GMOD

Chado Genetic Module

Contents

Introduction

See Dave Emmert’s presentation The new and improved chado genetics module for explanations of parts of this module.

Tables

Table: environment

The environmental component of a phenotype description.

F-Key Name Type Description
  environment_id serial PRIMARY KEY
  uniquename text UNIQUE NOT NULL
  description text  

environment Structure

Tables referencing this one via Foreign Key Constraints:


Table: environment_cvterm

F-Key Name Type Description
  environment_cvterm_id serial PRIMARY KEY
environment environment_id integer UNIQUE#1 NOT NULL
cvterm cvterm_id integer UNIQUE#1 NOT NULL

environment_cvterm Structure


Table: feature_genotype

feature_genotype Structure
F-Key Name Type Description
feature_genotype_id serial PRIMARY KEY

feature

feature_id integer UNIQUE#1 NOT NULL

genotype

genotype_id integer UNIQUE#1 NOT NULL

feature

chromosome_id integer UNIQUE#1

A feature of SO type "chromosome".
rank integer UNIQUE#1 NOT NULL

rank can be used for n-ploid organisms or to preserve order.
cgroup integer UNIQUE#1 NOT NULL

Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).

cvterm

cvterm_id integer UNIQUE#1 NOT NULL

feature_genotype Structure


Table: genotype

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

Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.

genotype Structure
F-Key Name Type Description
genotype_id serial PRIMARY KEY
name text

Optional alternative name for a genotype, for display purposes.
uniquename text UNIQUE NOT NULL

The unique name for a genotype; typically derived from the features making up the genotype.
description character varying(255)

genotype Structure

Tables referencing this one via Foreign Key Constraints:


Table: phendesc

A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.

F-Key Name Type Description
  phendesc_id serial PRIMARY KEY
genotype genotype_id integer UNIQUE#1 NOT NULL
environment environment_id integer UNIQUE#1 NOT NULL
  description text NOT NULL
cvterm type_id integer UNIQUE#1 NOT NULL
pub pub_id integer UNIQUE#1 NOT NULL

phendesc Structure


Table: phenotype_comparison

Comparison of phenotypes e.g., genotype1/environment1/phenotype1 “non-suppressible” with respect to genotype2/environment2/phenotype2.

F-Key Name Type Description
  phenotype_comparison_id serial PRIMARY KEY
genotype genotype1_id integer UNIQUE#1 NOT NULL
environment environment1_id integer UNIQUE#1 NOT NULL
genotype genotype2_id integer UNIQUE#1 NOT NULL
environment environment2_id integer UNIQUE#1 NOT NULL
phenotype phenotype1_id integer UNIQUE#1 NOT NULL
phenotype phenotype2_id integer  
cvterm type_id integer UNIQUE#1 NOT NULL
pub pub_id integer UNIQUE#1 NOT NULL

phenotype_comparison Structure


Table: 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.

F-Key Name Type Description
  phenstatement_id serial PRIMARY KEY
genotype genotype_id integer UNIQUE#1 NOT NULL
environment environment_id integer UNIQUE#1 NOT NULL
phenotype phenotype_id integer UNIQUE#1 NOT NULL
cvterm type_id integer UNIQUE#1 NOT NULL
pub pub_id integer UNIQUE#1 NOT NULL

phenstatement Structure


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