added new object property has roost for issue #453 #672

diatomsRcool · 2023-01-18T14:42:03Z

Added new object property "has roost" as child of "has habitat" to address issue #453

cthoyt · 2023-03-02T23:12:41Z

src/ontology/ro-edit.owl

+AnnotationAssertion(dce:creator obo:RO_0008509 <http://orcid.org/0000-0002-2908-3327>)
+AnnotationAssertion(dce:date obo:RO_0008509 "2023-01-18T14:28:21Z"^^xsd:dateTime)
+AnnotationAssertion(oboInOwl:inSubset obo:RO_0008509 subsets:ro-eco)
+AnnotationAssertion(rdfs:comment obo:RO_0008509 "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.")


can you please give a concrete example with terms in existing OBO ontologies as subject/predicate annotated with IAO:0000112 (example of usage)

@cthoyt Do you mean just an example of how the term is used? E.g., "bird has roost some nest"

yeah, that would be great, as long as it gives explicit references to Bird and Nest using OBO PURLs

I don't think examples of usage have to use obo purls. Free text is fine. The purpose of "example of usage" is to provide extra context to disambiguate the term.

I am just hoping there is a realistic, demonstrable scenario in which this relation will get used... like if there are no IRIs corresponding to entities that would actually use this, then how can we be sure this will be a useful relation? This is for the benefit of future users, who without a concrete example might not be able to figure out how to use the relationship

This is for the benefit of future users, who without a concrete example might not be able to figure out how to use the relationship

I agree. That is the purpose of the annotation. We haven't required that OBO PURLs be used. See examples for example of usage in adjacent to, capable of, characteristic of, and many more ...

But @diatomsRcool if you can provide an example OBO PURLs, that would be nice.

wdduncan · 2023-03-29T16:07:42Z

@diatomsRcool I added habitat as the range of has habitat. This change should propagate down to has roost. Can you confirm the range should be habitat?

I also change the dc:creator annotation to dcterms:contributor. @cthoyt Is this the current protocol for term attribution.

cthoyt · 2023-03-29T16:08:54Z

I'm not sure if we have a concrete choice on which predicate should be used, other than it should be DCTERMS and not DCE. Contributor is probably fine!

wdduncan · 2023-03-29T16:11:49Z

Thanks @cthoyt
@diatomsRcool you can change to dcterms:creator if you wish. I was going off my experience with uberon.

wdduncan · 2023-06-20T15:44:09Z

@cthoyt @diatomsRcool I think this is ready to merge. Please let me know if you disagree.

cthoyt · 2023-06-20T15:52:19Z

sorry I don't want to hold this up, but there was never any engagement with my request to get a concrete example. Can someone please suggest an actual example? Like "this kind of bird has roost on this kind of tree"? @diatomsRcool do you understand what I am asking? I just want an actual example of a bird and a tree.

diatomsRcool · 2023-06-22T12:27:57Z

Flying foxes (Pteropus giganteus) roost in a banyan tree (Ficus benghalensis). Is that what you need?

cthoyt · 2023-06-22T13:21:31Z

@diatomsRcool yes, that's perfect! You can annotate that on to the property with http://purl.obolibrary.org/obo/IAO_0000112 (example of usage)

wdduncan · 2023-06-23T13:35:52Z

@diatomsRcool I will merge after you provide the example of usage.

cthoyt · 2023-06-23T16:17:28Z

src/ontology/ro-edit.owl

-Import(<http://purl.obolibrary.org/obo/ro/imports/uberon_import.owl>)
-Import(<http://purl.obolibrary.org/obo/ro/imports/obi_import.owl>)
-Annotation(dc:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en)
+Import(<http://purl.obolibrary.org/obo/ro/annotations.owl>)


It would be important to resolve all of these spurious changes before finishing the PR

I'll update the branch from master.

I have no idea why that happened

This branch started before we changed the repository to use the ODK structure.

cthoyt · 2023-06-23T17:00:21Z

@wdduncan it seems you’ve merged before QC was passing, I would suggest immediately reverting this and @matentzn fixing the branch protection rules

wdduncan · 2023-06-23T17:05:53Z

@cthoyt Yes ... I did :(

I think the the violation concerns the use of dc elements.

Here is the sparql.

This reverts commit e16e307.

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.

