diff --git a/fbdv.obo b/fbdv.obo index bcb7f8d..00b0c7d 100644 --- a/fbdv.obo +++ b/fbdv.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2024-02-21 -date: 21:02:2024 14:18 +data-version: fbdv/releases/2024-04-18 +date: 18:04:2024 09:08 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: goslim_aspergillus "Aspergillus GO slim" @@ -14,10 +14,6 @@ subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" -subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" -subsetdef: ro-eco "" default-namespace: FlyBase_development_CV namespace-id-rule: * FBdv:$sequence(8,7000,10000)$ ontology: fbdv.obo @@ -32,7 +28,7 @@ property_value: IAO:0000700 FBdv:00000000 property_value: IAO:0000700 FBdv:00005259 property_value: IAO:0000700 FBdv:00007013 property_value: IAO:0000700 FBdv:00007024 -property_value: owl:versionInfo "2024-02-21" xsd:string +property_value: owl:versionInfo "2024-04-18" xsd:string [Term] id: FBdv:00000000 @@ -2157,32 +2153,16 @@ def: "A part of relation that applies only between occurrents." [] id: RO:0002087 name: immediately preceded by comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string inverse_of: RO:0002090 ! immediately precedes [Typedef] id: RO:0002090 name: immediately precedes comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 [Typedef] id: RO:0002092 name: happens during comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "d" xsd:string -property_value: IAO:0000118 "during" xsd:string -property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true diff --git a/fly_development.obo b/fly_development.obo index af563ed..ad782cf 100644 --- a/fly_development.obo +++ b/fly_development.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: 2024-02-21 -date: 21:02:2024 14:18 +data-version: 2024-04-18 +date: 18:04:2024 09:08 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: goslim_aspergillus "Aspergillus GO slim" @@ -14,10 +14,6 @@ subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" -subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" -subsetdef: ro-eco "" default-namespace: FlyBase development CV namespace-id-rule: * FBdv:$sequence(8,7000,10000)$ ontology: fbdv/fbdv-simple @@ -2054,10 +2050,6 @@ relationship: substage_of FBdv:00005369 ! adult stage id: happens_during name: happens_during comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco xref: RO:0002092 is_transitive: true diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 7a5d173..193a397 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 "2024-02-21") + +Annotation(owl:versionInfo "2024-04-18") Declaration(Class()) Declaration(Class()) @@ -173,63 +173,16 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -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()) -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()) @@ -240,10 +193,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) -Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ @@ -252,100 +203,6 @@ Declaration(AnnotationProperty() AnnotationAssertion(rdfs:label "definition") -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (is a defining property chain axiom) - -AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL") -AnnotationAssertion(rdfs:label "is a defining property chain axiom") - -# Annotation Property: (is a defining property chain axiom where second argument is reflexive) - -AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.") -AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: (subset_property) AnnotationAssertion(rdfs:label "subset_property") @@ -381,68 +238,22 @@ AnnotationAssertion(rdfs:label (part of) -AnnotationAssertion( "is part of"@en) -AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) -AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) AnnotationAssertion( "a core relation that holds between a part and its whole"@en) -AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) -AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants 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( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) -AnnotationAssertion( "part_of"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() # Object Property: (has part) -AnnotationAssertion( "has part"@en) -AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) -AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) AnnotationAssertion( "a core relation that holds between a whole and its part"@en) -AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) -AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants 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( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) -AnnotationAssertion( "has_part"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() # Object Property: (preceded by) -AnnotationAssertion( "preceded by"@en) AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) -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( ) AnnotationAssertion(rdfs:label "preceded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -452,9 +263,7 @@ ObjectPropertyRange( (precedes) -AnnotationAssertion( "precedes"@en) AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "precedes"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -463,12 +272,7 @@ ObjectPropertyRange( (characteristic of) -AnnotationAssertion( "inheres in"@en) -AnnotationAssertion( "this fragility is a characteristic of this vase"@en) -AnnotationAssertion( "this red color is a characteristic of this apple"@en) 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(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( ) @@ -477,26 +281,14 @@ FunctionalObjectProperty() # Object Property: (has characteristic) -AnnotationAssertion( "bearer of"@en) -AnnotationAssertion( "this apple is bearer of this red color"@en) -AnnotationAssertion( "this vase is bearer of this fragility"@en) AnnotationAssertion( "Inverse of characteristic_of"@en) -AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) -AnnotationAssertion( "bearer_of"@en) -AnnotationAssertion( "is bearer of"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has characteristic"@en) InverseFunctionalObjectProperty() ObjectPropertyRange( ) # Object Property: (participates in) -AnnotationAssertion( "participates in"@en) -AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) -AnnotationAssertion( "this input material (or this output material) participates in this process"@en) -AnnotationAssertion( "this investigator participates in this investigation"@en) AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "participates_in"@en) AnnotationAssertion(rdfs:label "participates in"@en) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -504,25 +296,14 @@ ObjectPropertyRange( (has participant) -AnnotationAssertion( "has participant"@en) -AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) -AnnotationAssertion( "this investigation has participant this investigator"@en) -AnnotationAssertion( "this process has participant this input material (or this output material)"@en) 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(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (function of) -AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -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(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( ) @@ -531,11 +312,7 @@ ObjectPropertyDomain( (quality of) -AnnotationAssertion( "this red color is a quality of this apple"@en) AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -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(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( ) @@ -543,11 +320,7 @@ InverseObjectProperties( (role of) -AnnotationAssertion( "this investigator role is a role of this person"@en) AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) -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(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( ) @@ -555,10 +328,7 @@ InverseObjectProperties( (has function) -AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) 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(rdfs:label "has function"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -566,20 +336,14 @@ ObjectPropertyRange( (has quality) -AnnotationAssertion( "this apple has quality this red color"@en) 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(rdfs:label "has quality"@en) SubObjectPropertyOf( ) ObjectPropertyRange( ) # Object Property: (has role) -AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) 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(rdfs:label "has role"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -597,7 +361,6 @@ ObjectPropertyRange( (disposition of) AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( ) 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( ) @@ -614,8 +377,6 @@ ObjectPropertyRange( (has regulatory component activity) AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "has regulatory component activity") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -623,8 +384,6 @@ SubObjectPropertyOf( (has negative regulatory component activity) AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively 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 negatively regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") AnnotationAssertion(rdfs:label "has negative regulatory component activity") SubObjectPropertyOf( ) @@ -633,8 +392,6 @@ SubObjectPropertyOf( (has positive regulatory component activity) AnnotationAssertion( "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(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( ) @@ -642,8 +399,6 @@ SubObjectPropertyOf( (has component activity) -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) 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( ) @@ -651,8 +406,6 @@ SubObjectPropertyOf( (has component process) AnnotationAssertion( "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(rdfs:label "has component process") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -660,8 +413,6 @@ ObjectPropertyRange( (directly regulated by) -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) 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( ) @@ -670,8 +421,6 @@ InverseObjectProperties( (directly negatively regulated by) AnnotationAssertion(Annotation( ) "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(rdfs:label "directly negatively regulated by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -679,8 +428,6 @@ InverseObjectProperties( (directly positively regulated by) AnnotationAssertion(Annotation( ) "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(rdfs:label "directly positively regulated by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -688,8 +435,6 @@ InverseObjectProperties( (has effector activity) AnnotationAssertion(Annotation( ) "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(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( ) @@ -697,8 +442,6 @@ FunctionalObjectProperty() # Object Property: (during which ends) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.") AnnotationAssertion(rdfs:label "during which ends"@en) SubObjectPropertyOf( ) @@ -706,8 +449,6 @@ InverseObjectProperties( (encompasses) -AnnotationAssertion( ) -AnnotationAssertion( "di") AnnotationAssertion(rdfs:comment "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.") AnnotationAssertion(rdfs:label "encompasses"@en) SubObjectPropertyOf( ) @@ -716,8 +457,6 @@ TransitiveObjectProperty() # Object Property: (ends after) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) AnnotationAssertion(rdfs:label "ends after"@en) SubObjectPropertyOf( ) @@ -725,8 +464,6 @@ TransitiveObjectProperty() # Object Property: (immediately preceded by) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "starts_at_end_of") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) AnnotationAssertion(rdfs:label "immediately preceded by"@en) SubObjectPropertyOf( ) @@ -734,8 +471,6 @@ InverseObjectProperties( (during which starts) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.") AnnotationAssertion(rdfs:label "during which starts"@en) SubObjectPropertyOf( ) @@ -743,21 +478,12 @@ InverseObjectProperties( (immediately precedes) -AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "ends_at_start_of") -AnnotationAssertion( "meets") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) AnnotationAssertion(rdfs:label "immediately precedes"@en) SubObjectPropertyOf( ) # Object Property: (starts during) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "io") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))"@en) AnnotationAssertion(rdfs:label "starts during"@en) SubObjectPropertyOf( ) @@ -766,63 +492,34 @@ ObjectPropertyRange( (happens during) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "d") -AnnotationAssertion( "during") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))"@en) AnnotationAssertion(rdfs:label "happens during"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Happens_during"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() # Object Property: (ends during) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "o") -AnnotationAssertion( "overlaps") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). "@en) AnnotationAssertion(rdfs:label "ends during"@en) SubObjectPropertyOf( ) # Object Property: (overlaps) -AnnotationAssertion( ) AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") -AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "overlaps"@en) SubObjectPropertyOf( ) SymmetricObjectProperty() # Object Property: (has component) -AnnotationAssertion( ) AnnotationAssertion( "w 'has component' p if 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( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") -AnnotationAssertion( "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has component"@en) -AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (develops from) -AnnotationAssertion( ) AnnotationAssertion( "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This is the transitive form of the develops from relation") AnnotationAssertion(rdfs:label "develops from"@en) SubObjectPropertyOf( ) @@ -834,12 +531,7 @@ ObjectPropertyRange( (develops into) -AnnotationAssertion( ) AnnotationAssertion( "inverse of develops from") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "develops into"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -849,17 +541,6 @@ TransitiveObjectProperty() # Object Property: (regulates) AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "GO") -AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") -AnnotationAssertion( "regulates (processual)") -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulates"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -870,13 +551,6 @@ ObjectPropertyRange( (negatively regulates) AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negatively regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -885,13 +559,6 @@ InverseObjectProperties( (positively regulates) AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positively regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -900,15 +567,7 @@ TransitiveObjectProperty() # Object Property: (capable of) -AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") -AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") -AnnotationAssertion( ) -AnnotationAssertion( "has function realized in") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capable of"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -917,21 +576,12 @@ ObjectPropertyRange( (capable of part of) AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") -AnnotationAssertion( ) -AnnotationAssertion( "has function in") AnnotationAssertion(rdfs:label "capable of part of"@en) -AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (temporally related to) -AnnotationAssertion( ) -AnnotationAssertion( ) -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( ) 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( ) @@ -939,47 +589,29 @@ ObjectPropertyRange( (has input) -AnnotationAssertion( ) AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") -AnnotationAssertion( ) -AnnotationAssertion( "consumes") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has input"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) # Object Property: (has developmental contribution from) -AnnotationAssertion( "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]") -AnnotationAssertion( ) AnnotationAssertion( "x has developmental contribution from y iff x has some part z such that z develops from y"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has developmental contribution from"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (developmentally contributes to) -AnnotationAssertion( ) AnnotationAssertion( "inverse of has developmental contribution from") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "developmentally contributes to"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (developmentally preceded by) -AnnotationAssertion( ) AnnotationAssertion( "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p") -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(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( ) @@ -989,142 +621,89 @@ ObjectPropertyRange( (acts upstream of) -AnnotationAssertion( "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( ) AnnotationAssertion(rdfs:label "acts upstream of") -AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (acts upstream of or within) -AnnotationAssertion( "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( "affects") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (developmentally succeeded by) -AnnotationAssertion( ) AnnotationAssertion( "Inverse of developmentally preceded by") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "developmentally succeeded by"@en) SubObjectPropertyOf( ) # Object Property: (causally upstream of, positive effect) AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") AnnotationAssertion(rdfs:label "causally upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (causally upstream of, negative effect) AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (characteristic of part of) AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") -AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") -AnnotationAssertion( ) -AnnotationAssertion( "inheres in part of") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "characteristic of part of"@en) -AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (mereotopologically related to) AnnotationAssertion( "A mereological relationship or a topological relationship") -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(rdfs:label "mereotopologically related to"@en) # Object Property: (developmentally related to) 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(rdfs:label "developmentally related to"@en) # Object Property: (enables) -AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion( "catalyzes") -AnnotationAssertion( "executes") -AnnotationAssertion( "has") -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( ) AnnotationAssertion(rdfs:label "enables"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (functionally related to) AnnotationAssertion( "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(rdfs:label "functionally related to"@en) # Object Property: (part of structure that is capable of) 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(rdfs:label "part of structure that is capable of"@en) SubObjectPropertyOf( ) # Object Property: (involved in) AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion( ) -AnnotationAssertion( "actively involved in") -AnnotationAssertion( "enables part of") AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (enabled by) AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (regulated by) AnnotationAssertion( "inverse of regulates") -AnnotationAssertion( ) -AnnotationAssertion( "regulated by (processual)") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulated by"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -1134,66 +713,49 @@ ObjectPropertyRange( (negatively regulated by) AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negatively regulated by"@en) SubObjectPropertyOf( ) # Object Property: (positively regulated by) AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positively regulated by"@en) SubObjectPropertyOf( ) # Object Property: (input of) AnnotationAssertion( "inverse of has input") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "input of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (has developmental potential involving) -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(rdfs:label "has developmental potential involving"@en) SubObjectPropertyOf( ) # Object Property: (has potential to developmentally contribute to) -AnnotationAssertion( ) 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(rdfs:label "has potential to developmentally contribute to"@en) SubObjectPropertyOf( ) # Object Property: (has potential to develop into) -AnnotationAssertion( ) 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(rdfs:label "has potential to develop into"@en) SubObjectPropertyOf( ) # Object Property: (has potential to directly develop into) -AnnotationAssertion( ) 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(rdfs:label "has potential to directly develop into"@en) SubObjectPropertyOf( ) # Object Property: (causally downstream of) -AnnotationAssertion( ) AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally downstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1201,8 +763,6 @@ InverseObjectProperties( (immediately causally downstream of) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1211,11 +771,7 @@ InverseObjectProperties( (indirectly positively regulates) AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly activates") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -1223,11 +779,7 @@ TransitiveObjectProperty() # Object Property: (indirectly negatively regulates) AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly inhibits") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -1235,31 +787,11 @@ TransitiveObjectProperty() # Object Property: (causally related to) AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") -AnnotationAssertion( "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. - -To define causal relations in an activity-flow type network, we make use of 3 primitives: - - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative? - -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. - -For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. - -For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. - -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(rdfs:label "causally related to"@en) # Object Property: (causally upstream of) AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally upstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1268,8 +800,6 @@ TransitiveObjectProperty() # Object Property: (immediately causally upstream of) AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1277,9 +807,6 @@ SubObjectPropertyOf( (causally upstream