update iao import #1700 #1754

stap-m · 2023-11-17T13:43:56Z

Summary of the discussion

Based on #1700 and #1755 and #1756 and #1651 and #1695 and #1689

remove OMO import since redundant
update iao import based on tidy oeo imports oeo-tools#4
update domains and ranges of imported object properties

Type of change (CHANGELOG.md)

Add

Automation

Closes #1755, #1700

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…1700

…testing #1700

…oeo-shared #1700

stap-m · 2023-11-28T08:47:25Z

Note: since we included has time stamp with hierarchy, we have its parent property has part imported twice, once by IAO and once by RO.

ToDo: fix that

EDIT: see OpenEnergyPlatform/oeo-tools#5 for the import procedure. For the immediate solution, I remove it in ro-extracted.owl

…ations to oeo-import-edits

stap-m · 2023-11-29T08:42:32Z

I just saw, the the newly imported journal article has two parents, report and pubclication. How do we deal with that? I'd vote for removing either of them and comment in oeo-import-edits.

…ools@af7bae9

This reverts commit cd385de.

stap-m · 2023-11-29T11:15:26Z

Todo:
clean oeo-import-edits. I'll do that in a separate issue once this PR is merged, for a better reviewability.

src/ontology/edits/oeo-import-edits.owl

l-emele · 2023-11-29T13:07:49Z

src/ontology/edits/oeo-import-edits.owl

@@ -35,6 +37,12 @@ Currently, it covers the `ro-extracted.owl`-file which is a subset of the Relati



+    <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>


I it is probably not the right line, but I noticed that editor note (IAO_0000116) has duplicate labels, one from BFO and one from IAO:

Yes, both contribute these annotation properties (there are several), since BFO imports them from iao obviously. With removing OMO, there are at least only doubled annotations left. I think, I won't fix that in this PR, unfortunatetly :(

From todays oeo-dev-meeting: @areleu opened a feature request for ROBOT some time ago with this topic. ontodev/robot#1099

src/ontology/edits/catalog-v001.xml

src/ontology/edits/oeo-shared.omn

stap-m · 2023-11-29T13:39:12Z

I just saw, the the newly imported journal article has two parents, report and pubclication. How do we deal with that? I'd vote for removing either of them and comment in oeo-import-edits.

Thanks for the review. Any opinion on this @l-emele ?

…gyPlatform/ontology into feature-1700-iao-update

stap-m · 2023-11-30T10:24:35Z

I just saw, the the newly imported journal article has two parents, report and pubclication. How do we deal with that? I'd vote for removing either of them and comment in oeo-import-edits.

Thanks for the review. Any opinion on this @l-emele ?

From todays oeo-dev-meeting: try to skip the import of publication and have only the already imported class report as parent

areleu · 2023-11-30T16:19:50Z

I could not reproduce the extraction process 1 to 1, did you do some manual changes after extracting or am I missing something?

stap-m · 2023-11-30T18:20:55Z

I could not reproduce the extraction process 1 to 1, did you do some manual changes after extracting or am I missing something?

Can you specify the diffs? I ran the script pushed in this commit: OpenEnergyPlatform/oeo-tools@b1cd5d4 All other changes have been done in oeo-import-edits.

stap-m · 2023-12-01T08:15:30Z

I could not reproduce the extraction process 1 to 1, did you do some manual changes after extracting or am I missing something?

Can you specify the diffs? I ran the script pushed in this commit: OpenEnergyPlatform/oeo-tools@b1cd5d4 All other changes have been done in oeo-import-edits.

@areleu could you also review this PR OpenEnergyPlatform/oeo-tools#4 please.

areleu · 2023-12-01T08:33:57Z

I could not reproduce the extraction process 1 to 1, did you do some manual changes after extracting or am I missing something?

Can you specify the diffs? I ran the script pushed in this commit: OpenEnergyPlatform/oeo-tools@b1cd5d4 All other changes have been done in oeo-import-edits.