* change dc:creator to dcterms:contributor * change orcid to https * change orcid to https for has phenotype or disease * change annotation to dcterms:creator for nominally disjoint with * change dc:creator to dcterms:creator for is antagonist of * change dc:contributor to dcterms:contributor for has characterizing marker set * change dc:creator to dcterms:creator for is inverse agonist of * change dc:contributor to dcterms:contributor for has disease * change dc:contributor to dcterms:contributor for has phenotype or disease * change dc:creator to dcterms:creator for is agonist of * change dc:date to dcterms:date for has phenotype or disease * change dc:date to dcterms:date for has exposure medium * change dc:date to dcterms:date for has roost * change dc:title to dcterms:title * change dc:description to dcterm:description for ontology * add xsd:dateTime datatype to dcterms:date * Fix broken annotations. 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. Somehow in #672, some "created_by" annotations were reverted to their "pre-ORCID" values, so we fix them again. --------- Co-authored-by: Damien Goutte-Gattat <dpg44@cam.ac.uk>

…oms for `has roost` (#730) * Revert "added new object property has roost for issue #453 (#672)" This reverts commit e16e307. * add back domain and range to `has roost` --------- Co-authored-by: Anita Caron <anitacaron@users.noreply.github.com>

added new object property has roost for issue #453

566eb46

diatomsRcool requested a review from wdduncan January 18, 2023 14:42

cthoyt reviewed Mar 2, 2023

View reviewed changes

wdduncan added 3 commits March 29, 2023 09:34

add habitat to other_import to be used as domain/range in relations

a722436

change range of to

952cbbc

change dc:creator to dcterms:contributor

ad439b1

wdduncan and others added 7 commits March 30, 2023 10:33

remove habitat from other_imports

15e1380

update branch with master

ecc9176

add "habitat" it envo_terms

b629fe0

fix dc/dce confusions

f00d557

add habitat class using ODK

a2e82f8

Update ro-edit.owl

33bed46

Delete other_import.owl

6ef9d13

anitacaron assigned diatomsRcool Jun 12, 2023

wdduncan added 3 commits June 20, 2023 11:35

merge in updates from master

ad6d846

add domain of organism

c34e8bf

add range habitat

a3eac0e

wdduncan approved these changes Jun 20, 2023

View reviewed changes

adding example of usage for has roost

875a457

cthoyt reviewed Jun 23, 2023

View reviewed changes

Merge branch 'master' into thessen-1

3f63c09

anitacaron requested a review from wdduncan June 23, 2023 16:32

wdduncan merged commit e16e307 into master Jun 23, 2023

wdduncan deleted the thessen-1 branch June 23, 2023 16:58

wdduncan restored the thessen-1 branch June 23, 2023 17:01

wdduncan added a commit that referenced this pull request Jun 23, 2023

Revert "added new object property has roost for issue #453 (#672)"

9c36a51

This reverts commit e16e307.

wdduncan mentioned this pull request Jun 23, 2023

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

Merged

wdduncan deleted the thessen-1 branch June 23, 2023 17:22

wdduncan mentioned this pull request Jun 23, 2023

Change dc:creator to dcterms:contributor #731

Merged

gouttegd mentioned this pull request Jun 26, 2023

Fix BFO incompatibility #709

Merged

gouttegd added a commit that referenced this pull request Jun 26, 2023

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.

gouttegd added a commit that referenced this pull request Jun 26, 2023

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

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added new object property has roost for issue #453 #672

added new object property has roost for issue #453 #672

diatomsRcool commented Jan 18, 2023

cthoyt Mar 2, 2023

wdduncan Mar 29, 2023

cthoyt Mar 29, 2023

wdduncan Mar 29, 2023

cthoyt Mar 29, 2023

wdduncan Mar 29, 2023

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diatomsRcool commented Jun 22, 2023

cthoyt commented Jun 22, 2023 •

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wdduncan commented Jun 23, 2023

cthoyt Jun 23, 2023

anitacaron Jun 23, 2023

diatomsRcool Jun 23, 2023

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cthoyt commented Jun 23, 2023

wdduncan commented Jun 23, 2023

added new object property has roost for issue #453 #672

added new object property has roost for issue #453 #672

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diatomsRcool commented Jan 18, 2023

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wdduncan commented Mar 29, 2023

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cthoyt commented Jun 23, 2023

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