of or within) AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") -AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") -AnnotationAssertion( ) -AnnotationAssertion( "influences (processual)") AnnotationAssertion( "affects") AnnotationAssertion(rdfs:label "causally upstream of or within") SubObjectPropertyOf( ) @@ -1289,9 +816,6 @@ TransitiveObjectProperty() # Object Property: (causally downstream of or within) AnnotationAssertion( "inverse of causally upstream of or within") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally downstream of or within") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -1299,7 +823,6 @@ TransitiveObjectProperty() # Object Property: (involved in regulation of) AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "involved in regulation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1307,25 +830,18 @@ SubObjectPropertyOf( (involved in positive regulation of) AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "involved in positive regulation of") SubObjectPropertyOf( ) # Object Property: (involved in negative regulation of) AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "involved in negative regulation of") SubObjectPropertyOf( ) # Object Property: (involved in or involved in regulation of) AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") -AnnotationAssertion( "OWL does not allow defining object properties via a Union") -AnnotationAssertion( ) -AnnotationAssertion( "involved in or reguates") AnnotationAssertion(rdfs:label "involved in or involved in regulation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1334,15 +850,8 @@ SubObjectPropertyOf( (interacts with) AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) -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( "in pairwise interaction with") -AnnotationAssertion( ) 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) SymmetricObjectProperty() ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -1350,20 +859,12 @@ ObjectPropertyRange( (molecularly interacts with) AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") -AnnotationAssertion( ) -AnnotationAssertion( "binds") -AnnotationAssertion( "molecularly binds with") AnnotationAssertion(rdfs:label "molecularly interacts with") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) SubObjectPropertyOf( ) SymmetricObjectProperty() # Object Property: (phosphorylates) -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(rdfs:label "phosphorylates") SubObjectPropertyOf( ) @@ -1372,8 +873,6 @@ SubObjectPropertyOf( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "molecularly controls") AnnotationAssertion(rdfs:label "directly regulates activity of") SubObjectPropertyOf( ) @@ -1385,9 +884,6 @@ ObjectPropertyRange( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly inhibits") AnnotationAssertion( "molecularly decreases activity of") AnnotationAssertion(rdfs:label "directly negatively regulates activity of") SubObjectPropertyOf( ) @@ -1398,9 +894,6 @@ ObjectPropertyRange( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly activates") AnnotationAssertion( "molecularly increases activity of") AnnotationAssertion(rdfs:label "directly positively regulates activity of") SubObjectPropertyOf( ) @@ -1409,20 +902,16 @@ ObjectPropertyRange( (helper property (not for use in curation)) -AnnotationAssertion( ) -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(rdfs:label "helper property (not for use in curation)") # Object Property: (is kinase activity) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "is kinase activity") SubObjectPropertyOf( ) # Object Property: (causal agent in process) AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causal agent in process") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -1430,9 +919,6 @@ InverseObjectProperties( (causal relation between processes) AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") -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(rdfs:label "causal relation between processes") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1440,16 +926,10 @@ ObjectPropertyRange( (depends on) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "depends on") -AnnotationAssertion(rdfs:seeAlso ) # Object Property: (causal relation between entities) -AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") -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(rdfs:label "causal relation between entities") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1457,34 +937,23 @@ ObjectPropertyRange( (causally influenced by) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influenced by (entity-centric)") AnnotationAssertion(rdfs:label "causally influenced by") SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (interaction relation helper property) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interaction relation helper property") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (molecular interaction relation helper property) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "molecular interaction relation helper property") SubObjectPropertyOf( ) # Object Property: (causally influences) AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influences (entity-centric)") AnnotationAssertion(rdfs:label "causally influences") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1493,22 +962,13 @@ ObjectPropertyRange( (directly regulates) AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly regulates (processual)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly regulates") SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (has part structure that is capable of) -AnnotationAssertion( "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(rdfs:label "has part structure that is capable of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1516,9 +976,6 @@ SubObjectPropertyOf( (causal relation between material entity and a process) AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") -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(rdfs:label "causal relation between material entity and a process") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1526,136 +983,85 @@ ObjectPropertyRange( (capable of regulating) -AnnotationAssertion( "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(rdfs:label "capable of regulating") SubObjectPropertyOf( ) # Object Property: (capable of negatively regulating) AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capable of negatively regulating") SubObjectPropertyOf( ) # Object Property: (capable of positively regulating) -AnnotationAssertion( "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(rdfs:label "capable of positively regulating") SubObjectPropertyOf( ) # Object Property: (process has causal agent) AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "process has causal agent") SubObjectPropertyOf( ) # Object Property: (directly positively regulates) AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly positively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (directly negatively regulates) AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly negatively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (enables subfunction) AnnotationAssertion( "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(rdfs:label "enables subfunction") SubObjectPropertyOf( ) # Object Property: (acts upstream of or within, positive effect) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( ) 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( ) # Object Property: (acts upstream of or within, negative effect) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( ) 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( ) # Object Property: (acts upstream of, positive effect) AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (acts upstream of, negative effect) AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (causally upstream of or within, negative effect) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) 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( ) # Object Property: (causally upstream of or within, positive effect) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (regulates activity of) AnnotationAssertion( "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(rdfs:label "regulates activity of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1664,29 +1070,19 @@ ObjectPropertyRange( (indirectly causally upstream of) AnnotationAssertion( "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(rdfs:label "indirectly causally upstream of"@en) SubObjectPropertyOf( ) # Object Property: (indirectly regulates) AnnotationAssertion( "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(rdfs:label "indirectly regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (device utilizes material) -AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -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"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) @@ -1801,7 +1197,6 @@ AnnotationAssertion( "M-phase of mitotic cell cycle") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0000087") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).") AnnotationAssertion(rdfs:label "mitotic M phase") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -1816,10 +1211,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "mitosis") AnnotationAssertion( "GO:0000278") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.") AnnotationAssertion(rdfs:label "mitotic cell cycle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -1833,7 +1224,6 @@ AnnotationAssertion( "M-phase") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0000279") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).") AnnotationAssertion(rdfs:label "M phase") SubClassOf( ) @@ -1844,7 +1234,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "karyokinesis") AnnotationAssertion( "GO:0000280") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nuclear division") SubClassOf( ) @@ -1855,12 +1244,6 @@ AnnotationAssertion( "molecular function") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0003674") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") AnnotationAssertion(rdfs:label "molecular_function") @@ -1871,21 +1254,12 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:tb") "enzyme activity") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0003824") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catalytic activity") SubClassOf( ) # Class: (organelle 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 an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2013-12-19T15:25:51Z") AnnotationAssertion( "GO:1902589") AnnotationAssertion( "organelle organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "single organism organelle organization") @@ -1893,8 +1267,6 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "organelle organization and biogenesis") AnnotationAssertion( "single-organism organelle organization") AnnotationAssertion( "GO:0006996") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle organization") SubClassOf( ) @@ -1905,25 +1277,14 @@ AnnotationAssertion( "cell-division cycle") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0007049") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell cycle") SubClassOf( ) # Class: (multicellular organism development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:ems") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21234"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0007275") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term