Difference between revisions of "Chado Genetic Module"

Revision as of 19:31, 19 February 2007

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

genotype

Table 4.35: genotype

ColumnDatatype Description genotype id integer uniquename text description varchar

feature_genotype

WARNING OPEN QUESTION: for multicopy transgenes, should we include a 'n_copies' column as well?

 Table 4.36: feature genotype

Column  Datatype Description
feature genotype id integer
feature id integer
genotype idinteger
chromosome id integer
rank integer
cgroup  integer
cvterm id  integer

environment

 Table 4.37: environment

 ColumnDatatype  Description
 environment id integer
 uniquename  text
 description text

environment_cvterm

 Table 4.38: environment cvterm

 Column Datatype Description
 environment cvterm id integer
 environment id  integer
 cvterm id integer