings/fbbt-mappings.sssom.tsv +++ b/src/ontology/mappings/fbbt-mappings.sssom.tsv @@ -2,6 +2,7 @@ # FBbt: "http://purl.obolibrary.org/obo/FBbt_" # UBERON: "http://purl.obolibrary.org/obo/UBERON_" # CL: "http://purl.obolibrary.org/obo/CL_" +# semapv: "https://w3id.org/semapv/vocab/" #mapping_provider: "http://purl.obolibrary.org/obo/FBbt.owl" subject_id subject_label predicate_id object_id mapping_justification FBbt:00000001 organism semapv:crossSpeciesExactMatch UBERON:0000468 semapv:ManualMappingCuration