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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"
- nonsense_mutation
- deletion
- nucleotide_mutation
- partial_amino_acid_deletion
- other
- partial_nucleotide_deletion
- unrecorded
- wild_type
- unknown
- amino_acid_mutation
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.
Phenotypes are annotated to genotypes via the feature_cvterm table
See the GMOD extension docs for an overview.
We store extensions using a post-composed terms in the cv "PomBase annotation extension terms". The new term names have the form " [] ...". eg. "O-phospho-L-threonine [absent_during] mitotic G1 phase". There may be multiple extensions:
- "kinetochore [during] mitotic cell cycle [during] meiotic cell cycle"
- "cell pole [dependent_on] actin cytoskeleton [occurs_during] mitosis [occurs_during] mitotic interphase"
The relation objects can be terms (as in the examples above) or can be genes as with localizes() here:
- "medial cortical node [localizes] SPAC57A10.02 [during] G2 phase"
See also: