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COB Transition Demo 1 #1812

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COB Transition Demo 1 #1812

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8a1044c
Switch non-versioned OMO import to the current version of OMO.
sebastianduesing Aug 5, 2024
0ed714a
Replace RO-core import with OntoFox RO import.
sebastianduesing Aug 5, 2024
43990a3
Prepare IAO import module.
sebastianduesing Aug 5, 2024
19d4e32
Remove BFO import.
sebastianduesing Aug 5, 2024
bce2c6b
Add COB import
sebastianduesing Aug 6, 2024
9fe2471
Rename 'alternative term' column to 'alternative label' in all templates
sebastianduesing Aug 6, 2024
9ea9345
Replace 'inheres in' and 'bearer of' with 'characteristic of' and 'ha…
sebastianduesing Aug 6, 2024
b3b54ad
Redirect references to CHEBI:atom to COB:atom
sebastianduesing Aug 6, 2024
05e16bd
Redirect references to CHEBI:molecular entity to COB:molecular entity
sebastianduesing Aug 6, 2024
5eca0d1
Update device module
sebastianduesing Aug 7, 2024
b650131
Obsolete OBI:device
sebastianduesing Aug 7, 2024
0ced5d7
Fix typo in RO import
sebastianduesing Aug 13, 2024
d02c932
Remove mentions of CHEBI:molecular entity from assays.owl
sebastianduesing Aug 13, 2024
fa7ddda
Remove BFO:0000028
sebastianduesing Aug 13, 2024
2a894e5
Redirect references to IAO:measurement datum to COB:measurement datum
sebastianduesing Aug 20, 2024
721f22a
Remove references to BFO:entity
sebastianduesing Aug 20, 2024
71cf811
Remove reference to BFO:continuant
sebastianduesing Aug 20, 2024
b2a2369
Remove references to BFO:quality
sebastianduesing Aug 20, 2024
d4897e7
Move IAO import of ICE out from under GDC
sebastianduesing Aug 20, 2024
be301b2
Remove unused information carrier term
sebastianduesing Aug 20, 2024
64f9314
Run make modules
sebastianduesing Aug 21, 2024
af55725
Remove references to BFO:0000055 (realizes)
sebastianduesing Aug 21, 2024
d2a24a0
Remove references to RO:0000059 (concretizes)
sebastianduesing Aug 21, 2024
b93ac97
Merge branch 'master' into cob_transition_1
jamesaoverton Aug 27, 2024
96ba715
Drop external-byhand.owl
jamesaoverton Aug 27, 2024
ec60b63
Fix almost all unsatisfiability issues
sebastianduesing Aug 27, 2024
09166e7
Remove unused unsatisfiable class
sebastianduesing Aug 29, 2024
ea65142
Merge branch 'master' into cob_transition_1
jamesaoverton Aug 30, 2024
a58f92c
Obsolete OBI:0001720
sebastianduesing Aug 30, 2024
72484fc
Merge branch 'cob_transition_1' of https://github.com/obi-ontology/ob…
sebastianduesing Aug 30, 2024
3f8b57e
Remove usage of BFO_0000001
sebastianduesing Aug 30, 2024
cd6485e
Remove usage of BFO_0000002
sebastianduesing Aug 30, 2024
d3ebf24
Remove usage of BFO_0000003
sebastianduesing Aug 30, 2024
934cb5a
Remove usage of BFO_0000004
sebastianduesing Aug 30, 2024
7813044
Remove usage of BFO_0000035
sebastianduesing Aug 30, 2024
5d13bb2
Fix multiple-definition conflict
sebastianduesing Sep 3, 2024
dccf1f4
Fix multiple-label conflicts
sebastianduesing Sep 3, 2024
492a5bf
Relabel templates
sebastianduesing Sep 3, 2024
bac8d74
Remove one missed label
sebastianduesing Sep 3, 2024
fd040da
Move 'region' out from under GDC
sebastianduesing Sep 3, 2024
dff4b02
Restore labels for six OBI terms used in COB
jamesaoverton Sep 5, 2024
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212 changes: 155 additions & 57 deletions src/ontology/OntoFox_inputs/ChEBI_input.txt
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7 changes: 3 additions & 4 deletions src/ontology/OntoFox_inputs/GO_input.txt
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Expand Up @@ -41,6 +41,7 @@ http://purl.obolibrary.org/obo/GO_0004448 # isocitrate dehydrogenase [NAD(P)+] a
http://purl.obolibrary.org/obo/GO_0004457 # lactate dehydrogenase activity
http://purl.obolibrary.org/obo/GO_0004540 # ribonuclease activity
http://purl.obolibrary.org/obo/GO_0005216
http://purl.obolibrary.org/obo/GO_0005488 # binding
http://purl.obolibrary.org/obo/GO_0005575
http://purl.obolibrary.org/obo/GO_0005577 # fibrinogen complex
http://purl.obolibrary.org/obo/GO_0005694
Expand Down Expand Up @@ -179,8 +180,6 @@ http://purl.obolibrary.org/obo/GO_0140730 # amphiregulin production
http://purl.obolibrary.org/obo/GO_0140779 # XCL1 production

