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COB Transition Demo 2 #1819

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COB Transition Demo 2 #1819

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971d697
Replace OMO import with versioned OMO import
sebastianduesing Sep 3, 2024
eda610e
Add OntoFox import for RO
sebastianduesing Sep 3, 2024
1e2bf6b
Update IAO import module & switch to computed intermediates
sebastianduesing Sep 3, 2024
38c0a7d
Replace BFO import with COB import
sebastianduesing Sep 3, 2024
3f07f56
Rename alternative term to alternative label column in templates
sebastianduesing Sep 3, 2024
0fae4d9
Replace 'inheres in' with 'characteristic of' and 'bearer of' with 'h…
sebastianduesing Sep 3, 2024
1e51788
Redirect usages of CHEBI:atom to COB:atom
sebastianduesing Sep 4, 2024
7191f60
Redirect usages of CHEBI:molecular entity to COB:molecular entity
sebastianduesing Sep 4, 2024
6e543b3
Redirect usages of OBI:device to COB:device and obsolete OBI:device
sebastianduesing Sep 4, 2024
8d657ba
Redirect usages of IAO:measurement datum to COB:measurement datum
sebastianduesing Sep 4, 2024
4b8964f
Redirect usages of BFO:realizes to COB:realizes
sebastianduesing Sep 4, 2024
4f49dfb
Redirect usages of RO:concretizes to COB:concretizes
sebastianduesing Sep 4, 2024
f8a2a0b
Remove unused duplicate 'action specification' IAO term
sebastianduesing Sep 4, 2024
dbf696b
Remove unused 'information carrier' IAO term
sebastianduesing Sep 4, 2024
8a1d9ff
Remove unused BFO_0000028
sebastianduesing Sep 4, 2024
31d3ee4
Line order update to obi-edit.owl by Protege
sebastianduesing Sep 4, 2024
fc43326
Remove BFO:0000001 and its usages
sebastianduesing Sep 4, 2024
7a81081
Remove BFO:0000002 and resolve its usages
sebastianduesing Sep 4, 2024
5ced43c
Drop external-byhand
sebastianduesing Sep 4, 2024
5166707
Remove BFO:0000003 and resolve its usages
sebastianduesing Sep 4, 2024
020f395
Remove BFO:0000004 and resolve its usages
sebastianduesing Sep 4, 2024
4362c18
Remove BFO:0000019 and resolve its usages
sebastianduesing Sep 4, 2024
12e9c23
Remove all non-OMO usages of BFO_0000031
sebastianduesing Sep 4, 2024
589bc0c
Remove BFO:0000035 and resolve its usages
sebastianduesing Sep 4, 2024
382d5d9
Run make modules
sebastianduesing Sep 4, 2024
3a6a982
Fix unsatisfiable classes
sebastianduesing Sep 4, 2024
38a6222
Fix multiple-textual-definitions-violation
sebastianduesing Sep 5, 2024
b85ac8d
Relabel is_specified_input_of to is specified input of
sebastianduesing Sep 5, 2024
bdd796f
Relabel is_specified_output_of to is specified output of
sebastianduesing Sep 5, 2024
f02b1b1
Relabel has_specified_input to has specified input
sebastianduesing Sep 5, 2024
d00f8f9
Relabel has_specified_output to has specified output
sebastianduesing Sep 5, 2024
7060af8
Relabel planned process to completely executed planned process
sebastianduesing Sep 5, 2024
cfbac28
Relabel processed material to processed material entity
sebastianduesing Sep 5, 2024
42d0b3b
Relabel duplicates
sebastianduesing Sep 16, 2024
d5ca609
Update obi.owl and obi-base.owl artifacts
jamesaoverton Sep 16, 2024
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14,489 changes: 6,949 additions & 7,540 deletions obi.owl
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190 changes: 133 additions & 57 deletions src/ontology/OntoFox_inputs/ChEBI_input.txt
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1 change: 1 addition & 0 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
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11 changes: 5 additions & 6 deletions src/ontology/OntoFox_inputs/IAO_input.txt
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Expand Up @@ -11,10 +11,8 @@ http://purl.obolibrary.org/obo/IAO_0000003 # measurement unit label
http://purl.obolibrary.org/obo/IAO_0000004 # has measurement value
http://purl.obolibrary.org/obo/IAO_0000005 # objective specification
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 +30,6 @@ 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 +43,7 @@ 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 @@ -64,16 +62,17 @@ 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
subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process
http://purl.obolibrary.org/obo/IAO_0000572 # documenting
subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process

http://purl.obolibrary.org/obo/IAO_0000032 # scalar measurement datum
subClassOf http://purl.obolibrary.org/obo/COB_0000121 # measurement datum
[Source term retrieval setting]
includeAllIntermediates
includeComputedIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
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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
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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
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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]
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43 changes: 43 additions & 0 deletions src/ontology/OntoFox_inputs/RO_input.txt
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@@ -0,0 +1,43 @@
[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_0000085 # has function
http://purl.obolibrary.org/obo/RO_0000079 # function of
http://purl.obolibrary.org/obo/RO_0000086 # has quality
http://purl.obolibrary.org/obo/RO_0000080 # quality of
http://purl.obolibrary.org/obo/RO_0002351 # has member
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
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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