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Basic Genetics Ontology

Basic Genetics Ontology. Onur Buk German Monroy. Gene-Pair-Description. (every Gene-Pair-Description has (controls-trait ((a Trait-Descr))) (dominant-trait ((a Trait))) (recessive-trait ((a Trait))) (dominant-symbol ((a Gene-Symbol))) (recessive-symbol ((a Gene-Symbol)))).

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Basic Genetics Ontology

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  1. Basic Genetics Ontology Onur Buk German Monroy

  2. Gene-Pair-Description (every Gene-Pair-Description has (controls-trait ((a Trait-Descr))) (dominant-trait ((a Trait))) (recessive-trait ((a Trait))) (dominant-symbol ((a Gene-Symbol))) (recessive-symbol ((a Gene-Symbol)))) (*Smoothness-Gene-Pair-Description has (instance-of (Gene-Pair-Description)) (controls-trait (*Smoothness)) (dominant-trait (*Smooth)) (recessive-trait (*Wrinkled)) (dominant-symbol (*S)) (recessive-symbol (*s)) )

  3. Eukaryote (Eukaryote has (superclasses (Organism))) (every Eukaryote has (genotype ((a Gene-Pair))) (phenotype ((the expressed-trait of (the genotype of Self)))) ) (*Fido has (instance-of (Eukaryote)) (genotype ((a Gene-Pair with (alleles ((:pair *S *s))) ) (a Gene-Pair with (alleles ((:pair *y *y)))) )) ) this is actually the potential phenotype

  4. Subclasses of Eukaryote (Homozygous-Dominant, Homozygous-Recessive, Heterozygous) (Heterozygous has (superclasses (Eukaryote)) ) (every Homozygous-Dominant has (for-trait ((a Trait-Descr))) (genotype ((a Gene-Pair with (alleles ((:pair (the dominant-symbol of (the controls-trait-of of (the for-trait of Self))) (the recessive-symbol of (the controls-trait-of of (the for-trait of Self))) ))) (gene-pair-descr ((the controls-trait-of of (the for-trait of Self)))) ))) ) KM> (the alleles of (the genotype of (a Heterozygous with (for-trait (*Smoothness)) ))) ((:pair *S *s))

  5. Probabilistic-Cross (Probabilistic-Cross has (superclasses (Event))) (every Probabilistic-Cross has (probability ((a Number))) (offspring ((a Eukaryote))) )

  6. Cross (Cross has (superclasses (Event))) (every Cross has ; assuming only 1 trait is considered (for now) (parents ((:pair (a Eukaryote) (a Eukaryote))) ) (filial-generation ( … )) (possible-genotypes ( … )) (possible-genotypes-probabilities ( … )) (possible-phenotypes ((the phenotype of (the offspring of (the possible-crosses of Self))))) (possible-phenotypes-probabilities ( … )) (possible-crosses ( { (a Probabilistic-Cross) }* )) ) KM> (the possible-phenotypes of (a Cross with (parents ((:pair (a Homozygous-Recessive with (for-trait (*Smoothness))) (a Homozygous-Dominant with (for-trait (*Smoothness))) ))))) (*Smooth) KM> (the possible-phenotypes-probabilities of (a Cross with (parents ((:pair (a Homozygous-Recessive with (for-trait (*Smoothness))) (a Homozygous-Dominant with (for-trait (*Smoothness))) ))))) ((:bag 1.0))

  7. TestCross (every TestCross has ; required slots (observed-phenotypes ((a Trait))) (observed-phenotypes-probabilities ((a Number))) ; output slot (unknown-parent ((if (the is-candidate1 of Self) then (the parent1-candidate1 of Self) else (if (the is-candidate2 of Self) then (the parent1-candidate2 of Self) else (if (the is-candidate3 of Self) then (the parent1-candidate3 of Self))))))

  8. Caption 2.5 Q: Do a cross between true-breeding peas with phenotypes smooth and wrinkled. What is the phenotype of the progeny? A: All are smooth (*pea1 has (instance-of (True-Breeding)) (trait (*Smooth))) (*pea2 has (instance-of (True-Breeding)) (trait (*Wrinkled))) (*cross2_5 has (instance-of (Cross)) (parents ((:pair *pea1 *pea2)))) KM> (the possible-phenotypes of *cross2_5) (*Smooth) KM> (the possible-phenotypes-probabilities of *cross2_5)))) ((:bag 1.0))

  9. Caption 2.6 Q: Self pollinate F1 individuals. What is the phenotype of the progeny? A: In a proportion approximately 5474 to 1850 between Smooth and Wrinkled. (*f1 has (instance-of (Eukaryote)) (genotype ((a Gene-Pair with (alleles ((the possible-genotypes of *cross2_5))))))) (*cross2_6 has (instance-of (SelfCross)) (parent (*f1)) ) KM> (the possible-phenotypes of *cross2_6) (*Smooth *Wrinkled) KM> (the possible-phenotypes-probabilities of *cross2_6)))) ((:bag 0.75 0.25))

  10. Caption 2.11 For each individual X of the F2 generation, the result of the cross of X with a homozygous recessive individual, is a progeny that when test-crossed, will find out the genotype of X correctly. KM> (forall-bag ?offspring in (the bag of (the filial-generation of *cross2_6)) ((?cross == (a Cross with (parents ((:pair ?offspring (a Homozygous-Recessive with (for-trait ((the for-trait of *cross2_6))))))))) and ( (the alleles of (the genotype of ?offspring) ) = (the alleles of (the genotype of (the unknown-parent of (a TestCross with (observed-phenotypes ((the possible-phenotypes of ?cross))) (observed-phenotypes-probabilities ((the possible-phenotypes-probabilities of ?cross)))))))))) ((:bag t t t))

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