PTFI FoodOn id assignment prep.

src/ontology/foodon-edit.ofn

@@ -17093,13 +17093,10 @@ SubClassOf(obo:FOODON_00003713 obo:FOODON_00001915)
 
 AnnotationAssertion(obo:IAO_0000117 obo:FOODON_00003714 <http://orcid.org/0000-0002-8844-9165>)
 
-# Class: obo:FOODON_00003715 (idaho potato)
-
-AnnotationAssertion(obo:IAO_0000117 obo:FOODON_00003715 <http://orcid.org/0000-0002-8844-9165>)
-
 # Class: obo:FOODON_00003716 (idaho russet potato)
 
 AnnotationAssertion(obo:IAO_0000117 obo:FOODON_00003716 <http://orcid.org/0000-0002-8844-9165>)
+AnnotationAssertion(obo:IAO_0000119 obo:FOODON_00003716 wikipedia:Russet_potato)
 
 # Class: obo:FOODON_00003717 (ginger root)
 
@@ -20371,10 +20368,7 @@ SubClassOf(obo:FOODON_00004505 obo:FOODON_00004503)
 
 # Class: obo:FOODON_00004529 (spring barley seed (raw))
 
-AnnotationAssertion(dcterms:contributor obo:FOODON_00004529 <https://orcid.org/0000-0002-8844-9165>)
 AnnotationAssertion(dcterms:date obo:FOODON_00004529 "2023-11-16T05:19:25Z"^^xsd:dateTime)
-AnnotationAssertion(rdfs:label obo:FOODON_00004529 "spring barley seed (raw)"@en)
-SubClassOf(obo:FOODON_00004529 obo:FOODON_00003108)
 
 # Class: obo:FOODON_00004530 (piece of cow)
 

src/ontology/imports/deprecation_import.ofn

@@ -14923,6 +14923,10 @@ AnnotationAssertion(owl:deprecated obo:FOODON_00003364 "true"^^xsd:boolean)
 AnnotationAssertion(obo:IAO_0100001 obo:FOODON_00003492 obo:FOODON_00003427)
 AnnotationAssertion(rdfs:label obo:FOODON_00003492 "obsolete: corn kernel"@en)
 AnnotationAssertion(owl:deprecated obo:FOODON_00003492 "true"^^xsd:boolean)
+AnnotationAssertion(obo:IAO_0100001 obo:FOODON_00003715 obo:FOODON_00003716)
+AnnotationAssertion(dcterms:date obo:FOODON_00003715 "2021-02-11T17:32:19"^^xsd:dateTime)
+AnnotationAssertion(rdfs:label obo:FOODON_00003715 "obsolete: idaho potato"@en)
+AnnotationAssertion(owl:deprecated obo:FOODON_00003715 "true"^^xsd:boolean)
 AnnotationAssertion(obo:IAO_0100001 obo:FOODON_00003751 obo:FOODON_03309978)
 AnnotationAssertion(rdfs:label obo:FOODON_00003751 "obsolete: sorghum seed (whole)"@en)
 AnnotationAssertion(owl:deprecated obo:FOODON_00003751 "true"^^xsd:boolean)

src/ontology/imports/foodon_product_import.ofn

@@ -2184,6 +2184,7 @@ Declaration(Class(obo:FOODON_00003708))
 Declaration(Class(obo:FOODON_00003710))
 Declaration(Class(obo:FOODON_00003711))
 Declaration(Class(obo:FOODON_00003713))
+Declaration(Class(obo:FOODON_00003716))
 Declaration(Class(obo:FOODON_00003717))
 Declaration(Class(obo:FOODON_00003718))
 Declaration(Class(obo:FOODON_00003719))
@@ -32528,11 +32529,11 @@ AnnotationAssertion(rdfs:label obo:FOODON_03301476 "corn dextrin"@en)
 SubClassOf(obo:FOODON_03301476 obo:FOODON_00001845)
 SubClassOf(obo:FOODON_03301476 ObjectSomeValuesFrom(obo:RO_0002350 obo:FOODON_03400149))
 
-# Class: obo:FOODON_03301477 (coffee bean (whole or ground))
+# Class: obo:FOODON_03301477 (coffee bean)
 
 AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03301477 obo:IAO_0000428)
 AnnotationAssertion(oboInOwl:hasDbXref obo:FOODON_03301477 siren:F1477)
-AnnotationAssertion(rdfs:label obo:FOODON_03301477 "coffee bean (whole or ground)"@en)
+AnnotationAssertion(rdfs:label obo:FOODON_03301477 "coffee bean"@en)
 SubClassOf(obo:FOODON_03301477 obo:FOODON_00001139)
 SubClassOf(obo:FOODON_03301477 ObjectSomeValuesFrom(obo:RO_0002350 obo:FOODON_03400268))
 
