Chado Phenotype Module

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Phenotypes are things like ”larval lethal”. Phenstatements are things like ”dpp[1] is recessive larval lethal”. So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.

 Table 4.39: phenstatement
Column  DatatypeDescription
phenstatement id integer
genotype idinteger
environment idinteger
phenotype id  integer
type id integer
pub id  integer


a summary of a set of phenotypic statements for any one gcontext made in any one publication

Table 4.40: phendesc

ColumnDatatype Description phendesc id integer genotype id integer environment id integer description text pub idinteger


comparison of phenotypes eg, genotype1/environment1/phenotype1 ”non-suppressible” wrt geno- type2/environment2/phenotype2

Table 4.41: phenotype comparison

ColumnDatatype Description phenotype comparison id integer genotype1 idinteger environment1 idinteger genotype2 idinteger environment2 idinteger phenotype1 id integer phenotype2 id integer type id integer pub idinteger


a phenotypic statement, or a single atomic phenotypic observation a controlled sentence describing observable effect of non-wt function – e.g. Obs=eye, attribute=color, cvalue=red

Table 4.42: phenotype

Column  Datatype Description
phenotype id  integer
uniquename text
observable id integer  The entity: e.g. anatomy part, biological process
attr id integer  Phenotypic attribute (quality, property, attribute,

character) - drawn from PATO

valuetext  value of attribute - unconstrained free text. Used

only if cvalue id is not appropriate

cvalue id  integer  Phenotype attribute value (state)
assay idinteger  evidence type



 Table 4.43: phenotype cvterm
 Column  Datatype Description
 phenotype cvterm id integer
 phenotype id  integer
 cvterm id  integer



Table 4.44: feature phenotype

 ColumnDatatype Description
 feature phenotype id integer
 feature id  integer
 phenotype idinteger