GMOD
Chado Genetic Module - Staging
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.
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.
| FK | Name | Type | Description |
|---|---|---|---|
| environment_id | serial | PRIMARY KEY | |
| uniquename | text | UNIQUE NOT NULL | |
| description | text |
public.environment Structure
Tables referencing this one via Foreign Key Constraints:
Table: environment_cvterm
| 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 |
public.environment_cvterm Structure
Table: feature_genotype
| FK | Name | Type | Description |
|---|---|---|---|
| feature_genotype_id | serial | PRIMARY KEY | |
| feature_id | integer | UNIQUE#1 NOT NULL | |
| genotype_id | integer | UNIQUE#1 NOT NULL | |
| 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_id | integer | UNIQUE#1 NOT NULL |
public.feature_genotype Structure
Table: genotype
Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
| 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) |
public.genotype Structure
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.
| 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 |
public.phendesc Structure
Table: phenotype_comparison
Comparison of phenotypes e.g., genotype1/environment1/phenotype1 “non-suppressible” with respect to genotype2/environment2/phenotype2.
| 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 |
public.phenotype_comparison Structure
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.
| 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 |
public.phenstatement Structure