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Add taxslim-disjoint-over-in-taxon.owl to the pipeline #2928

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Add taxslim-disjoint-over-in-taxon.owl to the pipeline #2928

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819a775
merge taxslim-disjoint-over-in-taxon in pipeline
anitacaron Jun 16, 2023
0a29862
update ncbitaxon_terms based on the edit file
anitacaron Jun 16, 2023
dad24f9
update taxslim-disjoint-over-in-taxon
anitacaron Jun 19, 2023
6631160
remove wings never_in_taxon Sauropsida
anitacaron Jun 20, 2023
e954525
Taxon disjointness unsat not showing up in pipeline
anitacaron Jul 20, 2023
149e472
Making induction relation between suture and DM mammal-only
anitacaron Jul 21, 2023
09caf74
Making induction relation between suture and DM mammal-only (#2978)
cmungall Sep 5, 2023
9d70842
Merge branch 'master' into issue2707
gouttegd Sep 6, 2023
49e2930
replace `taxslim-disjoint-over-in-taxon.owl` with `mirror/ncbitaxon.owl`
anitacaron Sep 13, 2023
a3f1092
Merge taxon disjointness axioms when doing the bridge checks.
gouttegd Sep 19, 2023
6c97be8
Merge branch 'master' into anitacaron/issue2707
Oct 11, 2023
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249 changes: 248 additions & 1 deletion src/ontology/imports/ncbitaxon_terms.txt
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Original file line number Diff line number Diff line change
@@ -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
3 changes: 1 addition & 2 deletions src/ontology/uberon-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -76309,7 +76308,7 @@ 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]
Expand Down
41 changes: 33 additions & 8 deletions src/ontology/uberon.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -109,9 +109,10 @@ quick-qc: $(REPORTDIR)/uberon-edit-obscheck.txt
# ----------------------------------------
# BUILDING UBERON ITSELF
# ----------------------------------------

# Step 1: Preprocessing. We Merge the edit file file with imports,
# disjointness axioms, and list of contributors, then expand macros.
# FIXME: Need explanation for not expanding RO:0002175 specifically.
# 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
@echo "STRONG WARNING: issues/contributor.owl needs to be manually updated."
$(ROBOT) merge -i $< \
Expand Down Expand Up @@ -410,7 +411,7 @@ $(TMPDIR)/uberon-taxon-constraints.obo: $(SRC)
cat [email protected] $(COMPONENTSDIR)/taxon_relations.obo > $@

$(TMPDIR)/uberon-taxon-constraints.owl: $(TMPDIR)/uberon-taxon-constraints.obo
$(OWLTOOLS) $< --expand-macros -o $@
$(ROBOT) expand --input $< -o $@


# %-xf: Product without "non-subclass cross-references"?
Expand Down Expand Up @@ -629,18 +630,33 @@ $(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
# probably be removed entirely from the repo anyway).
# (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).
# 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 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 $@
.PRECIOUS: $(TMPDIR)/uberon-edit-plus-tax-equivs.owl

Expand All @@ -664,8 +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 > $@

Expand All @@ -675,8 +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 $@
Expand Down
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