From 819a77515d9e94f11c1918212e5c175c6115192f Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Fri, 16 Jun 2023 18:07:33 +0100 Subject: [PATCH 1/8] merge taxslim-disjoint-over-in-taxon in pipeline --- src/ontology/uberon.Makefile | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 2f30bfb758..64cfdf4f3f 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -95,6 +95,9 @@ test: $(REPORTDIR)/uberon-edit-xp-check reports/bfo-check.txt tmp/uberon-merged.owl: $(SRC) $(ROBOT) merge -i $< -o $@ +$(TMPDIR)/taxslim-disjoint-over-in-taxon.owl: + wget http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl -O $@ + # TODO This goal needs to be revised carefully. remove_axioms removes RO labels to avoid duplicates # merge -i ro_import then adds them back to ensure they are canonical. # Cannot add $(IMPORTDIR)/ro_import.owl as dependency because it cause to be circular with tmp/seed.txt @@ -108,9 +111,9 @@ tmp/uberon-merged.owl: $(SRC) # $(SCRIPTSDIR)/expand-dbxref-literals.pl ## Turns some CURIES into expanded URI syntax ## TODO: Leave for now but make a ticket for replacment (maybe with SPARQL?) -$(OWLSRC): tmp/uberon-merged.owl $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(SCRIPTSDIR)/expand-dbxref-literals.pl +$(OWLSRC): tmp/uberon-merged.owl $(COMPONENTSDIR)/disjoint_union_over.ofn $(TMPDIR)/subset-taxslim-disjoint-over-in-taxon.owl $(REPORTDIR)/$(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 -o $@ && $(SCRIPTSDIR)/expand-dbxref-literals.pl $@ > $@.tmp + $(OWLTOOLS) --no-logging $< $(COMPONENTSDIR)/disjoint_union_over.ofn $(TMPDIR)/subset-taxslim-disjoint-over-in-taxon.owl issues/contributor.owl --merge-support-ontologies -o $@ && $(SCRIPTSDIR)/expand-dbxref-literals.pl $@ > $@.tmp # The previous step seems to be necessary because somehow the expand-dbxref-literals script expects the owtools output.. No idea why $(ROBOT) expand -i $@.tmp --no-expand-term http://purl.obolibrary.org/obo/RO_0002175 \ query \ @@ -700,7 +703,7 @@ $(TMPDIR)/uberon-taxon-constraints.obo: $(SRC) $(SCRIPTSDIR)/obo-filter-relationships.pl -t only_in_taxon -t never_in_taxon $< | $(SCRIPTSDIR)/obo-filter-tags.pl -t id -t name -t relationship - | $(SCRIPTSDIR)/obo-grep.pl --noheader -r relationship: - > $@.tmp && cat $@.tmp $(COMPONENTSDIR)/taxon-relations.obo > $@ $(TMPDIR)/uberon-taxon-constraints.owl: $(TMPDIR)/uberon-taxon-constraints.obo - $(OWLTOOLS) $< --expand-macros -o $@ + $(ROBOT) expand --input $< -o $@ # ---------------------------------------- # SYNTACTIC CHECKS @@ -744,7 +747,8 @@ $(TMPDIR)/GO.xrf_abbs: $(SRC) # * species anatomy bridge axioms # This can be used to reveal both internal inconsistencies within uberon, and the improper linking of a species AO class to an uberon class with a taxon constraint $(TMPDIR)/uberon-edit-plus-tax-equivs.owl: $(OWLSRC) $(TMPDIR)/external-disjoints.owl $(TMPDIR)/bridges $(CATALOG_DYNAMIC) - $(OWLTOOLS_CAT_DYNAMIC) $< $(TMPDIR)/external-disjoints.owl `ls $(BRIDGEDIR)/uberon-bridge-to-*.owl | grep -v emap.owl` --merge-support-ontologies -o -f ofn $@ + $(OWLTOOLS_CAT_DYNAMIC) $< $(TMPDIR)/external-disjoints.owl `ls $(BRIDGEDIR)/uberon-bridge-to-*.owl | grep -v emap.owl` --merge-support-ontologies -o -f ofn $@.tmp + $(ROBOT) expand -i $@.tmp -o $@ .PRECIOUS: $(TMPDIR)/uberon-edit-plus-tax-equivs.owl # uberon bridges to mba and dmba are now manually curated and generated in https://github.com/obophenotype/ABA_Uberon/tree/new_bridge From 0a29862fc3ae74900263f215fdf8a64e64cb1007 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Fri, 16 Jun 2023 18:08:18 +0100 Subject: [PATCH 2/8] update ncbitaxon_terms based on the edit file --- src/ontology/imports/ncbitaxon_terms.txt | 249 ++++++++++++++++++++++- 1 file changed, 248 insertions(+), 1 deletion(-) diff --git a/src/ontology/imports/ncbitaxon_terms.txt b/src/ontology/imports/ncbitaxon_terms.txt index ff6792faf3..6812f79f1c 100644 --- a/src/ontology/imports/ncbitaxon_terms.txt +++ b/src/ontology/imports/ncbitaxon_terms.txt @@ -1,4 +1,251 @@ NCBITaxon:1 +NCBITaxon:10047 +NCBITaxon:10088 +NCBITaxon:10090 +NCBITaxon:10114 +NCBITaxon:10116 +NCBITaxon:10135 +NCBITaxon:10205 +NCBITaxon:10219 +NCBITaxon:10220 +NCBITaxon:110815 +NCBITaxon:117565 +NCBITaxon:117569 +NCBITaxon:117570 +NCBITaxon:117893 +NCBITaxon:118040 +NCBITaxon:118072 +NCBITaxon:119203 +NCBITaxon:119825 +NCBITaxon:120557 +NCBITaxon:1206795 +NCBITaxon:1294634 +NCBITaxon:147099 +NCBITaxon:1476529 +NCBITaxon:181400 +NCBITaxon:186634 +NCBITaxon:189497 +NCBITaxon:207598 +NCBITaxon:261739 +NCBITaxon:264759 +NCBITaxon:270656 +NCBITaxon:27686 +NCBITaxon:28376 +NCBITaxon:29132 +NCBITaxon:30458 +NCBITaxon:30533 +NCBITaxon:30559 +NCBITaxon:30649 +NCBITaxon:31033 +NCBITaxon:311790 +NCBITaxon:314145 +NCBITaxon:314146 +NCBITaxon:314147 +NCBITaxon:314293 +NCBITaxon:314295 +NCBITaxon:32443 +NCBITaxon:32455 +NCBITaxon:32519 +NCBITaxon:32523 +NCBITaxon:32524 +NCBITaxon:32525 +NCBITaxon:32561 +NCBITaxon:32577 +NCBITaxon:33090 +NCBITaxon:33208 +NCBITaxon:33213 +NCBITaxon:33317 +NCBITaxon:33392 +NCBITaxon:33511 +NCBITaxon:33554 +NCBITaxon:337687 +NCBITaxon:338153 +NCBITaxon:35033 +NCBITaxon:35069 +NCBITaxon:35497 +NCBITaxon:37572 +NCBITaxon:376911 +NCBITaxon:376913 +NCBITaxon:377294 +NCBITaxon:37887 +NCBITaxon:379584 +NCBITaxon:38624 +NCBITaxon:38625 +NCBITaxon:39107 +NCBITaxon:399537 +NCBITaxon:40151 +NCBITaxon:40674 +NCBITaxon:41324 +NCBITaxon:41426 +NCBITaxon:41712 +NCBITaxon:43120 +NCBITaxon:43453 +NCBITaxon:436486 +NCBITaxon:436491 +NCBITaxon:436495 +NCBITaxon:4751 +NCBITaxon:50557 +NCBITaxon:51337 +NCBITaxon:569425 +NCBITaxon:57294 +NCBITaxon:6040 +NCBITaxon:6072 +NCBITaxon:6073 +NCBITaxon:6157 +NCBITaxon:6178 +NCBITaxon:6199 +NCBITaxon:6211 +NCBITaxon:6217 +NCBITaxon:6231 +NCBITaxon:6239 +NCBITaxon:63221 +NCBITaxon:6340 +NCBITaxon:6425 +NCBITaxon:6447 +NCBITaxon:6448 +NCBITaxon:6544 +NCBITaxon:65997 +NCBITaxon:6656 +NCBITaxon:6657 +NCBITaxon:6681 +NCBITaxon:6830 +NCBITaxon:6843 +NCBITaxon:70846 +NCBITaxon:7088 +NCBITaxon:7227 +NCBITaxon:7434 +NCBITaxon:7568 +NCBITaxon:7586 +NCBITaxon:7588 +NCBITaxon:7618 +NCBITaxon:7625 +NCBITaxon:7711 +NCBITaxon:7712 +NCBITaxon:7713 +NCBITaxon:7718 +NCBITaxon:7735 +NCBITaxon:7737 +NCBITaxon:7742 +NCBITaxon:7745 +NCBITaxon:7746 +NCBITaxon:7761 +NCBITaxon:7762 +NCBITaxon:7764 +NCBITaxon:7769 +NCBITaxon:7776 +NCBITaxon:7777 +NCBITaxon:7778 +NCBITaxon:7858 +NCBITaxon:7863 +NCBITaxon:7864 +NCBITaxon:7878 +NCBITaxon:7896 +NCBITaxon:7898 +NCBITaxon:7900 +NCBITaxon:7901 +NCBITaxon:7911 +NCBITaxon:7915 +NCBITaxon:7922 +NCBITaxon:7954 +NCBITaxon:7955 +NCBITaxon:79805 +NCBITaxon:8022 +NCBITaxon:8065 +NCBITaxon:8075 +NCBITaxon:80999 +NCBITaxon:8287 +NCBITaxon:8289 +NCBITaxon:8292 +NCBITaxon:8293 +NCBITaxon:8295 +NCBITaxon:8296 +NCBITaxon:8314 +NCBITaxon:8342 +NCBITaxon:8353 +NCBITaxon:8355 +NCBITaxon:8457 +NCBITaxon:8459 +NCBITaxon:8464 +NCBITaxon:8492 +NCBITaxon:8493 +NCBITaxon:8499 +NCBITaxon:8504 +NCBITaxon:8507 +NCBITaxon:8508 +NCBITaxon:8509 +NCBITaxon:8561 +NCBITaxon:8570 +NCBITaxon:8578 +NCBITaxon:8782 +NCBITaxon:8801 +NCBITaxon:8827 +NCBITaxon:88770 +NCBITaxon:8930 +NCBITaxon:89593 +NCBITaxon:9030 +NCBITaxon:9031 +NCBITaxon:9126 +NCBITaxon:91561 +NCBITaxon:9254 +NCBITaxon:9255 +NCBITaxon:9257 +NCBITaxon:9258 +NCBITaxon:9259 +NCBITaxon:9261 +NCBITaxon:9263 +NCBITaxon:9265 +NCBITaxon:9305 +NCBITaxon:9321 +NCBITaxon:9322 +NCBITaxon:9338 +NCBITaxon:9347 +NCBITaxon:9348 +NCBITaxon:9359 +NCBITaxon:9362 +NCBITaxon:9363 +NCBITaxon:9365 +NCBITaxon:9369 +NCBITaxon:9373 +NCBITaxon:9376 +NCBITaxon:9397 +NCBITaxon:9443 +NCBITaxon:9475 +NCBITaxon:9499 NCBITaxon:9539 +NCBITaxon:9590 +NCBITaxon:9596 +NCBITaxon:9599 +NCBITaxon:9604 +NCBITaxon:9605 +NCBITaxon:9606 +NCBITaxon:9608 +NCBITaxon:9611 +NCBITaxon:9632 NCBITaxon:9669 -NCBITaxon:4751 +NCBITaxon:9673 +NCBITaxon:9681 +NCBITaxon:9705 +NCBITaxon:9709 +NCBITaxon:9721 +NCBITaxon:9753 +NCBITaxon:9761 +NCBITaxon:9765 +NCBITaxon:9775 +NCBITaxon:9779 +NCBITaxon:9780 +NCBITaxon:9787 +NCBITaxon:9788 +NCBITaxon:9816 +NCBITaxon:9822 +NCBITaxon:9823 +NCBITaxon:9835 +NCBITaxon:9836 +NCBITaxon:9845 +NCBITaxon:9850 +NCBITaxon:9892 +NCBITaxon:9895 +NCBITaxon:9935 +NCBITaxon:9963 +NCBITaxon:9972 +NCBITaxon:9975 +NCBITaxon:9989 From dad24f98386bc66083dbe43c8dbb0b9ee3c4a3cc Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Mon, 19 Jun 2023 13:33:59 +0100 Subject: [PATCH 3/8] update taxslim-disjoint-over-in-taxon --- src/ontology/uberon.Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 64cfdf4f3f..b6dba9ac58 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -111,9 +111,9 @@ $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl: # $(SCRIPTSDIR)/expand-dbxref-literals.pl ## Turns some CURIES into expanded URI syntax ## TODO: Leave for now but make a ticket for replacment (maybe with SPARQL?) -$(OWLSRC): tmp/uberon-merged.owl $(COMPONENTSDIR)/disjoint_union_over.ofn $(TMPDIR)/subset-taxslim-disjoint-over-in-taxon.owl $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(SCRIPTSDIR)/expand-dbxref-literals.pl +$(OWLSRC): tmp/uberon-merged.owl $(COMPONENTSDIR)/disjoint_union_over.ofn $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl $(REPORTDIR)/$(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 $(TMPDIR)/subset-taxslim-disjoint-over-in-taxon.owl issues/contributor.owl --merge-support-ontologies -o $@ && $(SCRIPTSDIR)/expand-dbxref-literals.pl $@ > $@.tmp + $(OWLTOOLS) --no-logging $< $(COMPONENTSDIR)/disjoint_union_over.ofn $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl issues/contributor.owl --merge-support-ontologies -o $@ && $(SCRIPTSDIR)/expand-dbxref-literals.pl $@ > $@.tmp # The previous step seems to be necessary because somehow the expand-dbxref-literals script expects the owtools output.. No idea why $(ROBOT) expand -i $@.tmp --no-expand-term http://purl.obolibrary.org/obo/RO_0002175 \ query \ From 663116066fdf8c2d9652a99ad2ae3d64145153d9 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 20 Jun 2023 11:48:47 +0100 Subject: [PATCH 4/8] remove wings never_in_taxon Sauropsida --- src/ontology/uberon-edit.obo | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index f32928a405..15516fdd84 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -932,7 +932,6 @@ relationship: never_in_taxon NCBITaxon:314147 {source="bgee"} ! Glires relationship: never_in_taxon NCBITaxon:6231 {source="bgee"} ! Nematoda relationship: never_in_taxon NCBITaxon:7878 {source="bgee"} ! Dipnomorpha relationship: never_in_taxon NCBITaxon:8292 {notes="we do not consider flying frogs to have wings", source="bgee"} ! Amphibia -relationship: never_in_taxon NCBITaxon:8457 {source="bgee"} ! Sauropsida relationship: never_in_taxon NCBITaxon:91561 {source="bgee"} ! Artiodactyla relationship: never_in_taxon NCBITaxon:9254 {source="bgee"} ! Prototheria relationship: never_in_taxon NCBITaxon:9263 {source="bgee"} ! Metatheria From 149e47293d5254c07ed63b3bb76c67ca2c254560 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Fri, 21 Jul 2023 11:22:30 +0100 Subject: [PATCH 5/8] Making induction relation between suture and DM mammal-only --- src/ontology/uberon-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 94154b36e1..ecfc354400 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -76306,7 +76306,7 @@ is_a: UBERON:0009198 {source="GO"} ! craniofacial suture intersection_of: UBERON:0002209 ! fibrous joint intersection_of: part_of UBERON:0003128 ! cranium relationship: contributes_to_morphology_of UBERON:0003128 ! cranium -relationship: developmentally_induced_by UBERON:0002363 {source="PMID:16496288"} ! dura mater +relationship: developmentally_induced_by UBERON:0002363 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="PMID:16496288"} ! dura mater relationship: fma_set_term FMA:71385 [Term] From 09caf74bfecd4d4e337a64d5d075cae2523bb8ca Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 5 Sep 2023 02:53:42 -0700 Subject: [PATCH 6/8] Making induction relation between suture and DM mammal-only (#2978) See #2928 From 49e2930212dab9ff63af0d596c5460ef71a7ae09 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Wed, 13 Sep 2023 16:32:32 +0100 Subject: [PATCH 7/8] replace `taxslim-disjoint-over-in-taxon.owl` with `mirror/ncbitaxon.owl` --- src/ontology/uberon.Makefile | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 2d245c625d..7d975fcfda 