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Updated vessel and vessel organ crosswalk #5

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merged 19 commits into from
Feb 22, 2024
Merged

Updated vessel and vessel organ crosswalk #5

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de6c7de
draft add vessel organ crosswalk
anitacaron Oct 12, 2023
ca6da21
update vessel_organ_crosswalk etl script
anitacaron Oct 18, 2023
4205527
update script to transform crosswalk into robot template
anitacaron Nov 24, 2023
deefda1
update_repo
anitacaron Nov 24, 2023
92cf7c9
update vessel_organ_crosswalk component
anitacaron Nov 24, 2023
e4ce07c
update ro and uberon imports
anitacaron Nov 24, 2023
f38c2a2
add `directly_supplies_drains` temp definition
anitacaron Feb 9, 2024
5b75501
apply flake8 black formatting
anitacaron Feb 9, 2024
13da24f
update imports
anitacaron Feb 22, 2024
7028da0
remove temporary RO property
anitacaron Feb 22, 2024
e8f6d2c
update vessels and vessel organ crosswalk
anitacaron Feb 22, 2024
cb5a695
update python script path
anitacaron Feb 22, 2024
8d0781b
fix path to python script
anitacaron Feb 22, 2024
4932307
Create vessel_ETL.py in etl directory
Feb 22, 2024
4c19f1b
Create utils.py in etl directory
Feb 22, 2024
ac8c125
Rename vessel_organ_crosswalk_ETL.py to vessel_organ_crosswalk_ETL.py
Feb 22, 2024
58a3239
Delete src/scripts/ETL/utils.py
Feb 22, 2024
ba96695
Delete src/scripts/ETL/vessel_ETL.py
Feb 22, 2024
4a9a859
fix typo in scripts folder name
anitacaron Feb 22, 2024
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6 changes: 5 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -41,4 +41,8 @@ src/ontology/imports/*_terms_combined.txt
src/patterns/data/**/*.ofn
src/patterns/data/**/*.txt
src/patterns/pattern_owl_seed.txt
src/patterns/all_pattern_terms.txt
src/patterns/all_pattern_terms.txt

src/scripts/etl/__init__.py
src/scripts/etl/__pycache__
.vscode
26 changes: 12 additions & 14 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for vccf
# Generated using ontology-development-kit
# ODK Version: v1.4
# ODK Version: v1.4.3
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vccf.Makefile instead

Expand Down Expand Up @@ -44,14 +44,14 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE)
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by
SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
ODK_VERSION_MAKEFILE = v1.4
ODK_VERSION_MAKEFILE = v1.4.3

TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
VERSION= $(TODAY)
ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output [email protected] && mv [email protected] $@
OTHER_SRC = $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/vessel_relation.owl
OTHER_SRC = $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/vessel_relation.owl $(COMPONENTSDIR)/vessel_organ_crosswalk.owl
ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt
EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl
PATTERNDIR= ../patterns
Expand Down Expand Up @@ -335,16 +335,6 @@ $(IMPORTDIR)/uberon_import.owl: $(MIRRORDIR)/uberon.owl $(IMPORTDIR)/uberon_term
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/uberon_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: ro

$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/ro_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
remove --base-iri $(URIBASE)/RO --axioms external --preserve-structure false --trim false \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/ro_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: omo

$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combined.txt
Expand Down Expand Up @@ -406,11 +396,19 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)


$(COMPONENTSDIR)/vessel_relation.owl: $(TEMPLATEDIR)/vessel_relation.tsv
if [ $(COMP) = true ] ; then $(ROBOT) template --input imports/ro_import.owl --prefix 'RO: http://purl.obolibrary.org/obo/RO_' --prefix 'VCCF: http://purl.obolibrary.org/obo/VCCF_' \
if [ $(COMP) = true ] ; then $(ROBOT) template --input imports/ro_import.owl --prefix 'VCCF: http://purl.obolibrary.org/obo/VCCF_' \
$(patsubst %, --template %, $^) \
$(ANNOTATE_CONVERT_FILE); fi

.PRECIOUS: $(COMPONENTSDIR)/vessel_relation.owl


$(COMPONENTSDIR)/vessel_organ_crosswalk.owl: $(TEMPLATEDIR)/vessel_organ_crosswalk.tsv
if [ $(COMP) = true ] ; then $(ROBOT) template --input imports/ro_import.owl --prefix 'VCCF: http://purl.obolibrary.org/obo/VCCF_' \
$(patsubst %, --template %, $^) \
$(ANNOTATE_CONVERT_FILE); fi

.PRECIOUS: $(COMPONENTSDIR)/vessel_organ_crosswalk.owl
# ----------------------------------------
# Mirroring upstream ontologies
# ----------------------------------------
Expand Down
8 changes: 1 addition & 7 deletions src/ontology/catalog-v001.xml
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Original file line number Diff line number Diff line change
@@ -1,17 +1,11 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">


<uri name="http://purl.obolibrary.org/obo/vccf/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/vccf/imports/uberon_import.obo" uri="imports/uberon_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/vccf/imports/ro_import.owl" uri="imports/ro_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/vccf/imports/omo_import.owl" uri="imports/omo_import.owl"/>




<uri name="http://purl.obolibrary.org/obo/vccf/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
<uri name="http://purl.obolibrary.org/obo/vccf/components/vessel_relation.owl" uri="components/vessel_relation.owl"/>
<uri name="http://purl.obolibrary.org/obo/vccf/components/vessel_organ_crosswalk.owl" uri="components/vessel_organ_crosswalk.owl"/>
</group>
</catalog>
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