How to debug unsat in composite?

[matentzn]

MBASE = $(TMPDIR)/ext-weak.owl $(BRIDGEDIR)/bridges $(TMPDIR)/local-ma.owl $(TMPDIR)/local-ehdaa2.owl $(TMPDIR)/local-emapa.owl $(TMPDIR)/local-xao.owl \
    $(TMPDIR)/local-zfa.owl $(TMPDIR)/local-fbbt.owl $(TMPDIR)/local-fbdv.owl \
    $(TMPDIR)/local-wbbt.owl $(TMPDIR)/local-wbls.owl $(TMPDIR)/local-ceph.owl \
    $(TMPDIR)/local-cteno.owl $(TMPDIR)/local-poro.owl $(TMPDIR)/allen-mba.obo $(TMPDIR)/allen-pba.obo $(TMPDIR)/allen-hba.obo \
    $(TMPDIR)/allen-dmba.obo $(TMPDIR)/allen-dhba.obo \
    dependencies

# A subset of OPs will be turned into taxon GCIs
TAXON_GCI_RELS = RO:0002202 RO:0002496 RO:0002497 BFO:0000051

MERGESPECIES =\
  --merge-species-ontology -s 'mouse' -t NCBITaxon:10090 -q $(TAXON_GCI_RELS) \
  --merge-species-ontology -s 'human' -t NCBITaxon:9606 -q $(TAXON_GCI_RELS) \
  --merge-species-ontology -s 'primate' -t NCBITaxon:9443 \
  --merge-species-ontology -s 'Xenopus' -t NCBITaxon:8353 \
  --merge-species-ontology -s 'Danio' -t NCBITaxon:7954 \
  --merge-species-ontology -s 'Drosophila' -t NCBITaxon:7227 \
  --merge-species-ontology -s 'C elegans' -t NCBITaxon:6237 \

MERGE_EQSETS =  --merge-equivalence-sets -s UBERON 10 -s CL 9 -s CARO 5  -l UBERON 10 -l CL 9 -d UBERON 10 -d CL 9

MAKESPMERGE= $(UCAT)\
  --map-ontology-iri $(URIBASE)/uberon.owl $(TMPDIR)/ext-weak.owl\
  --map-ontology-iri $(URIBASE)/fma.owl $(COMPONENTSDIR)/null.owl\
  --map-ontology-iri $(URIBASE)/uberon/bridge/uberon-bridge-to-fma.owl $(COMPONENTSDIR)/null.owl\
 $(URIBASE)/uberon/$(BRIDGEDIR)/collected-$*.owl --merge-imports-closure

# bundled: collect all ontologies and do a basic (non-species) import closure merge
# primarily for testing: not released
bundled-%.owl: $(MBASE)
    OWLTOOLS_MEMORY=12G owltools $(MAKESPMERGE) --merge-import-closure -o -f ofn $@
.PRECIOUS: unreasoned-composite-%.owl

# stage1 of composite build: do a species merge, but no additional reasoning
unreasoned-composite-%.owl: $(MBASE)
    OWLTOOLS_MEMORY=12G owltools $(MAKESPMERGE) --reasoner elk $(MERGESPECIES) $(MERGE_EQSETS) -o -f ofn $@
.PRECIOUS: unreasoned-composite-%.owl

This whole block is very hard for me to understand - What should I do if unreasoned-composite-%.owl fails because of an unsatisfiable class?

For example, I get:

Exception in thread "main" owltools.mooncat.SpeciesMergeUtil$UnmergeableOntologyException: unsatisfiable class: <http://purl.obolibrary.org/obo/DHBA_146035008>
    at owltools.mooncat.SpeciesMergeUtil.merge(SpeciesMergeUtil.java:228)
    at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:823)
    at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
    at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
    at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)
uberon.Makefile:999: recipe for target 'unreasoned-composite-metazoan.owl' failed
make: *** [unreasoned-composite-metazoan.owl] Error 1

Now because SpeciesMergeUtil needs the reasoner, I cant dump an intermediate ontology that I can look and debug. Whats the best way to inspect this problem?