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -113,12 +113,12 @@ quick-qc: $(REPORTDIR)/uberon-edit-obscheck.txt # Step 1: Preprocessing. We Merge the edit file file with imports, # disjointness axioms, and list of contributors, then expand macros # (except RO:0002175, which only needs to be expanded for QC purposes). -$(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl +$(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(MIRRORDIR)/ncbitaxon.owl @echo "STRONG WARNING: issues/contributor.owl needs to be manually updated." $(ROBOT) merge -i $< \ -i $(COMPONENTSDIR)/disjoint_union_over.ofn \ -i issues/contributor.owl \ - -i $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl \ + -i $(MIRRORDIR)/ncbitaxon.owl \ expand --no-expand-term http://purl.obolibrary.org/obo/RO_0002175 \ -o $@ @@ -1303,13 +1303,6 @@ $(TMPDIR)/hra_depiction_3d_images.owl: $(COMPONENTSDIR)/hra_depiction_3d_images.owl: $(TMPDIR)/hra_depiction_3d_images.owl $(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@ -# Disjointness axioms over taxons. -# FIXME: Not treated as a "component", but it should be, since it is -# merged early in the pipeline (preprocessing step) and therefore ends -# up in all products. -$(TMPDIR)/taxslim-disjoint-over-in-taxon.owl: - wget http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl -O $@ - # ---------------------------------------- # RELEASE DEPLOYMENT From a3f10920aac287b6bd52a1a0dc607b95346a79a4 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Tue, 19 Sep 2023 18:49:11 +0100 Subject: [PATCH 8/8] Merge taxon disjointness axioms when doing the bridge checks. Do not merge the taxslim early in the pipeline (just merge the classes that are normally imported via merged_import). Instead, merge a version of the taxslim that includes inter-taxon disjointness axioms when performing the 'taxon-constraint-check' and all the bridge checks. --- src/ontology/uberon.Makefile | 32 ++++++++++++++++++++++++++------ 1 file changed, 26 insertions(+), 6 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 7d975fcfda..71d2ad05b8 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -113,12 +113,11 @@ quick-qc: $(REPORTDIR)/uberon-edit-obscheck.txt # Step 1: Preprocessing. We Merge the edit file file with imports, # disjointness axioms, and list of contributors, then expand macros # (except RO:0002175, which only needs to be expanded for QC purposes). -$(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(MIRRORDIR)/ncbitaxon.owl +$(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv @echo "STRONG WARNING: issues/contributor.owl needs to be manually updated." $(ROBOT) merge -i $< \ -i $(COMPONENTSDIR)/disjoint_union_over.ofn \ -i issues/contributor.owl \ - -i $(MIRRORDIR)/ncbitaxon.owl \ expand --no-expand-term http://purl.obolibrary.org/obo/RO_0002175 \ -o $@ @@ -631,10 +630,19 @@ $(TMPDIR)/external-disjoints.owl: components/external-disjoints.obo $(ROBOT) convert -i $< -f owl -o $@ .PRECIOUS: $(TMPDIR)/external-disjoints.owl +# We get a version of the NCBITaxon slim that includes