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/GO_0001047 # core promoter binding
subClassOf http://purl.obolibrary.org/obo/OBI_0001588 # binding
http://purl.obolibrary.org/obo/GO_0001788
subClassOf http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/GO_0001806
Expand Down Expand Up @@ -264,7 +263,7 @@ subClassOf http://purl.obolibrary.org/obo/GO_0032991
http://purl.obolibrary.org/obo/GO_0019882
subClassOf http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/GO_0019904
subClassOf http://purl.obolibrary.org/obo/OBI_0001588
subClassOf http://purl.obolibrary.org/obo/GO_0005488
http://purl.obolibrary.org/obo/GO_0030041
subClassOf http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/GO_0030097
Expand Down Expand Up @@ -394,7 +393,7 @@ subClassOf http://purl.obolibrary.org/obo/BFO_0000040
http://purl.obolibrary.org/obo/GO_0043316
subClassOf http://purl.obolibrary.org/obo/GO_0001906
http://purl.obolibrary.org/obo/GO_0043565
subClassOf http://purl.obolibrary.org/obo/OBI_0001588
subClassOf http://purl.obolibrary.org/obo/GO_0005488
http://purl.obolibrary.org/obo/GO_0048869
subClassOf http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/GO_0050896
Expand Down
7 changes: 3 additions & 4 deletions src/ontology/OntoFox_inputs/IAO_input.txt
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Expand Up @@ -14,7 +14,6 @@ http://purl.obolibrary.org/obo/IAO_0000006 # narrative object
http://purl.obolibrary.org/obo/IAO_0000007 # action specification
http://purl.obolibrary.org/obo/IAO_0000009 # datum label
http://purl.obolibrary.org/obo/IAO_0000010 # software
http://purl.obolibrary.org/obo/IAO_0000015 # information carrier
http://purl.obolibrary.org/obo/IAO_0000027 # data item
http://purl.obolibrary.org/obo/IAO_0000028 # symbol
http://purl.obolibrary.org/obo/IAO_0000030 # information content entity
Expand All @@ -32,7 +31,6 @@ http://purl.obolibrary.org/obo/IAO_0000098 # data format specification
http://purl.obolibrary.org/obo/IAO_0000100 # data set
http://purl.obolibrary.org/obo/IAO_0000101 # image
http://purl.obolibrary.org/obo/IAO_0000104 # plan specification
http://purl.obolibrary.org/obo/IAO_0000109 # measurement datum
http://purl.obolibrary.org/obo/IAO_0000136 # is about
http://purl.obolibrary.org/obo/IAO_0000144 # conclusion textual entity
http://purl.obolibrary.org/obo/IAO_0000178 # material information bearer
Expand All @@ -46,6 +44,7 @@ http://purl.obolibrary.org/obo/IAO_0000235 # denoted by
http://purl.obolibrary.org/obo/IAO_0000300 # textual entity
http://purl.obolibrary.org/obo/IAO_0000306 # table
http://purl.obolibrary.org/obo/IAO_0000310 # document
http://purl.obolibrary.org/obo/IAO_0000311 # publication
http://purl.obolibrary.org/obo/IAO_0000312 # publication about an investigation
http://purl.obolibrary.org/obo/IAO_0000401 # one dimensional cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000407 # has coordinate unit label
Expand All @@ -64,7 +63,7 @@ http://purl.obolibrary.org/obo/IAO_0000594 # software application

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/IAO_0000030 # information content entity
subClassOf http://purl.obolibrary.org/obo/BFO_0000031 # generically dependent continuant
subClassOf http://www.w3.org/2002/07/owl#Thing # owl:Thing
http://purl.obolibrary.org/obo/IAO_0000178 # material information bearer
subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity
http://purl.obolibrary.org/obo/IAO_0000574 # assigning a centrally registered identifier
Expand All @@ -73,7 +72,7 @@ http://purl.obolibrary.org/obo/IAO_0000572 # documenting
subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process

