Fixes to pipeline in-progress

EnvironmentOntology · May 12, 2018 · 252cb69 · 252cb69
1 parent ea44ccc
commit 252cb69
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Showing 20 changed files with 39,254 additions and 8,544 deletions.
diff --git a/src/envo/Makefile b/src/envo/Makefile
@@ -40,15 +40,19 @@ copy-release:
 
 #release: envo-basic.obo release-diffs
 
-# all release files are derived from the editors version.
-# we use the default Oort setup (hermit as reasoner)
-
+# Merge in all module files, whilst removing the corresponding import
 envo-edit-module-merge.owl: envo-edit.owl
-	owltools $(USECAT) $<  --merge-imports-closure -o $@
-	#owltools $(USECAT) $<  $(patsubst %, --remove-import-declaration $(OBO)/envo/modules/%.owl, $(MODS)) $(ALL_MODS_OWL) --merge-support-ontologies -o $@
+	owltools $(USECAT) $<  $(patsubst %, --remove-import-declaration $(OBO)/envo/modules/%.owl, $(MODS)) -o $@.tmp
+	owltools $(USECAT) $@.tmp  $(ALL_MODS_OWL) --merge-support-ontologies -o $@
+
+envo.owl: envo-edit-module-merge.owl
+	robot reason -i $< -r ELK relax reduce -o $@
+
+envo-simple.owl: envo.owl
+	owltools --use-catalog $< --remove-imports-declarations --remove-dangling-annotations -f -o $@
+
 
-envo.owl envo-simple.owl: envo-edit-module-merge.owl
-	ontology-release-runner --catalog-xml catalog-v001.xml --reasoner elk  --skip-format owx --skip-format obo  --error-report envo-errors.txt $< --allow-overwrite --asserted --simple
+###	ontology-release-runner --catalog-xml catalog-v001.xml --reasoner elk  --skip-format owx --skip-format obo  --error-report envo-errors.txt $< --allow-overwrite --asserted --simple
 ##	ontology-release-runner --catalog-xml catalog-v001.xml  --skip-format owx --run-obo-basic-dag-check --error-report envo-errors.txt $< --allow-overwrite --asserted --simple
 
 #envo.owl: envo-edit.owl

diff --git a/src/envo/imports/agro_import.owl b/src/envo/imports/agro_import.owl
@@ -2909,6 +2909,16 @@ clustering algorithm.</obo:IAO_0000115>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0001933 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001933">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+        <obo:IAO_0000115>An information content entity that specifies a value within a classification scheme or on a quantitative scale.</obo:IAO_0000115>
+        <rdfs:label>value specification</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0100026 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100026">

diff --git a/src/envo/imports/chebi_import.obo b/src/envo/imports/chebi_import.obo
@@ -340,6 +340,11 @@ id: CHEBI:17972
 name: ribonucleoside triphosphate
 is_a: CHEBI:17326 ! nucleoside triphosphate
 
+[Term]
+id: CHEBI:17992
+name: sucrose
+is_a: CHEBI:24407 ! glycosyl glycoside
+
 [Term]
 id: CHEBI:17996
 name: chloride
@@ -644,6 +649,11 @@ id: CHEBI:24373
 name: glycine derivative
 is_a: CHEBI:83811 ! proteinogenic amino acid derivative
 
+[Term]
+id: CHEBI:24407
+name: glycosyl glycoside
+is_a: CHEBI:36233 ! disaccharide
+
 [Term]
 id: CHEBI:24431
 name: chemical entity
@@ -1005,6 +1015,11 @@ name: aldopentose phosphate
 is_a: CHEBI:35131 ! aldose phosphate
 is_a: CHEBI:84055 ! pentose phosphate
 
+[Term]
+id: CHEBI:25944
+name: pesticide
+is_a: CHEBI:33232 ! application
+
 [Term]
 id: CHEBI:26020
 name: phosphate
@@ -1711,6 +1726,11 @@ id: CHEBI:33287
 name: fertilizer
 is_a: CHEBI:33286 ! agrochemical
 
+[Term]
+id: CHEBI:33290
+name: food
+is_a: CHEBI:52211 ! physiological role
+
 [Term]
 id: CHEBI:33292
 name: fuel
@@ -2620,6 +2640,11 @@ id: CHEBI:36125
 name: cyclitol carboxylic acid anion
 is_a: CHEBI:35757 ! monocarboxylic acid anion
 
+[Term]
+id: CHEBI:36233
+name: disaccharide
+is_a: CHEBI:50699 ! oligosaccharide
+
 [Term]
 id: CHEBI:36244
 name: dicarboxylic acid monoester
@@ -3533,6 +3558,11 @@ name: carbon nanotube
 is_a: CHEBI:50796 ! nanotube
 is_a: CHEBI:50812 ! carbon nanostructure
 
+[Term]
+id: CHEBI:50699
+name: oligosaccharide
+is_a: CHEBI:16646 ! carbohydrate
+
 [Term]
 id: CHEBI:50795
 name: nanostructure

diff --git a/src/envo/imports/chebi_import.owl b/src/envo/imports/chebi_import.owl
@@ -625,6 +625,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHEBI_17992 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_17992">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_24407"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sucrose</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CHEBI_17996 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_17996">
@@ -1153,6 +1162,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHEBI_24407 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_24407">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_36233"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glycosyl glycoside</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CHEBI_24431 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_24431">
@@ -1774,6 +1792,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHEBI_25944 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_25944">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33232"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pesticide</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CHEBI_26020 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_26020">
@@ -2996,6 +3023,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHEBI_33290 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33290">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_52211"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">food</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CHEBI_33292 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33292">
@@ -4557,6 +4593,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHEBI_36233 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36233">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_50699"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disaccharide</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CHEBI_36244 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36244">
@@ -6134,6 +6179,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHEBI_50699 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_50699">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_16646"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">oligosaccharide</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CHEBI_50795 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_50795">