Change dc:creator to dcterms:contributor #731

wdduncan · 2023-06-23T17:21:33Z

No description provided.

…arker set

…ease

wdduncan · 2023-06-23T19:20:12Z

@matentzn @cthoyt @anitacaron the qc is failing b/c of non-conforming values for the created_by annotation.
E.g., here is a list produced after running make test.

FAIL Rule ../sparql/term-editor-uri-violation.sparql: 33 violation(s)
subject,orcid
http://purl.obolibrary.org/obo/RO_0002207,has developmental precursor
http://purl.obolibrary.org/obo/valid_for_go_gp2term,pg
http://purl.obolibrary.org/obo/valid_for_go_annotation_extension,pg
http://purl.obolibrary.org/obo/RO_0002020,dos
http://purl.obolibrary.org/obo/RO_0012002,pg
http://purl.obolibrary.org/obo/RO_0002021,dos
http://purl.obolibrary.org/obo/RO_0012012,pg
http://purl.obolibrary.org/obo/RO_0002023,dos
http://purl.obolibrary.org/obo/RO_0002019,dos
http://purl.obolibrary.org/obo/RO_0012004,pg
http://purl.obolibrary.org/obo/RO_0002026,dos
http://purl.obolibrary.org/obo/RO_0012001,pg
http://purl.obolibrary.org/obo/RO_0012005,pg
http://purl.obolibrary.org/obo/RO_0002029,dos
http://purl.obolibrary.org/obo/RO_0002017,dos
http://purl.obolibrary.org/obo/RO_0002015,dos
http://purl.obolibrary.org/obo/RO_0012006,pg
http://purl.obolibrary.org/obo/RO_0002018,dos
http://purl.obolibrary.org/obo/RO_0012003,pg
http://purl.obolibrary.org/obo/RO_0002022,dos
http://purl.obolibrary.org/obo/valid_for_go_ontology,pg
http://purl.obolibrary.org/obo/RO_0012007,pg
http://purl.obolibrary.org/obo/RO_0012008,pg
http://purl.obolibrary.org/obo/RO_0002024,dos
http://purl.obolibrary.org/obo/RO_0002025,dos
http://purl.obolibrary.org/obo/RO_0002013,dos
http://purl.obolibrary.org/obo/RO_0012000,pg
http://purl.obolibrary.org/obo/RO_0012009,pg
http://purl.obolibrary.org/obo/RO_0002014,dos
http://purl.obolibrary.org/obo/RO_0012010,pg
http://purl.obolibrary.org/obo/valid_for_gocam,pg
http://purl.obolibrary.org/obo/RO_0012011,pg
http://purl.obolibrary.org/obo/RO_0002016,dos

balhoff

It looks like some xsd:dateTime datatypes were lost. Also a bunch of xsd:strings, but that doesn't matter—was it on purpose?

How does this relate to 'has roost'? It seems like a general cleanup.

src/ontology/ro-edit.owl

wdduncan · 2023-06-23T20:15:09Z

@balhoff when I changed the annotation property I didn't specify the datatype. I assumed the datatype would carry over to the new annotation. My mistake :(

This PR originated from my oversight of merging NTR: has roost prior to the qc checks finishing :(

gouttegd · 2023-06-26T14:55:30Z

@wdduncan Mind if I commit directly to this PR to fix the remaining QC issues?

Fix two annotations that were broken as part of #672: a removed label and an exact synonym that had been changed into another annotation.

Somehow in #672, some "created_by" annotations were reverted to their "pre-ORCID" values, so we fix them again.

wdduncan · 2023-06-26T19:46:57Z

@gouttegd I don't mind at all!
Thanks!

gouttegd · 2023-06-26T21:34:10Z

Done and the CI checks now pass.

cthoyt · 2023-06-26T21:34:51Z

Please please please do not merge this until the commit history on the main branch is fixed

wdduncan · 2023-06-26T21:42:48Z

What needs to be fixed? I'm not following.

gouttegd · 2023-06-26T21:47:18Z

@cthoyt The point of this PR is precisely to fix the breakage that was introduced by the merging of #672.

I agree that a hard reset to cancel #672 would be cleaner, but not now that the merge has occurred on the public master branch. Hard resets are good on a local repository to cancel commits that have never been published, but once they have been pushed on a public repo, it’s too late. Rewriting history on a public branch is a bad idea.

cthoyt · 2023-06-26T21:53:23Z

please see #732. @gouttegd either way, can you help remove all of the spurious diff in this PR? like tons of changes are totally irrelevant to the content update

I'm not sure I agree about rewriting history on a public branch. This only happened a day ago and I don't think that changing it will affect anyone who isn't already involved in PRs on this repo anyway

gouttegd · 2023-06-26T22:02:13Z

@cthoyt Those “spurious changes” are not irrelevant: they are here to fix the real spurious changes that were introduced in #672. Obviously, when you introduced a spurious change, the fix to it also looks like a spurious change.

