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PomBase Chado notes

Alleles

Alleles are stored as features with SO type allele.

Allele feature have these possible featureprops:

• allele_type - see below
• canto_session - the Canto session ID if this allele was created in Canto
• description - eg. "A123K", "1-159,274-372", "119->opal"

Allele types

• nonsense_mutation
• deletion
• nucleotide_mutation
• partial_amino_acid_deletion
• other
• partial_nucleotide_deletion
• unrecorded
• wild_type
• unknown
• amino_acid_mutation

Genotype modelling

Genotypes are stored as features with SO type genotype. allele features are part_of genotype feature via the feature_relationship table.

The expression of an allele is stored as a feature_relationshipprop of the part_of relation.

Genotype/phenotype annotation

Phenotypes are annotated to genotypes via the feature_cvterm table