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27 import mop directly #44

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838300e
#27 compare MOP entities
StroemPhi Apr 7, 2022
5ca9a4a
#27 add MOPvsRXNO as excel and suggest solution for MOP:0000003
StroemPhi Apr 7, 2022
c2183dc
correct the axioms needed to also have "acylation" as inferred parent…
StroemPhi Apr 7, 2022
3f61525
#27 reconcile: MOP:0000339, MOP:0000364, MOP:0000369, MOP:0000410, MO…
StroemPhi Apr 7, 2022
28a0508
#27 reconciling: MOP:0000422, MOP:0000458, MOP:0000479, MOP:0000539
StroemPhi Apr 7, 2022
c2fb1db
reconcile classes
StroemPhi Apr 7, 2022
44ded96
#27 reconcile: MOP:0000566, MOP:0000567, MOP:0000568
StroemPhi Apr 7, 2022
f6f60f2
reconcile: MOP:0000569, MOP:0000570, MOP:0000571,
StroemPhi Apr 19, 2022
29b4cd1
#27 reconcile: MOP:0000582, MOP:0000583,
StroemPhi Apr 19, 2022
5cb2c4f
#27 propose how to classify 'alkene oxidative cleavage' for now
StroemPhi Apr 19, 2022
df185e2
#27 reconcile: MOP:0000589, MOP:0000596, MOP:0000618, ...
StroemPhi Apr 20, 2022
bab158d
#27 reconcile last batch in XLSX
StroemPhi Apr 20, 2022
0526d1a
#27 adding comment in xlsx regarding acylation superclass
StroemPhi Apr 21, 2022
b0bf4e2
#27 import MOP into RXNO
StroemPhi Apr 21, 2022
d9a6663
#27 delete MOP_0000003 (formylation) from rxno.owl and correct its su…
StroemPhi Apr 21, 2022
3202209
Revert "#27 import MOP into RXNO"
StroemPhi Apr 21, 2022
912e3bc
Revert "#27 delete MOP_0000003 (formylation) from rxno.owl and correc…
StroemPhi Apr 21, 2022
122e49c
#27 add editor files
StroemPhi Apr 21, 2022
5318ef4
rename editor files
StroemPhi Apr 21, 2022
f1d94f3
delete MOP_0000339 silylation from rxno_edit.owl
StroemPhi Apr 21, 2022
b660cab
delete MOP_0000364 methylation from rxno-edit.owl
StroemPhi Apr 21, 2022
2ca1447
delete MOP_0000369 alkylation from rxno-edit.owl
StroemPhi Apr 21, 2022
1b25d80
delete MOP_0000410 hydrocarbylation from rxno-edit.owl
StroemPhi Apr 21, 2022
759beae
delete MOP_0000411 arylation from rxno-edit.owl but add its additiona…
StroemPhi Apr 21, 2022
a7350fa
delete MOP_0000422 allylation in rxno-edit.owl
StroemPhi Apr 21, 2022
3ea45b1
delete MOP_0000458 organylation from rxno-edit.owl
StroemPhi Apr 21, 2022
202e215
delete MOP_0000479 acylation from rxno-edit.owl
StroemPhi Apr 21, 2022
4bf2a47
delete MOP_0000539 sulfonylation from rxno-edit.owl but copy comment …
StroemPhi Apr 21, 2022
118492c
delete MOP_0000543, MOP:0000555, MOP:0000562, MOP:0000563, MOP:000056…
StroemPhi Apr 21, 2022
902f837
delete identical MOP classes from rxno-edit.owl
StroemPhi Apr 21, 2022
1bf9635
delete more identical MOP classes from rxno.edit
StroemPhi Apr 21, 2022
1280a90
cut MOP classes only declared in rxno-edit.owl to mop-edit.owl
StroemPhi Apr 21, 2022
4aaf4fe
Update MOP_vs_RXNO.xlsx
StroemPhi Apr 21, 2022
99a2cdd
delete MOP:0000550 halogenation in rxno-edit.owl
StroemPhi Apr 21, 2022
2e1d0e1
clean up after copying classes from RXNO to MOP and adding of needed …
StroemPhi Apr 21, 2022
1ef4b86
delete MOP_0000556 nitration from rxno-edit.owl
StroemPhi Apr 21, 2022
24521ba
fix exidently deleted metadata of nitration
StroemPhi Apr 21, 2022
25d6a1b
delete cyclization from RXNO and use its has_participant axiom instea…
StroemPhi Apr 21, 2022
e3c2323
delete MOP:0000571 from rxno but copy missing axioms to mop
StroemPhi Apr 21, 2022
f9a7602
delete MOP_0000565 from rxno but copy axiom to mop
StroemPhi Apr 21, 2022
8a90c36
delete MOP_0000572 from rxno but copy axiom to mop
StroemPhi Apr 21, 2022
02266e1
delete MOP_0000573 from rxno but copy missing axioms to mop
StroemPhi Apr 21, 2022
bc3fffa
delete MOP_0000574 from rxno but copy missing axioms and altLabel to mop
StroemPhi Apr 21, 2022
921ce46
delete MOP_0000575 from rxno but change its parent in mop
StroemPhi Apr 21, 2022
bf9e7d1
delete MOP_0000556 in rxno, as parent in mop is more precise
StroemPhi Apr 21, 2022
577bb43
delete MOP_0000577 in rxno but copy axiom to mop
StroemPhi Apr 21, 2022
542027b
delete MOP_0000578 from rxno but copy axiom to mop
StroemPhi Apr 21, 2022
66d472c
delete deprecated MOP_0000524 from rxno as it's already in mop
StroemPhi Apr 21, 2022
ee1c463
delete MOP_0000579 from rxno but copy axiom to mop
StroemPhi Apr 21, 2022
ac4bd96
delete MOP_0000580 from RXNO but copy axioms to MOP
StroemPhi Apr 21, 2022
f02643b
delete MOP_0002411 from rxno
StroemPhi Apr 21, 2022
426bdcf
add IAO AP labels
StroemPhi Apr 21, 2022
419c565
merge MOP:0000708 and RXNO:0000344 and make the latter obsolete
StroemPhi Apr 21, 2022
970a35f
make secondary and primary alcohol children of alcohol
StroemPhi Apr 21, 2022
f47a486
delete wrong injected disjoint axiom
StroemPhi Apr 21, 2022
4c2059b
minted MOP:ID for "oxidation state" which was falsely using MOP:00007…
StroemPhi May 5, 2022
bbaac2c
move #27 workfiles into docs
StroemPhi May 5, 2022
bfd80cc
Create catalog-v001.xml
StroemPhi May 5, 2022
f6532ef
resolve conflict between MOP:0000591 & MOP:0000713 in RXNO
StroemPhi May 10, 2022
b478c83
move "carbonyl oxidation to alkyne" to MOP properly
StroemPhi May 10, 2022
d2a8879
move "[3+2] cycloaddition" to MOP
StroemPhi May 10, 2022
d9c03bd
add iao:ICE as parent for "'oxidation state'" (MOP:0005561)
StroemPhi May 10, 2022
ddf8b5b
move deprecated RXNO classes from MOP to RXNO
StroemPhi May 10, 2022
3d3d99d
delete MOP_0000627 in RXNO
StroemPhi May 10, 2022
5f01203
delete MOP_0000628 from RXNO
StroemPhi May 10, 2022
de1dab2
delete MOP_0000671 from RXNO but "cyclization" (MOP_0000561) as paren…
StroemPhi May 11, 2022
fc764ae
delete enolisation (with wrong ID) in RXNO but
StroemPhi May 11, 2022
25ad7d0
add header to mop_vs_rxno.tsv
StroemPhi May 11, 2022
6c333a6
Merge branch '27_importMOP_directly' of https://github.com/NFDI4Chem/…
StroemPhi May 11, 2022
4ec07aa
Update MOP_vs_RXNO.xlsx
StroemPhi May 12, 2022
06f3cdf
Merge pull request #21 from rsc-ontologies/master
StroemPhi May 19, 2022
276fdc2
delete parent MOP_0000800 from MOP_0000028
StroemPhi May 19, 2022
2ca0a4d
revert MOP_0000479 (acylation) being child and instead sibling of MOP…
StroemPhi May 19, 2022
d68c8f8
don't use axiomatization proposed in #27 on "oxidative cleavage" and …
StroemPhi May 19, 2022
ccb5a8f
keep longer labels from the previous RXNO duplicates
StroemPhi May 19, 2022
da7fe3c
fix wrong namespace annotation
StroemPhi May 19, 2022
baad263
update Protégé formatation
StroemPhi May 19, 2022
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Binary file added docs/#27_workfiles/MOP_vs_RXNO.xlsx
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4 changes: 4 additions & 0 deletions docs/#27_workfiles/README.md
Original file line number Diff line number Diff line change
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These two files where genereate as layed out in [27#issuecomment-1091415293](https://github.com/rsc-ontologies/rxno/issues/27#issuecomment-1091415293).
They were created to resolve the [issue#72](https://github.com/rsc-ontologies/rxno/issues/27) with some classes of MOP being declared twice, once in mop.owl and once in rxno.owl.
The detailed documentation of what has been done with each conflicting class in the PR draft #... is inside the Excel file.
The TSV thus records the *ID, label* and *SubclassOf axioms* of the conflicting MOP classes within *2022-02-01/mop.owl* & *2021-12-16/rxno.owl*
Empty file.
3,631 changes: 3,631 additions & 0 deletions docs/#27_workfiles/mop_vs_rxno.tsv

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39 changes: 39 additions & 0 deletions mop_odk/src/ontology/mop-odk.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
catalog_file: catalog-v001.xml
ci:
- github_actions
components: null
contact: null
contributors: null
create_obo_metadata: true
creators: null
description: None
edit_format: owl
id: mop
title: "Molecular Process Ontology"
github_org: rsc-ontologies
repo: rxno
report_fail_on: ERROR
edit_format: owl
export_formats:
- owl
- obo
- json
release_artefacts:
- base
- full
primary_release: full
import_group:
products:
- id: ro
module_type: slme
module_type_slme: BOT
slme_individuals: include
- id: bfo
module_type: mirror
- id: obi
module_type: custom
- id: iao
module_type: custom
- id: omo
module_type: mirror
robot_java_args: '-Xmx8G'
8 changes: 8 additions & 0 deletions src/catalog-v001.xml
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/mop/releases/2022-02-01/mop.owl" uri="http://purl.obolibrary.org/obo/mop.owl"/>
<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
<uri id="Automatically generated entry, Timestamp=1650975684046" name="http://purl.obolibrary.org/obo/mop.owl" uri="mop-edit.owl"/>
<uri id="Automatically generated entry, Timestamp=1650975684046" name="http://purl.obolibrary.org/obo/rxno.obo.owl" uri="rxno-edit.owl"/>
</group>
</catalog>
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