Chado Phenotype Module
Contents
Introduction
Tables
phenstatement
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
phendesc
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
phenotype_comparison
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
phenotype
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
phenotype_cvterm
NULL
Table 4.43: phenotype cvterm
Column Datatype Description phenotype cvterm id integer phenotype id integer cvterm id integer
feature_phenotype
NULL
Table 4.44: feature phenotype
ColumnDatatype Description feature phenotype id integer feature id integer phenotype idinteger
