Merge pull request #123 from KrishnaTO/batch-fertilizer-concentrations

Batch fertilizer concentrations

.gitignore

@@ -7,3 +7,4 @@ src/ontology/catalog-v001.xml
 src/ontology/catalog-v001.xml
 src/ontology/mirror
 src/ontology/mirror/*
+src/ontology/envo-test/Makefile

src/ontology/Makefile

@@ -45,15 +45,28 @@ imports/%_import.owl: mirror/%.owl imports/%_terms.txt
 #	$(OWLTOOLS) $(USECAT) $< -o -f obo $@
 
 #patterns
-PATTERNS = eq
+PATTERNS = eq chemical_area_density
 PATTERNS_OWL = $(patsubst %, patterns/%.owl,$(PATTERNS))
 
 # Make this target to regenerate ALL patterns
 all_patterns: $(PATTERNS_OWL)
 
 patterns/%.owl: patterns/%.tsv
-	$(DOSDPTOOLS) generate --outfile=$@ --obo-prefixes=true --template=patterns/$*.yaml --ontology=imports/pato_import.owl --infile=$<
-	robot annotate -O "http://purl.obolibrary.org/obo/agro/patterns/$*.owl" -i $@ -o $@
+	$(DOSDPTOOLS) generate \
+		--outfile=$@ \
+		--obo-prefixes=true \
+		--template=patterns/$*.yaml \
+		--infile=$<
+	robot annotate \
+		-i $@ \
+		-O "http://purl.obolibrary.org/obo/agro/patterns/$*.owl" \
+		-o $@
+	robot merge \
+		--input agro-edit.owl \
+		--input $@ \
+		--collapse-import-closure false convert \
+		--format ofn \
+		--output agro-edit.owl
 .PRECIOUS: patterns/%.owl
 
 # clone remote ontology locally, perfoming some excision of relations and annotations

src/ontology/patterns/chemical_area_density.tsv

@@ -0,0 +1,39 @@
+defined_class	defined_class_label	chemical	chemical_label
+AGRO:00040000		CHEBI:62982	ammonium dihydrogen phosphate
+AGRO:00040001		CHEBI:149425	ammonium magnesium phosphate
+AGRO:00040002		CHEBI:149427	ammonium magnesium phosphate hexahydrate
+AGRO:00040003		CHEBI:63038	ammonium nitrate
+AGRO:00040004		CHEBI:147420	ammonium nitrate phosphate
+AGRO:00040005		CHEBI:147419	ammonium phosphate sulfate
+AGRO:00040006		CHEBI:147408	ammonium polyphosphate
+AGRO:00040007		CHEBI:62946	ammonium sulfate
+AGRO:00040008		CHEBI:140457	ammonium sulfate nitrate
+AGRO:00040009		CHEBI:91240	ammonium sulfate urea
+AGRO:00040010		CHEBI:147402	ammonium thiosulfate
+AGRO:00040011		CHEBI:91238	calcium ammonium nitrate
+AGRO:00040012		CHEBI:35433	calcium bis(dihydrogenphosphate)
+AGRO:00040013		CHEBI:3311	calcium carbonate
+AGRO:00040014		CHEBI:64301	calcium cyanamide
+AGRO:00040015		CHEBI:3312	calcium dichloride
+AGRO:00040016		CHEBI:64205	calcium nitrate
+AGRO:00040017		CHEBI:31344	calcium oxide
+AGRO:00040018		CHEBI:23414	copper(II) sulfate
+AGRO:00040019		CHEBI:147423	cyanoguanidine
+AGRO:00040020		CHEBI:63051	diammonium hydrogen phosphate
+AGRO:00040021		CHEBI:48838	gypsum
+AGRO:00040022		ENVO:00002053	limestone
+AGRO:00040023		CHEBI:31793	magnesium carbonate
+AGRO:00040024		CHEBI:64736	magnesium nitrate
+AGRO:00040025		CHEBI:31794	magnesium oxide
+AGRO:00040026		CHEBI:32599	magnesium sulfate
+AGRO:00040027		CHEBI:26078	phosphoric acid
+AGRO:00040028		CHEBI:131526	potassium carbonate
+AGRO:00040029		CHEBI:32588	potassium chloride
+AGRO:00040030		CHEBI:63036	potassium dihydrogen phosphate
+AGRO:00040031		CHEBI:148438	potassium metaphosphate
+AGRO:00040032		CHEBI:63043	potassium nitrate
+AGRO:00040033		CHEBI:63005	sodium nitrate
+AGRO:00040034		CHEBI:77775	sodium selenate
+AGRO:00040035		CHEBI:16199	urea
+AGRO:00040036		CHEBI:88276	urea ammonium nitrate
+AGRO:00040037		CHEBI:35176	zinc sulfate

src/ontology/patterns/chemical_area_density.yaml

@@ -0,0 +1,50 @@
+pattern_name: agro/patterns/chemical_area_density
+contributors:
+- https://orcid.org/0000-0002-2627-0696
+
+#### owl_entity Dictionaries
+classes:
+  chemical entity: CHEBI:24431
+  area density: PATO:0001351
+
+relations:
+  inheres in: RO:0000052
+  has_part: BFO:0000051
+
+# Var types
+vars:
+  chemical: "'chemical entity'"
+
+subClassOf: 
+  text: "'area density'"
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+
+  # OBO fields 
+name:
+  text: "%s area density"
+  vars:
+    - chemical
+
+# Specifying axioms:
+annotations:
+  - annotationProperty: exact_synonym
+    text: "amount of %s applied"
+    vars:
+      - chemical
+
+def:
+  text: "An area density quality which inheres in %s by virtue of some influence exerted by the mass of %s applied in a given surface area."
+  vars:
+    - chemical
+    - chemical
+
+equivalentTo:
+  text: "'area density' and 'inheres in' some %s"
+  vars:
+    - chemical
+
+comment:
+  text: "Generated by pattern 'agro/patterns/chemical_area_density', using dosdp-tools and ROBOT tool"
+