See Dave Emmert’s presentation The new and improved chado genetics module for explanations of parts of this module.
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:
| 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
| F-Key | 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 |
feature_genotype Structure
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.
| 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:
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
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
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