#97 robot to dosdp migration completed except individuals

obophenotype · Aug 12, 2021 · 633bd1e · 633bd1e
1 parent 19bdc80
commit 633bd1e
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Showing 21 changed files with 164,312 additions and 60,516 deletions.
diff --git a/bdscratch-full.owl b/bdscratch-full.owl
diff --git a/src/dendrograms/Makefile b/src/dendrograms/Makefile
@@ -1,20 +1,20 @@
 JOBS = CCN202002013 #CCN201908210 CCN201810310 CCN201908211
 
 TEMPLATE_FILES = $(patsubst %, ../templates/%.tsv, $(JOBS))
-TEMPLATE_CLASS_FILES = $(patsubst %, ../templates/%_class.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 %, ../templates/%_equivalent_reification.tsv, $(JOBS))
-TEMPLATE_MINIMAL_MARKER_FILES = $(patsubst %, ../templates/%_minimal_markers.tsv, $(JOBS))
-NOMENCLATURE_TEMPLATE_FILES = $(patsubst %, ../templates/%_non_taxonomy_classification.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))
 
 
 all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_FILES) $(MARKER_DENORMALIZED_FILES) $(EQUIVALENT_CLASS_MARKER_FILES) $(EQUIVALENT_CLASS_REIFICATION_FILES) $(TEMPLATE_MINIMAL_MARKER_FILES) $(NOMENCLATURE_TEMPLATE_FILES)
 
 ../templates/%.tsv: %.json
 	python ../scripts/template_runner.py $< $@
 
-../templates/%_class.tsv: %.json
+../patterns/data/bds/%_class.tsv: %.json
 	python ../scripts/template_runner.py -c $< $@
 
 ../markers/%_markers_denormalized.tsv: %.json
@@ -23,12 +23,12 @@ all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_FILES) $(MARKER_DENORMALIZED_FILES) $(EQ
 ../templates/%_equivalent_markers.tsv: %.json
 	python ../scripts/template_runner.py -em $< $@
 
-../templates/%_equivalent_reification.tsv: %.json
+../patterns/data/bds/%_equivalent_reification.tsv: %.json
 	python ../scripts/template_runner.py -er $< $@
 
-../templates/%_minimal_markers.tsv: %.json
+../patterns/data/bds/%_minimal_markers.tsv: %.json
 	python ../scripts/template_runner.py -mm $< $@
 
-../templates/%_non_taxonomy_classification.tsv: %.json
+../patterns/data/bds/%_non_taxonomy_classification.tsv: %.json
 	python ../scripts/template_runner.py -n $< $@
 
diff --git a/src/ontology/bdscratch.Makefile b/src/ontology/bdscratch.Makefile
@@ -31,11 +31,10 @@ $(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERND
 	if [ $(PAT) = true ]; then $(DOSDPT) terms --prefixes=template_prefixes.yaml --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi
 
 # hard wiring for now.  Work on patsubst later
-mirror/ensmusg.owl: ../templates/ensmusg.tsv
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) template --input bdscratch-edit.owl --template $< \
-      --add-prefixes template_prefixes.json \
-      annotate --ontology-iri ${BDS_BASE}$@ \
-      convert --format ofn --output $@; fi
+mirror/ensmusg.owl: ../patterns/data/bds/ensmusg_data.tsv ../patterns/dosdp-patterns/ensmusg.yaml bdscratch-edit.owl
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
+        --infile=$< --template=../patterns/dosdp-patterns/ensmusg.yaml \
+        --ontology=bdscratch-edit.owl --obo-prefixes=true --outfile=$@; fi
 
 components/all_templates.owl: $(OWL_FILES) $(OWL_CLASS_FILES) $(OWL_EQUIVALENT_CLASS_FILES) $(OWL_MIN_MARKER_FILES) $(OWL_NOMENCLATURE_FILES)
 	$(ROBOT) merge $(patsubst %, -i %, $^) \
@@ -52,27 +51,23 @@ components/%.owl: ../templates/%.tsv bdscratch-edit.owl
     		annotate --ontology-iri ${BDS_BASE}$@ \
     		convert --format ofn --output $@
 
