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fixed some deprecated terms not being ^^xsd:boolean
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undeprecated yeast since it was different from yeast (ground ...)
Moved a few annotations to food_product_import.ofn
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@ddooley
ddooley committed Jun 27, 2024
1 parent cde8bcb commit 36d4fee
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Showing 3 changed files with 54 additions and 417 deletions.
94 changes: 6 additions & 88 deletions src/ontology/foodon-edit.ofn
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Original file line number Diff line number Diff line change
Expand Up @@ -10726,13 +10726,6 @@ AnnotationAssertion(rdfs:label go:hasSynonym "has synonym"@en)
AnnotationAssertion(rdfs:label obo:FOODON_00001301 "has food substance analog"@en)
SymmetricObjectProperty(obo:FOODON_00001301)

# Object Property: obo:FOODON_00001303 (obsolete - has taxonomic identifier)

AnnotationAssertion(obo:IAO_0100001 obo:FOODON_00001303 obo:RO_0002160)
AnnotationAssertion(rdfs:label obo:FOODON_00001303 "obsolete - has taxonomic identifier"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_00001303 "true"^^xsd:boolean)
SubObjectPropertyOf(obo:FOODON_00001303 owl:topObjectProperty)

# Object Property: obo:FOODON_00001563 (has defining ingredient)

AnnotationAssertion(obo:IAO_0000115 obo:FOODON_00001563 "A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient."@en)
Expand Down Expand Up @@ -13178,23 +13171,13 @@ AnnotationAssertion(obo:IAO_0000412 obo:FOODON_00001088 <http://langual.org>)
AnnotationAssertion(obo:IAO_0000117 obo:FOODON_00001141 <https://orcid.org/0000-0002-8844-9165>)
AnnotationAssertion(dcterms:date obo:FOODON_00001141 "2023-05-03T04:59:00Z"^^xsd:dateTime)

# Class: obo:FOODON_00001144 (yeast food product)

EquivalentClasses(obo:FOODON_00001144 ObjectIntersectionOf(obo:FOODON_00001143 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03411345)))

# Class: obo:FOODON_00001258 (food (fermented))

AnnotationAssertion(obo:IAO_0000114 obo:FOODON_00001258 obo:IAO_0000428)
AnnotationAssertion(obo:IAO_0000116 obo:FOODON_00001258 "Are all fermented foods considered preserved to some extent?"@en)
AnnotationAssertion(obo:IAO_0000117 obo:FOODON_00001258 "Damion Dooley"@en)
SubClassOf(obo:FOODON_00001258 ObjectSomeValuesFrom(obo:RO_0002353 obo:FOODON_00001304))

# Class: obo:FOODON_00001287 (obsolete: mushroom (whole organism))

AnnotationAssertion(obo:IAO_0100001 obo:FOODON_00001287 obo:NCBITaxon_4751)
AnnotationAssertion(rdfs:label obo:FOODON_00001287 "obsolete: mushroom (whole organism)"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_00001287 "true"^^xsd:boolean)

# Class: obo:FOODON_00001304 (food fermentation)

AnnotationAssertion(go:hasDbXref obo:FOODON_00001304 langual:J0104)
Expand Down Expand Up @@ -20264,10 +20247,10 @@ SubClassOf(obo:FOODON_00004472 obo:FOODON_00004338)

# Class: obo:FOODON_00004474 (slicing process)

AnnotationAssertion(obo:IAO_0000115 obo:FOODON_00004474 "A cutting process which outputs sliced material."@en)
AnnotationAssertion(dcterms:contributor obo:FOODON_00004474 <https://orcid.org/0000-0002-8844-9165>)
AnnotationAssertion(dcterms:date obo:FOODON_00004474 "2023-08-01T23:32:07Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:FOODON_00004474 "slicing process"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_00004474 "A cutting process which outputs sliced material."@en)
SubClassOf(obo:FOODON_00004474 obo:FOODON_00000071)

# Class: obo:FOODON_00004475 (clown featherback)
Expand Down Expand Up @@ -22597,10 +22580,6 @@ SubClassOf(obo:FOODON_03304091 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03

