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Remove injection of property chains over 'develops from'.
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For years, Uberon had been injecting the following property chains over
RO’s 'develops from' relation (RO:0002202):

  'develops from' o 'part of' SubPropertyOf 'develops from'

  'part of' o 'develops from' SubPropertyOf 'develops from'

An attempt to upstream those property chains into RO did not find any
support, and in fact the weak consensus is rather that those chains
serve no useful purpose (oborel/obo-relations#814).

So, we completely remove those chains from Uberon.
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gouttegd committed Feb 7, 2025
1 parent e775060 commit 10c7794
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Showing 4 changed files with 1 addition and 21 deletions.
1 change: 0 additions & 1 deletion src/ontology/catalog-v001.xml
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Expand Up @@ -43,7 +43,6 @@
<uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl" uri="bridge/uberon-bridge-to-wbbt.owl"/>
<uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbls.owl" uri="bridge/uberon-bridge-to-wbls.owl"/>
<uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-xao.owl" uri="bridge/uberon-bridge-to-xao.owl"/>
<uri name="http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl" uri="components/develops-from-chains.owl"/>
<uri name="http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl" uri="components/disjoint_union_over.owl"/>
<uri name="http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl" uri="components/hra_depiction_3d_images.owl"/>
<uri name="http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl" uri="components/hra_subset.owl"/>
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13 changes: 0 additions & 13 deletions src/ontology/components/develops-from-chains.owl

This file was deleted.

1 change: 0 additions & 1 deletion src/ontology/uberon-edit.obo
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Expand Up @@ -55,7 +55,6 @@ treat-xrefs-as-equivalent: VSAO
treat-xrefs-as-is_a: BFO
treat-xrefs-as-is_a: VHOG
remark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.
import: http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl
import: http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl
import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl
import: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl
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7 changes: 1 addition & 6 deletions src/ontology/uberon.Makefile
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Expand Up @@ -117,9 +117,6 @@ $(OWLSRC): $(SRC) $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv
-o $@

# Step 2: Reasoning.
# For the temporary injection of property chains, see
# <https://github.com/obophenotype/uberon/issues/2381>
DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl
# The 'materialize' step is too resource-intensive for the GitHub
# Action runners, so we leave it out when running online QC checks, see
# <https://github.com/obophenotype/uberon/pull/3087#issuecomment-1755553647>
Expand All @@ -128,13 +125,11 @@ MATERIALIZE=
else
MATERIALIZE = materialize -T $(CONFIGDIR)/basic_properties.txt -r elk
endif
$(POSTPROCESS_SRC): $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl $(DEVELOPS_FROM_CHAIN)
$(POSTPROCESS_SRC): $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl
$(ROBOT) merge -i $(OWLSRC) -i $(BRIDGEDIR)/uberon-bridge-to-bfo.owl \
-i $(DEVELOPS_FROM_CHAIN) \
relax $(MATERIALIZE) \
reason -r elk --exclude-duplicate-axioms true \
--equivalent-classes-allowed asserted-only \
unmerge -i $(DEVELOPS_FROM_CHAIN) \
annotate -O $(URIBASE)/uberon.owl -V $(RELEASE)/uberon.owl -o $@

# Step 3: Postprocessing. We merge some files that are derived from the
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