#97 equivalent_reification template merged with class template

obophenotype · Sep 8, 2021 · 191241b · 191241b
1 parent 29ac975
commit 191241b
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Showing 10 changed files with 165 additions and 760 deletions.
diff --git a/src/dendrograms/Makefile b/src/dendrograms/Makefile
@@ -1,29 +1,21 @@
 JOBS = CCN202002013 #CCN201912131 CCN201912132 CCN201908210 CCN201810310 CCN201908211
 
 TEMPLATE_FILES = $(patsubst %, ../templates/%.tsv, $(JOBS))
-TEMPLATE_CLASS_FILES = $(patsubst %, ../patterns/data/default/%_class.tsv, $(JOBS))
 MARKER_DENORMALIZED_FILES = $(patsubst %, ../markers/%_markers_denormalized.tsv, $(JOBS))
-EQUIVALENT_CLASS_MARKER_FILES = $(patsubst %, ../templates/%_equivalent_markers.tsv, $(JOBS))
-EQUIVALENT_CLASS_REIFICATION_FILES = $(patsubst %, ../patterns/data/default/%_equivalent_reification.tsv, $(JOBS))
+TEMPLATE_CLASS_FILES = $(patsubst %, ../patterns/data/default/%_class.tsv, $(JOBS))
 NOMENCLATURE_TEMPLATE_FILES = $(patsubst %, ../patterns/data/default/%_non_taxonomy_classification.tsv, $(JOBS))
 
 
-all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_FILES) $(MARKER_DENORMALIZED_FILES) $(EQUIVALENT_CLASS_MARKER_FILES) $(EQUIVALENT_CLASS_REIFICATION_FILES) $(NOMENCLATURE_TEMPLATE_FILES)
+all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_FILES) $(MARKER_DENORMALIZED_FILES) $(NOMENCLATURE_TEMPLATE_FILES)
 
 ../templates/%.tsv: %.json
  python ../scripts/template_runner.py $< $@
 
-../patterns/data/default/%_class.tsv: %.json
- python ../scripts/template_runner.py -c $< $@
-
 ../markers/%_markers_denormalized.tsv: %.json
  python ../scripts/template_runner.py -md $< $@
 
-../templates/%_equivalent_markers.tsv: %.json
- python ../scripts/template_runner.py -em $< $@
-
-../patterns/data/default/%_equivalent_reification.tsv: %.json
- python ../scripts/template_runner.py -er $< $@
+../patterns/data/default/%_class.tsv: %.json
+ python ../scripts/template_runner.py -c $< $@
 
 ../patterns/data/default/%_non_taxonomy_classification.tsv: %.json
  python ../scripts/template_runner.py -n $< $@

diff --git a/src/ontology/bdscratch.Makefile b/src/ontology/bdscratch.Makefile
@@ -10,7 +10,6 @@ BDS_BASE = http://www.semanticweb.org/brain_data_standards/
 
 OWL_FILES = $(patsubst %, components/%.owl, $(JOBS))
 OWL_CLASS_FILES = $(patsubst %, components/%_class.owl, $(JOBS))
-OWL_EQUIVALENT_CLASS_FILES = $(patsubst %, components/%_equivalent_class.owl, $(JOBS))
 GENE_FILES = $(patsubst %, mirror/%.owl, $(JOBS))
 OWL_NOMENCLATURE_FILES = $(patsubst %, components/%_non_taxonomy_classification.owl, $(JOBS))
 
@@ -43,8 +42,7 @@ dosdp_patterns_default: $(SRC) all_imports .FORCE
 # extract pattern terms even template name is different
 $(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/data/default/%.tsv .FORCE
  if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_class.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_class.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/data/default/CCN202002013_class.txt; fi
- if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_equivalent_reification.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_equivalent_class.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/data/default/CCN202002013_equivalent_reification.txt; fi
- if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_non_taxonomy_classification.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/CCN202002013_non_taxonomy_classification.txt; fi
+ if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_non_taxonomy_classification.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/data/default/CCN202002013_non_taxonomy_classification.txt; fi
 
 # hard wiring for now. Work on patsubst later
 mirror/ensmusg.owl: ../templates/ensmusg.tsv .FORCE
@@ -53,7 +51,7 @@ mirror/ensmusg.owl: ../templates/ensmusg.tsv .FORCE
  annotate --ontology-iri ${BDS_BASE}$@ \
  convert --format ofn --output $@; fi
 
-components/all_templates.owl: $(OWL_FILES) $(OWL_CLASS_FILES) $(OWL_EQUIVALENT_CLASS_FILES) $(OWL_MIN_MARKER_FILES) $(OWL_NOMENCLATURE_FILES)
+components/all_templates.owl: $(OWL_FILES) $(OWL_CLASS_FILES) $(OWL_MIN_MARKER_FILES) $(OWL_NOMENCLATURE_FILES)
  $(ROBOT) merge $(patsubst %, -i %, $^) \
  --collapse-import-closure false \
  annotate --ontology-iri ${BDS_BASE}$@ \
@@ -73,11 +71,6 @@ components/%_class.owl: ../patterns/data/default/%_class.tsv bdscratch-edit.owl
  --infile=$< --template=../patterns/dosdp-patterns/taxonomy_class.yaml \
  --ontology=$(SRC) --obo-prefixes=true --outfile=$@
 
-components/%_equivalent_class.owl: ../patterns/data/default/%_equivalent_reification.tsv ../patterns/dosdp-patterns/taxonomy_equivalent_class.yaml $(SRC) all_imports .FORCE
- $(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
- --infile=$< --template=../patterns/dosdp-patterns/taxonomy_equivalent_class.yaml \
- --ontology=$(SRC) --obo-prefixes=true --outfile=$@
-
 components/%_non_taxonomy_classification.owl: ../patterns/data/default/%_non_taxonomy_classification.tsv ../patterns/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml $(SRC) all_imports .FORCE
  $(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
  --infile=$< --template=../patterns/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml \