Merge pull request #367 from ontologyportal/J20230918

new terms created in cell biology related to WheatGrass

Economy.kif

@@ -3844,11 +3844,175 @@ in the Poaceae &%Grass family.")
 &%Grass family.")
 (termFormat EnglishLanguage SorghumGrass "sorghum grass")
 
+(subclass AegilopsGrass Grass)
+(documentation AegilopsGrass EnglishLanguage "Aegilops is a genus of Eurasian and North American plants 
+in the grass family, Poaceae. They are known generally as goatgrasses. It is a diploid (2 sets of chromosomes) 
+goatgrass. Genus Aegilops has played an important role in the taxonomy of wheat. The familiar common wheat
+(Triticum aestivum) arose when cultivated emmer wheat hybridized with Aegilops tauschii about 8,000 years 
+ago.[wikipedia]")
+(termFormat EnglishLanguage AegilopsGrass "Aegilops grass")
+(names "goat grass" AegilopsGrass)
+
+(=>
+  (and
+    (instance ?A AegilopsGrass)
+    (part ?C ?A)
+    (instance ?C ?CLASS))
+  (subclass ?CLASS DiploidCell))
+
+(subclass AegilopsTauschii AegilopsGrass)
+(documentation AegilopsTauschii EnglishLanguage "Aegilops tauschii, the Tausch's goatgrass or
+ rough-spike hard grass, is an annual grass species. Aegilops tauschii is part of the tribe Triticeae, 
+ along with wheat. This diploid (2 sets of chromosomes) goatgrass species has contributed 
+ the D genome to common wheat.[wikipedia]")
+(termFormat EnglishLanguage AegilopsTauschii "Aegilops Tauschii")
+
+(subclass AegilopsSpeltoides AegilopsGrass)
+(documentation AegilopsSpeltoides EnglishLanguage "Aegilops speltoides is an edible goatgrass in the family 
+Poaceae native to Southeastern Europe and Western Asia, which is often used for animal feed, and it has 
+grown in cultivated beds. Aegilops speltoides is a diploid (2 sets of chromosomes). [wikipedia]")
+(termFormat EnglishLanguage AegilopsSpeltoides "Aegilops Speltoides")
+
 (subclass WheatGrass CerealGrass)
 (documentation WheatGrass EnglishLanguage "Wheat is widely cultivated for its &%seed, &%WheatGrain. 
-It is a worldwide staple food. The many species of wheat plant make up the genus Triticum.")
+It is a worldwide staple food. The many species of wheat plant make up the genus Triticum.[wikipedia]")
 (termFormat EnglishLanguage WheatGrass "wheat grass")
 
