wiki:PhenotypeImportExportFormats

Version 23 (modified by val_wood, 10 years ago) (diff)

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DatatypeExampleCardinalityInput format requirementExport format requirement
Gene systematic ID SPCPB16A4.03c 1 (single gene) >1 (multigene) See 1 mandatory mandatory
Gene name ade100 or greateroptionaloptional
Allele name ade10-10 or 1 optionaloptional
Allele description e.g deletion, overexpression or See 2 1 (single gene) >1 (multigene) See 1 mandatory mandatory
Allele synonymade101 See 3 0 or greater optionaloptional
FYPO IDFYPO:0000000 1 mandatory mandatory
Evidence codecell growth assay See 41 mandatory mandatory
Condition at high temperature See 51 mandatory mandatory
Penetrance %, range%, or small CV (did we say high/low)?0 or 1optional optional
Expressivity integer/units AND|OR small CV (high/low)0 or 1optional optional
Background strain ID972h- See 61mandatory mandatory
Date ID201201011mandatory mandatory
Export only fields
DatabasePomBase?1optional mandatory
  1. Cardinality is one for single genes, >1 for multigenes. Q How should these be separated ? comma/pipe? need to be able to combine with allele description to make genotype, so should be colinear?
  1. https://sourceforge.net/apps/trac/pombase/wiki/DescribingResidues
  1. If the user wants to submit an alternative name for an allele
  1. ECO subset
  1. Currently a list, will be a vocabulary http://sourceforge.net/apps/trac/pombase/wiki/PhenotypeConditions\

  1. Background strain, plus information about changes (but not info in allele description?) including selectable markers to be used in genotype description...this will get complicated....will be used in construction of genotype? what happens with legacy data where we do't have this info without checking? syntax?