[matentzn]

Found a way to debug:

xxz:
    robot merge --catalog $(CATALOG) -i tmp/ext-weak.owl -i bridge/collected-metazoan.owl -i tmp/allen-dhba.obo -o tmp/debugme.owl

xxx:
    robot explain -i tmp/debugme.owl -M unsatisfiability  --unsatisfiable random:3 --explanation tmp/debug_unsat_dhba.md -o tmp/debug_unsat.owl

[matentzn]

If anyone can see any obvious problems here, please let me know @cmungall @balhoff @dosumis

pulmonary valve leaflet mesenchyme SubClassOf Nothing

• pulmonary valve leaflet mesenchyme SubClassOf develops_from some aortico-pulmonary spiral septum mesenchyme
  • aortico-pulmonary spiral septum mesenchyme SubClassOf develops_from some outflow tract neural crest
    • outflow tract neural crest SubClassOf located_in some outflow tract cardiac jelly
    • outflow tract cardiac jelly EquivalentTo outflow tract cardiac jelly and (part of some NCBITaxon_9606)
      • outflow tract cardiac jelly SubClassOf acellular anatomical structure
      • outflow tract cardiac jelly EquivalentTo cardiac jelly and (part of some outflow tract)
      • cardiac jelly SubClassOf tissue
        • tissue SubClassOf multicellular anatomical structure
• acellular anatomical structure DisjointWith multicellular anatomical structure

trachea basement membrane SubClassOf Nothing

• trachea basement membrane EquivalentTo trachea basement membrane and (part of some NCBITaxon_10090)
  • trachea basement membrane SubClassOf respiratory system basement membrane
    • respiratory system basement membrane SubClassOf basement membrane of epithelium
    • basement membrane of epithelium SubClassOf acellular membrane
      • acellular membrane EquivalentTo acellular anatomical structure and (bounding layer of some connected anatomical structure)
• tissue SubClassOf multicellular anatomical structure
• trachea basement membrane EquivalentTo trachea basement membrane and (part of some NCBITaxon_10090)
• trachea non-cartilage connective tissue SubClassOf trachea connective tissue
• trachea connective tissue EquivalentTo connective tissue and (part of some trachea)
• trachea non-cartilage connective tissue EquivalentTo trachea non-cartilage connective tissue and (part of some NCBITaxon_10090)
• acellular anatomical structure DisjointWith multicellular anatomical structure
• connective tissue SubClassOf tissue
• trachea basement membrane SubClassOf trachea non-cartilage connective tissue

outflow tract cardiac jelly SubClassOf Nothing

• outflow tract cardiac jelly EquivalentTo outflow tract cardiac jelly and (part of some NCBITaxon_9606)
  • outflow tract cardiac jelly SubClassOf cardiac jelly
    • cardiac jelly SubClassOf tissue
    • tissue SubClassOf multicellular anatomical structure
  • outflow tract cardiac jelly SubClassOf acellular anatomical structure
• acellular anatomical structure DisjointWith multicellular anatomical structure

trachea reticular lamina SubClassOf Nothing

• trachea reticular lamina EquivalentTo trachea reticular lamina and (part of some NCBITaxon_10090)
• tissue SubClassOf multicellular anatomical structure
• trachea basement membrane EquivalentTo trachea basement membrane and (part of some NCBITaxon_10090)
• trachea non-cartilage connective tissue SubClassOf trachea connective tissue
• trachea basement membrane SubClassOf respiratory system basement membrane
• basement membrane of epithelium SubClassOf acellular membrane
• trachea connective tissue EquivalentTo connective tissue and (part of some trachea)
• acellular membrane EquivalentTo acellular anatomical structure and (bounding layer of some connected anatomical structure)
• respiratory system basement membrane SubClassOf basement membrane of epithelium
• trachea reticular lamina SubClassOf part of some trachea basement membrane
• trachea reticular lamina EquivalentTo trachea reticular lamina and (part of some NCBITaxon_10090)
• trachea non-cartilage connective tissue EquivalentTo trachea non-cartilage connective tissue and (part of some NCBITaxon_10090)
• acellular anatomical structure DisjointWith multicellular anatomical structure
• connective tissue SubClassOf tissue
• trachea basement membrane SubClassOf trachea non-cartilage connective tissue

aortico-pulmonary spiral septum mesenchyme SubClassOf Nothing

• aortico-pulmonary spiral septum mesenchyme SubClassOf develops_from some outflow tract neural crest
  • outflow tract neural crest SubClassOf located_in some outflow tract cardiac jelly
    • outflow tract cardiac jelly EquivalentTo outflow tract cardiac jelly and (part of some NCBITaxon_9606)
    • outflow tract cardiac jelly SubClassOf acellular anatomical structure
    • outflow tract cardiac jelly EquivalentTo cardiac jelly and (part of some outflow tract)
      • cardiac jelly SubClassOf tissue
      • tissue SubClassOf multicellular anatomical structure
• acellular anatomical structure DisjointWith multicellular anatomical structure

