From 65bb0c93250665a71b7c7ac36fd411ab3fffb92d Mon Sep 17 00:00:00 2001
From: oliviahobai <119642653+oliviahobai@users.noreply.github.com>
Date: Mon, 2 Sep 2024 17:05:17 -0400
Subject: [PATCH 1/3] Create no-orphaned-subclasses.sparql

There is probably some trouble with lines 10-11. When it's convenient, could somebody else look at this file, please?
---
 .../sparql/no-orphaned-subclasses.sparql      | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .github/deployment/sparql/no-orphaned-subclasses.sparql

diff --git a/.github/deployment/sparql/no-orphaned-subclasses.sparql b/.github/deployment/sparql/no-orphaned-subclasses.sparql
new file mode 100644
index 0000000..a327d96
--- /dev/null
+++ b/.github/deployment/sparql/no-orphaned-subclasses.sparql
@@ -0,0 +1,21 @@
+# Title: 
+#     No Orphaned Subclasses
+# Constraint Description: 
+#     All classes must have some parent class. The only result otherwise should be “entity”.
+# Severity:
+#     Warning
+# Author:
+#	 github.com/swartik
+
+Severity:
+    (select "Warning" or "Error")
+
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?cls
+WHERE {
+  ?cls a owl:Class
+  FILTER isIRI(?cls)
+  FILTER NOT EXISTS { ?cls rdfs:subClassOf ?supercls }
+}

From 51efd29ffae96241e4cb9235feba356f4c61f0d5 Mon Sep 17 00:00:00 2001
From: oliviahobai <119642653+oliviahobai@users.noreply.github.com>
Date: Tue, 3 Sep 2024 18:24:41 -0400
Subject: [PATCH 2/3] Update no-orphaned-subclasses.sparql

Based on the updates provided by @swartik, thank you. Tell me if there are any remaining edits that need to be made.
---
 .github/deployment/sparql/no-orphaned-subclasses.sparql | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/deployment/sparql/no-orphaned-subclasses.sparql b/.github/deployment/sparql/no-orphaned-subclasses.sparql
index a327d96..07c185c 100644
--- a/.github/deployment/sparql/no-orphaned-subclasses.sparql
+++ b/.github/deployment/sparql/no-orphaned-subclasses.sparql
@@ -1,15 +1,12 @@
 # Title: 
 #     No Orphaned Subclasses
 # Constraint Description: 
-#     All classes must have some parent class. The only result otherwise should be “entity”.
+#     All CCO classes must have a superclass.
 # Severity:
-#     Warning
+#     Error
 # Author:
 #	 github.com/swartik
 
-Severity:
-    (select "Warning" or "Error")
-
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
@@ -18,4 +15,5 @@ WHERE {
   ?cls a owl:Class
   FILTER isIRI(?cls)
   FILTER NOT EXISTS { ?cls rdfs:subClassOf ?supercls }
+  FILTER (?cls != <http://purl.obolibrary.org/obo/BFO_0000001>)
 }

From f512eaf41ff1dbd3a8efd05cf0a0573ba95d2c84 Mon Sep 17 00:00:00 2001
From: oliviahobai <119642653+oliviahobai@users.noreply.github.com>
Date: Wed, 11 Sep 2024 12:55:55 -0400
Subject: [PATCH 3/3] Change no-orphaned-subclasses.sparql to
 all-CCO-classes-have-a-BFO-superclass

This is a query designed by @neilotte after an issue originally raised by @swartik .
---
 .../all-CCO-classes-have-a-BFO-superclass     | 19 +++++++++++++++++++
 .../sparql/no-orphaned-subclasses.sparql      | 19 -------------------
 2 files changed, 19 insertions(+), 19 deletions(-)
 create mode 100644 .github/deployment/sparql/all-CCO-classes-have-a-BFO-superclass
 delete mode 100644 .github/deployment/sparql/no-orphaned-subclasses.sparql

diff --git a/.github/deployment/sparql/all-CCO-classes-have-a-BFO-superclass b/.github/deployment/sparql/all-CCO-classes-have-a-BFO-superclass
new file mode 100644
index 0000000..eeea2f5
--- /dev/null
+++ b/.github/deployment/sparql/all-CCO-classes-have-a-BFO-superclass
@@ -0,0 +1,19 @@
+# Title: 
+#    No CCO Class Should Be Outside the BFO Hierarchy
+# Constraint Description: 
+#     All CCO classes must have a BFO superclass.
+# Severity:
+#     Error
+# Author:
+#	 github.com/neilotte
+
+PREFIX owl: http://www.w3.org/2002/07/owl#
+PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#
+
+SELECT DISTINCT ?class ?label
+WHERE {
+?class a owl:Class .
+FILTER contains(str(?class),"http://www.ontologyrepository.com/CommonCoreOntologies/")
+FILTER NOT EXISTS {?class rdfs:subClassOf+ http://purl.obolibrary.org/obo/BFO_0000001 }
+OPTIONAL {?class rdfs:label ?label}
+}
diff --git a/.github/deployment/sparql/no-orphaned-subclasses.sparql b/.github/deployment/sparql/no-orphaned-subclasses.sparql
deleted file mode 100644
index 07c185c..0000000
--- a/.github/deployment/sparql/no-orphaned-subclasses.sparql
+++ /dev/null
@@ -1,19 +0,0 @@
-# Title: 
-#     No Orphaned Subclasses
-# Constraint Description: 
-#     All CCO classes must have a superclass.
-# Severity:
-#     Error
-# Author:
-#	 github.com/swartik
-
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-SELECT DISTINCT ?cls
-WHERE {
-  ?cls a owl:Class
-  FILTER isIRI(?cls)
-  FILTER NOT EXISTS { ?cls rdfs:subClassOf ?supercls }
-  FILTER (?cls != <http://purl.obolibrary.org/obo/BFO_0000001>)
-}