SubClassOf(obo:FOODON_03304096 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03411012))

# Class: obo:FOODON_03304099 (sourdough starter)

SubClassOf(obo:FOODON_03304099 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03411312))

# Class: obo:FOODON_03304103 (swiss almond cookie)

SubClassOf(obo:FOODON_03304103 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03411012))
Expand Down Expand Up @@ -28513,11 +28492,6 @@ SubClassOf(obo:FOODON_03316372 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03

SubClassOf(obo:FOODON_03316389 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03411011))

# Class: obo:FOODON_03316405 (obsolete: malto dextrin)

AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03316405 obo:CHEBI_25140)
AnnotationAssertion(owl:deprecated obo:FOODON_03316405 "true"^^xsd:boolean)

# Class: obo:FOODON_03316413 (glucose syrup (exclusively for commercial production of sweets and candies))

SubClassOf(obo:FOODON_03316413 ObjectSomeValuesFrom(obo:RO_0001000 obo:FOODON_03411016))
Expand Down Expand Up @@ -36223,13 +36197,6 @@ AnnotationAssertion(go:hasSynonym obo:FOODON_03412033 "penny bun"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03412033 "yellow boletus"@en)
AnnotationAssertion(rdfs:comment obo:FOODON_03412033 "A basidiomycete fungus, a species of the genus Boletus. Widely distributed in the Northern Hemisphere across Europe, Asia, and North America."@en)

# Class: obo:FOODON_03412034 (obsolete: ascomycetes)

AnnotationAssertion(obo:IAO_0000412 obo:FOODON_03412034 <http://langual.org>)
AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03412034 obo:NCBITaxon_4890)
AnnotationAssertion(rdfs:label obo:FOODON_03412034 "obsolete: ascomycetes"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_03412034 "true"^^xsd:boolean)

# Class: obo:FOODON_03412038 (corinth grape plant)

AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03412038 obo:IAO_0000122)
Expand Down Expand Up @@ -41685,29 +41652,6 @@ AnnotationAssertion(go:hasSynonym obo:FOODON_03412936 "epigonus spp."@en)
AnnotationAssertion(rdfs:label obo:FOODON_03412936 "cardinalfish"@en)
SubClassOf(obo:FOODON_03412936 obo:FOODON_03412886)

# Class: obo:FOODON_03412937 (obsolete: cultivated mushroom (organism))

AnnotationAssertion(obo:IAO_0000115 obo:FOODON_03412937 "An edible basidiomycete mushroom native to grasslands in Europe and North America."@en)
AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03412937 obo:NCBITaxon_5341)
AnnotationAssertion(go:hasNarrowSynonym obo:FOODON_03412937 "Agaricus bisporus (J.E. Lange) Imbach, 1946")
AnnotationAssertion(go:hasNarrowSynonym obo:FOODON_03412937 "Agaricus bisporus (Lange) Imbach")
AnnotationAssertion(go:hasNarrowSynonym obo:FOODON_03412937 "Agaricus bisporus (Lange) Imbach forma albidus (Lange) Singer")
AnnotationAssertion(go:hasSynonym obo:FOODON_03412937 "button mushroom"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03412937 "champignon"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03412937 "champignon mushroom"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03412937 "common mushroom"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03412937 "cremini"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03412937 "crimini"@en)
AnnotationAssertion(rdfs:comment obo:FOODON_03412937 "Agaricus bisporus has two color states while immature - white and brown - both of which have various names. When mature, the same mushroom has yet another popular name.

When immature and white - this mushroom may be known as common mushroom, button mushroom, white mushroom, cultivated mushroom, table mushroom, and champignon mushroom. When immature and brown - this mushroom may be known variously as Swiss brown mushroom, Roman brown mushroom, Italian brown, Italian mushroom, cremini or crimini mushroom, brown cap mushroom, or chestnut mushroom. When mature, the same mushroom is known as Portobello mushroom.