+(subclass EmmerWheatGrass WheatGrass)
+(documentation EmmerWheatGrass EnglishLanguage "Emmer wheat or hulled wheat is a type of awned wheat. 
+Emmer is a tetraploid (4 sets of chromosomes). This tetraploid wheat is formed by the hybridization 
+of two diploid wild grasses (2 sets of chromomsomes), Triticum urartu, closely related to wild einkorn 
+(T. boeoticum), and an as yet unidentified Aegilops species related to A. searsii or A. speltoides. [wikipedia]")
+(termFormat EnglishLanguage EmmerWheatGrass "emmer wheat grass")
+
+(=>
+  (and
+    (instance ?E EmmerWheatGrass)
+    (part ?C ?E)
+    (instance ?C ?CLASS))
+  (subclass ?CLASS TetraploidCell))
+
+(=>
+  (and
+    (instance ?COLL Collection)
+    (memberType ?COLL Chromosome)
+    (member ?M ?COLL)
+    (part ?M EmmerWheatGrass))
+  (exists (?A ?B ?X ?Y)
+    (and
+      (subCollection ?A ?COLL)
+      (instance ?A HomologousChromosomeSet)
+      (memberType ?A ?X)      
+      (initialPart ?X EinkornWheatGrass)
+      (subCollection ?B ?COLL)
+      (instance ?B HomologousChromosomeSet)
+      (memberType ?B ?Y)      
+      (initialPart ?Y AegilopsGrass))))
+
+(subclass DurumWheatGrass WheatGrass)
+(documentation DurumWheatGrass EnglishLanguage "Durum wheat also called pasta wheat 
+or macaroni wheat (Triticum durum or Triticum turgidum subsp. durum), is a tetraploid 
+species of wheat, having four sets of chromosomes. Durum wheat originated through 
+intergeneric hybridization and polyploidization involving two diploid grass species: 
+T. urartu and a Aegilops speltoides.[wikipedia]")
+(termFormat EnglishLanguage DurumWheatGrass "durum wheat grass")
+
+(=>
+  (and
+    (instance ?E DurumWheatGrass)
+    (part ?C ?E)
+    (instance ?C ?CLASS))
+  (subclass ?CLASS TetraploidCell))
+
+(=>
+  (and
+    (instance ?COLL Collection)
+    (memberType ?COLL Chromosome)
+    (member ?M ?COLL)
+    (part ?M DurumWheatGrass))
+  (exists (?A ?B ?X ?Y)
+    (and
+      (subCollection ?A ?COLL)
+      (instance ?A HomologousChromosomeSet)
+      (memberType ?A ?X)      
+      (initialPart ?X TriticumUrartu)
+      (subCollection ?B ?COLL)
+      (instance ?B HomologousChromosomeSet)
+      (memberType ?B ?Y)      
+      (initialPart ?Y AegilopsSpeltoides))))
+
+(subclass EinkornWheatGrass WheatGrass)
+(documentation EinkornWheatGrass EnglishLanguage "Einkorn wheat can refer either to a wild species of wheat (Triticum) 
+or to its domesticated form. The wild form is T. boeoticum, and the domesticated form is T. monococcum.Einkorn is a 
+diploid species (2 sets of chromosomes) of hulled wheat, with tough glumes ('husks') that tightly enclose the grains.[wikipedia]")
+(termFormat EnglishLanguage EinkornWheatGrass "einkorn wheat grass")
+
+(=>
+  (and
+    (instance ?E EinkornWheatGrass)
+    (part ?C ?E)
+    (instance ?E ?CLASS))
+  (subclass ?CLASS DiploidCell))
+
+(subclass TriticumUrartu WheatGrass)
+(documentation TriticumUrartu EnglishLanguage "riticum urartu, 
+also known as red wild einkorn wheat,[2] and a form of einkorn wheat, is a grass species 
+related to wheat, and native to western Asia. It is a diploid (2 sets of chromosome. [wikipedia]")
+(termFormat EnglishLanguage TriticumUrartu "Triticum urartu")
+(names "red wild einkron wheat" TriticumUrartu)    
+
+(=>
+  (and
+    (instance ?E TriticumUrartu)
+    (part ?C ?E)
+    (instance ?E ?CLASS))
+  (subclass ?CLASS DiploidCell))
+
+(subclass CommonWheatGrass WheatGrass)
+(documentation CommonWheatGrass EnglishLanguage "&%CommonWheatGrass, (Triticum.aestivum), also 
+known as bread wheat, is a cultivated wheat species. Itis an allohexaploid – a combination of 
+six sets of chromosomes from different species. Of the six sets of chromosomes, four come from 
+emmer (Triticum turgidum, itself a tetraploid) and two from Aegilops tauschii (a wild diploid 
+goatgrass). [wikiepedia]")
+(termFormat EnglishLanguage CommonWheatGrass "common wheat grass") 
+
+(=>
+  (and
+    (instance ?C CommonWheatGrass)
+    (part ?CELL ?C)
+    (instance ?CELL ?CLASS))
+  (subclass ?CLASS HexaploidCell))
+
+(=>
+  (and
+    (instance ?COLL Collection)
+    (memberType ?COLL Chromosome)
+    (member ?M ?COLL)
+    (part ?M CommonWheatGrass))
+  (exists (?A ?B ?X ?Y)
+    (and
+      (subCollection ?A ?COLL)
+      (instance ?A HomologousChromosomeSet)
+      (memberType ?A ?X)      
+      (initialPart ?X EmmerWheatGrass)
+      (subCollection ?B ?COLL)
+      (instance ?B HomologousChromosomeSet)
+      (memberType ?B ?Y)      
+      (initialPart ?Y AegilopsTauschii))))
+
+(subclass SpeltWheatGrass WheatGrass)
+(documentation SpeltWheatGrass EnglishLanguage "&%SpeltWheatGrass, (Triticum.spelta)
+, also known as dinkel wheat or hulled wheat.  Like common wheat, it is a hexaploid 
+wheat, which means it has six sets of chromosomes.[wikiepedia]")
+(termFormat EnglishLanguage SpeltWheatGrass "spelt wheat grass") 
+
+(=>
+  (and
+    (instance ?C SpeltWheatGrass)
+    (part ?CELL ?C)
+    (instance ?CELL ?CLASS))
+  (subclass ?CLASS HexaploidCell))
+
 (subclass RyeGrass CerealGrass)
 (documentation RyeGrass EnglishLanguage "Rye (Secale cereale) is a member of the tibe Triticeae related 
 to both wheat (Triticum) and barley (genus Hordeum). Rye is a &%CerealGrass and should not be 
@@ -3876,6 +4040,7 @@ as a grazing forage crop. It is an important crops in the semiarid tropics of As
 ;; MaizeGrain, WheatGrain and RiceGrain are defined in MILO
 
 (subclass CerealGrain Seed)
+(subclass CerealGrain Grain)
 (documentation CerealGrain EnglishLanguage "Any &%Seed which is produced by the cereal grasses,
 e.g. rice, corn, wheat, etc.")
 
