Strains have phenotype, but no genotype

[ypandit]

• The data model for phenotype is strain -> genotype -> phenotype <- environment
• However, there are 3255 strains that do not have a genotype, but still have phenotypes.
  • In such cases, a genotype (CGM_CHADO.genotype) is created with the uniquename => DBS ID, description => strain_name; although CGM_DDB.stock_center.genotype IS NULL
• The complete list of these strains is available here

For these strains a genotype can be generated from the following string, where the <gene-name> is variable depending on the associated genes for respective strains.

axeA1,axeB1,axeC1,<gene_name>-,[pBSR1],bsR

Note:

1. This only applies to strains where strain_name LIKE [V]{5} e.g V31836, V31821.
   • Total of 3057/3255.
   • Data available here
2. The rest to be curated manually
   • Data available here

cc: @dictyBase, @pfey03

[ypandit]

Only a few (241) [V]{5} like strains have any associated genes. The default genotype for the rest 2017 strains would be:

axeA1,axeB1,axeC1,[pBSR1],bsR

[ypandit]

• Genotypes for [V0-9]{6} like strains (from their parent AX4) can be found here

cc: @pfey03

[ypandit]

• If genotype doesn't exist, create entry with stock.name in genotype and link to phenotype