Merge pull request #438 from rctauber/report_feedback

Report query updates based on feedback

docs/Makefile

@@ -14,7 +14,7 @@
 ### Configuration
 
 # Collect the list of query files for report.
-REPORT_QUERIES := $(wildcard ../robot-core/src/main/resources/queries/*.rq)
+REPORT_QUERIES := $(wildcard ../robot-core/src/main/resources/report_queries/*.rq)
 REPORT_DOCS := $(foreach x, $(REPORT_QUERIES), report_queries/$(notdir $(basename $(x))).md)
 
 
@@ -29,7 +29,7 @@ report_queries:
 	mkdir -p $@
 
 # Convert each SPARQL file to a Markdown file.
-report_queries/%.md: ../robot-core/src/main/resources/queries/%.rq | report_queries
+report_queries/%.md: ../robot-core/src/main/resources/report_queries/%.rq | report_queries
 	awk '/^PREFIX/ && !x {print "```sparql"; x=1} 1' $< \
 	| sed 's/^#//' \
 	| sed 's/^ //' \

docs/report_queries/annotation_whitespace.md

@@ -1,15 +1,14 @@
 # Annotation Whitespace
 
-Problem: An annotation has leading or trailing whitespace, usually a single space.
+**Problem:** An annotation has leading or trailing whitespace, usually a single space.
 
-Solution: Re-format the annotation to remove additional whitespace.
+**Solution:** Re-format the annotation to remove additional whitespace.
 
 ```sparql
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  {?property a owl:AnnotationProperty .
   ?entity ?property ?value .
   FILTER STRENDS(str(?value), " ")}
@@ -18,4 +17,5 @@ WHERE {
   ?entity ?property ?value .
   FILTER STRSTARTS(str(?value), " ")}
 }
+ORDER BY ?entity
 ```

docs/report_queries/deprecated_class_reference.md

@@ -1,34 +1,32 @@
 # Deprecated Class Reference
 
-Problem: A deprecated class is used in a logical axiom. A deprecated class can be the child of another class (e.g. ObsoleteClass), but it cannot have children or be used in blank nodes or equivalent class statements. Additionally, a deprecated class should not have any equivalent classes or anonymous parents.
+**Problem:** A deprecated class is used in a logical axiom. A deprecated class can be the child of another class (e.g. ObsoleteClass), but it cannot have children or be used in blank nodes or equivalent class statements. Additionally, a deprecated class should not have any equivalent classes or anonymous parents.
 
-Solution: Replace deprecated class.
+**Solution:** Replace deprecated class.
 
 ```sparql
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  {
   VALUES ?property {
     owl:equivalentClass
     rdfs:subClassOf
   }
-  ?entity owl:deprecated ?dep .
-  FILTER regex(str(?dep), "true") .
+  ?entity owl:deprecated true .
   ?value ?property ?entity .
-  FILTER (!STRENDS(str(?property), "owl#deprecated"))
+  FILTER NOT EXISTS { ?entity rdfs:subClassOf oboInOwl:ObsoleteClass }
  }
  UNION
  {
-  ?entity owl:deprecated ?dep .
-  FILTER regex(str(?dep), "true") .
+  ?entity owl:deprecated true .
   ?entity ?property ?value .
-  FILTER (!STRENDS(str(?property), "owl#deprecated")) .
+  FILTER (?property != obo:IAO_0000231)
+  FILTER (?property != rdf:type)
   FILTER NOT EXISTS { ?property a owl:AnnotationProperty }
   FILTER NOT EXISTS {
     ?entity rdfs:subClassOf ?value .
@@ -38,6 +36,8 @@ WHERE {
     ?entity rdfs:subPropertyOf ?value .
     FILTER (!isBlank(?value))
   }
+  FILTER NOT EXISTS { ?entity rdfs:subClassOf oboInOwl:ObsoleteClass }
  }
 }
+ORDER BY ?entity
 ```

docs/report_queries/duplicate_definition.md

@@ -1,20 +1,25 @@
 # Duplicate Definition
 
-Problem: An entity shares an exact definition with another entity.
+**Problem:** An entity shares an exact definition or elucidation with another entity. Excludes deprecated entities.
 
-Solution: Update the definition to reflect the entities, or determine if the entities are the same.
+**OBO Foundry Principle:** [6 - Textual Definitions](http://obofoundry.org/principles/fp-006-textual-definitions.html)
+
+**Solution:** Update the definition to reflect the entities, or determine if the entities are the same.
 
 ```sparql
 PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
- VALUES ?property {obo:IAO_0000115}
- ?entity obo:IAO_0000115 ?value .
- ?entity2 obo:IAO_0000115 ?value .
- FILTER (?entity != ?entity2) .
+SELECT DISTINCT ?entity ?property ?value WHERE {
+ VALUES ?property { obo:IAO_0000115
+                    obo:IAO_0000600 }
+ ?entity ?property ?value .
+ ?entity2 ?property ?value .
+ FILTER NOT EXISTS { ?entity owl:deprecated true }
+ FILTER NOT EXISTS { ?entity2 owl:deprecated true }
+ FILTER (?entity != ?entity2)
  FILTER (!isBlank(?entity))
 }
-ORDER BY ?value
+ORDER BY DESC(UCASE(str(?value)))
 ```

docs/report_queries/duplicate_exact_synonym.md

@@ -1,22 +1,25 @@
 # Duplicate Exact Synonym
 
-Problem: Two entities share an exact synonym. This causes ambiguity.
+**Problem:** Two entities share an exact synonym. This causes ambiguity. Excludes deprecated entities.
 
-Solution: Avoid ambiguity by assigning unique exact synonyms or changing the exact synonym to a different annotation (e.g. broad synonym).
+**Solution:** Avoid ambiguity by assigning unique exact synonyms or changing the exact synonym to a different annotation (e.g. broad synonym).
 
 ```sparql
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  VALUES ?property {
    obo:IAO_0000118
    oboInOwl:hasExactSynonym
  }
- ?entity ?property ?value .
+ ?entity ?property ?value.
  ?entity2 ?property ?value .
+ FILTER NOT EXISTS { ?entity owl:deprecated true }
+ FILTER NOT EXISTS { ?entity2 owl:deprecated true }
  FILTER (?entity != ?entity2)
 }
+ORDER BY DESC(UCASE(str(?value)))
 ```

docs/report_queries/duplicate_label.md

@@ -1,19 +1,20 @@
 # Duplicate Label
 
-Problem: Two different subjects have been assigned the same label. This causes ambiguity.
+**Problem:** Two different subjects have been assigned the same label. This causes ambiguity.
 
-Solution: Avoid ambiguity by assigning distinct labels to each subject.
+**OBO Foundry Principle:** [12 - Naming Conventions](http://www.obofoundry.org/principles/fp-012-naming-conventions.html)
+
+**Solution:** Avoid ambiguity by assigning distinct labels to each subject.
 
 ```sparql
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  VALUES ?property {rdfs:label}
  ?entity ?property ?value .
  ?entity2 ?property ?value .
  FILTER (?entity != ?entity2)
  FILTER (!isBlank(?entity))
 }
-ORDER BY ?value
+ORDER BY DESC(UCASE(str(?value)))
 ```

docs/report_queries/duplicate_label_synonym.md

@@ -1,24 +1,27 @@
 # Duplicate Label-Synonym
 
-Problem: An entity shares a label with an exact synonym. This causes ambiguity.
+**Problem:** An entity shares a label with an exact synonym. This causes ambiguity. Excludes deprecated entities.
 
-Solution: Avoid ambiguity by changing the exact synonym or label.
+**Solution:** Avoid ambiguity by changing the exact synonym or label.
 
 ```sparql
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  VALUES ?property {
    obo:IAO_0000118
    oboInOwl:hasExactSynonym
    oboInOwl:hasRelatedSynonym
    oboInOwl:hasNarrowSynonym
    oboInOwl:hasBroadSynonym
  }
+ FILTER NOT EXISTS { ?entity owl:deprecated true }
+ FILTER NOT EXISTS { ?entity2 owl:deprecated true }
  ?entity rdfs:label ?value .
- ?entity ?property ?value
+ ?entity ?property ?value .
 }
+ORDER BY ?entity
 ```

docs/report_queries/duplicate_scoped_synonym.md

@@ -1,16 +1,15 @@
 # Duplicate Scoped Synonyms
 
-Problem: An entity has duplicate synonyms with different properties (e.g. the same broad and related synonym). This causes ambiguity.
+**Problem:** An entity has duplicate synonyms with different properties (e.g. the same broad and related synonym). This causes ambiguity.
 
-Solution: Remove duplicate synonyms and determine the correct scope.
+**Solution:** Remove duplicate synonyms and determine the correct scope.
 
 ```sparql
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  VALUES ?property {
    obo:IAO_0000118
    oboInOwl:hasExactSynonym

docs/report_queries/equivalent_pair.md

@@ -1,16 +1,16 @@
 # Equivalent Pair
 
-Problem: An entity has a one-to-one equivalency with another entity. This may be intentional (assuming it is not annotated with `is_inferred true`), or it may be due to incorrect logic and the reasoner asserting the equivalency.
+**Problem:** An entity has a one-to-one equivalency with another entity. This may be intentional (assuming it is not annotated with `is_inferred true`), or it may be due to incorrect logic and the reasoner asserting the equivalency.
 
-Solution: Ensure the reasoner is not incorrectly inferring equivalency. If so, update the logical axioms.
+**Solution:** Ensure the reasoner is not incorrectly inferring equivalency. If so, update the logical axioms.
 