aortic valve leaflet mesenchyme SubClassOf Nothing

• aortic valve leaflet mesenchyme SubClassOf develops_from some aortico-pulmonary spiral septum mesenchyme
  • aortico-pulmonary spiral septum mesenchyme SubClassOf develops_from some outflow tract neural crest
    • outflow tract neural crest SubClassOf located_in some outflow tract cardiac jelly
    • outflow tract cardiac jelly EquivalentTo outflow tract cardiac jelly and (part of some NCBITaxon_9606)
      • outflow tract cardiac jelly SubClassOf acellular anatomical structure
      • outflow tract cardiac jelly EquivalentTo cardiac jelly and (part of some outflow tract)
      • cardiac jelly SubClassOf tissue
        • tissue SubClassOf multicellular anatomical structure
• acellular anatomical structure DisjointWith multicellular anatomical structure

bronchus basement membrane SubClassOf Nothing

• bronchus basement membrane EquivalentTo bronchus basement membrane and (part of some NCBITaxon_10090)
  • bronchus basement membrane SubClassOf respiratory system basement membrane
    • respiratory system basement membrane SubClassOf basement membrane of epithelium
    • basement membrane of epithelium SubClassOf acellular membrane
      • acellular membrane EquivalentTo acellular anatomical structure and (bounding layer of some connected anatomical structure)
• bronchus connective tissue SubClassOf lower respiratory tract connective tissue
• tissue SubClassOf multicellular anatomical structure
• lower respiratory tract connective tissue SubClassOf respiratory system connective tissue
• bronchus basement membrane SubClassOf bronchus connective tissue
• bronchus basement membrane EquivalentTo bronchus basement membrane and (part of some NCBITaxon_10090)
• bronchus connective tissue EquivalentTo bronchus connective tissue and (part of some NCBITaxon_10090)
• respiratory system connective tissue EquivalentTo connective tissue and (part of some respiratory system)
• acellular anatomical structure DisjointWith multicellular anatomical structure
• connective tissue SubClassOf tissue

outflow tract neural crest SubClassOf Nothing

• outflow tract neural crest SubClassOf located_in some outflow tract cardiac jelly
  • outflow tract cardiac jelly EquivalentTo outflow tract cardiac jelly and (part of some NCBITaxon_9606)
    • outflow tract cardiac jelly SubClassOf acellular anatomical structure
    • outflow tract cardiac jelly EquivalentTo cardiac jelly and (part of some outflow tract)
    • cardiac jelly SubClassOf tissue
      • tissue SubClassOf multicellular anatomical structure
• acellular anatomical structure DisjointWith multicellular anatomical structure

membranous interventricular septum mesenchyme SubClassOf Nothing

• membranous interventricular septum mesenchyme SubClassOf develops_from some aortico-pulmonary spiral septum mesenchyme
  • aortico-pulmonary spiral septum mesenchyme SubClassOf develops_from some outflow tract neural crest
    • outflow tract neural crest SubClassOf located_in some outflow tract cardiac jelly
    • outflow tract cardiac jelly EquivalentTo outflow tract cardiac jelly and (part of some NCBITaxon_9606)
      • outflow tract cardiac jelly SubClassOf acellular anatomical structure
      • outflow tract cardiac jelly EquivalentTo cardiac jelly and (part of some outflow tract)
      • cardiac jelly SubClassOf tissue
        • tissue SubClassOf multicellular anatomical structure
• acellular anatomical structure DisjointWith multicellular anatomical structure

trachea basal lamina SubClassOf Nothing

• trachea basal lamina SubClassOf part of some trachea basement membrane
  • trachea basement membrane EquivalentTo trachea basement membrane and (part of some NCBITaxon_10090)
    • trachea basement membrane SubClassOf respiratory system basement membrane
    • respiratory system basement membrane SubClassOf basement membrane of epithelium
      • basement membrane of epithelium SubClassOf acellular membrane
      • acellular membrane EquivalentTo acellular anatomical structure and (bounding layer of some connected anatomical structure)
• tissue SubClassOf multicellular anatomical structure
• trachea basement membrane EquivalentTo trachea basement membrane and (part of some NCBITaxon_10090)
• trachea non-cartilage connective tissue SubClassOf trachea connective tissue
• trachea connective tissue EquivalentTo connective tissue and (part of some trachea)
• trachea non-cartilage connective tissue EquivalentTo trachea non-cartilage connective tissue and (part of some NCBITaxon_10090)
• acellular anatomical structure DisjointWith multicellular anatomical structure
• connective tissue SubClassOf tissue
• trachea basement membrane SubClassOf trachea non-cartilage connective tissue

