diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 38cd188f3..b0abf9ce8 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -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: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index b48d3eda5..c78d4be7e 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 0fcd636feea85fce01a9e5009487aad06aedf4ba32833cb10c92bcf68fbc2cc2 +CONFIG_HASH= 3a5afcd02a25dc79d50036cccc5351438f736858c55ac01f7abd367aa2dd6172 # ---------------------------------------- @@ -63,7 +63,7 @@ PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern. TRANSLATIONSDIR= ../translations BABELONPY= babelon -q -TRANSLATIONS_OWL=$(TRANSLATIONSDIR)/hp-de.babelon.owl $(TRANSLATIONSDIR)/hp-it.babelon.owl $(TRANSLATIONSDIR)/hp-nl.babelon.owl $(TRANSLATIONSDIR)/hp-nl.synonyms.owl $(TRANSLATIONSDIR)/hp-fr.babelon.owl $(TRANSLATIONSDIR)/hp-fr.synonyms.owl $(TRANSLATIONSDIR)/hp-cs.babelon.owl $(TRANSLATIONSDIR)/hp-cs.synonyms.owl $(TRANSLATIONSDIR)/hp-pt.babelon.owl $(TRANSLATIONSDIR)/hp-pt.synonyms.owl $(TRANSLATIONSDIR)/hp-tr.babelon.owl $(TRANSLATIONSDIR)/hp-zh.babelon.owl $(TRANSLATIONSDIR)/hp-nna.babelon.owl $(TRANSLATIONSDIR)/hp-tw.babelon.owl $(TRANSLATIONSDIR)/hp-dtp.babelon.owl $(TRANSLATIONSDIR)/hp-ja.babelon.owl $(TRANSLATIONSDIR)/hp-es.babelon.owl +TRANSLATIONS_OWL=$(TRANSLATIONSDIR)/hp-de.babelon.owl $(TRANSLATIONSDIR)/hp-de.synonyms.owl $(TRANSLATIONSDIR)/hp-it.babelon.owl $(TRANSLATIONSDIR)/hp-it.synonyms.owl $(TRANSLATIONSDIR)/hp-nl.babelon.owl $(TRANSLATIONSDIR)/hp-nl.synonyms.owl $(TRANSLATIONSDIR)/hp-fr.babelon.owl $(TRANSLATIONSDIR)/hp-fr.synonyms.owl $(TRANSLATIONSDIR)/hp-cs.babelon.owl $(TRANSLATIONSDIR)/hp-cs.synonyms.owl $(TRANSLATIONSDIR)/hp-pt.babelon.owl $(TRANSLATIONSDIR)/hp-pt.synonyms.owl $(TRANSLATIONSDIR)/hp-tr.babelon.owl $(TRANSLATIONSDIR)/hp-tr.synonyms.owl $(TRANSLATIONSDIR)/hp-zh.babelon.owl $(TRANSLATIONSDIR)/hp-zh.synonyms.owl $(TRANSLATIONSDIR)/hp-nna.babelon.owl $(TRANSLATIONSDIR)/hp-tw.babelon.owl $(TRANSLATIONSDIR)/hp-dtp.babelon.owl $(TRANSLATIONSDIR)/hp-ja.babelon.owl $(TRANSLATIONSDIR)/hp-ja.synonyms.owl $(TRANSLATIONSDIR)/hp-es.babelon.owl $(TRANSLATIONSDIR)/hp-es.synonyms.owl TRANSLATIONS_TSV=$(TRANSLATIONSDIR)/hp-de-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-it-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-nl-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-fr-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-cs-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-pt-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-tr-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-zh-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-nna-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-tw-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-dtp-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-ja-preprocessed.babelon.tsv $(TRANSLATIONSDIR)/hp-es-preprocessed.babelon.tsv TRANSLATION_FILES=$(TRANSLATIONSDIR)/$(ONT)-all.babelon.tsv $(TRANSLATIONSDIR)/$(ONT)-all.babelon.json @@ -690,6 +690,9 @@ TRANSLATE_PREDICATES=rdfs:label $(TRANSLATIONSDIR)/hp-de.babelon.tsv: wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-de.babelon.tsv" -O $@ +$(TRANSLATIONSDIR)/hp-de.synonyms.tsv: + wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-de.synonyms.tsv" -O $@ + $(TRANSLATIONSDIR)/hp-de-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TRANSLATIONSDIR)/hp-de.babelon.tsv @@ -709,6 +712,9 @@ $(TRANSLATIONSDIR)/hp-de-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TR $(TRANSLATIONSDIR)/hp-it.babelon.tsv: wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-it.babelon.tsv" -O $@ +$(TRANSLATIONSDIR)/hp-it.synonyms.tsv: + wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-it.synonyms.tsv" -O $@ + $(TRANSLATIONSDIR)/hp-it-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TRANSLATIONSDIR)/hp-it.babelon.tsv @@ -816,6 +822,9 @@ $(TRANSLATIONSDIR)/hp-pt-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TR $(TRANSLATIONSDIR)/hp-tr.babelon.tsv: wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-tr.babelon.tsv" -O $@ +$(TRANSLATIONSDIR)/hp-tr.synonyms.tsv: + wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-tr.synonyms.tsv" -O $@ + $(TRANSLATIONSDIR)/hp-tr-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TRANSLATIONSDIR)/hp-tr.babelon.tsv @@ -835,6 +844,9 @@ $(TRANSLATIONSDIR)/hp-tr-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TR $(TRANSLATIONSDIR)/hp-zh.babelon.tsv: wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-zh.babelon.tsv" -O $@ +$(TRANSLATIONSDIR)/hp-zh.synonyms.tsv: + wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-zh.synonyms.tsv" -O $@ + $(TRANSLATIONSDIR)/hp-zh-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TRANSLATIONSDIR)/hp-zh.babelon.tsv @@ -909,7 +921,10 @@ $(TRANSLATIONSDIR)/hp-dtp-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(T $(TRANSLATIONSDIR)/hp-ja.babelon.tsv: - wget "https://raw.githubusercontent.com/ogishima/HPO-Japanese/master/HPO-japanese.alpha.21Jul2023.tsv" -O $@ + wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-ja.babelon.tsv" -O $@ + +$(TRANSLATIONSDIR)/hp-ja.synonyms.tsv: + wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-ja.synonyms.tsv" -O $@ @@ -930,6 +945,9 @@ $(TRANSLATIONSDIR)/hp-ja-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TR $(TRANSLATIONSDIR)/hp-es.babelon.tsv: wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-es.babelon.tsv" -O $@ +$(TRANSLATIONSDIR)/hp-es.synonyms.tsv: + wget "https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-es.synonyms.tsv" -O $@ + $(TRANSLATIONSDIR)/hp-es-preprocessed.babelon.tsv: $(TRANSLATIONS_ONTOLOGY) $(TRANSLATIONSDIR)/hp-es.babelon.tsv diff --git a/src/ontology/build-without-imports.sh b/src/ontology/build-without-imports.sh index 9c0debf31..47c0a1957 100644 --- a/src/ontology/build-without-imports.sh +++ b/src/ontology/build-without-imports.sh @@ -8,7 +8,6 @@ echo docker pull obolibrary/odkfull:$ODK ODK_TAG=$ODK sh run.sh make hpoa_clean -B test -f tmp/hpo-annotation-data/README.md -ODK_TAG=$ODK sh run.sh make MIR=false IMP=false prepare_release -B ODK_TAG=$ODK sh run.sh make MIR=false IMP=false babelon prepare_release -B ODK_TAG=$ODK sh run.sh make hpoa -B ODK_TAG=$ODK sh run.sh make hpo_diff -B diff --git a/src/ontology/hp-odk.yaml b/src/ontology/hp-odk.yaml index bc633100c..35044778b 100644 --- a/src/ontology/hp-odk.yaml +++ b/src/ontology/hp-odk.yaml @@ -109,13 +109,17 @@ babelon_translation_group: products: - id: hp-de auto_translate: FALSE + include_robot_template_synonyms: TRUE maintenance: mirror + mirror_synonyms_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-de.synonyms.tsv mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-de.babelon.tsv language: de - id: hp-it auto_translate: FALSE + include_robot_template_synonyms: TRUE maintenance: mirror mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-it.babelon.tsv + mirror_synonyms_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-it.synonyms.tsv language: it - id: hp-nl include_robot_template_synonyms: TRUE @@ -142,13 +146,17 @@ babelon_translation_group: mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-pt.babelon.tsv mirror_synonyms_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-pt.synonyms.tsv - id: hp-tr + include_robot_template_synonyms: TRUE language: tr maintenance: mirror mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-tr.babelon.tsv + mirror_synonyms_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-tr.synonyms.tsv - id: hp-zh + include_robot_template_synonyms: TRUE language: zh maintenance: mirror mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-zh.babelon.tsv + mirror_synonyms_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-zh.synonyms.tsv - id: hp-nna language: nna maintenance: mirror @@ -162,13 +170,17 @@ babelon_translation_group: maintenance: mirror mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-dtp.babelon.tsv - id: hp-ja + include_robot_template_synonyms: TRUE language: ja maintenance: mirror - mirror_babelon_from: https://raw.githubusercontent.com/ogishima/HPO-Japanese/master/HPO-japanese.alpha.21Jul2023.tsv + mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-ja.babelon.tsv + mirror_synonyms_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-ja.synonyms.tsv - id: hp-es + include_robot_template_synonyms: TRUE language: es maintenance: mirror mirror_babelon_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-es.babelon.tsv + mirror_synonyms_from: https://raw.githubusercontent.com/obophenotype/hpo-translations/main/babelon/hp-es.synonyms.tsv robot_report: release_reports: True fail_on : ERROR diff --git a/src/ontology/hp.Makefile b/src/ontology/hp.Makefile index 8b16d0c58..1fb388562 100644 --- a/src/ontology/hp.Makefile +++ b/src/ontology/hp.Makefile @@ -637,3 +637,5 @@ $(TMPDIR)/hp-%-merged.owl: hp-base.owl tmp/%.owl mappings: $(MAKE_FAST) ../mappings/hp-snomed.lexmatch.sssom.tsv +babelon: + pip install -U babelon==0.3.4 --break-system-packages \ No newline at end of file diff --git a/src/translations/hp-es.synonyms.tsv b/src/translations/hp-es.synonyms.tsv new file mode 100644 index 000000000..659eb1826 --- /dev/null +++ b/src/translations/hp-es.synonyms.tsv @@ -0,0 +1,2 @@ +subject_id translation_value comment +ID AL oboInOwl:hasExactSynonym@es diff --git a/src/translations/hp-it.synonyms.tsv b/src/translations/hp-it.synonyms.tsv new file mode 100644 index 000000000..db30ec402 --- /dev/null +++ b/src/translations/hp-it.synonyms.tsv @@ -0,0 +1,2 @@ +subject_id translation_value comment +ID AL oboInOwl:hasExactSynonym@it diff --git a/src/translations/hp-tr.synonyms.tsv b/src/translations/hp-tr.synonyms.tsv new file mode 100644 index 000000000..38c50ae4a --- /dev/null +++ b/src/translations/hp-tr.synonyms.tsv @@ -0,0 +1,2 @@ +subject_id translation_value comment +ID AL oboInOwl:hasExactSynonym@tr