Chado Genetic Module - Staging

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Under Construction

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.

public.environment Structure
FK Name Type Description
environment_id serial PRIMARY KEY
uniquename text UNIQUE NOT NULL
description text

Tables referencing this one via Foreign Key Constraints:



Table: environment_cvterm

public.environment_cvterm Structure
FK 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


Table: feature_genotype

public.feature_genotype Structure
FK 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


Table: genotype

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

public.genotype Structure
FK 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)

Tables referencing this one via Foreign Key Constraints:


Discussion

OPEN QUESTION: for multicopy transgenes, should we include a 'n_copies' column as well? -- Brain Osborne, Feb 2007


Table: phendesc

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

public.phendesc Structure
FK 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


Table: phenotype_comparison

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

public.phenotype_comparison Structure
FK 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

pub

pub_id integer UNIQUE#1 NOT NULL

organism

organism_id integer NOT NULL

Tables referencing this one via Foreign Key Constraints:



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.

public.phenstatement Structure
FK 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