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Merge pull request #262 from mcwdsi/minor-fixes
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Removes FMA and updates ontology annotations
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@hoganwr
hoganwr authored Jan 24, 2025
2 parents 576778e + 8e94b1c commit 21938c0
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Showing 11 changed files with 5,064 additions and 4,747 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/qc.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5.2
container: obolibrary/odkfull:v1.5.4

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
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3 changes: 2 additions & 1 deletion docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -25,9 +25,10 @@ These are the current imports in OMRSE
| oae | http://purl.obolibrary.org/obo/oae.owl | None |
| pco | http://purl.obolibrary.org/obo/pco.owl | None |
| bfo | http://purl.obolibrary.org/obo/bfo.owl | slme |
| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | filter |
| oostt | http://purl.obolibrary.org/obo/oostt.owl | None |
| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
| pno | http://purl.obolibrary.org/obo/iao/pno.owl | mirror |
| iao | http://purl.obolibrary.org/obo/iao.owl | mirror |
| d-acts | http://purl.obolibrary.org/obo/iao/d-acts.owl | filter |
| geo | http://purl.obolibrary.org/obo/geo.owl | None |
| mf | http://purl.obolibrary.org/obo/mf.owl | None |
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40 changes: 29 additions & 11 deletions src/ontology/Makefile
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@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for omrse
# Generated using ontology-development-kit
# ODK Version: v1.5.2
# ODK Version: v1.5.4
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use omrse.Makefile instead

Expand All @@ -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= e982da79af6e23c70c7eacfef4b1468d45fe5e4f48d15d34bbff904800ec1fb4
CONFIG_HASH= b702d082982fc2813887ba9432052e4a47f0ea1b41fc62348d450d34d4ef7d1b


# ----------------------------------------
Expand Down Expand Up @@ -53,7 +53,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE)
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference iri-range
SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
ODK_VERSION_MAKEFILE = v1.5.2
ODK_VERSION_MAKEFILE = v1.5.4

TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
Expand Down Expand Up @@ -166,7 +166,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = ro ogms obi apollo_sv obib go oae pco bfo oostt omo pno d-acts geo mf
IMPORTS = ro ogms obi apollo_sv obib go oae pco bfo ncbitaxon oostt omo iao d-acts geo mf

IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -425,15 +425,25 @@ $(IMPORTDIR)/bfo_import.owl: $(MIRRORDIR)/bfo.owl $(IMPORTDIR)/bfo_terms_combine
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: ncbitaxon

$(IMPORTDIR)/ncbitaxon_import.owl: $(MIRRORDIR)/ncbitaxon.owl $(IMPORTDIR)/ncbitaxon_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/ncbitaxon_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
remove --base-iri http://purl.obolibrary.org/obo/NCBITaxon_ --axioms external --preserve-structure false --trim false \
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/ncbitaxon_terms_combined.txt --select complement \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: omo

$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: pno
## Module for ontology: iao

$(IMPORTDIR)/pno_import.owl: $(MIRRORDIR)/pno.owl $(IMPORTDIR)/pno_terms_combined.txt
$(IMPORTDIR)/iao_import.owl: $(MIRRORDIR)/iao.owl $(IMPORTDIR)/iao_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

Expand Down Expand Up @@ -583,6 +593,13 @@ mirror-bfo: | $(TMPDIR)
$(ROBOT) convert -i $(TMPDIR)/bfo-download.owl -o $(TMPDIR)/$@.owl


## ONTOLOGY: ncbitaxon
.PHONY: mirror-ncbitaxon
.PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl
mirror-ncbitaxon: | $(TMPDIR)
$(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $(TMPDIR)/$@.owl


## ONTOLOGY: oostt
.PHONY: mirror-oostt
.PRECIOUS: $(MIRRORDIR)/oostt.owl
Expand All @@ -599,11 +616,12 @@ mirror-omo: | $(TMPDIR)
$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl


## ONTOLOGY: pno
.PHONY: mirror-pno
.PRECIOUS: $(MIRRORDIR)/pno.owl
mirror-pno: | $(TMPDIR)
$(ROBOT) convert -I http://purl.obolibrary.org/obo/iao/pno.owl -o $(TMPDIR)/$@.owl
## ONTOLOGY: iao
.PHONY: mirror-iao
.PRECIOUS: $(MIRRORDIR)/iao.owl
mirror-iao: | $(TMPDIR)
curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl


## ONTOLOGY: d-acts
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5 changes: 4 additions & 1 deletion src/ontology/catalog-v001.xml
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@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/omrse/releases/2025-01-18/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/omrse/releases/2023-09-08/imports/mf_import.owl" uri="imports/mf_import.owl"/>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/omrse/external_import.owl" uri="imports/external_import.owl"/>
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
Expand Down Expand Up @@ -34,7 +35,9 @@
<uri name="http://purl.obolibrary.org/obo/omrse/imports/geo_import.obo" uri="imports/geo_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/omrse/imports/mf_import.owl" uri="imports/mf_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/omrse/imports/mf_import.obo" uri="imports/mf_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/omrse/components/pno.owl" uri="components/pno.owl"/>
<uri name="http://purl.obolibrary.org/obo/omrse/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/omrse/imports/ncbitaxon_import.obo" uri="imports/ncbitaxon_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/omrse/imports/iao.owl" uri="imports/iao.owl"/>
<uri name="http://purl.obolibrary.org/obo/omrse/components/d-acts.owl" uri="components/d-acts.owl"/>
<uri name="http://purl.obolibrary.org/obo/omrse/components/import_terms.owl" uri="components/import_terms.owl"/>
<uri name="http://purl.obolibrary.org/obo/omrse/language-individuals/" uri="components/language/language-individuals.owl"/>
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5 changes: 5 additions & 0 deletions src/ontology/imports/external_import.owl
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Expand Up @@ -25,6 +25,11 @@ Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0021009>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0021031>))
Declaration(Class(<http://purl.obolibrary.org/obo/MF_0000030>))
Declaration(Class(<http://purl.obolibrary.org/obo/MF_0000031>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_131567>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2759>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_40674>))
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/OAE_0000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/OAE_0000067>))
Declaration(Class(<http://purl.obolibrary.org/obo/OAE_0002807>))
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