Merge pull request #249 from obophenotype/marker_set

Marker set

Author: hkir-dev

src/dendrograms/Makefile

@@ -7,11 +7,12 @@ TEMPLATE_CLASS_CURATION_FILES = $(patsubst %, ../patterns/data/default/%_class_c
 TEMPLATE_CLASS_HOMOLOGOUS_FILES = $(patsubst %, ../patterns/data/default/%_class_homologous.tsv, $(JOBS))
 APP_SPECIFIC_TEMPLATE_FILES = $(patsubst %, ../templates/%_app_specific.tsv, $(JOBS))
 DATASET_TEMPLATE_FILES = $(patsubst %, ../templates/%_dataset.tsv, $(JOBS))
+MARKER_SET_TEMPLATE_FILES = $(patsubst %, ../patterns/data/default/%_marker_set.tsv, $(JOBS))
 TAXONOMY_TEMPLATE_FILE = ../templates/Taxonomies.tsv
 
 
 
-all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_BASE_FILES) $(TEMPLATE_CLASS_CURATION_FILES) $(MARKER_DENORMALIZED_FILES) $(TAXONOMY_TEMPLATE_FILE) $(APP_SPECIFIC_TEMPLATE_FILES) $(TEMPLATE_CLASS_HOMOLOGOUS_FILES) $(DATASET_TEMPLATE_FILES)
+all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_BASE_FILES) $(TEMPLATE_CLASS_CURATION_FILES) $(MARKER_DENORMALIZED_FILES) $(TAXONOMY_TEMPLATE_FILE) $(APP_SPECIFIC_TEMPLATE_FILES) $(TEMPLATE_CLASS_HOMOLOGOUS_FILES) $(DATASET_TEMPLATE_FILES) $(MARKER_SET_TEMPLATE_FILES)
 
 ../templates/%.tsv: %.json nomenclature_table_%.csv
 	if [ $< = CS1908210.json ]; then python ../scripts/template_runner.py generator -i $< -o $@ ;\
@@ -40,6 +41,10 @@ all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_BASE_FILES) $(TEMPLATE_CLASS_CURATION_FI
 ../templates/%_dataset.tsv: MOp_taxonomies_ontology/%_landingpage_dataset_info.csv
 	python ../scripts/template_runner.py generator -ds -i $< -o $@
 
+../patterns/data/default/%_marker_set.tsv: %.json nomenclature_table_%.csv
+	if [ $< = CS1908210.json ]; then python ../scripts/template_runner.py generator -ms -i $< -o $@ ;\
+	else python ../scripts/template_runner.py generator -ms -i $(word 2, $^) -o $@ ; fi
+
 ../templates/Taxonomies.tsv: MOp_taxonomies_ontology/Taxonomy_Info_Panel.csv
 	python ../scripts/template_runner.py generator -tx -i $< -o $@
 

src/ontology/bdso.Makefile

@@ -12,10 +12,12 @@ ONTBASE=                    $(URIBASE)/pcl
 
 TSV_CLASS_FILES = $(patsubst %, ../patterns/data/default/%_class.tsv, $(JOBS))
 TSV_CLASS_HOMOLOGOUS_FILES = $(patsubst %, ../patterns/data/default/%_class_homologous.tsv, $(JOBS))
+TSV_MARKER_SET_FILES = $(patsubst %, ../patterns/data/default/%_marker_set.tsv, $(JOBS))
 
 OWL_FILES = $(patsubst %, components/%.owl, $(JOBS))
 OWL_CLASS_FILES = $(patsubst %, components/%_class.owl, $(JOBS))
 OWL_CLASS_HOMOLOGOUS_FILES = $(patsubst %, components/%_class_homologous.owl, $(JOBS))
+OWL_MARKER_SET_FILES = $(patsubst %, components/%_marker_set.owl, $(JOBS))
 GENE_FILES = $(patsubst %, mirror/%.owl, $(GENE_LIST))
 OWL_APP_SPECIFIC_FILES = $(patsubst %, components/%_app_specific.owl, $(JOBS))
 OWL_DATASET_FILES = $(patsubst %, components/%_dataset.owl, $(JOBS))
@@ -62,6 +64,9 @@ $(PATTERNDIR)/data/default/%_class_curation.txt: $(PATTERNDIR)/data/default/%_cl
 $(PATTERNDIR)/data/default/%_class_homologous.txt: $(PATTERNDIR)/data/default/%_class_homologous.tsv $(TSV_CLASS_FILES) .FORCE
 	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$< --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_class_homologous.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$@; fi
 
+$(PATTERNDIR)/data/default/%_marker_set.txt: $(PATTERNDIR)/data/default/%_marker_set.tsv $(TSV_MARKER_SET_FILES) .FORCE
+	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$< --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_marker_set.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$@; fi
+
 $(PATTERNDIR)/data/default/Protein2GeneExpression.txt: $(PATTERNDIR)/data/default/Protein2GeneExpression.tsv .FORCE
 	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$< --template=$(PATTERNDIR)/dosdp-patterns/Protein2GeneExpression.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$@; fi
 
@@ -93,7 +98,7 @@ mirror/ensmusg.owl: ../templates/ensmusg.tsv .FORCE
 .PRECIOUS: imports/simple_marmoset_import.owl
 
 # merge all templates except application specific ones
-components/all_templates.owl: $(OWL_FILES) $(OWL_CLASS_FILES) $(OWL_MIN_MARKER_FILES) $(OWL_TAXONOMY_FILE) $(OWL_PROTEIN2GENE_FILE) $(OWL_APP_SPECIFIC_FILES) $(PCL_LEGACY_FILE) $(OWL_CLASS_HOMOLOGOUS_FILES) $(OWL_DATASET_FILES)
+components/all_templates.owl: $(OWL_FILES) $(OWL_CLASS_FILES) $(OWL_MIN_MARKER_FILES) $(OWL_TAXONOMY_FILE) $(OWL_PROTEIN2GENE_FILE) $(OWL_APP_SPECIFIC_FILES) $(PCL_LEGACY_FILE) $(OWL_CLASS_HOMOLOGOUS_FILES) $(OWL_DATASET_FILES) $(OWL_MARKER_SET_FILES)
 	$(ROBOT) merge $(patsubst %, -i %, $(filter-out $(OWL_APP_SPECIFIC_FILES), $^)) \
 	 --collapse-import-closure false \
 	 annotate --ontology-iri ${BDS_BASE}$@  \
@@ -118,6 +123,11 @@ components/%_class_homologous.owl: $(PATTERNDIR)/data/default/%_class_homologous
         --infile=$< --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_class_homologous.yaml \
         --ontology=$(SRC) --obo-prefixes=true --outfile=$@
 
+components/%_marker_set.owl: $(PATTERNDIR)/data/default/%_marker_set.tsv $(SRC) $(PATTERNDIR)/dosdp-patterns/taxonomy_marker_set.yaml $(SRC) all_imports .FORCE
+	$(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
+        --infile=$< --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_marker_set.yaml \
+        --ontology=$(SRC) --obo-prefixes=true --outfile=$@
+
 components/taxonomies.owl: ../templates/Taxonomies.tsv $(SRC)
 	$(ROBOT) template --input $(SRC) --template $< \
     		--add-prefixes template_prefixes.json \

src/ontology/helper.owl

@@ -27,4 +27,8 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002215> "capa
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002292> "expresses")
 
+# Object Property: <http://purl.obolibrary.org/obo/PCL_0010062> (has_characterizing_marker_set)
+
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010062> "has_characterizing_marker_set")
+
 )