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Exclude deprecated from lowercase_definition check #1224

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merged 4 commits into from
Nov 13, 2024
Merged

Exclude deprecated from lowercase_definition check #1224

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38df8b5
Exclude deprecated terms from lowercase_definition check
jamesaoverton Nov 12, 2024
74bfb1d
Update lowercase_definition doc
jamesaoverton Nov 12, 2024
8b91ae7
Update changelog, with fix
jamesaoverton Nov 12, 2024
b5f9c05
Add missing owl prefix
jamesaoverton Nov 12, 2024
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7 changes: 6 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,11 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

## Fixed
- Add missing filter for deprecated in lowercase_definition check [#1220]
- Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations [#1223]

## [1.9.7] - 2024-10-30

### Fixed
- Output inferred object property assertions using Whelk reasoner, by updating to Whelk 1.1.3. [#1121]
- Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations [#1223]

### Changed
- Update Whelk to 1.2.1 [#1221]
Expand Down Expand Up @@ -413,7 +416,9 @@ First official release of ROBOT!
[`validate`]: http://robot.obolibrary.org/validate
[`verify`]: http://robot.obolibrary.org/verify

[#1223]: https://github.com/ontodev/robot/pull/1223
[#1221]: https://github.com/ontodev/robot/pull/1221
[#1220]: https://github.com/ontodev/robot/issues/1220
[#1211]: https://github.com/ontodev/robot/pull/1211
[#1194]: https://github.com/ontodev/robot/pull/1194
[#1193]: https://github.com/ontodev/robot/pull/1193
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4 changes: 3 additions & 1 deletion docs/report_queries/lowercase_definition.md
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Expand Up @@ -7,14 +7,16 @@
**Solution:** Capitalize the first letter of the definition, or disregard this INFO.

```sparql
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?entity ?property ?value WHERE {
VALUES ?property { obo:IAO_0000115
obo:IAO_0000600 }
?entity ?property ?value .
FILTER (!regex(?value, "^[A-Z0-9]"))
FILTER NOT EXISTS { ?entity owl:deprecated true }
FILTER (!isBlank(?entity))
FILTER (!regex(?value, "^[A-Z0-9]"))
}
ORDER BY ?entity
```
4 changes: 3 additions & 1 deletion robot-core/src/main/resources/report_queries/lowercase_definition.rq
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Expand Up @@ -6,13 +6,15 @@
#
# **Solution:** Capitalize the first letter of the definition, or disregard this INFO.

PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?entity ?property ?value WHERE {
VALUES ?property { obo:IAO_0000115
obo:IAO_0000600 }
?entity ?property ?value .
FILTER (!regex(?value, "^[A-Z0-9]"))
FILTER NOT EXISTS { ?entity owl:deprecated true }
FILTER (!isBlank(?entity))
FILTER (!regex(?value, "^[A-Z0-9]"))
}
ORDER BY ?entity
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