From f719cd47e96e37667a6a92a66e66f08593471b1b Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sun, 17 Mar 2024 11:37:18 +0100
Subject: [PATCH 1/2] Added additional recognised prefixes (expected to be used
 by FOOPS)

---
 ontopy/ontology.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 02e1a217f..31fba7222 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -1004,15 +1004,17 @@ def save(
             # Make a copy of the owlready2 graph object to not mess with
             # owlready2 internals
             graph = rdflib.Graph()
-            graph_owlready2 = self.world.as_rdflib_graph()
-            for triple in graph_owlready2.triples((None, None, None)):
+            for triple in self.world.as_rdflib_graph():
                 graph.add(triple)
 
-            # Add namespaces
-            graph.namespace_manager.bind("", rdflib.Namespace(self.base_iri))
-            graph.namespace_manager.bind(
-                "swrl", rdflib.Namespace("http://www.w3.org/2003/11/swrl#")
-            )
+            # Add common namespaces unknown to rdflib
+            extra_namespaces = [
+                ("", self.base_iri),
+                ("swrl", "http://www.w3.org/2003/11/swrl#"),
+                ("bibo", "http://purl.org/ontology/bibo/"),
+            ]
+            for prefix, iri in extra_namespaces:
+                graph.namespace_manager.bind(prefix, rdflib.Namespace(iri))
 
             # Remove all ontology-declarations in the graph that are
             # not the current ontology.

From 802232ef5f0b74453390c29e77c8a937cd92d1b3 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sun, 17 Mar 2024 11:45:54 +0100
Subject: [PATCH 2/2] Do not override existing namespaces in save()

---
 ontopy/ontology.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 31fba7222..47425c771 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -1014,7 +1014,9 @@ def save(
                 ("bibo", "http://purl.org/ontology/bibo/"),
             ]
             for prefix, iri in extra_namespaces:
-                graph.namespace_manager.bind(prefix, rdflib.Namespace(iri))
+                graph.namespace_manager.bind(
+                    prefix, rdflib.Namespace(iri), override=False
+                )
 
             # Remove all ontology-declarations in the graph that are
             # not the current ontology.