Skip to content

removed obsolated UBERON class life-death temporal boundary. To do so… #265

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
hoganwr merged 2 commits into from
Mar 13, 2026
Merged

removed obsolated UBERON class life-death temporal boundary. To do so… #265

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1cbb141
removed obsolated UBERON class life-death temporal boundary. To do so…
hoganwr Mar 6, 2026
34e84c5
not sure what this apollo-sv.owl file was doing here, but it's out of…
hoganwr Mar 6, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ These are the current imports in APOLLO_SV
| omrse | http://purl.obolibrary.org/obo/omrse.owl | slme |
| dron | http://purl.obolibrary.org/obo/dron.owl | filter |
| ogms | http://purl.obolibrary.org/obo/ogms.owl | filter |
| uberon | http://purl.obolibrary.org/obo/uberon.owl | filter |
## Components
Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

Expand Down
12 changes: 10 additions & 2 deletions src/ontology/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
# 3. [Update repo to latest ODK](update_repo)

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= f10687d13b9fb4d82c6a832e60b296d76dadc31432fe22bb1f06ab3cc66d4a02
CONFIG_HASH= 0625a31aff99dcab0d48bca6e3dddd2614c7f65055668a9ae139332d9e4f5f5f


# ----------------------------------------
Expand Down Expand Up @@ -193,7 +193,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = ro geo ido mf go iao omrse dron ogms
IMPORTS = ro geo ido mf go iao omrse dron ogms uberon

IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -647,6 +647,14 @@ mirror-ogms: | $(TMPDIR)
$(ROBOT) remove -i $(TMPDIR)/ogms-download.owl --base-iri http://purl.obolibrary.org/obo/OGMS_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl


## ONTOLOGY: uberon
.PHONY: mirror-uberon
.PRECIOUS: $(MIRRORDIR)/uberon.owl
mirror-uberon: | $(TMPDIR)
curl -L $(OBOBASE)/uberon.owl --create-dirs -o $(TMPDIR)/uberon-download.owl --retry 4 --max-time 200 && \
$(ROBOT) remove -i $(TMPDIR)/uberon-download.owl --base-iri http://purl.obolibrary.org/obo/UBERON_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl


$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
Expand Down
30,071 changes: 0 additions & 30,071 deletions src/ontology/apollo-sv.owl
View file
Open in desktop

This file was deleted.

240 changes: 10 additions & 230 deletions src/ontology/apollo_sv-edit.owl
View file
Open in desktop

Large diffs are not rendered by default.

5 changes: 5 additions & 0 deletions src/ontology/apollo_sv-odk.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,11 @@ import_group:
make_base: true
base_iris:
- http://purl.obolibrary.org/obo/OGMS_
- id: uberon
module_type: filter
make_base: true
base_iris:
- http://purl.obolibrary.org/obo/UBERON_
use_custom_import_module: TRUE
robot_java_args: '-Xmx16G'
custom_makefile_header: |
Expand Down
1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/omrse_import.owl" uri="imports/omrse_import.owl" />
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/dron_import.owl" uri="imports/dron_import.owl" />
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/ogms_import.owl" uri="imports/ogms_import.owl" />
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/uberon_import.owl" uri="imports/uberon_import.owl" />
</group>
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public">
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/ro_import.obo" uri="imports/ro_import.obo" />
Expand Down
8 changes: 0 additions & 8 deletions src/ontology/imports/ido_import.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000045>))
Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000063>))
Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000087>))
Declaration(Class(<http://purl.obolibrary.org/obo/TRANS_0000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0035944>))
Declaration(Class(<http://www.geneontology.org/formats/oboInOwl#ObsoleteClass>))
Declaration(Class(<http://www.geneontology.org/formats/oboInOwl#Subset>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
Expand Down Expand Up @@ -1635,13 +1634,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000412> <http://purl.ob
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/TRANS_0000000> "transmission process")
SubClassOf(<http://purl.obolibrary.org/obo/TRANS_0000000> <http://purl.obolibrary.org/obo/BFO_0000015>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0035944> (life-death temporal boundary)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0035944> "A life cycle temporal boundary that marks the end of the life cycle of the organism.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000412> <http://purl.obolibrary.org/obo/UBERON_0035944> <http://purl.obolibrary.org/obo/uberon.owl>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0035944> "life-death temporal boundary")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0035944> <http://purl.obolibrary.org/obo/BFO_0000015>)

# Class: <http://www.geneontology.org/formats/oboInOwl#ObsoleteClass> (Obsolete Class)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#ObsoleteClass> "Obsolete Class")
Expand Down
10 changes: 0 additions & 10 deletions src/ontology/imports/omrse_import.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9443>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9606>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000245>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0200000>))
Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000045>))
Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000096>))
Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000097>))
Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000100>))
Expand Down Expand Up @@ -2555,15 +2554,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.ob
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0200000> "data transformation"@en)
SubClassOf(<http://purl.obolibrary.org/obo/OBI_0200000> <http://purl.obolibrary.org/obo/COB_0000035>)

# Class: <http://purl.obolibrary.org/obo/OGMS_0000045> (disorder)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OGMS_0000045> "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OGMS_0000045> "Albert Goldfain")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OGMS_0000045> "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/OGMS_0000045> "creation date: 2009-06-23T11:39:44Z")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OGMS_0000045> "disorder")
SubClassOf(<http://purl.obolibrary.org/obo/OGMS_0000045> <http://purl.obolibrary.org/obo/BFO_0000040>)

# Class: <http://purl.obolibrary.org/obo/OGMS_0000096> (health care process)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OGMS_0000096> "A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient"@en)
Expand Down
18 changes: 1 addition & 17 deletions src/ontology/imports/ro_import.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000061>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000465>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0010000>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000054>))
Expand Down Expand Up @@ -211,9 +210,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#commo
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#human_subset>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#mouse_subset>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#uberon_slim>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#upper_level>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#vertebrate_core>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
Expand Down Expand Up @@ -450,7 +447,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://www.gen
AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> "has broad synonym"@en)
AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> "has_broad_synonym")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (database_cross_reference)
# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (has cross-reference)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.")
Expand Down Expand Up @@ -2249,19 +2246,6 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001062> "
EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0001062> ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0020105>))
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001062> <http://purl.obolibrary.org/obo/BFO_0000004>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0010000> (multicellular anatomical structure)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "CARO:0010000") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0010000> "An anatomical structure that has more than one cell as a part.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0010000> "CARO:0010000")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBbt:00100313") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular structure")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0010000> "UBERON:0010000")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#common_anatomy>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#human_subset>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#mouse_subset>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#upper_level>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular anatomical structure")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/UBERON_0000061>)


############################
# Named Individuals
Expand Down
Loading