 ```sparql
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  VALUES ?property {owl:equivalentClass}
  ?entity ?property ?value .
  FILTER (!isBlank(?value))
 }
+ORDER BY ?entity
 ```

docs/report_queries/index.md

@@ -21,9 +21,12 @@ See [`report`](../report) for more details.
 | [missing definition](missing_definition)  | WARN
 | [missing label](missing_label)  | ERROR
 | [missing obsolete label](missing_obsolete_label)  | WARN
+| [missing ontology description](missing_ontology_description)  | ERROR
+| [missing ontology license](missing_ontology_license)  | ERROR
+| [missing ontology title](missing_ontology_title)  | ERROR
 | [missing superclass](missing_superclass)  | INFO
 | [misused obsolete label](misused_obsolete_label)  | ERROR
 | [multiple asserted superclasses](multiple_asserted_superclasses)  | WARN
 | [multiple definitions](multiple_definitions)  | ERROR
+| [multiple equivalent classes](multiple_equivalent_classes)  | ERROR
 | [multiple labels](multiple_labels)  | ERROR
-| [ontology metadata](ontology_metadata)  | ERROR

docs/report_queries/invalid_xref.md

@@ -1,18 +1,18 @@
 # Invalid Xref
 
-Problem: A database_cross_reference is not in CURIE format.
+**Problem:** A database_cross_reference is not in CURIE format.
 
-Solution: Replace the reference with a [CURIE](https://www.w3.org/TR/2010/NOTE-curie-20101216/).
+**Solution:** Replace the reference with a [CURIE](https://www.w3.org/TR/2010/NOTE-curie-20101216/).
 
 ```sparql
 PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  VALUES ?property {oboInOwl:hasDbXref}
  ?entity ?property ?value .
- FILTER (!regex(?value, "^[a-z|A-Z|_|0-9]*:(?!$)\\S*$"))
+ FILTER (!regex(?value, "^[a-z|A-Z|_|\\-|0-9]*:(?!$)\\S*$"))
  FILTER (!isBlank(?entity))
 }
+ORDER BY ?entity
 ```

docs/report_queries/label_formatting.md

@@ -1,15 +1,14 @@
 # Label Formatting
 
-Problem: Formatting characters are used in a label. This may cause issues when trying to reference the entity by label.
+**Problem:** Formatting characters are used in a label. This may cause issues when trying to reference the entity by label.
 
-Solution: Remove formatting characters from label.
+**Solution:** Remove formatting characters from label.
 
 ```sparql
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  {
   VALUES ?property {rdfs:label}
   ?entity ?property ?value .
@@ -22,4 +21,5 @@ WHERE {
   FILTER regex(?value, "\t")
  }
 }
+ORDER BY ?entity
 ```

docs/report_queries/label_whitespace.md

@@ -1,15 +1,14 @@
 # Label Whitespace
 
-Problem: A label has leading or trailing whitespace. This may cause issues when trying to reference the entity by label.
+**Problem:** A label has leading or trailing whitespace. This may cause issues when trying to reference the entity by label.
 
-Solution: Remove the additional whitespace.
+**Solution:** Remove the additional whitespace.
 
 ```sparql
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
+SELECT DISTINCT ?entity ?property ?value WHERE {
  {
   VALUES ?property {rdfs:label}
   ?entity ?property ?value .
@@ -22,4 +21,5 @@ WHERE {
   FILTER STRSTARTS(str(?value), " ")
  }
 }
+ORDER BY ?entity
 ```

docs/report_queries/lowercase_definition.md

@@ -1,16 +1,17 @@
 # Lowercase Definition
 
-Problem: A definition does not begin with an uppercase letter. This may be indicative of inconsistent formatting.
+**Problem:** A definition or elucidation does not begin with an uppercase letter. This may be indicative of inconsistent formatting.
 
-Solution: Capitalize the first letter of the definition, or disregard this INFO.
+**Solution:** Capitalize the first letter of the definition, or disregard this INFO.
 
 ```sparql
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 
-SELECT DISTINCT ?entity ?property ?value
-WHERE {
- VALUES ?property {obo:IAO_0000115}
+SELECT DISTINCT ?entity ?property ?value WHERE {
+ VALUES ?property { obo:IAO_0000115
+                    obo:IAO_0000600 }
  ?entity ?property ?value .
  FILTER (!regex(?value, "^[A-Z]"))
 }
+ORDER BY ?entity
 ```