@@ -3890,6 +4055,11 @@ e.g. rice, corn, wheat, etc.")
       (instance ?X ?CLASS)
       (equal ?CLASS (FoodForFn Animal)))))
 
+
+(subclass MaizeGrain CerealGrain)
+(documentation MaizeGrain EnglishLanguage "A &%CerealGrain which is found on long ears of a &%Plant
+native to the Americas.")
+
 (subclass RiceGrain CerealGrain)
 (documentation RiceGrain EnglishLanguage "A &%CerealGrain which has short and long grain varieties
 and which is usually prepared for eating by steaming.")
@@ -3904,13 +4074,15 @@ which is used to make &%BreadOrBiscuits.")
 
 (subclass CommonWheatGrain WheatGrain)
 (documentation CommonWheatGrain EnglishLanguage "&%CommonWheatGrain is the seed of (T.aestivum). 
-[wikiepedia]")
+Bread wheat is an allohexaploid – a combination of six sets of chromosomes from different species. 
+Of the six sets of chromosomes, four come from emmer (Triticum turgidum, itself a tetraploid) and 
+two from Aegilops tauschii (a wild diploid goatgrass). [wikiepedia]")
 (termFormat EnglishLanguage CommonWheatGrain "common wheat grain")  
 
 (=>
   (equal ?X
     (PlantFn CommonWheatGrain))
-  (subclass ?X WheatGrass))
+  (subclass ?X CommonWheatGrass))
 
 (subclass DurumWheatGrain WheatGrain)
 (documentation DurumWheatGrain EnglishLanguage "&%DurumWheatGrain is the seed (T.durum). 
@@ -3920,18 +4092,38 @@ which is used to make &%BreadOrBiscuits.")
 (=>
   (equal ?X
     (PlantFn DurumWheatGrain))
-  (subclass ?X WheatGrass))
+  (subclass ?X DurumWheatGrass))
+
+(subclass EmmerWheatGrain WheatGrain)
+(documentation EmmerWheatGrain EnglishLanguage "&%EmmerWheatGrain is the seed 
+of Wild Emmer (T.dicoccoides) or Domesticated form (T. dicoccum). [wikipedia]")
+(termFormat EnglishLanguage EmmerWheatGrain "Emmer wheat grain") 
+
+(=>
+  (equal ?X
+    (PlantFn EmmerWheatGrain))
+  (subclass ?X EmmerWheatGrass))
+
+(subclass EinkornWheatGrain WheatGrain)
+(documentation EinkornWheatGrain EnglishLanguage "&%EinkornWheatGrain is the seed 
+of Wild Einkorn (T.boeoticum) or the domesticated form (T. monococcum). [wikipedia]")
+(termFormat EnglishLanguage EinkornWheatGrain "Einkorn wheat grain") 
+
+(=>
+  (equal ?X
+    (PlantFn EinkornWheatGrain))
+  (subclass ?X EinkornWheatGrass))
 
-(subclass SpeltGrain WheatGrain)
-(documentation SpeltGrain EnglishLanguage "&%SpeltGrain is the seed of  (Triticum spelta),
-also known as dinkel wheat. It is a species of &%WheatGrass that has been cultivated since
-approximately 5000 BC.[wikipedia]")
-(termFormat EnglishLanguage SpeltGrain "Spelt grain") 
+(subclass SpeltWheatGrain WheatGrain)
+(documentation SpeltWheatGrain EnglishLanguage "&%SpeltWheatGrain is the seed of 
+(Triticum spelta),also known as dinkel wheat. It is a species of &%WheatGrass that 
+has been cultivated sinceapproximately 5000 BC.[wikipedia]")
+(termFormat EnglishLanguage SpeltWheatGrain "spelt wheat grain") 
 
 (=>
   (equal ?X
-    (PlantFn SpeltGrain))
-  (subclass ?X WheatGrass))
+    (PlantFn SpeltWheatGrain))
+  (subclass ?X SpeltWheatGrass))
 
 (subclass Pea Seed)
 (subclass Pea (FoodForFn Animal))

Food.kif

@@ -1509,6 +1509,9 @@ wheat flour (T.durum) is the second most used. There are also Semolina and Spelt
 It is the flour most often used for making &%BreadOrBiscuits. [wikiepedia]")
 (termFormat EnglishLanguage CommonWheatFlour "common wheat flour")  
 (initialPart CommonWheatFlour CommonWheatGrain)
+(=>
+  (instance ?WF (OrganicObjectFn CommonWheatGrain))
+  (instance ?WF CommonWheatFlour))
 