Note that if you go the #732 route and reset the main branch to before #672 was merged, then this PR becomes irrelevant, so I don’t know why your last item in the description of #732 is to ”fix #731”.

(I am personally opposed to any form of history re-writing on a public repo. That being said, I don’t know what is the OBO policy on the matter – if even there is one –, so if nobody else has a problem with that, I won’t object ~~too much~~. All I want is to fix the master branch so that I can then update and merge #709.)

wdduncan · 2023-06-26T22:04:47Z

All I want is to fix the master branch so that I can then update and merge #709.

That is what is most important. Github purity is secondary to do this.

gouttegd · 2023-06-26T22:06:47Z

This only happened a day ago and I don't think that changing it will affect anyone who isn't already involved in PRs on this repo anyway

#672 was merged 3 days ago. Hard-resetting the master branch to before it was merged will affect anyone who has updated their local copy since then. That’s reason enough for not doing so, in my opinion.

wdduncan · 2023-06-27T12:16:33Z

Thanks for your help @balhoff and @gouttegd !

anitacaron · 2023-06-28T09:07:19Z

src/ontology/ro-edit.owl

+Declaration(Class(obo:CARO_0000000))
+Declaration(Class(obo:CARO_0000003))
+Declaration(Class(obo:CARO_0000006))
+Declaration(Class(obo:CARO_0000007))
+Declaration(Class(obo:CARO_0001001))
+Declaration(Class(obo:CARO_0001010))
+Declaration(Class(obo:CARO_0010000))


Still, have to redo some changes! No CARO is imported anymore.

change dc:creator to dcterms:contributor

77e9e1b

wdduncan changed the title ~~change dc:creator to dcterms:contributor~~ 'has roost' change dc:creator to dcterms:contributor Jun 23, 2023

wdduncan added 14 commits June 23, 2023 13:25

change orcid to https

a8ea295

change orcid to https for has phenotype or disease

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change annotation to dcterms:creator for nominally disjoint with

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change dc:creator to dcterms:creator for is antagonist of

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change dc:contributor to dcterms:contributor for has characterizing m…

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…arker set

change dc:creator to dcterms:creator for is inverse agonist of

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change dc:contributor to dcterms:contributor for has disease

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change dc:contributor to dcterms:contributor for has phenotype or dis…

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…ease

change dc:creator to dcterms:creator for is agonist of

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change dc:date to dcterms:date for has phenotype or disease

cd4262a

change dc:date to dcterms:date for has exposure medium

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change dc:date to dcterms:date for has roost

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change dc:title to dcterms:title

c3c516d

change dc:description to dcterm:description for ontology

cd6d111

wdduncan self-assigned this Jun 23, 2023

wdduncan requested review from anitacaron, matentzn and balhoff June 23, 2023 19:20

balhoff requested changes Jun 23, 2023

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add xsd:dateTime datatype to dcterms:date

d767ca0

gouttegd mentioned this pull request Jun 26, 2023

Fix BFO incompatibility #709

Merged

gouttegd added 2 commits June 26, 2023 16:20

Fix broken annotations.

b9b2386

Fix two annotations that were broken as part of #672: a removed label and an exact synonym that had been changed into another annotation.

Fix "created_by" annotations.

6d7e155

Somehow in #672, some "created_by" annotations were reverted to their "pre-ORCID" values, so we fix them again.

cthoyt mentioned this pull request Jun 26, 2023

Fix broken commit history and dangerous project settings #732

Closed

balhoff approved these changes Jun 27, 2023

View reviewed changes

gouttegd merged commit 5f05336 into master Jun 27, 2023
1 check passed

wdduncan deleted the fix-dc-creator-for-has-roost branch June 27, 2023 12:16

anitacaron reviewed Jun 28, 2023

View reviewed changes

anitacaron changed the title ~~'has roost' change dc:creator to dcterms:contributor~~ Change dc:creator to dcterms:contributor Jun 28, 2023

gouttegd mentioned this pull request Jun 28, 2023

Revert previous committed changes made in PR #672 and add missing axioms for has roost #730

Merged

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Change dc:creator to dcterms:contributor #731

Change dc:creator to dcterms:contributor #731

wdduncan commented Jun 23, 2023

wdduncan commented Jun 23, 2023

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wdduncan commented Jun 23, 2023

gouttegd commented Jun 26, 2023

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gouttegd commented Jun 26, 2023

cthoyt commented Jun 26, 2023

wdduncan commented Jun 26, 2023

gouttegd commented Jun 26, 2023

cthoyt commented Jun 26, 2023 •

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gouttegd commented Jun 26, 2023

wdduncan commented Jun 26, 2023

gouttegd commented Jun 26, 2023

wdduncan commented Jun 27, 2023

anitacaron Jun 28, 2023

Change dc:creator to dcterms:contributor #731

Change dc:creator to dcterms:contributor #731

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cthoyt commented Jun 26, 2023 •

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