Revision as of 20:32, 10 December 2010

This page or section is under construction.

This page is a working area for updating the revised genetic module that came out of the GMOD Evo Hackathon. Please edit the table and column descriptions below. These updates will be added to the PostgreSQL comments before the next Chado release.

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.

Tables referencing this one via Foreign Key Constraints:

• environment_cvterm

• phendesc

• phenotype_comparison

• phenstatement

Table: environment_cvterm

Table: feature_genotype

Table: genotype

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

Tables referencing this one via Foreign Key Constraints:

• feature_genotype

• nd_experiment_genotype

• phendesc

• phenotype_comparison

• phenstatement

• stock_genotype

Table: phendesc

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

Table: phenotype_comparison

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

Tables referencing this one via Foreign Key Constraints:

• phenotype_comparison_cvterm

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.