Strip BFO continuant/occurrent disjointness before reasoning (VFB2#457)

pip_vfb-pipeline-dumps has been failing construct_all.owl since build #872
with 'The ontology is inconsistent' under ELK. One of the mechanisms (the
other is a separate FBbt laterality curation issue, tracked separately on
VFB2#457): scRNAseq Clustering individuals assert 'has_part' to their Assay
(vfb-scRNAseq-ontology's schema, unchanged since well before this started
failing). Assay is a BFO occurrent; 'Clustering has_part Assay' is
equivalent to 'Assay part_of Clustering', and once Clustering is inferred
continuant that collides with BFO's DisjointClasses(continuant, part_of
some occurrent) (and its mirror, and the plain continuant/occurrent
disjointness) - both fbbt.owl and vfbext.owl carry their own copy of these
axioms via their bundled BFO/RO import closure, and both get merged into
all.ttl.

vfb-scRNAseq-ontology's schema can't easily change without touching the
TSV-building scripts, and that ontology is being migrated to
VirtualFlyBrain/vfb-scRNAseq anyway, where the real fix belongs. As a
stopgap to get builds passing again, strip the three continuant/occurrent
disjointness axioms from the merged all.ttl right before reasoning, in the
construct_all.owl rule:

  robot merge -i all.ttl     remove --term BFO:0000002 --term BFO:0000003            --axioms DisjointClasses --preserve-structure false     reason --reasoner ELK ...

Verified with robot merge+reason (ELK) against a minimal reproducer (one
scRNAseq dataset file's individual assertions + the BFO/RO axioms that
trip this): the full construct_all.owl command chain (merge, reason with
the same axiom-generators/relax/reduce/annotate/convert steps used here)
reproduces 'The ontology is inconsistent' without this remove step, and
completes cleanly with it.

This only removes the continuant/occurrent disjointness - no other
DisjointClasses axioms are touched. Temporary: revert once the scRNAseq
migration lands a real fix.

Refs VirtualFlyBrain/VFB2#457.

Author: claude

dumps.Makefile

@@ -95,10 +95,27 @@ $(RAW_DUMPS_DIR)/%.ttl:
 $(RAW_DUMPS_DIR)/construct_%.owl: $(RAW_DUMPS_DIR)/%.ttl
 	$(call log, $@, $(ROBOT) merge -i $< annotate --ontology-iri "http://virtualflybrain.org/data/VFB/OWL/raw/$*.owl" convert -f owl -o $@ $(STDOUT_FILTER))
 
+# TEMPORARY (VFB2#457): BFO's continuant/occurrent disjointness --
+# DisjointClasses(BFO:0000002, BFO:0000003) and the two GCI forms
+# DisjointClasses(BFO:0000002, part_of some BFO:0000003) / mirror -- is tripped
+# by 'Clustering has_part Assay' in the scRNAseq data (Assay is an occurrent,
+# Clustering ends up inferred continuant, so 'Assay part_of Clustering' hits the
+# GCI form). vfb-scRNAseq-ontology's schema can't change without touching the
+# TSV-building scripts it's about to be migrated away from anyway
+# (VirtualFlyBrain/vfb-scRNAseq), so as a stopgap we strip these three axioms
+# from the merged all.ttl right before reasoning, wherever they came from
+# (fbbt.owl and vfbext.owl both carry a copy via their own BFO/RO import
+# closure). Remove this step once the scRNAseq migration lands the real fix.
+# Verified with robot merge+reason (ELK): a scRNAseq dataset file that
+# reproduces "The ontology is inconsistent" on its own reasons cleanly once
+# this remove step runs first.
+#
 # Generates an OWL file from multiple TTL files, infers annotations and relations,
 # reduces the ontology, annotates it, and saves it to disk.
 $(RAW_DUMPS_DIR)/construct_all.owl: $(RAW_DUMPS_DIR)/all.ttl
-	$(call log, $@, $(ROBOT) merge -i $< reason --reasoner ELK --axiom-generators "SubClass EquivalentClass ClassAssertion" --exclude-tautologies structural relax reduce --reasoner ELK annotate --ontology-iri "http://virtualflybrain.org/data/VFB/OWL/raw/all.owl" convert -f owl -o $@ $(STDOUT_FILTER) || { $(EXPLAIN_ALL) ; false ; })
+	$(call log, $@, $(ROBOT) merge -i $< \
+		remove --term BFO:0000002 --term BFO:0000003 --axioms "DisjointClasses" --preserve-structure false \
+		reason --reasoner ELK --axiom-generators "SubClass EquivalentClass ClassAssertion" --exclude-tautologies structural relax reduce --reasoner ELK annotate --ontology-iri "http://virtualflybrain.org/data/VFB/OWL/raw/all.owl" convert -f owl -o $@ $(STDOUT_FILTER) || { $(EXPLAIN_ALL) ; false ; })
 
 # Infers annotations and relations for the virtual fly brain ontology using the ROBOT inference engine.
 $(RAW_DUMPS_DIR)/inferred_annotation.owl: $(FINAL_DUMPS_DIR)/owlery.owl $(RAW_DUMPS_DIR)/vfb-config.yaml