was 'developmental process'.") AnnotationAssertion(rdfs:label "multicellular organism development") SubClassOf( ) @@ -1932,9 +1293,6 @@ SubClassOf( (biological_process) AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-09-19T15:05:24Z") AnnotationAssertion( "GO:0000004") AnnotationAssertion( "GO:0007582") AnnotationAssertion( "GO:0044699") @@ -1945,13 +1303,6 @@ AnnotationAssertion( "single organism process") AnnotationAssertion( "single-organism process") AnnotationAssertion( "GO:0008150") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") AnnotationAssertion(rdfs:label "biological_process") @@ -1965,17 +1316,12 @@ AnnotationAssertion( "embryonal development") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009790") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryo development") SubClassOf( ) # Class: (cellular process) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-12-11T16:56:55Z") AnnotationAssertion( "GO:0008151") AnnotationAssertion( "GO:0044763") AnnotationAssertion( "GO:0050875") @@ -1985,8 +1331,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism cellular process") AnnotationAssertion( "GO:0009987") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") AnnotationAssertion(rdfs:label "cellular process") SubClassOf( ) @@ -2005,10 +1349,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mah") "cell organization and biogenesis") AnnotationAssertion( "GO:0016043") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component organization") SubClassOf( ) @@ -2020,11 +1360,6 @@ AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "phosphokinase activity") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0016301") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -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( ) @@ -2040,16 +1375,6 @@ AnnotationAssertion(Annotation(rdfs:label "TRAF2 ubiquitinates cIAP1,2 in cIAP1, AnnotationAssertion(Annotation(rdfs:label "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248") "Reactome:R-HSA-8868783") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0016740") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "transferase activity") SubClassOf( ) @@ -2059,7 +1384,6 @@ AnnotationAssertion(Annotation( "EC:2.7.-.-") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0016772") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.") AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") SubClassOf( ) @@ -2069,7 +1393,6 @@ SubClassOf( "GOC:isa_complete") Annotation( "GOC:mtg_cell_cycle") "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022402") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell cycle process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -2080,7 +1403,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mtg_cell_cycle") "One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022403") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).") AnnotationAssertion(rdfs:label "cell cycle phase") SubClassOf( ) @@ -2088,20 +1410,12 @@ SubClassOf( (multicellular organismal process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-09-19T16:07:47Z") AnnotationAssertion( "GO:0044707") AnnotationAssertion( "GO:0050874") AnnotationAssertion( "organismal physiological process") AnnotationAssertion( "biological_process") AnnotationAssertion( "single-multicellular organism process") AnnotationAssertion( "GO:0032501") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "multicellular organismal process") SubClassOf( ) DisjointClasses( ) @@ -2109,16 +1423,11 @@ DisjointClasses( (developmental process) AnnotationAssertion(Annotation( "GOC:isa_complete") "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-12-19T12:21:31Z") AnnotationAssertion( "GO:0044767") AnnotationAssertion( "development") AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism developmental process") AnnotationAssertion( "GO:0032502") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "developmental process") SubClassOf( ) DisjointClasses( ) @@ -2126,11 +1435,8 @@ DisjointClasses( (biological phase) AnnotationAssertion(Annotation( "GOC:jl") "A distinct period or stage in a biological process or cycle.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2014-07-16T13:12:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044848") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.") AnnotationAssertion(rdfs:label "biological phase") SubClassOf( ) @@ -2150,22 +1456,15 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:jid") "The creation of two or more organelles by division of one organelle.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048285") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle fission") SubClassOf( ) # Class: (anatomical structure development) AnnotationAssertion(Annotation( "GO_REF:0000021") "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "development of an anatomical structure") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048856") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anatomical structure development") SubClassOf( ) @@ -2177,7 +1476,6 @@ AnnotationAssertion( "karyostasis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051325") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).") AnnotationAssertion(rdfs:label "interphase") SubClassOf( ) @@ -2188,7 +1486,6 @@ AnnotationAssertion(Annotation( "interphase of mitotic cell cycle") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051329") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).") AnnotationAssertion(rdfs:label "mitotic interphase") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -2198,16 +1495,12 @@ SubClassOf( (cellular component organization or biogenesis) AnnotationAssertion(Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2010-09-10T01:39:16Z") AnnotationAssertion( "GO:0071841") AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation or biogenesis") AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation or biogenesis at cellular level") AnnotationAssertion( "cellular component organization or biogenesis at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071840") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component organization or biogenesis") SubClassOf( ) @@ -2216,7 +1509,6 @@ SubClassOf( "GOC:dos") "One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098763") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).") AnnotationAssertion(rdfs:label "mitotic cell cycle phase") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -2226,14 +1518,9 @@ SubClassOf( ObjectSomeValuesFrom( (mitotic nuclear division) AnnotationAssertion(Annotation( "ISBN:0198547684") "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19910"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2017-03-23T14:44:23Z") AnnotationAssertion( "mitosis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140014") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mitotic nuclear division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -2242,11 +1529,8 @@ SubClassOf( (mitotic cell cycle process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cell_cycle") Annotation( "GO_REF:0000060") "A process that is part of the mitotic cell cycle.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2014-05-22T14:22:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903047") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mitotic cell cycle process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -2257,13 +1541,10 @@ SubClassOf(ObjectSomeValuesFrom( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -2276,7 +1557,6 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -2317,10 +1597,8 @@ DLSafeRule(Body(ClassAtom( Variable( DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv new file mode 100644 index 0000000..488f6de --- /dev/null +++ b/src/ontology/reports/basic-report.tsv @@ -0,0 +1,264 @@ +?cls ?def ?xrefs + "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." + "Oogenesis stage that begins when the nurse cells chromosomes become bulbous. Nurse cell chromosomes during this stage are polytene and reach a ploidy of 32C. The egg chamber is oval shaped." + "The execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module." "GO:0008150" + "Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying)." + "67th day after eclosion." + "Secretion of innermost chorionic layer and endochorion begins in the main follicle cells." + "Oogenesis stage during which 12-15 nurse cell nuclei remain at the anterior of the oocyte. At this stage, the oocyte nucleus has reached its maximum volume and its chromosomes are compressed into a 5-7 micrometer karyosome." + "The 13th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "The second larval instar begins at the first larval molt and ends at the second larval molt. Larvae are actively feeding and crawling in the food. Distinct anterior spiracles are present as enlargements at the end of the tracheal trunk, but not open to the outside; posterior spiracles have three openings each, and four groups of small unbranched hairs. The salivary glands extend to the first abdominal segment, and have cells that are uniform in size. Mouth hooks typically have two or three teeth. Duration at 25 degrees C: approximately 23 hours (49-72 hours after egg laying; 25-48 hours after hatching)." "UBERON:8000001" + "The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "69th day after eclosion." + "Stage 11 begins with the invagination of the tracheal placodes. Para-segmental furrow form and segment boundary furrows become deep folds. Within the head, gnathal protuberances become apparent. The end of this stage is signaled by the appearance of a distinct cleft at the posterior pole of the embryo, which becomes detached from the vitelline membrane. This marks the beginning of germ-band retraction. Duration at 25 degrees C: approximately 120 minutes (320-440 minutes after egg laying)." + "The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents." + "41st day after eclosion." + "The developing adult after pupal-adult apolysis, i.e.- from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. Duration at 25 degrees C: approximately 55.7 hours (164.3-220 hours after egg laying; 44.3-100 hours after puparium formation)." + "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." + "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." + "A collective term for stages 13-15." + "Stage 17 begins when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. It lasts until hatching of the embryo (approximately 24 hours after egg laying), during which time much terminal differentiation occurs, the tracheal tree fills with air, so becoming completely visible, and the ventral cord continues to retract. Duration at 25 degrees C: approximately 8 hours (16-24 hours after egg laying)." + "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation." + "21st day after eclosion." + "Male gonads become less distinct. Oral armature stops moving permanently. Dorsal medial abdominal contractions stop. Gas bubble becomes visible within abdomen. Duration at 25 degrees C: approximately 100 minutes. (120.3-122 hours after egg laying; 0.3-2 hours after puparium formation)." + "The life of an individual of the species Drosophila melanogaster, from fertilization to death." + "Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying)." + "The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs." "Wikipedia:Interphase" + "58th day after eclosion." + "Oogenesis stage that begins when the micropyle begins to form. At the beginning of this stage, about 12-15 nurse cell nuclei remain at the anterior of the oocyte. By the end of this stage, none of these nuclei remain. Oocyte meiosis up to arrest at full metaphase I occurs during this stage." + "11th day after eclosion." + "24th day after eclosion." + "The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3)." + "An entity that has temporal parts and that happens, unfolds or develops through time."