[Source term retrieval setting]
includeAllIntermediates
includeComputedIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/OntoFox_inputs/OBA_input.txt
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Expand Up @@ -22,7 +22,7 @@ http://purl.obolibrary.org/obo/OBA_2060190 # brachioradialis functionality
[Top level source term URIs and target direct superclass URIs]
# WARN: OBA subclasses PATO:0000001 'quality' not BFO:0000019 'quality'
http://purl.obolibrary.org/obo/OBA_0000001 # biological attribute
subClassOf http://purl.obolibrary.org/obo/BFO_0000019 # quality
subClassOf http://purl.obolibrary.org/obo/BFO_0000020 # characteristic

[Source term retrieval setting]
includeNoIntermediates
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/OntoFox_inputs/OGMS_input.txt
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Expand Up @@ -18,7 +18,7 @@ http://purl.obolibrary.org/obo/OGMS_0000123 # clinical data item
http://purl.obolibrary.org/obo/OGMS_0000015
subClassOf http://purl.obolibrary.org/obo/IAO_0000030
http://purl.obolibrary.org/obo/OGMS_0000023
subClassOf http://purl.obolibrary.org/obo/BFO_0000019
subClassOf http://purl.obolibrary.org/obo/BFO_0000020 # characteristic
http://purl.obolibrary.org/obo/OGMS_0000063
subClassOf http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/OGMS_0000090
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/OntoFox_inputs/PATO_input.txt
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Expand Up @@ -58,7 +58,7 @@ http://purl.obolibrary.org/obo/PATO_0002027 # osmolality

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/PATO_0001241
subClassOf http://purl.obolibrary.org/obo/BFO_0000019
subClassOf http://purl.obolibrary.org/obo/BFO_0000020 # characteristic


[Source term retrieval setting]
Expand Down
38 changes: 38 additions & 0 deletions src/ontology/OntoFox_inputs/RO_input.txt
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@@ -0,0 +1,38 @@
[URI of the OWL(RDF/XML) output file]
http://purl.obolibrary.org/obo/obi/dev/import/RO_imports.owl

[Source ontology]
# OBO Relations Ontology
RO

[Low level source term URIs]
http://purl.obolibrary.org/obo/BFO_0000062 # preceded by
http://purl.obolibrary.org/obo/BFO_0000063 # precedes
http://purl.obolibrary.org/obo/RO_0000079 # function of
http://purl.obolibrary.org/obo/RO_0000080 # quality of
http://purl.obolibrary.org/obo/RO_0000081 # role of
http://purl.obolibrary.org/obo/RO_0000085 # has function
http://purl.obolibrary.org/obo/RO_0000086 # has quality
http://purl.obolibrary.org/obo/RO_0000087 # has role
http://purl.obolibrary.org/obo/RO_0000091 # has disposition
http://purl.obolibrary.org/obo/RO_0000092 # disposition of
http://purl.obolibrary.org/obo/RO_0001000 # derives from
http://purl.obolibrary.org/obo/RO_0001025 # located in
http://purl.obolibrary.org/obo/RO_0002087 # immediately preceded by
http://purl.obolibrary.org/obo/RO_0002090 # immediately precedes
http://purl.obolibrary.org/obo/RO_0002180 # has component
http://purl.obolibrary.org/obo/RO_0002215 # capable of
http://purl.obolibrary.org/obo/RO_0002219 # surrounded by
http://purl.obolibrary.org/obo/RO_0002222 # temporal relation
http://purl.obolibrary.org/obo/RO_0002223 # starts
http://purl.obolibrary.org/obo/RO_0002351 # has member

[Top level source term URIs and target direct superclass URIs]

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
copyTo http://purl.obolibrary.org/obo/IAO_0000111
http://purl.obolibrary.org/obo/IAO_0000115
4 changes: 2 additions & 2 deletions src/ontology/OntoFox_inputs/SO_input.txt
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Expand Up @@ -19,7 +19,7 @@ http://purl.obolibrary.org/obo/SO_0000235 # TF_binding_site

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/SO_0000001
subClassOf http://purl.obolibrary.org/obo/BFO_0000031
subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity
http://purl.obolibrary.org/obo/SO_0000104
subClassOf http://purl.obolibrary.org/obo/SO_0000001
http://purl.obolibrary.org/obo/SO_0000276
Expand Down Expand Up @@ -49,4 +49,4 @@ includeNoIntermediates
[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
copyTo http://purl.obolibrary.org/obo/IAO_0000111
http://purl.obolibrary.org/obo/IAO_0000115
http://purl.obolibrary.org/obo/IAO_0000115
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