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new release
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@cmungall
cmungall committed Jan 6, 2018
1 parent a3ea088 commit ed7f3ad
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Showing 39 changed files with 10,790 additions and 1,727 deletions.
1,834 changes: 1,267 additions & 567 deletions ro.json
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326 changes: 295 additions & 31 deletions ro.obo
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491 changes: 468 additions & 23 deletions ro.owl
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2 changes: 1 addition & 1 deletion src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ ONTS= ro.obo ro.owl ro.json annotations.owl core.owl go-biotic.owl pato_import.o

all: build

build: ro.owl ro.obo all_subsets
build: ro.owl ro.obo ro.json all_subsets

release:
cp -pr catalog-v001.xml $(ONTS) subsets ../..
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95 changes: 69 additions & 26 deletions src/ontology/ro.obo
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219 changes: 159 additions & 60 deletions src/ontology/ro.owl
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103 changes: 74 additions & 29 deletions src/ontology/subsets/ro-causal.obo
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197 changes: 149 additions & 48 deletions src/ontology/subsets/ro-causal.owl
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59 changes: 41 additions & 18 deletions src/ontology/subsets/ro-chado.obo
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Expand Up @@ -417,6 +417,12 @@ is_functional: true
is_a: RO:0002017 ! has component activity
is_a: RO:0002211 ! regulates

[Typedef]
id: RO:0002026
name: in_register_with
def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos]
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002081
name: before_or_simultaneous_with
Expand Down Expand Up @@ -2914,21 +2920,6 @@ name: has_partial_material_basis_in_germline_mutation_in
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to

[Typedef]
id: RO:0004007
name: TEST_1
is_a: RO:0004000 ! condition has genetic basis in

[Typedef]
id: RO:0004008
name: TEST_2
is_a: RO:0004000 ! condition has genetic basis in

[Typedef]
id: RO:0004009
name: TEST_3
is_a: RO:0004000 ! condition has genetic basis in

[Typedef]
id: RO:0004010
name: is_genetic_basis_for_condition
Expand Down Expand Up @@ -2985,6 +2976,7 @@ is_a: RO:0002410 ! causally related to
id: RO:0004019
name: disease_has_basis_in
is_a: RO:0004017 ! realizable has basis in
is_a: RO:0004023 ! causal relationship with disease as subject

[Typedef]
id: RO:0004020
Expand All @@ -3007,22 +2999,53 @@ is_a: RO:0004019 ! disease has basis in

[Typedef]
id: RO:0004023
name: causal_relationship_between_a_disease_and_something
name: causal_relationship_with_disease_as_subject
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0004024
name: disease_causes_disruption_of
def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." []
is_a: RO:0004023 ! causal relationship between a disease and something
is_a: RO:0004023 ! causal relationship with disease as subject
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0004025
name: disease_causes_dysfunction_of
is_a: RO:0004023 ! causal relationship between a disease and something
is_a: RO:0004023 ! causal relationship with disease as subject
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0004026
name: disease_has_location
def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." []
is_a: RO:0004023 ! causal relationship with disease as subject

[Typedef]
id: RO:0004027
name: disease_has_inflammation_site
def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" []
is_a: RO:0004026 ! disease has location

[Typedef]
id: RO:0004028
name: realized_in_response_to_stimulus
def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." []
holds_over_chain: RO:0009501 RO:0002233
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0004029
name: disease_has_feature
def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." []
is_a: RO:0004023 ! causal relationship with disease as subject

[Typedef]
id: RO:0004030
name: disease_arises_from_structure
def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure." []
is_a: RO:0004019 ! disease has basis in

[Typedef]
id: RO:0008501
name: epiphyte_of
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59 changes: 41 additions & 18 deletions src/ontology/subsets/ro-chado.obo.tmp
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Original file line number Diff line number Diff line change
Expand Up @@ -417,6 +417,12 @@ is_functional: true
is_a: RO:0002017 ! has component activity
is_a: RO:0002211 ! regulates

[Typedef]
id: RO:0002026
name: in register with
def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos]
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002081
name: before or simultaneous with
Expand Down Expand Up @@ -2914,21 +2920,6 @@ name: has partial material basis in germline mutation in
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to

[Typedef]
id: RO:0004007
name: TEST 1
is_a: RO:0004000 ! condition has genetic basis in

[Typedef]
id: RO:0004008
name: TEST 2
is_a: RO:0004000 ! condition has genetic basis in

[Typedef]
id: RO:0004009
name: TEST 3
is_a: RO:0004000 ! condition has genetic basis in

[Typedef]
id: RO:0004010
name: is genetic basis for condition
Expand Down Expand Up @@ -2985,6 +2976,7 @@ is_a: RO:0002410 ! causally related to
id: RO:0004019
name: disease has basis in
is_a: RO:0004017 ! realizable has basis in
is_a: RO:0004023 ! causal relationship with disease as subject

[Typedef]
id: RO:0004020
Expand All @@ -3007,22 +2999,53 @@ is_a: RO:0004019 ! disease has basis in

[Typedef]
id: RO:0004023
name: causal relationship between a disease and something
name: causal relationship with disease as subject
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0004024
name: disease causes disruption of
def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." []
is_a: RO:0004023 ! causal relationship between a disease and something
is_a: RO:0004023 ! causal relationship with disease as subject
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0004025
name: disease causes dysfunction of
is_a: RO:0004023 ! causal relationship between a disease and something
is_a: RO:0004023 ! causal relationship with disease as subject
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0004026
name: disease has location
def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." []
is_a: RO:0004023 ! causal relationship with disease as subject

[Typedef]
id: RO:0004027
name: disease has inflammation site
def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" []
is_a: RO:0004026 ! disease has location

[Typedef]
id: RO:0004028
name: realized in response to stimulus
def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." []
holds_over_chain: RO:0009501 RO:0002233
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0004029
name: disease has feature
def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." []
is_a: RO:0004023 ! causal relationship with disease as subject

[Typedef]
id: RO:0004030
name: disease arises from structure
def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure." []
is_a: RO:0004019 ! disease has basis in

[Typedef]
id: RO:0008501
name: epiphyte of
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