@en + "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." "Wikipedia:Mitosis" + "The 16th cell cycle division of embryogenesis. Asynchronous." + "The M-phase of embryonic cycle 14. This is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains." + "Oogenesis stage that begins when nurse cell chromosomes are no longer bulbous - the association between homologs weakens so that these chromosomes no longer have a polytene structure. During this stage, posterior nurse cell nuclei have a higher ploidy (64C) than anterior ones." + "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en + "Pale yellow pigmentation spreads inwards across the eye. Eye color becomes bright yellow, then changes to amber. Duration at 25 degrees C: approximately 12 hours 20 minutes. (164.3-176.6 hours after egg laying; 44.3-56.6 hours after puparium formation)." + "Thoracic bristles become visible, and the tips of the wings turn grey. Duration at 25 degrees C: approximately 2 hours. (194.6-196.6 hours after egg laying; 74.6-76.6 hours after puparium formation)." + "39th day after eclosion." + "The 15th cell cycle of embryogenesis. Asynchronous." + "The stage of the Drosophila life-cycle from maturation of an egg to the end of fertilization. At the beginning of this stage, the nucleus is arrested in meiotic metaphase I. The completion of meiosis and the start of protein synthesis are triggered by ovulation. If the female has already mated, fertilization begins during meiosis." + "Embryonic stages 4 and 5." + "37th day after eclosion." + "Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage." + "1st day after eclosion." + "Oogenesis stage that begins when the border cells begin to migrate. During this stage: the oocyte is about 1/3 the length of the egg chamber with its nucleus located antero-dorsally; follicle cell migration results in an anterior to posterior gradient of follicle cell thickness with posterior cells being thicker (-> columnar) and posterior cells thinner ( -> squamous); border cell migration begins and ends; secretion of vitelline membrane begins." + "43rd day after eclosion." + "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." + "Oogenesis stage that begins when the cyst leaves the germarium (from this point the cyst is referred to as an egg chamber). During this stage, polyploidation of the nurse cells begins, they reach a ploidy of 8C, and follicle cells start to divide." + "Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL)." + + "64th day after eclosion." + + "Eyes become bright red. Orbital and ocellar bristles and vibrissae darken. Duration at 25 degrees C: approximately 6 minutes. (194.5-194.6 hours after egg laying; 74.5-74.6 hours after puparium formation)." + "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle." + "One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." + "The 11th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "The anterior spiracles are fully everted, with 7-9 finger-like projections. The body shortens, withdrawing three apparent abdominal segments and the larva sticks to its substrate." + "19th day after eclosion." + "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en + "16th day after eclosion." + "13th day after eclosion." + "Oogenesis stage during which polyploidation and enlargement of follicle cells begins. Nurse cell ploidy ranges from 256C (anterior) to 512C (posterior) and the egg chamber gains an elongated shape." + "Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 5 hours, 25 minutes. (133.3-138.7 hours after egg laying; 13.3-18.7 hours after puparium formation)." + "The 12th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "Embryonic stage 1-3." + + "Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying)." + "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." + "The M-phase (GO:0000279) of an embryonic cycle." + "47th day after eclosion." + "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en + "36th day after eclosion." + "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase." "Wikipedia:M_phase" + "Oogenesis stage that begins when the centripetal follicle cells begin to migrate. As a result, the vitelline membrane extends into the opercular region. This stage ends when nurse cell dumping begins." + "A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition." "GO:0032502" + "The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying)." + "The stage of the Drosophila life-cycle from eclosion to death." + + "The last stage of oogenesis. This stage begins when no nurse cell nuclei remain at the anterior of the egg (chamber). Exochorion formation and secretion occurs during this stage. The dorsal appendages complete their elongation and the follicle cells die." + "Stage 6 begins when the ventral furrow becomes apparent, an event which is followed rapidly by the formation of the cephalic furrow. Stage 6 ends when the pole cells have adopted a dorsal (horizontal) position at the posterior. Duration at 25 degrees C: approximately 10 minutes (170-180 minutes after egg laying)." + + "32nd day after eclosion." + "The third larval instar begins at the second larval molt and ends at puparium formation. Anterior spiracles are open to the outside; posterior spiracles have three openings each, and four groups of large branched hairs. The salivary glands extend to the second abdominal segment, with cells larger in the posterior than in the anterior of the gland. Mouth hooks typically have 9-12 teeth. About 24 hours before pupariation (at 25 degree C), larvae stop feeding and climb away from their food. Duration at 25 degrees C: approximately 48 hours (72-120 hours after egg laying; 48-96 hours after hatching)." "UBERON:8000002" + "Pharate adult stage P12 begins as the abdominal tergite bristles become visible, and ends as the wings darken to black. Duration at 25 degrees C: approximately 2 hours. (196.6-198.6 hours after egg laying; 76.6-78.6 hours after puparium formation)." + "Secretion of the exochorion begins and ends." + "The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "10th day after eclosion." + "The stage of the Drosophila life-cycle from fertilization to hatching." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." + "Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying)." + "23rd day after eclosion." + "61st day after eclosion." + "Tips of folded wings become grey. Duration at 25 degrees C: approximately 45 minutes (195.5-196.6 hours after egg laying; 75.9-76.6 hours after puparium formation)." + "46th day after eclosion." + "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." "Reactome:R-HSA-8868783 EC:2.-.-.- Reactome:R-HSA-5668414 Reactome:R-HSA-1483186 Reactome:R-HSA-1483089" + "51st day after eclosion." + "31st day after eclosion." + "The pupal stage starts once larval/pupal apolysis is complete as indicated by the expulsion of the larval armature. Early in this stage, the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. Duration at 25 degrees C: approximately 32 hours. (132.2-164.3 hours after egg laying; 12.2-44.3 hours after puparium formation)." + "The 'yellow body' moves back between the Malpighian tubules. The transparent pupal cuticle separates from the underlying epidermis. Eye cup becomes yellow at its perimeter. Duration at 25 degrees C: approximately 12 hours. (152.4-164.3 hours after egg laying; 32.4-44.3 hours after puparium formation)." + "70th day after eclosion." + "The 14th mitotic cell cycle of embryogenesis. This is the first round of nuclear division to occur in a cellularized embryo, so this is the first round of cell division. Embryonic cycle 14 mitosis is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains." + "Extends from puparium formation through tanning of the pupal cuticle. Posterior spiracles and ridge between anterior spiracles tan orange. Wriggling stops completely. Puparium becomes brown to the unaided eye. Duration at 25 degrees C: approximately 20 minutes. (120-120.3 hours after egg laying; 0-0.3 hours after puparium formation)." + "66th day after eclosion." + "Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm." + "25th day after eclosion." + "29th day after eclosion." + "Temporal subdivision of adulthood in days post-eclosion." + "A collective term for stages 11 and 12." + "Tanning of the tergites obscures the Malpighian tubules and the 'yellow body'. Legs begin to twitch; fly is able to walk if puparium is removed prematurely. Ptilinum expands by hydrostatic pressure, opening the operculum. Duration at 25 degrees C: approximately 8 hours, 6 minutes. (211.5-219.6 hours after egg laying; 91.5-99.6 hours after puparium formation)." + + "The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs." + "A distinct period or stage in a biological process or cycle." + "The embryonic stage that lasts from the end of fertilization to the end of the second nuclear division. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying)." + "Developmental stage that starts with sperm entry until the first mitotic division of the zygote." + "The eukaryotic cell cycle in which a cell is duplicated without changing ploidy, occurring in the embryo." + "54th day after eclosion." + "17th day after eclosion." + "Bubble is displaced to anterior end of the puparium, and pupa withdraws to the posterior end. Imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 12 minutes. (132-132.2 hours after egg laying; 12-12.2 hours after puparium formation)." + "9th day after eclosion." + "The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion." + "Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying)." + "7th day after eclosion." + "Oogenesis stage during which follicle cell division ceases." + "3rd day after eclosion." + "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en + "Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying)." + "The day of eclosion." + "2nd day after eclosion." + "Oogenesis stage that begins when endochorion begins to form at the anterior pole, a process which includes the beginning of formation of the dorsal appendages. During this stage, the follicle cells secrete membranous vesicles that form irregular extracellular plaques. This stage ends when dying nurse cells form an anterior cap to the oocyte." + "Oogenesis stage during which only 7-8 nurse cell nuclei remain at the anterior of the oocyte. At the beginning of this stage, oocyte chromosome bivalents separate from each other - indicating mid-prometaphase of oocyte meiosis." + "The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + + "60th day after eclosion." + "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." "Wikipedia:Biological_process" + "49th day after eclosion." + "The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "Prepupal stage P4 begins as the lateral trunk trachea become obscured and ends when the imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 5 hours, 30 minutes. (126.75-132.2 hours after egg laying; 6.75-12.2 hours after puparium formation)." + "A collective term for stages 1-4." + "Oogenesis stage which begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends when centripetal follicle migration begins. During this stage, the migrating border cells reach the oocyte. The oocyte is about 50% egg chamber length." + "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." "Wikipedia:Cell_cycle" + "The interphase of embryonic cycle 14. This begins at the same time as cellularization and is of variable length depending on cell identity: embryonic cycle 14 M phase (14B) is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains." + "Lateral trunk tracheae become obscured. Dorsal medial abdominal contractions occur. Everted leg and wing discs become visible. Bubble appears in posterior of puparium, displacing the pupa anteriorly; abdominal bubble disappears. Duration at 25 degrees C: approximately 5 hours, 15 minutes. (126.75-132 hours after egg laying; 6.75-12 hours after puparium formation)." + "Stage, shortly after eclosion, during which the wings expand. During wing expansion, the abdomen pulsates and the hind legs stroke the wings vigorously for several minutes at a time. The stage ends when the wings are folded down over the abdomen, which has become broader and shorter, and the wing cuticle has lost its folds. The stage lasts around 15 minutes at 25'C." + "The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut." + "22nd day after eclosion." + "The interphase (GO:0051325) of an embryonic cycle." + "The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "38th day after eclosion." + "Embryonic stages 16-17." + "A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion." + "Stages during which gastrulation occurs. 