disjointness +# axioms between taxons. For the checks below, we need the *entire* +# slim, not just the classes that are used in Uberon. So to avoid making +# Uberon itself needlessly large, the slim will only be merged as part +# of the checks. +$(TMPDIR)/taxslim-disjoint-over-in-taxon.owl: + wget -O $@ http://purl.obolibrary.org/obo/ncbitaxon/taxslim-disjoint-over-in-taxon.owl + # We create a merged ontology consisting of # (1) Uberon itself; # (2) the external-disjoints component; -# (3) all the bridges to Uberon (except the EMAP bridge, which should +# (3) the taxslim including inter-taxon disjointness axioms; +# (4) all the bridges to Uberon (except the EMAP bridge, which should # probably be removed entirely from the repo anyway); # and we expand RO:0002175 (which was left unexpanded at the # preprocessing step, as it is only required for this check). @@ -642,8 +650,11 @@ $(TMPDIR)/external-disjoints.owl: components/external-disjoints.obo # Uberon, and the improper linking of a species AO class to an Uberon # class with a taxon constraints. ALL_UBERON_BRIDGES=$(shell ls $(BRIDGEDIR)/uberon-bridge-to-*.owl | grep -v emap.owl) -$(TMPDIR)/uberon-edit-plus-tax-equivs.owl: $(OWLSRC) $(TMPDIR)/external-disjoints.owl $(TMPDIR)/bridges +$(TMPDIR)/uberon-edit-plus-tax-equivs.owl: $(OWLSRC) $(TMPDIR)/external-disjoints.owl \ + $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl \ + $(TMPDIR)/bridges $(ROBOT) merge -i $< -i $(TMPDIR)/external-disjoints.owl \ + -i $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl \ $(foreach bridge, $(ALL_UBERON_BRIDGES), -i $(bridge)) \ expand \ convert -f ofn -o $@ @@ -669,8 +680,12 @@ extra-full-bridge-checks: $(foreach ao, $(EXTRA_FULL_CHECK_AO_LIST), $(REPORTDIR # A quick bridge check uses only uberon plus taxon constraints plus # bridging axioms, *not* the axioms in the source ontology itself. -$(REPORTDIR)/quick-bridge-check-%.txt: uberon.owl $(TMPDIR)/external-disjoints.owl $(TMPDIR)/bridges +$(REPORTDIR)/quick-bridge-check-%.txt: uberon.owl \ + $(TMPDIR)/external-disjoints.owl \ + $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl \ + $(TMPDIR)/bridges $(ROBOT) merge -i $< -i $(TMPDIR)/external-disjoints.owl \ + -i $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl \ -i $(BRIDGEDIR)/uberon-bridge-to-$*.owl \ reason -r ELK > $@ @@ -680,8 +695,13 @@ $(REPORTDIR)/quick-bridge-check-%.txt: uberon.owl $(TMPDIR)/external-disjoints.o # For this check, we separate the production of the merged ontology # from the production of the report. # 1. The merge -$(REPORTDIR)/bridge-check-%.owl: uberon.owl $(TMPDIR)/external-disjoints.owl $(TMPDIR)/bridges $(IMPORTDIR)/local-%.owl +$(REPORTDIR)/bridge-check-%.owl: uberon.owl \ + $(TMPDIR)/external-disjoints.owl \ + $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl \ + $(TMPDIR)/bridges \ + $(IMPORTDIR)/local-%.owl $(ROBOT) merge -i $< -i $(TMPDIR)/external-disjoints.owl \ + -i $(TMPDIR)/taxslim-disjoint-over-in-taxon.owl \ -i $(BRIDGEDIR)/uberon-bridge-to-$*.owl \ -i $(IMPORTDIR)/local-$*.owl \ convert -f ofn -o $@