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Related to #1810 unresolvable IRIs #1854

Merged
2 commits merged into from
Feb 24, 2023
Merged

Related to #1810 unresolvable IRIs #1854

2 commits merged into from
Feb 24, 2023

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ghost
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@ghost ghost commented Feb 22, 2023

Related to #1810 unresolvable IRIs
assigned numeric IDs to native CL object properties

assign numeric IDs to native CL object properties
@ghost ghost self-assigned this Feb 22, 2023
@ghost ghost requested review from anitacaron, dosumis and balhoff February 22, 2023 10:56
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ghost commented Feb 22, 2023

QC appears to fail because two of the three renamed entities have an 'expand expression to' annotation, which is not permitted for terms with CL IRIs per ../sparql/illegal-annotation-property-violation.sparql:

FAIL Rule ../sparql/illegal-annotation-property-violation.sparql: 2 violation(s)
[32](https:/obophenotype/cell-ontology/actions/runs/4241973672/jobs/7372881034#step:4:33)
term,annotation
[33](https:/obophenotype/cell-ontology/actions/runs/4241973672/jobs/7372881034#step:4:34)
http://purl.obolibrary.org/obo/CL_4030046,http://purl.obolibrary.org/obo/IAO_0000424
[34](https:/obophenotype/cell-ontology/actions/runs/4241973672/jobs/7372881034#step:4:35)
http://purl.obolibrary.org/obo/CL_4030045,http://purl.obolibrary.org/obo/IAO_0000424

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ghost commented Feb 23, 2023

Thanks for reviewing, @balhoff.
@matentzn, can you comment on the QC failure noted above? Is there a reason why that annotation is blocked for CL terms?

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This failure gives me great peace of mind. All you need to do is edit the

../sparql/illegal-annotation-property-violation.sparql file and add the new property to the list of allowed properties. You can do this on this branch here, and assign me as a reviewer

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ghost commented Feb 24, 2023

Thanks, @matentzn. SPARQL file updated.
Why are some annotations blocked for CL terms?

@ghost ghost requested a review from matentzn February 24, 2023 08:58
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Looks great! Now QC should pass. Thanks!

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ghost commented Feb 24, 2023

Looks great! Now QC should pass. Thanks!

Why are some annotations blocked for CL terms?

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Generally, this solves two purposes:

  1. Make sure wrong annotations are not added accidentally (it's cheaper to list the allowed properties then to anticipate the millions of wrong combinations)
  2. make sure to avoid uncontrolled annotation proliferation. Like in a datamodel, we want adding annotations to be an explicitly sanctioned process by the CL editors committee and not something left to the discretion of individual taste.

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ghost commented Feb 24, 2023

Generally, this solves two purposes:
...

Thank you for the context and for the review!

@ghost ghost merged commit 69694c3 into master Feb 24, 2023
@ghost ghost deleted the 1810_fix-unresolvable-iris branch February 24, 2023 09:17
@ghost ghost mentioned this pull request Feb 24, 2023
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2 participants