6-8." + "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." + "65th day after eclosion." + "A temporal subdivision of a developmental process." + "Third instar larva prior to the wandering stage (approximately the first 24 hours of the third instar larval stage under standard conditions at 25'C.)." + "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." + "40th day after eclosion." + + "Stage 9 begins when mesodermal segmentation becomes (transiently) visible, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying)." + "A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized." + "The creation of two or more organelles by division of one organelle." + "Pupal stage P5 starts when the legs and wings reach full extension along the abdomen and ends as the Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 6 hours, 30 minutes. (132.2-138.7 hours after egg laying; 12.2-18.7 hours after puparium formation)." + "Oogenesis stage during which 9-11 nurse cell nuclei remain at the anterior of the oocyte. During this stage, the nuclear membrane of the oocyte nucleus disappears, indicating the start of meiotic pro-metaphase." + "Stage 13 begins at the completion of germ-band retraction, when the prospective anal plate occupy the posterior pole. The dorsal ridge becomes apparent externally; the clypeolabrum retracts, leaving a triangular shaped gap at the anterior pole; the labium moves to the ventral midline. This stage ends when head involution begins. Duration at 25 degrees C: Approximately 60 minutes (560-620 minutes after egg laying)." + "12th day after eclosion." + "The tenth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "Oogenesis stage that begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends with the beginning of nurse cell dumping." + "Dorsal thoracic microchaetes and macrochaetes become visible. Duration at 25 degrees C: approximately 80 minutes (194.6-195.5 hours after egg laying; 74.6-75.9 hours after puparium formation)." + "Pharate adult stage P15 begins with the tanning of the tergites and ends with eclosion. Duration at 25 degrees C: approximately 8 hours, 30 minutes. (211.5-220 hours after egg laying; 91.5-100 hours after puparium formation)." + "Newly eclosed adult stage. Animal free of pupal case. Runs rapidly to find site for wing expansion. Wings are folded back and black against a very pale abdomen." + "Stage 14 begins with the initiation of head involution. Closure of the midgut around the yolk and dorsal closure continue. Dorsal closure is 80% complete by the end of this stage. This stage ends with the appearance of the second midgut constriction. Duration at 25 degrees C: approximately 60 minutes (620-680 minutes after egg laying)." + "4th day after eclosion." + "6th day after eclosion." + + "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." "EC:2.7.-.-" + "Oogenesis stage that begins when the oocyte chromosomes condense into a karyosome attached to a distinctive spherical structure known as an endobody. The oocyte nucleolus disappears completely. During this stage, nurse cell ploidy reaches 16C." + "A collective term for stages 9 and 10." + "20th day after eclosion." + "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." + "Stage 7 begins when the pole cells have adopted a dorsal (horizontal) position at the posterior. Invagination of the anterior and posterior midgut and hindgut follows. The 'discoid plate' that carries the pole cells forms a pocket. Transverse furrows (dorsal folds) form on the dorsal surface. This stage ends when the anterior wall of the amnioproctodeal invagination starts moving anteriorly and the pole cells are no longer visible externally. Duration at 25 degrees C: approximately 10 minutes (180-190 minutes after egg laying)." + "One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." + "68th day after eclosion." + "27th day after eclosion." + "Sex combs darken in males. Wings darken to black. Duration at 25 degrees C: approximately 65 minutes. (197.5-198.6 hours after egg laying; 77.5-78.6 hours after puparium formation)." + "A process that is part of the mitotic cell cycle." + "35th day after eclosion." + "Oogenesis stage during which the number of nurse cell nuclei at the anterior of the oocyte reduce from 4 to zero. The oocyte chromosomes reach full metaphase I during this stage, at which point meiosis is arrested (until fertilization)." + + "The meconium appears dorsally at the posterior tip of the abdomen. Duration at 25 degrees C: approximately 9 hours, 30 minutes (201.9-211.5 hours after egg laying; 81.9-91.5 hours after puparium formation)." + "Stages during which the germ band is extended - 9-12." + "Legs and wings reach full extension along abdomen. Enlarged initial segments of anterior pair Malpighian tubules move from thorax into abdomen. Translucent patch that lacks adhering fat body cells becomes discernible in the middle of the eye region. Pair of white Malpighian tubules becomes visible dorsally in the abdomen. Duration at 25 degrees C: approximately 66 minutes. (132.2-133.3 hours after egg laying; 12.2-13.3 hours after puparium formation)." + "Nuclear division 9. The cleavage nuclei complete their migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying)." + "15th day after eclosion." + "Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins. The dorsal appendages begin to form during this stage. This stage ends when dying nurse cells form an anterior cap to the oocyte." + "14th day after eclosion." + "Oogenesis stage which begins when yolk first appears in the oocyte. Follicle cell migration over the oocyte begins during this stage (although mostly occurs during stage 9)." + "Bristles of the abdominal tergites become visible, and the wings become grey. Duration at 25 degrees C: approximately 55 minutes. (196.6-197.5 hours after egg laying; 76.6-77.5 hours after puparium formation)." + "52nd day after eclosion." + "Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C." + "Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3)." + "33rd day after eclosion." + + "57th day after eclosion." + + "59th day after eclosion." + "Third instar larva from the beginning of wandering to the beginning of puparium formation." + "55th day after eclosion." + "Stage of the third larval instar during which the larva wanders out of the food and climbs. Under optimum conditions at 25'C, this occurs approximately 24 hours after the start of the third instar larval stage." + "Dark green 'yellow body' appears between the anterior ends of the two Malpighian tubule segments, mid-dorsally at the anterior of the abdomen. Duration at 25 degrees C: approximately 13 hours, 45 minutes. (138.7-152.4 hours after egg laying; 18.7-32.4 hours after puparium formation)." + "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." "Reactome:R-HSA-6788855 Reactome:R-HSA-6788867" + "The prepupal stage begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C: approximately 12 hours. (120-132.2 hours after egg laying; 0-12.2 hours after puparium formation)." + "63rd day after eclosion." + "Oogenesis stage during which only 5-6 nurse cell nuclei remain at the anterior of the oocyte. The oocyte nucleus is in late prometaphase:the bivalents arrange themselves in on the equatorial plane of the spindle; homologous centromeres are pulled towards the poles." + "Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins and ends when the dorsal appendages begin to form." + "26th day after eclosion." + "62nd day after eclosion." + "28th day after eclosion." + + "42nd day after eclosion." + + "The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells." + "Oogenesis stage that begins when dying nurse cells form an anterior cap to the oocyte. Shortly after this, nurse cell dumping and growth of the oocyte are complete. Elongation of the dorsal appendages and formation of the innermost chorionic layer and endochorion begins during this stage." + "The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "30th day after eclosion." + "Innermost chorionic layer and endochorion begin to form in the anterior of the follicle." + "Ridge of the operculum becomes distinct. Puparium begins to separate from underlying epidermis. Becomes positively buoyant. Duration at 25 degrees C: approximately 4 hours, 45 minutes. (122-126.75 hours after egg laying; 2-6.75 hours after puparium formation)." + "8th day after eclosion." + "56th day after eclosion." + "The first larval instar begins at hatching and ends at the first larval molt. Anterior spiracles are not yet present; posterior spiracles have two openings each. Salivary glands are very small and all cells are uniform in size. Mouth hooks typically have one tooth. Duration at 25 degrees C: approximately 25 hours (24-49 hours after egg laying; 0-25 hours after hatching)." "UBERON:8000000" + "53rd day after eclosion." + "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." "Wikipedia:Embryogenesis" + "Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion." + "48th day after eclosion." + "Stage 16 begins when the intersegmental grooves can be distinguished at mid-dorsal level, and ends when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. During this stage the ventral cord retracts to about 60% egg length. Duration at 25 degrees C: approximately 180 minutes (780-960 minutes after egg laying)." + "The substage of the wandering third instar larval stage when the larva has cleared its gut contents." + "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." + "Tarsal bristles darken and claws become black. Duration at 25 degrees C: approximately 3 hours, 20 minutes. (198.6-201.9 hours after egg laying; 78.6-81.9 hours after puparium formation)." + "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en + "Eye color darkens to deep amber, then becomes pale pink. Duration at 25 degrees C: approximately 18 hours. (176.6-194.5 hours after egg laying; 56.6-74.5 hours after puparium