It is cultivated in more than seventy countries, and it is one of the most commonly and widely consumed mushrooms in the world.[Wikipedia]"@en)
AnnotationAssertion(rdfs:label obo:FOODON_03412937 "obsolete: cultivated mushroom (organism)"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_03412937 "true"^^xsd:boolean)
SubClassOf(obo:FOODON_03412937 obo:FOODON_00003528)
SubClassOf(obo:FOODON_03412937 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_5341))

# Class: obo:FOODON_03412940 (red beet plant)

AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03412940 obo:IAO_0000428)
Expand Down Expand Up @@ -54427,12 +54371,6 @@ AnnotationAssertion(go:hasSynonym obo:FOODON_03414941 "turnip-root mustard"@en)
AnnotationAssertion(rdfs:label obo:FOODON_03414941 "tuberous-root mustard plant"@en)
SubClassOf(obo:FOODON_03414941 obo:FOODON_03411092)

# Class: obo:FOODON_03414943 (obsolete: fusarium venenatum)

AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03414943 obo:NCBITaxon_56646)
AnnotationAssertion(rdfs:label obo:FOODON_03414943 "obsolete: fusarium venenatum"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_03414943 "true"^^xsd:boolean)

# Class: obo:FOODON_03414944 (scotch bonnet)

AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03414944 obo:IAO_0000122)
Expand Down Expand Up @@ -55586,12 +55524,6 @@ The most common kiwifruit is the fuzzy kiwifruit, from the species *Actinidia de
AnnotationAssertion(rdfs:label obo:FOODON_03415177 "actinidia plant"@en)
SubClassOf(obo:FOODON_03415177 obo:FOODON_03411231)

# Class: obo:FOODON_03415178 (obsolete: kiwifruit plant (A. deliciosa))

AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03415178 obo:NCBITaxon_3627)
AnnotationAssertion(rdfs:label obo:FOODON_03415178 "obsolete: kiwifruit plant (A. deliciosa)"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_03415178 "true"^^xsd:boolean)

# Class: obo:FOODON_03415181 (arenga palm plant)

AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03415181 obo:IAO_0000428)
Expand Down Expand Up @@ -55972,21 +55904,14 @@ AnnotationAssertion(obo:IAO_0000412 obo:FOODON_03420154 <http://langual.org>)

# Class: obo:FOODON_03420155 (obsolete: seed (anatomical part))

AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03420155 obo:IAO_0000428)
AnnotationAssertion(obo:IAO_0000115 obo:FOODON_03420155 "The main propagative part of a plant, especially the kernel of a grain or nut. The bulk of the seed is formed by the endosperm, which encloses the germ and is covered by skin (bran)."@en)
AnnotationAssertion(obo:IAO_0000412 obo:FOODON_03420155 <http://langual.org>)
AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03420155 obo:PO_0009010)
AnnotationAssertion(go:hasDbXref obo:FOODON_03420155 langual:C0155)
AnnotationAssertion(go:hasExactSynonym obo:FOODON_03420155 "seed"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03420155 "dehulled seed"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03420155 "kernel"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03420155 "nut, shelled (part or portion)"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03420155 "seed or kernel, skin undetermined"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03420155 "seed without shell or hull"@en)
AnnotationAssertion(go:hasSynonym obo:FOODON_03420155 "shelled seed"@en)
AnnotationAssertion(rdfs:comment obo:FOODON_03420155 "LanguaL curation note: The factor values under *SEED* are arrayed so that the indexer can check first whether the skin is present, removed or undetermined and then check the same information for the germ.

Renamed from *SEED OR KERNEL* in LanguaL 2008."@en)
AnnotationAssertion(rdfs:label obo:FOODON_03420155 "obsolete: seed (anatomical part)"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_03420155 "true"^^xsd:boolean)
SubClassOf(obo:FOODON_03420155 obo:FOODON_03420167)
Expand Down Expand Up @@ -56179,13 +56104,6 @@ AnnotationAssertion(go:hasSynonym obo:FOODON_03420202 "roe"@en)
AnnotationAssertion(rdfs:label obo:FOODON_03420202 "ovary, roe"@en)
SubClassOf(obo:FOODON_03420202 obo:FOODON_03420145)