 (subclass DurumWheatFlour WheatFlour)
 (documentation DurumWheatFlour EnglishLanguage "&%DurumWheatFlour is prepared from(T.durum). 
@@ -1528,7 +1531,7 @@ It is often used to make &%Pasta, breakfast cereals, puddings, and couscous.[wik
 also known as dinkel wheat. It is a species of &%WheatGrass that has been cultivated since
 approximately 5000 BC.[wikipedia]")
 (termFormat EnglishLanguage SpeltFlour "Spelt flour") 
-(initialPart SpeltFlour SpeltGrain)
+(initialPart SpeltFlour SpeltWheatGrain)
 
 (subclass RyeFlour Flour)
 (documentation RyeFlour EnglishLanguage "&%RyeFlour is a four refined from &%RyeGrain.[wikipedia]")

Mid-level-ontology.kif

@@ -10119,7 +10119,7 @@ Mitochondria generate most of the cell's supply of
 (termFormat EnglishLanguage Mitochondrion "mitochondria")
 (secretesSubstance Mitochondrion AdenosineTriphosphate)
 
-(subclass BloodCell Cell)
+(subclass BloodCell SomaticCell)
 (subclass BloodCell AnimalAnatomicalStructure)
 (documentation BloodCell EnglishLanguage "A &%Cell that is normally present in &%Blood.")
 
@@ -10721,7 +10721,7 @@ undergoing &%MuscularContract and then a &%MuscleRelaxing to pump
         (moves ?T ?B)
         (causes ?HB ?T)))))
 
-(subclass NerveCell Cell)
+(subclass NerveCell SomaticCell)
 (subclass NerveCell AnimalAnatomicalStructure)
 (documentation NerveCell EnglishLanguage "The &%Cells that make up a &%NervousSystem.")
 
@@ -21589,10 +21589,6 @@ continuous &%Liquid medium. Examples of Sol includes &%Blood &%Paint.")
       (instance ?B Bee)
       (result ?P ?H))))
 
-(subclass MaizeGrain CerealGrain)
-(documentation MaizeGrain EnglishLanguage "A &%CerealGrain which is found on long ears of a &%Plant
-native to the Americas.")
-
 (subclass Caffeine Molecule)
 (subclass Caffeine Stimulant)
 (subclass Caffeine Diuretic)
@@ -23885,12 +23881,34 @@ has not had any menstrual bleeding for a year. [from Wikipedia]")
   (attribute ?F Menopausal)
   (attribute ?F Female))
 
-(subclass Gamete Cell)
+(subclass SomaticCell EukaryoticCell)
+(documentation SomaticCell EnglishLanguage "&%SomaticCells are the cells in the 
+body other than a &%Gamete, germ cell, gametocyte or undifferentiated stem cell.
+In humans, somatic cells are diploid, meaning they contain two sets of chromosomes. 
+[Wikipedia]")
+(termFormat EnglishLanguage SomaticCell "somatic cell")
+(disjoint SomaticCell Gamete)
+
+(subclass Gamete EukaryoticCell)
+(documentation Gamete EnglishLanguage "A &%Gamete is a haploid cell 
+that fuses with another haploid cell during fertilization in organisms that 
+reproduce sexually.Gametes are an organism's reproductive cells, also referred 
+to as sex cells. In species that produce two morphologically distinct types of 
+gametes, and in which each individual produces only one type, a female is any 
+individual that produces the larger type of gamete—called an &%Ovum and a male 
+produces the smaller type, called a &%Sperm.[Wikipedia]")
+(termFormat EnglishLanguage Gamete "gamete")
+
 (subclass Ovum Gamete)
+(documentation Ovum EnglishLanguage "An &%Ovum is a female gamate.[Wikipedia]")
+(termFormat EnglishLanguage Ovum "ovum")
+
 (subclass Sperm Gamete)
+(documentation Sperm EnglishLanguage "A &%Sperm is a male gamate.[Wikipedia]")
+(termFormat EnglishLanguage Sperm "sperm")
+
 (subclass Fertilisation OrganOrTissueProcess)
 (subclass Fertilisation Attaching)
-
 (documentation Fertilisation EnglishLanguage "Fertilisation or
 fertilization, also known as generative
 fertilisation, syngamy and impregnation, is the fusion of gametes
@@ -23917,7 +23935,7 @@ called fertilization. [from Wikipedia]")
   (subclass ?F Fertilisation)
   (capability ?F patient Organism))
 
-(subclass Zygote Cell)
+(subclass Zygote EukaryoticCell)
 (termFormat EnglishLanguage Zygote "zygote")
 
 (documentation Zygote EnglishLanguage "A zygote is a &%EukaryoticCell