-components/%_class.owl: ../templates/%_class.tsv bdscratch-edit.owl
-	$(ROBOT) template --input bdscratch-edit.owl --template $< \
-    		--add-prefixes template_prefixes.json \
-    		annotate --ontology-iri ${BDS_BASE}$@ \
-    		convert --format ofn --output $@
-
-components/%_equivalent_class.owl: ../templates/%_equivalent_reification.tsv bdscratch-edit.owl
-	$(ROBOT) template --input bdscratch-edit.owl --template $< \
-	        --add-prefixes template_prefixes.json \
-    		annotate --ontology-iri ${BDS_BASE}$@ \
-    		convert --format ofn --output $@
-
-components/%_minimal_markers.owl: ../templates/%_minimal_markers.tsv bdscratch-edit.owl
-	$(ROBOT) template --input bdscratch-edit.owl --template $< \
-    		--add-prefixes template_prefixes.json \
-    		annotate --ontology-iri ${BDS_BASE}$@ \
-    		convert --format ofn --output $@
-
-components/%_non_taxonomy_classification.owl: ../templates/%_non_taxonomy_classification.tsv bdscratch-edit.owl
-	$(ROBOT) template --input bdscratch-edit.owl --template $< \
-    		--add-prefixes template_prefixes.json \
-    		annotate --ontology-iri ${BDS_BASE}$@ \
-    		convert --format ofn --output $@
+components/%_class.owl: ../patterns/data/bds/%_class.tsv bdscratch-edit.owl ../patterns/dosdp-patterns/taxonomy_class.yaml bdscratch-edit.owl
+	$(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
+        --infile=$< --template=../patterns/dosdp-patterns/taxonomy_class.yaml \
+        --ontology=bdscratch-edit.owl --obo-prefixes=true --outfile=$@
+
+components/%_equivalent_class.owl: ../patterns/data/bds/%_equivalent_reification.tsv ../patterns/dosdp-patterns/taxonomy_equivalent_class.yaml bdscratch-edit.owl
+	$(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
+        --infile=$< --template=../patterns/dosdp-patterns/taxonomy_equivalent_class.yaml \
+        --ontology=bdscratch-edit.owl --obo-prefixes=true --outfile=$@
+
+components/%_minimal_markers.owl: ../patterns/data/bds/%_minimal_markers.tsv ../patterns/dosdp-patterns/taxonomy_minimal_markers.yaml bdscratch-edit.owl
+	$(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
+        --infile=$< --template=../patterns/dosdp-patterns/taxonomy_minimal_markers.yaml \
+        --ontology=bdscratch-edit.owl --obo-prefixes=true --outfile=$@
+
+components/%_non_taxonomy_classification.owl: ../patterns/data/bds/%_non_taxonomy_classification.tsv ../patterns/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml bdscratch-edit.owl
+	$(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
+        --infile=$< --template=../patterns/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml \
+        --ontology=bdscratch-edit.owl --obo-prefixes=true --outfile=$@
 
diff --git a/...terns/data/default/CCN202002013_class.tsv → src/patterns/data/bds/CCN202002013_class.tsv b/...terns/data/default/CCN202002013_class.tsv → src/patterns/data/bds/CCN202002013_class.tsv
diff --git a/...t/CCN202002013_equivalent_reification.tsv → ...s/CCN202002013_equivalent_reification.tsv b/...t/CCN202002013_equivalent_reification.tsv → ...s/CCN202002013_equivalent_reification.tsv
diff --git a/.../default/CCN202002013_minimal_markers.tsv → ...data/bds/CCN202002013_minimal_markers.tsv b/.../default/CCN202002013_minimal_markers.tsv → ...data/bds/CCN202002013_minimal_markers.tsv
diff --git a/...202002013_non_taxonomy_classification.tsv → ...202002013_non_taxonomy_classification.tsv b/...202002013_non_taxonomy_classification.tsv → ...202002013_non_taxonomy_classification.tsv
diff --git a/src/templates/ensmusg.tsv → src/patterns/data/bds/ensmusg_data.tsv b/src/templates/ensmusg.tsv → src/patterns/data/bds/ensmusg_data.tsv
@@ -1,5 +1,4 @@
-ID	TYPE	NAME
-ID	SC %	A rdfs:label
+defined_class	TYPE	NAME
 ensembl:ENSMUSG00000064372	SO:0000704	mt-Tp
 ensembl:ENSMUSG00000064371	SO:0000704	mt-Tt
 ensembl:ENSMUSG00000064370	SO:0000704	mt-Cytb

diff --git a/src/patterns/dosdp-patterns/ensmusg.yaml b/src/patterns/dosdp-patterns/ensmusg.yaml
@@ -0,0 +1,27 @@
+pattern_name: bdsEnsmusg
+pattern_iri: http://purl.obolibrary.org/obo/odk/bdsEnsmusg.yaml
+description: "Ensmusg template for BDS."
+
+classes:
+  "thing": "owl:Thing"
+
+vars:
+  TYPE: "'thing'"
+
+data_vars:
+  NAME: "xsd:string"
+
+annotationProperties:
+  rdfsLabel: "rdfs:label"
+
+logical_axioms:
+   - axiom_type: subClassOf
+     text: "%s"
+     vars:
+        - TYPE
+
+annotations:
+  - annotationProperty: rdfsLabel
+    text: "%s"
+    vars:
+      - NAME
diff --git a/src/patterns/dosdp-patterns/taxonomy_equivalent_class.yaml b/src/patterns/dosdp-patterns/taxonomy_equivalent_class.yaml
@@ -18,7 +18,7 @@ logical_axioms:
      text: "'has_exemplar' value %s"
      vars:
         - Exemplar_SC
-   - axiom_type: subClassOf
+   - axiom_type: equivalentTo
      text: "'native_cell' and 'has_exemplar' value %s"
      vars:
         - Exemplar
diff --git a/src/scripts/template_generation_tools.py b/src/scripts/template_generation_tools.py
@@ -79,32 +79,31 @@ def generate_curated_class_template(dend_json_path, output_filepath):
 
     if taxonomy_config:
         subtrees = get_subtrees(dend_tree, taxonomy_config)
-        robot_class_curation_seed = {'ID': 'ID',
-                                     'prefLabel': 'A skos:prefLabel',
-                                     'Synonyms_from_taxonomy': "A oboInOwl:hasExactSynonym SPLIT=|",
-                                     'Curated_synonyms': "A oboInOwl:hasExactSynonym SPLIT=|",
-                                     'Comment': 'A rdfs:comment',
-                                     'Classification': 'SC %',
-                                     'Classification_comment': ">A rdfs:comment",
-                                     'Classification_pub': ">A oboInOwl:hasDbXref SPLIT=|",
-                                     'Expresses': "SC 'expresses' some % SPLIT=|",
-                                     'Expresses_comment': ">A rdfs:comment",
-                                     'Expresses_pub': ">A oboInOwl:hasDbXref SPLIT=|"
-                                     }
-        class_template = [robot_class_curation_seed]
+        robot_class_curation_seed = ['defined_class',
+                                     'prefLabel',
+                                     'Synonyms_from_taxonomy',
+                                     'Curated_synonyms',
+                                     'Comment',
+                                     'Classification',
+                                     'Classification_comment',
+                                     'Classification_pub',
+                                     'Expresses',
+                                     'Expresses_comment',
+                                     'Expresses_pub']
+        class_template = []
 
         for o in dend['nodes']:
             if o['cell_set_accession'] in set.union(*subtrees) and (o['cell_set_preferred_alias'] or
                                                                     o['cell_set_additional_aliases']):
                 d = dict()
-                d['ID'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
+                d['defined_class'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
                 if o['cell_set_preferred_alias']:
                     d['prefLabel'] = o['cell_set_preferred_alias']
                 elif o['cell_set_additional_aliases']:
                     d['prefLabel'] = str(o['cell_set_additional_aliases']).split(EXPRESSION_SEPARATOR)[0]
                 d['Synonyms_from_taxonomy'] = get_synonyms_from_taxonomy(o)
                 d['Comment'] = get_synonym_pairs(o)
-                for k in robot_class_curation_seed.keys():
+                for k in robot_class_curation_seed:
                     if not (k in d.keys()):
                         d[k] = ''
                 class_template.append(d)
@@ -123,18 +122,13 @@ def generate_equivalent_class_reification_template(dend_json_path, output_filepa
 
     subtrees = get_subtrees(dend_tree, config_yaml)
 
-    robot_class_equivalent_seed = {'ID': 'ID',
-                                   'Exemplar': "EC CL:0000003 and 'has_exemplar' value %",
-                                   'Exemplar_SC': "SC 'has_exemplar' value %"
-                                   }
-
-    equivalent_template = [robot_class_equivalent_seed]
+    equivalent_template = []
 
     for o in dend['nodes']:
         if o['cell_set_accession'] in set().union(*subtrees) and (o['cell_set_preferred_alias'] or
                                                                   o['cell_set_additional_aliases']):
             d = dict()
-            d['ID'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
+            d['defined_class'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
             d['Exemplar'] = 'AllenDend:' + o['cell_set_accession']
             d['Exemplar_SC'] = 'AllenDend:' + o['cell_set_accession']
             equivalent_template.append(d)
@@ -174,7 +168,7 @@ def generate_equivalent_class_marker_template(dend_json_path, marker_path, outpu
     for o in dend['nodes']:
         if o['cell_set_accession'] in set().union(*subtrees) and o['cell_set_accession'] in denormalized_markers.keys():
             d = dict()
-            d['ID'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
+            d['defined_class'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
             d['CLASS_TYPE'] = 'equivalent'
             d['Evidence'] = 'http://www.semanticweb.org/brain_data_standards/AllenDend_' + o['cell_set_accession']
 
@@ -209,18 +203,13 @@ def generate_minimal_marker_template(dend_json_path, flat_marker_path, output_ma
 
     if taxonomy_config:
         subtrees = get_subtrees(dend_tree, taxonomy_config)
-        robot_min_marker_seed = {'ID': "ID",
-                                 'Markers': "SC 'expresses' some % SPLIT=|",
-                                 'part_of': "SC 'part of' some %",
-                                 'has_soma_location': "SC 'has soma location' some %"
-                                 }
-        min_marker_template = [robot_min_marker_seed]
+        min_marker_template = []
 
         for o in dend['nodes']:
             if o['cell_set_accession'] in set.union(*subtrees) and (o['cell_set_preferred_alias'] or
                                                                     o['cell_set_additional_aliases']):
                 d = dict()
-                d['ID'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
+                d['defined_class'] = 'http://www.semanticweb.org/brain_data_standards/AllenDendClass_' + o['cell_set_accession']
 
                 if o['cell_set_accession'] in marker_expressions:
                     d['Markers'] = EXPRESSION_SEPARATOR.join(marker_expressions[o['cell_set_accession']][EXPRESSIONS])
@@ -257,11 +246,7 @@ def generate_non_taxonomy_classification_template(dend_json_path, output_filepat
 
     if taxonomy_config and os.path.exists(nomenclature_path):
         nomenclature_records = read_csv(nomenclature_path, id_column=cell_set_accession)
-
-        nomenclature_table_seed = {'ID': "ID",
-                                   'Classification': "SC %"
-                                   }
-        nomenclature_template = [nomenclature_table_seed]
+        nomenclature_template = []
 
         non_taxo_roots = {}
         for root in taxonomy_config['non_taxonomy_roots']:
@@ -278,7 +263,7 @@ def generate_non_taxonomy_classification_template(dend_json_path, output_filepat
                     # child of root with cell_set_preferred_alias
                     if child not in non_taxo_roots and nomenclature_records[child][0]:
                         d = dict()
-                        d['ID'] = ALLEN_DEND_CLASS + child
+                        d['defined_class'] = ALLEN_DEND_CLASS + child
                         d['Classification'] = non_taxo_roots[columns[cell_set_accession]]
                         nomenclature_template.append(d)