diff --git a/docs/examples/uvular_muscle.ofn b/docs/examples/uvular_muscle.ofn
index d56aa6847..1e7203e4e 100644
--- a/docs/examples/uvular_muscle.ofn
+++ b/docs/examples/uvular_muscle.ofn
@@ -1,4 +1,4 @@
-Prefix(:=<urn:unnamed:ontology#ont31#>)
+Prefix(:=<https://github.com/ontodev/robot/examples/uvular_muscle.ofn#>)
 Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
 Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
 Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
@@ -6,7 +6,8 @@ Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
 Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
-Ontology(<urn:unnamed:ontology#ont31>
+Ontology(<https://github.com/ontodev/robot/examples/uvular_muscle.ofn>
+Annotation(rdfs:label "Uvular Muscle Explanation"^^xsd:string)
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000100>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001134>))
@@ -112,4 +113,4 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0014892> "
 EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0014892> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001630> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/UBERON_0003082>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002219> <http://purl.obolibrary.org/obo/UBERON_0011899>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> <http://purl.obolibrary.org/obo/UBERON_0001134>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/uberon/core#synapsed_by> <http://purl.obolibrary.org/obo/CL_0000100>)))
 
 
-)
+)
\ No newline at end of file
diff --git a/docs/explain.md b/docs/explain.md
index 3ecfe1307..85be32ffb 100644
--- a/docs/explain.md
+++ b/docs/explain.md
@@ -3,7 +3,7 @@
 When reviewing inferred axioms, such as after applying the [`reason`](/reason) command,
 you may like more information about why a particular axiom was inferred:
 
-    robot explain -i uvula.ofn -r ELK \
+    robot explain --input uvula.ofn --reasoner ELK \
       --axiom "'uvular muscle' SubClassOf 'muscle organ' and 'part of' some 'jaw region'" \
       --explanation results/uvular_muscle.md
 
@@ -27,9 +27,11 @@ GitHub issues:
 In addition to outputting the explanation axioms in Markdown using `--explanation` (or `-e`), an ontology containing just
 those axioms can be output with `-o` or passed to any subsequent chained commands:
 
-    robot explain -i uvula.ofn -r ELK \
+    robot explain --input uvula.ofn --reasoner ELK \
       --axiom "'uvular muscle' SubClassOf 'muscle organ' and 'part of' some 'jaw region'" \
-      annotate --annotation rdfs:label "Uvular Muscle Explanation" -o uvular_muscle.ofn
+      annotate --annotation rdfs:label "Uvular Muscle Explanation" \
+      --ontology-iri "https://github.com/ontodev/robot/examples/uvular_muscle.ofn" \
+      --output results/uvular_muscle.ofn
 
 Finally, since there can be more than one way to derive an inference from an ontology,
 `explain` includes one more option, `--max`, which allows you to specify the maximum