Include SubObjectPropertyOf axioms when reducing.

By default, ROBOT's `reduce` command does not take SubObjectPropertyOf
axioms into account, which leads it to leave in place some axioms that
are in fact redundant.

We pass the `--include-subproperties true` option to all calls to
`reduce` to change that behaviour.

This is configurable at the Makefile level (by overriding the
REDUCE_OPTIONS variable, either on the command line or in the custom
Makefile), _not_ at the ODK level (as we already do with RELAX_OPTIONS).

Author: gouttegd

template/src/ontology/Makefile.jinja2

@@ -69,6 +69,7 @@ SPARQL_VALIDATION_CHECKS =  {% for x in project.robot_report.custom_sparql_check
 SPARQL_EXPORTS =            {% for x in project.robot_report.custom_sparql_exports|default(['basic-report', 'class-count-by-prefix', 'edges', 'xrefs', 'obsoletes', 'synonyms']) %}{{ x }} {% endfor %}
 ODK_VERSION_MAKEFILE =      {% if env is defined %}{{env['ODK_VERSION'] or "Unknown" }}{% else %}"Unknown"{% endif %}
 RELAX_OPTIONS =             --include-subclass-of true
+REDUCE_OPTIONS =            --include-subproperties true
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -1340,7 +1341,7 @@ $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 	reason --reasoner $(REASONER) --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms|default('false')|lower }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %}
 	materialize {% for iri in project.release_materialize_object_properties %}--term {{iri}} {% endfor %} \{% endif %}{% endif %}
 	relax $(RELAX_OPTIONS) \{% if project.release_use_reasoner %}
-	reduce -r $(REASONER) \{% endif %}
+	reduce -r $(REASONER) $(REDUCE_OPTIONS) \{% endif %}
 	remove {% if project.namespaces is not none %}{% for iri in project.namespaces %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(URIBASE)/{{ project.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false \
 	$(SHARED_ROBOT_COMMANDS) \
 	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
@@ -1363,7 +1364,7 @@ $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 		reason --reasoner $(REASONER) --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %}
 		materialize {% for iri in project.release_materialize_object_properties %}--term {{iri}} {% endfor %} \{% endif %}
 		relax $(RELAX_OPTIONS) \
-		reduce -r $(REASONER) \
+		reduce -r $(REASONER) $(REDUCE_OPTIONS) \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
 {% endif -%}
 
@@ -1384,7 +1385,7 @@ $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILE
 		relax $(RELAX_OPTIONS) \
 		remove --axioms equivalent \
 		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \{% if project.release_use_reasoner %}
-		reduce -r $(REASONER) \{% endif %}
+		reduce -r $(REASONER) $(REDUCE_OPTIONS) \{% endif %}
 		odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true \
 		repair --merge-axiom-annotations true \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
@@ -1397,7 +1398,7 @@ $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILE
 $(ONT)-simple-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE_BASE) \
 		remove --axioms equivalent \{% if project.release_use_reasoner %}
-		reduce -r $(REASONER) \{% endif %}
+		reduce -r $(REASONER) $(REDUCE_OPTIONS) \{% endif %}
 		filter --select ontology --term-file $(SIMPLESEED) --trim false \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
 {% endif -%}
@@ -1422,7 +1423,7 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
 		remove --axioms disjoint \
 		remove --term-file $(KEEPRELATIONS) --select complement --select object-properties --trim true \
 		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
-		reduce -r $(REASONER) \
+		reduce -r $(REASONER) $(REDUCE_OPTIONS) \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
 {% endif -%}
 {% for r in project.release_artefacts %}