Error on uberon.makefile ln100

[shawntanzk]

$(OWLSRC): tmp/uberon-merged.owl $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(SCRIPTSDIR)/expand-dbxref-literals.pl
	echo "STRONG WARNING: issues/contributor.owl needs to be manually updated."
	$(OWLTOOLS) --no-logging $< $(COMPONENTSDIR)/disjoint_union_over.ofn issues/contributor.owl --merge-support-ontologies --expand-macros -o  $@ &&  $(SCRIPTSDIR)/expand-dbxref-literals.pl $@ > $@.tmp
	$(ROBOT) query -i $@.tmp --update $(SPARQLDIR)/taxon_constraint_never_in_taxon.ru --update $(SPARQLDIR)/remove_axioms.ru -o $@ \
           query --update ../sparql/delete-definition-dot.ru merge -i imports/ro_import.owl -o $@

The above is the command in the makefile where it is failing.

tmp/uberon-merged.owl seems to be built alright, but seems to be failing at the line that starts with $(OWLTOOLS)

make: *** [uberon.Makefile:100: tmp/uberon-edit.owl] Error 1

This is the same failure with trying to build imports and mirrors and trying to make tmp/uberon-edit.owl

making tmp/uberon-merged.owl is fine though

[shawntanzk]

full documentation of this: #2231 (comment)

[dosumis]

This is sufficient to prompt the error:

./run.sh owltools tmp/uberon-merged.owl --expand-macros
(assuming tmp/uberon-merged.owl is built).

hypothesis - this is caused by an issue in never_in_taxon AP axioms that have changed since the last release

@shawntanzk can you do a diff of uberon-edit.owl since the last release and grep the results for never_in_taxon to see if any look odd?

[shawntanzk]

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/Users/shawntan/Documents/GitHub/uberon/src/ontology/tmp.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/Users/shawntan/Documents/GitHub/uberon/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

UBERON_8410068 http://purl.obolibrary.org/obo/UBERON_8410068

Added

• UBERON_8410068 label "capillary of small intestine"^^string

• UBERON_8410068 id "UBERON:8410068"^^string

• UBERON_8410068 in_subset location_grouping

• UBERON_8410068 date "2021-12-21T15:14:31Z"^^dateTime

• UBERON_8410068 has_exact_synonym "blood vessel capillary of small intestine"^^string

• UBERON_8410068 created_by "http://orcid.org/0000-0002-2825-0621"^^[string](http://www.w3.org/2001/XMLSchema#string)

• UBERON_8410068 definition "A capillary that is part of a small intestine."^^string

  • database_cross_reference "http://orcid.org/0000-0003-3440-1876"^^[string](http://www.w3.org/2001/XMLSchema#string)

• UBERON_8410068 has_obo_namespace "uberon"^^string

• UBERON_8410068 has_exact_synonym "small intestine capillary"^^string

• Class: UBERON_8410068

• UBERON_8410068 EquivalentTo capillary and (part of some small intestine)

echolocation organ http://purl.obolibrary.org/obo/UBERON_0010053

Added

• echolocation organ never_in_taxon "Euarchontoglires"^^string

exoskeleton http://purl.obolibrary.org/obo/UBERON_0006611

Added

• exoskeleton never_in_taxon "Euarchontoglires"^^string

feather http://purl.obolibrary.org/obo/UBERON_0000022

Added

• feather never_in_taxon "Euarchontoglires"^^string

fimbria of uterine tube http://purl.obolibrary.org/obo/UBERON_8410010

Removed

• fimbria of uterine tube has_exact_synonym "fimbriae of uterine tube"^^string

• fimbria of uterine tube has_exact_synonym "fimbriae of fallopian tube"^^string

Added

• fimbria of uterine tube has_exact_synonym "fimbriae of uterine tube"^^string

  • has_synonym_type plural term

• fimbria of uterine tube has_exact_synonym "fimbriae of fallopian tube"^^string

  • has_synonym_type plural term

laminar subdivision of the cortex http://purl.obolibrary.org/obo/UBERON_8440004

Added

• laminar subdivision of the cortex SubClassOf part of some neocortex

peripheral nervous system http://purl.obolibrary.org/obo/UBERON_0000010

Removed

• peripheral nervous system mutually_spatially_disjoint_with central nervous system

  • exceptions "ZFA"^^string

  • source "https://github.com/obophenotype/uberon/issues/378"^^[string](http://www.w3.org/2001/XMLSchema#string)

  • status "pending"^^string

[shawntanzk]

@dosumis not sure how to grep with old version and all, but the above is the diff between the last uberon release and current, the following are the ones that have never in taxon:

echolocation organ http://purl.obolibrary.org/obo/UBERON_0010053
Added
echolocation organ never_in_taxon "Euarchontoglires"^^string
exoskeleton http://purl.obolibrary.org/obo/UBERON_0006611
Added
exoskeleton never_in_taxon "Euarchontoglires"^^string
feather http://purl.obolibrary.org/obo/UBERON_0000022
Added
feather never_in_taxon "Euarchontoglires"^^string

[dosumis]

Values should be classes, not strings! Fixing now.

[shawntanzk]

Fixed in #2248