Unified DOSDP template

src/config/config_schema.json

@@ -56,6 +56,13 @@
             "description": "Brain region abbreviation."
           }
         },
+        "Reference_gene_list": {
+          "type": "array",
+          "items": {
+            "type": "string",
+            "description": "Reference gene list."
+          }
+        },
         "Root_nodes": {
           "type": "array",
           "items": {

src/dendrograms/Makefile

@@ -1,34 +1,26 @@
 JOBS = CCN202002013 #CCN201912131 CCN201912132 CCN201908210 CCN201810310 CCN201908211
 
 TEMPLATE_FILES = $(patsubst %, ../templates/%.tsv, $(JOBS))
-TEMPLATE_CLASS_FILES = $(patsubst %, ../patterns/data/bds/%_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/bds/%_equivalent_reification.tsv, $(JOBS))
-TEMPLATE_MINIMAL_MARKER_FILES = $(patsubst %, ../patterns/data/bds/%_minimal_markers.tsv, $(JOBS))
-NOMENCLATURE_TEMPLATE_FILES = $(patsubst %, ../patterns/data/bds/%_non_taxonomy_classification.tsv, $(JOBS))
+TEMPLATE_CLASS_BASE_FILES = $(patsubst %, ../patterns/data/default/%_class_base.tsv, $(JOBS))
+TEMPLATE_CLASS_CURATION_FILES = $(patsubst %, ../patterns/data/default/%_class_curation.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) $(TEMPLATE_MINIMAL_MARKER_FILES) $(NOMENCLATURE_TEMPLATE_FILES)
+all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_BASE_FILES) $(TEMPLATE_CLASS_CURATION_FILES) $(MARKER_DENORMALIZED_FILES) $(NOMENCLATURE_TEMPLATE_FILES)
 
 ../templates/%.tsv: %.json
-	python ../scripts/template_runner.py $< $@
-
-../patterns/data/bds/%_class.tsv: %.json
-	python ../scripts/template_runner.py -c $< $@
+	python ../scripts/template_runner.py generator -i $< -o $@
 
 ../markers/%_markers_denormalized.tsv: %.json
-	python ../scripts/template_runner.py -md $< $@
-
-../templates/%_equivalent_markers.tsv: %.json
-	python ../scripts/template_runner.py -em $< $@
+	python ../scripts/template_runner.py generator -md -i $< -o $@
 
-../patterns/data/bds/%_equivalent_reification.tsv: %.json
-	python ../scripts/template_runner.py -er $< $@
+../patterns/data/default/%_class_base.tsv: %.json
+	python ../scripts/template_runner.py generator -cb -i $< -o $@
 
-../patterns/data/bds/%_minimal_markers.tsv: %.json
-	python ../scripts/template_runner.py -mm $< $@
+../patterns/data/default/%_class_curation.tsv: %.json
+	python ../scripts/template_runner.py generator -cc -i $< -o $@
 
-../patterns/data/bds/%_non_taxonomy_classification.tsv: %.json
-	python ../scripts/template_runner.py -n $< $@
+../patterns/data/default/%_non_taxonomy_classification.tsv: %.json
+	python ../scripts/template_runner.py generator -n -i $< -o $@
 

src/dendrograms/taxonomy_details.yaml

@@ -12,6 +12,8 @@
     - UBERON:0001384
   Brain_region_abbv:
     - MOp
+  Reference_gene_list:
+    - Ensmusg
   Root_nodes:
     - Node: CS202002013_123
       Cell_type: CL:0011005 
@@ -143,6 +145,8 @@
     - NCBITaxon:9606
   Brain_region:
     - UBERON:0001384
+  Reference_gene_list:
+    - Ensg
   Root_nodes:
     - Node: CS201912131_149
       Cell_type: CL:0011005 
@@ -171,34 +175,27 @@
   non_taxonomy_roots:      
     - Node: CS201912131_128
       Cell_type: CL:4023011
-      Location_relation: has_soma_location
       #Lamp5
     - Node: CS201912131_129
       Cell_type: CL:4023015
-      Location_relation: has_soma_location
       #Sncg
     - Node: CS201912131_130
       Cell_type: CL:4023016
-      Location_relation: has_soma_location
       #Vip
     - Node: CS201912131_131
       Cell_type: CL:4023017
-      Location_relation: has_soma_location
       #Sst
     - Node: CS201912131_132
       Cell_type: CL:4023018
-      Location_relation: part_of
       #Pvalb
     - Node: CS201912131_147
       Cell_type: CL:0002453
-      Location_relation: part_of
       #OPC
     - Node: CS201912131_151
       Cell_type: CL:0000125
       # non-neuronal currently mapped as glial cell
     - Node: CS201912131_140
       Cell_type: CL:0000128
-      Location_relation: part_of
       #Oligodendrocyte
 -
   Taxonomy_id: CCN201912132
@@ -210,9 +207,11 @@
     - NCBITaxon:9483
   Brain_region:
     - UBERON:0001384
+  Reference_gene_list:
+    - Enscjag
   Root_nodes:
     - Node: CS201912132_116
-      Cell_type: CL:0011005 
+      Cell_type: CL:0011005
       Location_relation: has_soma_location
       #GABAergic interneuron
     - Node: CS201912132_117
@@ -246,27 +245,21 @@
   non_taxonomy_roots:  
     - Node: CS201912132_105
       Cell_type: CL:0000128
-      Location_relation: part_of
       #Oligodendrocyte
     - Node: CS201912132_95
       Cell_type: CL:4023011
-      Location_relation: has_soma_location
       #Lamp5
     - Node: CS201912132_96
       Cell_type: CL:4023015
-      Location_relation: has_soma_location
       #Sncg
     - Node: CS201912132_97
       Cell_type: CL:4023016
-      Location_relation: has_soma_location
       #Vip
     - Node: CS201912132_98
       Cell_type: CL:4023017
-      Location_relation: has_soma_location
       #Sst
     - Node: CS201912132_99
       Cell_type: CL:4023018
-      Location_relation: part_of
       #Pvalb
     - Node: CS201912131_151
       Cell_type: CL:0000125