formation)." + "The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoon." "GO:0007283" + + "Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior midgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying)." + "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." + "44th day after eclosion." + "The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation." + "18th day after eclosion." + "Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying)." + "Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying)." + "Life stage from the end of adult stage A3, when tanning is complete, to death." + "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." "Wikipedia:Enzyme" + "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en + "Stage which starts when the operculum opens and ends when eclosion is completed. Duration at 25 degrees C: approximately 24 minutes. (219.6-220 hours after egg laying; 99.6-100 hours after puparium formation)." + "50th day after eclosion." + "34th day after eclosion." + "The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell." "GO:0048477" + "5th day after eclosion." + "The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "45th day after eclosion." + "Formation of specialized endochorion structures in the anterior of the follicle: branches in the developing dorsal appendages; compact endochorion lacking the pillars seen in the rest of the follicle." + "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en diff --git a/src/ontology/reports/edges.tsv b/src/ontology/reports/edges.tsv new file mode 100644 index 0000000..909fa86 --- /dev/null +++ b/src/ontology/reports/edges.tsv @@ -0,0 +1,721 @@ +?x ?p ?y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/reports/obo_qc_fbdv.obo.txt b/src/ontology/reports/obo_qc_fbdv.obo.txt index 833b98e..45cb0d6 100644 --- a/src/ontology/reports/obo_qc_fbdv.obo.txt +++ b/src/ontology/reports/obo_qc_fbdv.obo.txt @@ -15,7 +15,6 @@ WARN missing_definition oboInOwl:hasOBOFormatVersion IAO:0000115 WARN missing_definition oboInOwl:hasOBONamespace IAO:0000115 WARN missing_definition oboInOwl:hasRelatedSynonym IAO:0000115 WARN missing_definition oboInOwl:id IAO:0000115 -WARN missing_definition oboInOwl:inSubset IAO:0000115 WARN missing_superclass FBdv:00000000 rdfs:subClassOf WARN missing_superclass FBdv:00005259 rdfs:subClassOf WARN missing_superclass FBdv:00007013 rdfs:subClassOf diff --git a/src/ontology/reports/obsoletes.tsv b/src/ontology/reports/obsoletes.tsv new file mode 100644 index 0000000..ffacc1c --- /dev/null +++ b/src/ontology/reports/obsoletes.tsv @@ -0,0 +1,13 @@ +?cls ?replCls ?consCls + + + + + "FBdv:00005330" + + + + + + + diff --git a/src/ontology/reports/robot_simple_diff.txt b/src/ontology/reports/robot_simple_diff.txt index 5de61e6..5be432b 100644 --- a/src/ontology/reports/robot_simple_diff.txt +++ b/src/ontology/reports/robot_simple_diff.txt @@ -1,119 +1,35 @@ -113 axioms in left ontology but not in right ontology: -- Annotation( "21:02:2024 14:18") -- Annotation( "2024-02-21") -- AnnotationAssertion( [day 61 of adulthood] ) -- AnnotationAssertion( [day 62 of adulthood] ) -- AnnotationAssertion( [day 63 of adulthood] ) -- AnnotationAssertion( [day 64 of adulthood] ) -- AnnotationAssertion( [day 65 of adulthood] ) -- AnnotationAssertion( [day 66 of adulthood] ) -- AnnotationAssertion( [day 67 of adulthood] ) -- AnnotationAssertion( [day 68 of adulthood] ) -- AnnotationAssertion( [day 69 of adulthood] ) -- AnnotationAssertion( [day 70 of adulthood] ) -- AnnotationAssertion( [day 61 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 62 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 63 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 64 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 65 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 66 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 67 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 68 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 69 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion( [day 70 of adulthood] "2024-01-15T17:54:59Z"^^xsd:dateTime) -- AnnotationAssertion([has_obo_namespace] [day 61 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 62 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 63 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 64 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 65 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 66 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 67 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 68 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 69 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([has_obo_namespace] [day 70 of adulthood] "FlyBase_development_CV") -- AnnotationAssertion([id] [day 61 of adulthood] "FBdv:0010001") -- AnnotationAssertion([id] [day 62 of adulthood] "FBdv:0010002") -- AnnotationAssertion([id] [day 63 of adulthood] "FBdv:0010003") -- AnnotationAssertion([id] [day 64 of adulthood] "FBdv:0010004") -- AnnotationAssertion([id] [day 65 of adulthood] "FBdv:0010005") -- AnnotationAssertion([id] [day 66 of adulthood] "FBdv:0010006") -- AnnotationAssertion([id] [day 67 of adulthood] "FBdv:0010007") -- AnnotationAssertion([id] [day 68 of adulthood] "FBdv:0010008") -- AnnotationAssertion([id] [day 69 of adulthood] "FBdv:0010009") -- AnnotationAssertion([id] [day 70 of adulthood] "FBdv:0010010") -- AnnotationAssertion( [day 61 of adulthood] "Temporal ordering number - 1410.") -- AnnotationAssertion( [day 62 of adulthood] "Temporal ordering number - 1420.") -- AnnotationAssertion( [day 63 of adulthood] "Temporal ordering number - 1430.") -- AnnotationAssertion( [day 64 of adulthood] "Temporal ordering number - 1440.") -- AnnotationAssertion( [day 65 of adulthood] "Temporal ordering number - 1450.") -- AnnotationAssertion( [day 66 of adulthood] "Temporal ordering number - 1460.") -- AnnotationAssertion( [day 67 of adulthood] "Temporal ordering number - 1470.") -- AnnotationAssertion( [day 68 of adulthood] "Temporal ordering number - 1480.") -- AnnotationAssertion( [day 69 of adulthood] "Temporal ordering number - 1490.") -- AnnotationAssertion( [day 70 of adulthood] "Temporal ordering number - 1500.") -- AnnotationAssertion( [day 61 of adulthood] "day 61 of adulthood") -- AnnotationAssertion( [day 62 of adulthood] "day 62 of adulthood") -- AnnotationAssertion( [day 63 of adulthood] "day 63 of adulthood") -- AnnotationAssertion( [day 64 of adulthood] "day 64 of adulthood") -- AnnotationAssertion( [day 65 of adulthood] "day 65 of adulthood") -- AnnotationAssertion( [day 66 of adulthood] "day 66 of adulthood") -- AnnotationAssertion( [day 67 of adulthood] "day 67 of adulthood") -- AnnotationAssertion( [day 68 of adulthood] "day 68 of adulthood") -- AnnotationAssertion( [day 69 of adulthood] "day 69 of adulthood") -- AnnotationAssertion( [day 70 of adulthood] "day 70 of adulthood") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 61 of adulthood] "61st day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 62 of adulthood] "62nd day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 63 of adulthood] "63rd day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 64 of adulthood] "64th day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 65 of adulthood] "65th day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 66 of adulthood] "66th day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 67 of adulthood] "67th day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 68 of adulthood] "68th day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 69 of adulthood] "69th day after eclosion.") -- AnnotationAssertion(Annotation([database_cross_reference] "FBC:DPG") [definition] [day 70 of adulthood] "70th day after eclosion.") -- Declaration(Class([day 61 of adulthood])) -- Declaration(Class([day 62 of adulthood])) -- Declaration(Class([day 63 of adulthood])) -- Declaration(Class([day 64 of adulthood])) -- Declaration(Class([day 65 of adulthood])) -- Declaration(Class([day 66 of adulthood])) -- Declaration(Class([day 67 of adulthood])) -- Declaration(Class([day 68 of adulthood])) -- Declaration(Class([day 69 of adulthood])) -- Declaration(Class([day 70 of adulthood])) -- OntologyID(OntologyIRI() VersionIRI()) -- SubClassOf([day 61 of adulthood] [adult age in days]) -- SubClassOf([day 61 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 61 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 60 of adulthood])) -- SubClassOf([day 62 of adulthood] [adult age in days]) -- SubClassOf([day 62 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 62 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 61 of adulthood])) -- SubClassOf([day 63 of adulthood] [adult age in days]) -- SubClassOf([day 63 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 63 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 62 of adulthood])) -- SubClassOf([day 64 of adulthood] [adult age in days]) -- SubClassOf([day 64 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 64 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 63 of adulthood])) -- SubClassOf([day 65 of adulthood] [adult age in days]) -- SubClassOf([day 65 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 65 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 64 of adulthood])) -- SubClassOf([day 66 of adulthood] [adult age in days]) -- SubClassOf([day 66 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 66 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 65 of adulthood])) -- SubClassOf([day 67 of adulthood] [adult age in days]) -- SubClassOf([day 67 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 67 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 66 of adulthood])) -- SubClassOf([day 68 of adulthood] [adult age in days]) -- SubClassOf([day 68 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 68 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 67 of adulthood])) -- SubClassOf([day 69 of adulthood] [adult age in days]) -- SubClassOf([day 69 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 69 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 68 of adulthood])) -- SubClassOf([day 70 of adulthood] [adult age in days]) -- SubClassOf([day 70 of adulthood] ObjectSomeValuesFrom([substage of] [adult stage])) -- SubClassOf([day 70 of adulthood] ObjectSomeValuesFrom([immediately preceded by] [day 69 of adulthood])) +3 axioms in left ontology but not in right ontology: +- Annotation( "18:04:2024 09:08") +- Annotation( "2024-04-18") +- OntologyID(OntologyIRI() VersionIRI()) -3 axioms in right ontology but not in left ontology: -+ Annotation( "07:12:2023 07:29") -+ Annotation( "2023-12-07") -+ OntologyID(OntologyIRI() VersionIRI()) +29 axioms in right ontology but not in left ontology: ++ Annotation( "21:02:2024 14:18") ++ Annotation( "2024-02-21") ++ AnnotationAssertion([obo:IAO_0000117] [immediately preceded by] "David Osumi-Sutherland") ++ AnnotationAssertion([obo:IAO_0000117] [immediately precedes] "David Osumi-Sutherland") ++ AnnotationAssertion([obo:IAO_0000117] [immediately precedes] ) ++ AnnotationAssertion([obo:IAO_0000117] [happens during] "David Osumi-Sutherland") ++ AnnotationAssertion([obo:IAO_0000118] [immediately preceded by] "starts_at_end_of") ++ AnnotationAssertion([obo:IAO_0000118] [immediately precedes] "ends_at_start_of") ++ AnnotationAssertion([obo:IAO_0000118] [immediately precedes] "meets") ++ AnnotationAssertion([obo:IAO_0000118] [happens during] "d") ++ AnnotationAssertion([obo:IAO_0000118] [happens during] "during") ++ AnnotationAssertion([obo:RO_0002575] [immediately precedes] [obo:BFO_0000063]) ++ AnnotationAssertion( [happens during] "https://wiki.geneontology.org/Happens_during"^^xsd:anyURI) ++ AnnotationAssertion([in_subset] [immediately precedes] ) ++ AnnotationAssertion([in_subset] [happens during] ) ++ AnnotationAssertion([in_subset] [happens during] [obo:valid_for_gocam]) ++ AnnotationAssertion([in_subset] [happens during] [obo:valid_for_go_ontology]) ++ AnnotationAssertion([in_subset] [happens during] [obo:valid_for_go_annotation_extension]) ++ AnnotationAssertion( "") ++ AnnotationAssertion( [obo:valid_for_gocam] "") ++ AnnotationAssertion( [obo:valid_for_go_ontology] "") ++ AnnotationAssertion( [obo:valid_for_go_annotation_extension] "") ++ AnnotationAssertion( [in_subset] "in_subset") ++ Declaration(AnnotationProperty([in_subset])) ++ OntologyID(OntologyIRI() VersionIRI()) ++ SubAnnotationPropertyOf( [subset_property]) ++ SubAnnotationPropertyOf([obo:valid_for_gocam] [subset_property]) ++ SubAnnotationPropertyOf([obo:valid_for_go_ontology] [subset_property]) ++ SubAnnotationPropertyOf([obo:valid_for_go_annotation_extension] [subset_property]) diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv new file mode 100644 index 0000000..5445287 --- /dev/null +++ b/src/ontology/reports/synonyms.tsv @@ -0,0 +1,380 @@ +?cls ?pred ?val ?synType + "day 28 of adulthood" + "pharate adult stage P15" + "oogenesis stage S10B" + "obsolete gamete" + "day 70 of adulthood" + "day 21 of adulthood" + "embryonic cycle interphase" + "oogenesis stage S14B" + "embryonic stage 4" + "embryonic cycle 3" + "embryonic stage 17(ii)" + "day 15 of adulthood" + "day 69 of adulthood" + "wandering third instar larval stage" + "day 39 of adulthood" + "day 33 of adulthood" + "day 29 of adulthood" + "day 42 of adulthood" + "oogenesis stage S10A" + "oogenesis stage S6" + "embryonic cycle M-phase" + "embryonic cycle 4" + "oogenesis" + "day 57 of adulthood" + "embryonic cycle 9" + "embryonic stage 1" + "day 68 of adulthood" + "embryonic stage 11" + "extended germ band stage" + "day 62 of adulthood" + "day 53 of adulthood" + "day 50 of adulthood" + "obsolete occurrent" + "pupal stage" + "embryonic stage 15" + "oogenesis stage S7" + "prepupal stage P3" + "Drosophila life" + "day 2 of adulthood" + "oogenesis stage S12C" + "day 25 of adulthood" + "pharate adult stage P9" + "oogenesis stage S2" + "day 58 of adulthood" + "embryonic cycle 14A" + "unfertilized egg stage" + "pupal stage P5" + "obsolete germ band stage" + "day 5 of adulthood" + "late extended germ band stage" + "obsolete contracted germ band stage" + "embryonic stage 8" + "day 51 of adulthood" + "larval stage" + "developmental process" + "day 63 of adulthood" + "third instar - uncleared gut stage" + "day 3 of adulthood" + "prepupal stage P1" + "oogenesis stage S13" + "spermatogenesis" + "oogenesis stage S3" + "day 45 of adulthood" + "pharate adult stage P15(i)" + "oogenesis stage S11" + "day 22 of adulthood" + "immature adult stage" + "embryonic cycle 11" + "egg stage" + "pupal stage P5(i)" + "embryonic cycle 6" + "pharate adult stage P12" + "day 6 of adulthood" + "day 16 of adulthood" + "embryonic stage 17(iii)" + "first instar larval stage" + "late embryonic stage" + "oogenesis stage S13B" + "prepupal stage P2" + "adult stage A2" + "P-stage" + "day 34 of adulthood" + "day 30 of adulthood" + "embryonic cycle" + "oogenesis stage S12" + "day 43 of adulthood" + "day 27 of adulthood" + "biological process" + "embryonic cycle 12" + "embryonic stage 6" + "embryonic cycle 5" + "pharate adult stage P12(i)" + "third instar - cleared gut stage" + "day 60 of adulthood" + "embryonic cycle 10" + "day 17 of adulthood" + "day 12 of adulthood" + "oogenesis stage S13C" + "embryonic stage 13" + "adult stage A1" + "life stage" + "day 44 of adulthood" + "day 40 of adulthood" + "oogenesis stage S8" + "day 65 of adulthood" + "day 54 of adulthood" + "day 26 of adulthood" + "day 35 of adulthood" + "embryonic stage 7" + "prepupal stage P4" + "third instar - partially cleared gut stage" + "day 59 of adulthood" + "blastoderm stage" + "embryonic cycle 8" + "embryonic cycle 14B" + "obsolete cellular blastoderm stage" + "pharate adult stage P10" + "pupal stage P6" + "day 11 of adulthood" + "day 23 of adulthood" + "embryonic cycle 1" + "day 8 of adulthood" + "embryonic stage 12" + "developmental stage" + "embryonic stage 9" + "third instar larval stage" + "oogenesis stage S13E" + "day 64 of adulthood" + "day 4 of adulthood" + "oogenesis stage S13A" + "oogenesis stage S11b" + "day 36 of adulthood" + "day 61 of adulthood" + "day 46 of adulthood" + "mature adult stage" + "embryonic cycle 15" + "embryonic stage 5" + "pupal stage P5(ii)" + "embryonic cycle 7" + "pharate adult stage P15(ii)" + "pharate adult stage P13" + "day 55 of adulthood" + "day 7 of adulthood" + "day 19 of adulthood" + "second instar larval stage" + "embryonic stage 16" + "oogenesis stage S14" + "pharate adult stage" + "oogenesis stage S11a" + "embryonic stage 17(iv)" + "adult age in days" + "day 47 of adulthood" + "oogenesis stage S12A" + "embryonic cycle 13" + "day 31 of adulthood" + "pharate adult stage P12(ii)" + "pharate adult stage P11(ii)" + "day 18 of adulthood" + "day 13 of adulthood" + "oogenesis stage S13D" + "embryonic cycle 2" + "obsolete head involution stage" + "age" + "day 41 of adulthood" + "day 66 of adulthood" + "early third instar larval stage" + "cleavage stage" + "day 38 of adulthood" + "oogenesis stage S10" + "oogenesis stage S9" + "oogenesis stage S5" + "early extended germ band stage" + "prepupal stage P4(i)" + "obsolete syncytial blastoderm stage" + "embryonic stage 3" + "gastrula stage" + "day 14 of adulthood" + "pupal stage P7" + "day 24 of adulthood" + "embryonic stage 2" + "fertilized egg stage" + "day 56 of adulthood" + "day 9 of adulthood" + "pre-blastoderm stage" + "day 67 of adulthood" + "day 52 of adulthood" + "third instar larval stage L1" + "embryonic stage 10" + "day 37 of adulthood" + "day 49 of adulthood" + "late third instar larval stage" + "dorsal closure stage" + "oogenesis stage S4" + "oogenesis stage S12B" + "prepupal stage P4(ii)" + "day 1 of adulthood" + "pharate adult stage P11" + "embryonic cycle 16" + "embryonic cycle 14" + "pharate adult stage P8" + "oogenesis stage S1" + "adult stage" + "pharate adult stage P14" + "embryonic stage" + "day 10 of adulthood" + "day 20 of adulthood" + "oogenesis stage S14A" + "adult stage A3" + "third instar larval stage L2" + "embryonic stage 17(i)" + "embryonic stage 17" + "day 48 of adulthood" + "embryonic stage 14" + "prepupal stage" + "day 0 of adulthood" + "pharate adult stage P11(i)" + "day 32 of adulthood" + "catalytic activity" + "mitotic cell cycle phase" + "M phase" + "interphase" + "specifically dependent continuant"@en + "multicellular organismal process" + "process"@en + "quality"@en + "independent continuant"@en + "biological_process" + "cellular process" + "material entity"@en + "mitotic cell cycle" + "function"@en + "realizable entity"@en + "cell cycle process" + "mitotic cell cycle, embryonic" + "continuant"@en + "mitotic cell cycle process" + "anatomical structure development" + "mitotic M phase" + "cellular component organization or biogenesis" + "nuclear division" + "mitotic interphase" + "occurrent"@en + "organelle fission" + "cellular component organization" + "transferase activity, transferring phosphorus-containing groups" + "biological phase" + "organelle organization" + "transferase activity" + "embryo development" + "role"@en + "molecular_function" + "cell cycle" + "mitotic nuclear division" + "multicellular organism development" + "cell cycle phase" + "kinase activity" + "developmental process" + "disposition"@en + "adult stage II" + "pupal stage" + "adult stage I" + "third instar larva" + "adult stage III" + "white prepupa" + "single-multicellular organism process" + "single-organism process" + "single organism process" + "single-organism cellular process" + "mitosis" + "karyokinesis" + "cell organization and biogenesis" + "single-organism organelle organization" + "organelle organization and biogenesis" + "single-organism developmental process" + "pupal stage P0" + "white prepupa" + "cell growth and/or maintenance" + "development" + "post-feeding larva" + "late third instar" + "metamorphosis" + "resting phase" + "embryogenesis and morphogenesis" + "pupal stage P15" + "syncytial blastoderm stage" + "syncytial blastoderm" + "oogenesis stage" + "phanerocephalic pupa" + "bubble prepupa stage" + "pupal stage P3" + "Drosophila life cycle" + "pupal stage P9" + "amber-eyed stage" + "embryonic cycle 14 interphase" + "rapidly extending germ band stage" + "white puparium stage" + "pupal stage P1" + "puparium formation" + "meconium stage" + "pupal stage P15(i)" + "Malpighian tubules migrating" + "pupal stage P12" + "first instar larva" + "L1" + "brown puparium stage" + "pupal stage P2" + "pupal stage P12(i)" + "wing tips grey stage" + "contracted germ band stage" + "life cycle stage" + "cryptocephalic pupa" + "pupal stage P4" + "blastoderm" + "embryonic cycle 14 M-phase" + "red-eye bald stage" + "pupal stage P10" + "green Malpighian tubules stage" + "retracting germ band stage" + "L3" + "second blastoderm mitosis" + "cellular blastoderm stage" + "cellular blastoderm" + "white Malpighian tubules stage" + "pupal stage P15(ii)" + "eclosion stage" + "pupal stage P13" + "wings black stage" + "L2" + "second instar larva" + "wings grey stage" + "pupal stage P12(ii)" + "pupal stage P11(ii)" + "thoracic bristles stage" + "pupal stage P4(i)" + "buoyant stage" + "gastrula" + "yellow body stage" + "pre-blastoderm" + "moving bubble stage" + "pupal stage P4(ii)" + "pupal stage P11" + "third blastoderm mitosis" + "first blastoderm mitosis" + "yellow-eyed stage" + "pupal stage P8" + "mature bristles stage" + "pupal stage P14" + "spiracles everted larva" + "head involution stage" + "pupal stage P11(i)" + "head bristles stage" + "enzyme activity" + "M-phase" + "karyostasis" + "organismal physiological process" + "physiological process" + "biological process" + "cellular physiological process" + "cell physiology" + "development of an anatomical structure" + "M-phase of mitotic cell cycle" + "M phase of mitotic cell cycle" + "cellular component organisation or biogenesis" + "cellular component organization or biogenesis at cellular level" + "cellular component organisation or biogenesis at cellular level" + "interphase of mitotic cell cycle" + "cellular component organisation at cellular level" + "cell organisation" + "cellular component organization in other organism" + "cellular component organization at cellular level" + "cellular component organisation in other organism" + "single organism organelle organization" + "organelle organisation" + "embryogenesis" + "embryonal development" + "molecular function" + "cell-division cycle" + "mitosis" + "phosphokinase activity" diff --git a/src/ontology/reports/xrefs.tsv b/src/ontology/reports/xrefs.tsv new file mode 100644 index 0000000..538a364 --- /dev/null +++ b/src/ontology/reports/xrefs.tsv @@ -0,0 +1,23 @@ +?cls ?xref + "GO:0048477" + "GO:0032502" + "GO:0007283" + "UBERON:8000000" + "GO:0008150" + "UBERON:8000002" + "UBERON:8000001" + "Wikipedia:Enzyme" + "Wikipedia:M_phase" + "Wikipedia:Interphase" + "Wikipedia:Biological_process" + "Wikipedia:Mitosis" + "EC:2.7.-.-" + "Reactome:R-HSA-8868783" + "EC:2.-.-.-" + "Reactome:R-HSA-5668414" + "Reactome:R-HSA-1483186" + "Reactome:R-HSA-1483089" + "Wikipedia:Embryogenesis" + "Wikipedia:Cell_cycle" + "Reactome:R-HSA-6788855" + "Reactome:R-HSA-6788867"