Axiom Impact

Axioms used 10 times

• tissue SubClassOf multicellular anatomical structure [ext.owl]
• acellular anatomical structure DisjointWith multicellular anatomical structure [ext.owl]

Axioms used 6 times

• outflow tract cardiac jelly EquivalentTo outflow tract cardiac jelly and (part of some NCBITaxon_9606) [ext.owl]
• outflow tract cardiac jelly SubClassOf acellular anatomical structure [ext.owl]
• cardiac jelly SubClassOf tissue [ext.owl]

Axioms used 5 times

• outflow tract cardiac jelly EquivalentTo cardiac jelly and (part of some outflow tract) [ext.owl]
• outflow tract neural crest SubClassOf located_in some outflow tract cardiac jelly [ext.owl]

Axioms used 4 times

• acellular membrane EquivalentTo acellular anatomical structure and (bounding layer of some connected anatomical structure) [ext.owl]
• aortico-pulmonary spiral septum mesenchyme SubClassOf develops_from some outflow tract neural crest [ext.owl]
• connective tissue SubClassOf tissue [ext.owl]
• basement membrane of epithelium SubClassOf acellular membrane [ext.owl]
• respiratory system basement membrane SubClassOf basement membrane of epithelium [ext.owl]

Axioms used 3 times

• trachea basement membrane EquivalentTo trachea basement membrane and (part of some NCBITaxon_10090) [ext.owl]
• trachea non-cartilage connective tissue EquivalentTo trachea non-cartilage connective tissue and (part of some NCBITaxon_10090) [ext.owl]
• trachea connective tissue EquivalentTo connective tissue and (part of some trachea) [ext.owl]
• trachea basement membrane SubClassOf trachea non-cartilage connective tissue [ext.owl]
• trachea non-cartilage connective tissue SubClassOf trachea connective tissue [ext.owl]
• trachea basement membrane SubClassOf respiratory system basement membrane [ext.owl]

Axioms used 2 times

• trachea basement membrane EquivalentTo trachea basement membrane and (part of some NCBITaxon_10090) [ext.owl]

Axioms used 1 times

• trachea reticular lamina EquivalentTo trachea reticular lamina and (part of some NCBITaxon_10090) [ext.owl]
• bronchus basement membrane EquivalentTo bronchus basement membrane and (part of some NCBITaxon_10090) [ext.owl]
• bronchus connective tissue EquivalentTo bronchus connective tissue and (part of some NCBITaxon_10090) [ext.owl]
• bronchus basement membrane EquivalentTo bronchus basement membrane and (part of some NCBITaxon_10090) [ext.owl]
• trachea reticular lamina EquivalentTo trachea reticular lamina and (part of some NCBITaxon_10090) [ext.owl]
• respiratory system connective tissue EquivalentTo connective tissue and (part of some respiratory system) [ext.owl]
• aortic valve leaflet mesenchyme SubClassOf develops_from some aortico-pulmonary spiral septum mesenchyme [ext.owl]
• pulmonary valve leaflet mesenchyme SubClassOf develops_from some aortico-pulmonary spiral septum mesenchyme [ext.owl]
• membranous interventricular septum mesenchyme SubClassOf develops_from some aortico-pulmonary spiral septum mesenchyme [ext.owl]
• trachea basal lamina SubClassOf part of some trachea basement membrane [ext.owl]
• bronchus basement membrane SubClassOf bronchus connective tissue [ext.owl]
• trachea reticular lamina SubClassOf part of some trachea basement membrane [ext.owl]
• lower respiratory tract connective tissue SubClassOf respiratory system connective tissue [ext.owl]
• bronchus connective tissue SubClassOf lower respiratory tract connective tissue [ext.owl]
• outflow tract cardiac jelly SubClassOf cardiac jelly [ext.owl]
• bronchus basement membrane SubClassOf respiratory system basement membrane [ext.owl]

Ontologies used:

• ext.owl (http://purl.obolibrary.org/obo/uberon/ext.owl)

Ontologies used:

• ext.owl (http://purl.obolibrary.org/obo/uberon/ext.owl)

[matentzn]

Ignore this ticket. Found the proble I think.

[matentzn]

Update to self: seems poro carries in disjoint axioms.

[dosumis]

This doesn't look right to me:

brain SubClassOf part of some neural tube [ext.owl]

[matentzn]

@dosumis where did you see this? I don't see that axiom (anymore?) it was there in the first version of the ticket, but I have corrected that since.

[matentzn]

Superceded.