@@ -61943,6 +61944,7 @@ SubClassOf(obo:FOODON_03307035 obo:FOODON_03301449)
 AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03307036 obo:IAO_0000428)
 AnnotationAssertion(oboInOwl:hasDbXref obo:FOODON_03307036 siren:F7036)
 AnnotationAssertion(rdfs:label obo:FOODON_03307036 "idaho russet potato (raw)"@en)
+SubClassOf(obo:FOODON_03307036 obo:FOODON_00003716)
 SubClassOf(obo:FOODON_03307036 obo:FOODON_03301449)
 
 # Class: obo:FOODON_03307037 (potato chip (cheese-flavored))
@@ -72675,11 +72677,11 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:FOODON_03309388 "baby carrot"@e
 AnnotationAssertion(rdfs:label obo:FOODON_03309388 "baby carrot root (raw)"@en)
 SubClassOf(obo:FOODON_03309388 obo:FOODON_00001687)
 
-# Class: obo:FOODON_03309389 (carrot root ((whole or pieces), raw))
+# Class: obo:FOODON_03309389 (carrot root (whole or pieces, raw))
 
 AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03309389 obo:IAO_0000428)
 AnnotationAssertion(oboInOwl:hasDbXref obo:FOODON_03309389 siren:F9389)
-AnnotationAssertion(rdfs:label obo:FOODON_03309389 "carrot root ((whole or pieces), raw)"@en)
+AnnotationAssertion(rdfs:label obo:FOODON_03309389 "carrot root (whole or pieces, raw)"@en)
 SubClassOf(obo:FOODON_03309389 obo:FOODON_00002490)
 
 # Class: obo:FOODON_03309390 (bulk grain)
@@ -84873,11 +84875,13 @@ AnnotationAssertion(rdfs:label obo:FOODON_03311672 "radish root (japanese)"@en)
 SubClassOf(obo:FOODON_03311672 obo:FOODON_00002184)
 SubClassOf(obo:FOODON_03311672 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03411513))
 
-# Class: obo:FOODON_03311673 (carrot (peeled))
+# Class: obo:FOODON_03311673 (carrot root (peeled))
 
-AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03311673 obo:IAO_0000428)
+AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03311673 obo:IAO_0000122)
+AnnotationAssertion(obo:IAO_0000115 obo:FOODON_03311673 "A peeled carrot root."@en)
 AnnotationAssertion(oboInOwl:hasDbXref obo:FOODON_03311673 siren:F11673)
-AnnotationAssertion(rdfs:label obo:FOODON_03311673 "carrot (peeled)"@en)
+AnnotationAssertion(oboInOwl:hasExactSynonym obo:FOODON_03311673 "peeled carrot"@en)
+AnnotationAssertion(rdfs:label obo:FOODON_03311673 "carrot root (peeled)"@en)
 SubClassOf(obo:FOODON_03311673 obo:FOODON_00001687)
 
 # Class: obo:FOODON_03311676 (corn (sweet, frozen))
@@ -101961,11 +101965,13 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:FOODON_03601071 "besan"@en)
 AnnotationAssertion(rdfs:label obo:FOODON_03601071 "gram flour"@en)
 SubClassOf(obo:FOODON_03601071 obo:FOODON_03304537)
 
-# Class: obo:FOODON_3000001 (carrot (raw, peeled))
+# Class: obo:FOODON_3000001 (carrot root (raw, peeled))
 
+AnnotationAssertion(obo:IAO_0000114 obo:FOODON_3000001 obo:IAO_0000122)
+AnnotationAssertion(obo:IAO_0000115 obo:FOODON_3000001 "A raw peeled carrot root."@en)
 AnnotationAssertion(dcterms:contributor obo:FOODON_3000001 <https://orcid.org/0000-0002-8844-9165>)
 AnnotationAssertion(dcterms:date obo:FOODON_3000001 "2023-07-14T17:34:13Z"^^xsd:dateTime)
-AnnotationAssertion(rdfs:label obo:FOODON_3000001 "carrot (raw, peeled)"@en)
+AnnotationAssertion(rdfs:label obo:FOODON_3000001 "carrot root (raw, peeled)"@en)
 SubClassOf(obo:FOODON_3000001 obo:FOODON_03311673)
 
 # Class: obo:GENEPIO_0002240 (za'atar)

src/ontology/imports/ncbitaxon_import.ofn

@@ -10,6 +10,7 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
 
 Ontology(<http://purl.obolibrary.org/obo/foodon/imports/ncbitaxon_import.ofn>
 
+Declaration(Class(obo:FOODON_03411458))
 Declaration(Class(obo:NCBITaxon_1000425))
 Declaration(Class(obo:NCBITaxon_1001333))
 Declaration(Class(obo:NCBITaxon_100186))
@@ -5230,7 +5231,7 @@ Declaration(AnnotationProperty(oboInOwl:hasExactSynonym))
 
 AnnotationAssertion(rdfs:label obo:IAO_0000412 "imported from"@en)
 
-# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym)
+# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym)
 
 AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym")
 
@@ -14863,6 +14864,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:NCBITaxon_223891 "brinjal")
 AnnotationAssertion(oboInOwl:hasExactSynonym obo:NCBITaxon_223891 "eggplant")
 AnnotationAssertion(oboInOwl:hasExactSynonym obo:NCBITaxon_223891 "yellow-fruit nightshade")
 AnnotationAssertion(rdfs:label obo:NCBITaxon_223891 "Solanum virginianum")
+SubClassOf(obo:NCBITaxon_223891 obo:FOODON_03411458)
 SubClassOf(obo:NCBITaxon_223891 obo:NCBITaxon_4107)
 
 # Class: obo:NCBITaxon_224270 (Diplectrum formosum)

src/ontology/imports/ncbitaxon_ontofox.txt

@@ -70,6 +70,7 @@ http://purl.obolibrary.org/obo/NCBITaxon_2849586 # Anethum foeniculum
 # DELETED http://purl.obolibrary.org/obo/NCBITaxon_5400 # species:Agrocybe aegerita REPLACED WITH
 http://purl.obolibrary.org/obo/NCBITaxon_1973307 # Cyclocybe aegerita
 
+http://purl.obolibrary.org/obo/NCBITaxon_4182 # Sesamum indicum 
 http://purl.obolibrary.org/obo/NCBITaxon_7705 # Holothuroidea / sea cucumber
 http://purl.obolibrary.org/obo/NCBITaxon_9878 # Odocoileus hemionus sitkensis / sitka deer
 http://purl.obolibrary.org/obo/NCBITaxon_9000 # Bonasa umbellus / Ruffed grouse

src/ontology/imports/ons_ontofox.txt

@@ -8,12 +8,19 @@ ONS
 http://purl.obolibrary.org/obo/ONS_1000001 # diet
 includeAllChildren
 http://purl.obolibrary.org/obo/ONS_0000094 # dietary pattern
-includeAllChildren
 http://purl.obolibrary.org/obo/ONS_0000085 # Meal
 http://purl.obolibrary.org/obo/ONS_1000064 # dietary pattern data item
 
 [Top level source term URIs and target direct superclass URIs]
-http://purl.obolibrary.org/obo/BFO_0000001 # entity
+http://purl.obolibrary.org/obo/IAO_0000030 # information
+http://purl.obolibrary.org/obo/BFO_0000020 # characteristic
+http://purl.obolibrary.org/obo/PATO_0000001 # characteristic
+subClassOf http://purl.obolibrary.org/obo/BFO_0000020
+
+http://purl.obolibrary.org/obo/BFO_0000141 # immaterial entity
+http://purl.obolibrary.org/obo/BFO_0000040 # material entity
+http://purl.obolibrary.org/obo/BFO_0000015 # process
+
 
 [Source term retrieval setting]
 includeAllIntermediates

src/ontology/imports/robot_plant_parts.ofn

@@ -5338,19 +5338,9 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FOODON_00003714> "sweet onion"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/FOODON_00003714> <http://purl.obolibrary.org/obo/FOODON_03316347>)
 
-# Class: <http://purl.obolibrary.org/obo/FOODON_00003715> (idaho potato)
-
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FOODON_00003715> "A shoot axis tuber of an idaho potato plant."@en)
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/FOODON_00003715> "https://en.wikipedia.org/wiki/Russet_potato")
-AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/obo/FOODON_00003715> "2021-02-11T17:32:19"^^xsd:dateTime)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FOODON_00003715> "idaho potato"@en)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FOODON_00003715> "russet potato"@en)
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FOODON_00003715> "idaho potato"@en)
-SubClassOf(<http://purl.obolibrary.org/obo/FOODON_00003715> <http://purl.obolibrary.org/obo/FOODON_03315354>)
-
 # Class: <http://purl.obolibrary.org/obo/FOODON_00003716> (idaho russet potato)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FOODON_00003716> "A shoot axis tuber of an idaho russet potato plant."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FOODON_00003716> "A russet potato which is trademarked by the Idaho Potato Commission (IPC) to certify that it has been grown in the state of Idaho."@en)
 AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/obo/FOODON_00003716> "2021-02-11T17:32:38"^^xsd:dateTime)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FOODON_00003716> "idaho russet potato"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/FOODON_00003716> <http://purl.obolibrary.org/obo/FOODON_03315354>)