Just checked it out, and I could reproduce the imports

I could not reproduce the extraction process 1 to 1, did you do some manual changes after extracting or am I missing something?

Can you specify the diffs? I ran the script pushed in this commit: OpenEnergyPlatform/oeo-tools@b1cd5d4 All other changes have been done in oeo-import-edits.

@areleu could you also review this PR OpenEnergyPlatform/oeo-tools#4 please.

I guess this check works as validation of this too.

add updated iao-extracted for testing #1700

40eb756

github-actions bot added the oeo-shared changes the oeo-shared module label Nov 17, 2023

stap-m added 2 commits November 17, 2023 15:46

remove omo-import from oeo-shared for testing #1700

4904ffa

import iao-extracted and ro-extracted to oeo-import-edits for testing #…

5fba8a3

…1700

github-actions bot added the oeo.omn changes the oeo.omn -module label Nov 17, 2023

remove oeo-import-edits from oeo.omn and import it to oeo-shared for …

cd21d09

…testing #1700

stap-m mentioned this pull request Nov 20, 2023

tidy oeo imports OpenEnergyPlatform/oeo-tools#4

Merged

8 tasks

stap-m added 3 commits November 21, 2023 09:55

undo changes in oeo-import-edits #1700

e54c5cd

add subclassof to information content entity in oeo-import-edits #1700

597a97d

add domain to is about in oeo-import-edits #1700

8a09cea

This was referenced Nov 21, 2023

OEO Import Structures #1756

Open

Update IAO imports #1700

Closed

stap-m added 2 commits November 23, 2023 12:12

remove direct import of bfo to oeo.omn since indirectly imported via …

f3de88b

…oeo-shared #1700

add further terms to iao-extracted based on #1700

42c6448

stap-m added 2 commits November 28, 2023 17:16

remove has part from ro-extracted

fc34336

remove remnant annotations from has part and shift oeo-specific annot…

c0a8baa

…ations to oeo-import-edits

l-emele mentioned this pull request Nov 28, 2023

check classification of policy #1684

Closed

5 tasks

stap-m added 5 commits November 29, 2023 09:49

update iao import once again based on commit OpenEnergyPlatform/oeo-t…

4049903

…ools@af7bae9

add domain and editor note to has time stamp

534c12e

update changelog

cd385de

Revert "update changelog"

530282c

This reverts commit cd385de.

update changelog

1c3314d

stap-m marked this pull request as ready for review November 29, 2023 10:07

stap-m requested review from l-emele, areleu, nelekoehler and h-spinde November 29, 2023 10:07

stap-m self-assigned this Nov 29, 2023

Merge branch 'dev' into feature-1700-iao-update

d193519

l-emele reviewed Nov 29, 2023

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stap-m added 3 commits November 29, 2023 20:10

delete omo-extracted

670622b

remove local path and outdated imports from catalog

3f8bb8c

Merge branch 'feature-1700-iao-update' of https://github.com/OpenEner…

2e28f60

…gyPlatform/ontology into feature-1700-iao-update

stap-m added 2 commits November 30, 2023 11:58

update iao-extracted with journal article imported without hierarchy

9d784db

annotate journal article in oeo-import-edits

d3f669a

areleu approved these changes Dec 1, 2023

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stap-m merged commit 874bbc0 into dev Dec 1, 2023
4 checks passed

stap-m deleted the feature-1700-iao-update branch December 1, 2023 08:38

stap-m mentioned this pull request Dec 5, 2023

[meta] review RO imports and (conservative?) extensions #1783

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update iao import #1700 #1754

update iao import #1700 #1754

stap-m commented Nov 17, 2023 •

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stap-m commented Dec 1, 2023

areleu commented Dec 1, 2023

		@@ -35,6 +37,12 @@ Currently, it covers the `ro-extracted.owl`-file which is a subset of the Relati



		<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->

		<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>

update iao import #1700 #1754

update iao import #1700 #1754

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stap-m commented Nov 17, 2023 • edited Loading

Summary of the discussion

Type of change (CHANGELOG.md)

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