From 167a948eab3bd956476808334b13c19750ba8cbb Mon Sep 17 00:00:00 2001
From: Anita Caron <anitac@ebi.ac.uk>
Date: Mon, 4 Apr 2022 06:11:15 -0300
Subject: [PATCH] Add obsolete report with replaced_by information (#2372)

* add sparql query

* add sparql check config
---
 src/ontology/Makefile                         |  2 +-
 src/ontology/uberon-odk.yaml                  |  1 +
 .../obsolete-replaced_by-violation.sparql     | 67 +++++++++++++++++++
 3 files changed, 69 insertions(+), 1 deletion(-)
 create mode 100644 src/sparql/obsolete-replaced_by-violation.sparql

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index 1fe4230a2d..842192dfa6 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -39,7 +39,7 @@ REPORT_FAIL_ON =            ERROR
 REPORT_LABEL =              
 REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
-SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor 
+SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by 
 SPARQL_EXPORTS =            basic-report 
 ODK_VERSION_MAKEFILE =      v1.3.0
 
diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml
index 2edf1907dc..d17438371e 100644
--- a/src/ontology/uberon-odk.yaml
+++ b/src/ontology/uberon-odk.yaml
@@ -98,6 +98,7 @@ robot_report:
     - illegal-annotation-property
     - taxon-range
     - orcid-contributor
+    - obsolete-replaced_by
   custom_sparql_exports:
     - basic-report
 owltools_memory: '20G'
diff --git a/src/sparql/obsolete-replaced_by-violation.sparql b/src/sparql/obsolete-replaced_by-violation.sparql
new file mode 100644
index 0000000000..9860902be6
--- /dev/null
+++ b/src/sparql/obsolete-replaced_by-violation.sparql
@@ -0,0 +1,67 @@
+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 replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
+
+SELECT DISTINCT ?entity ?property ?value ?replaced_by WHERE {
+  {
+   VALUES ?property {
+     rdfs:subClassOf
+   }
+   ?entity a owl:Class;
+           owl:deprecated true ;
+           ?property ?value .
+   OPTIONAL { ?entity replaced_by: ?replaced_by }
+   FILTER ( ?value NOT IN (oboInOwl:ObsoleteClass, owl:Thing) )
+  }
+  UNION
+  {
+   VALUES ?property {
+     owl:equivalentClass
+     owl:disjointWith
+   }
+   ?entity a owl:Class;
+           owl:deprecated true ;
+           ?property ?value .
+    OPTIONAL { ?entity replaced_by: ?replaced_by }
+  }
+  UNION
+  {
+     VALUES ?property {
+       rdfs:subClassOf
+       owl:equivalentClass
+       owl:disjointWith
+     }
+     ?entity a owl:Class;
+             owl:deprecated true .
+     ?value ?property ?entity .
+     OPTIONAL { ?entity replaced_by: ?replaced_by }
+  }
+  UNION
+  {
+   VALUES ?property {
+     owl:ObjectProperty
+     owl:DataProperty
+   }
+   ?entity a owl:Class ;
+           owl:deprecated true ;
+           ?property ?value .
+    OPTIONAL { ?entity replaced_by: ?replaced_by }
+  }
+  UNION
+  {
+   VALUES ?property {
+     owl:someValuesFrom
+     owl:allValuesFrom
+   }
+   ?value a owl:Class ;
+          owl:deprecated true .
+   ?rest a owl:Restriction ;
+         ?property ?value .
+   OPTIONAL { ?value replaced_by: ?replaced_by }
+   BIND("blank node" as ?entity)
+  }
+}
+ORDER BY ?entity
\ No newline at end of file