# Class: obo:FOODON_03420203 (obsolete: starch)

AnnotationAssertion(obo:IAO_0000412 obo:FOODON_03420203 <http://langual.org>)
AnnotationAssertion(rdfs:label obo:FOODON_03420203 "obsolete: starch"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_03420203 "true"^^xsd:boolean)
SubClassOf(obo:FOODON_03420203 obo:CHEBI_18154)

# Class: obo:FOODON_03420208 (seed, skin removed, germ removed (endosperm))

AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03420208 obo:IAO_0000428)
Expand Down Expand Up @@ -96916,6 +96834,10 @@ SubClassOf(obo:PO_0000003 obo:FOODON_03411564)

AnnotationAssertion(rdfs:seeAlso obo:PO_0009001 "https://en.wikipedia.org/wiki/Fruit_anatomy"^^xsd:anyURI)

# Class: obo:PO_0009010 (seed)

AnnotationAssertion(go:hasExactSynonym obo:PO_0009010 "shelled seed"@en)

# Class: obo:PO_0009011 (plant structure)

AnnotationAssertion(go:hasDbXref obo:PO_0009011 langual:C0174)
Expand All @@ -96930,7 +96852,7 @@ EquivalentClasses(obo:PO_0009084 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:B

# Class: obo:PO_0009090 (aril)

AnnotationAssertion(rdfs:label obo:PO_0009090 "aril"@en)
AnnotationAssertion(go:hasDbXref obo:PO_0009090 langual:C0287)
SubClassOf(obo:PO_0009090 obo:FOODON_03420178)

# Class: obo:PO_0020006 (funicle)
Expand Down Expand Up @@ -97372,8 +97294,6 @@ AnnotationAssertion(obo:IAO_0000117 obo:FOODON_03309824 "Damion Dooley"@en)
AnnotationAssertion(obo:IAO_0000119 obo:FOODON_03309824 "https://en.wikipedia.org/wiki/Khoa"^^xsd:anyURI)
AnnotationAssertion(go:hasExactSynonym obo:FOODON_03310120 "purslane"@en)
AnnotationAssertion(go:hasExactSynonym obo:FOODON_03310141 "groundsel leaf")
AnnotationAssertion(obo:IAO_0000115 obo:FOODON_03310334 "Baker's yeast is the common name for the strains of yeast commonly used in baking bread and bakery products, serving as a leavening agent which causes the bread to rise (expand and become lighter and softer) by converting the fermentable sugars present in the dough into carbon dioxide and ethanol"@en)
AnnotationAssertion(obo:IAO_0000119 obo:FOODON_03310334 "https://en.wikipedia.org/wiki/Baker%27s_yeast"^^xsd:anyURI)
AnnotationAssertion(obo:IAO_0000115 obo:FOODON_03310591 "A beef steak product which is raw and is cut from the outer part of the round of a cow."@en)
AnnotationAssertion(obo:IAO_0000119 obo:FOODON_03310591 "https://en.wikipedia.org/wiki/Round_steak"@en)
AnnotationAssertion(dcterms:contributor obo:FOODON_03310591 "https://orcid.org/0000-0001-5193-0062 | https://orcid.org/0000-0001-8008-8249"@en)
Expand All @@ -97384,8 +97304,6 @@ AnnotationAssertion(go:hasNarrowSynonym obo:FOODON_03310591 "top round"@en)
AnnotationAssertion(obo:IAO_0000115 obo:FOODON_03311719 "A carcass of a swine."@en)
AnnotationAssertion(dcterms:contributor obo:FOODON_03311719 <https://orcid.org/0000-0001-5275-8866>)
AnnotationAssertion(rdfs:seeAlso obo:FOODON_03311870 <https://scottishforestgarden.wordpress.com/2017/04/08/leaf-sauce/>)
AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03315025 "http://purl.obolibrary.org/obo/FOODON_03306041"@en)
AnnotationAssertion(owl:deprecated obo:FOODON_03315025 "true"^^xsd:boolean)
AnnotationAssertion(go:hasDbXref obo:FOODON_03315177 langual:H0154)
AnnotationAssertion(obo:IAO_0100001 obo:FOODON_03315305 langual:H0105)
AnnotationAssertion(obo:IAO_0000114 obo:FOODON_03316443 "requires discussion"@en)
Expand Down
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