Difference between revisions of "Chado Genetic Module"

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==Introduction==
+
=Introduction=
  
  
−
==Tables==
+
=Tables=
 +
 
 +
== Table: environment ==
 +
 
 +
The environmental component of a phenotype description.
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ environment Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| environment_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
| uniquename
 +
| text
 +
| '' UNIQUE NOT NULL ''
 +
|- class="tr0"
 +
|
 +
| description
 +
| text
 +
| '' ''
 +
|}
 +
 
 +
Tables referencing this one via Foreign Key Constraints:
 +
 
 +
* [[Chado_Tables#Table:_environment_cvterm| environment_cvterm]]
 +
 
 +
* [[Chado_Tables#Table:_phendesc| phendesc]]
 +
 
 +
* [[Chado_Tables#Table:_phenotype_comparison| phenotype_comparison]]
 +
 
 +
* [[Chado_Tables#Table:_phenstatement| phenstatement]]
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: environment_cvterm ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ environment_cvterm Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| environment_cvterm_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_environment| environment]]
 +
| environment_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| cvterm_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: feature_genotype ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ feature_genotype Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| feature_genotype_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| feature_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_genotype| genotype]]
 +
| genotype_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| chromosome_id
 +
| integer
 +
| '' UNIQUE#1 ''<br /><br />A feature of SO type "chromosome".
 +
|- class="tr0"
 +
|
 +
| rank
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''<br /><br />rank can be used for n-ploid organisms or to preserve order.
 +
|- class="tr1"
 +
|
 +
| cgroup
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''<br /><br />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).
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| 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.
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ genotype Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| genotype_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
| name
 +
| text
 +
| '' ''<br /><br />Optional alternative name for a genotype, for display purposes.
 +
|- class="tr0"
 +
|
 +
| uniquename
 +
| text
 +
| '' UNIQUE NOT NULL ''<br /><br />The unique name for a genotype; typically derived from the features making up the genotype.
 +
|- class="tr1"
 +
|
 +
| description
 +
| character varying(255)
 +
| '' ''
 +
|}
 +
 
 +
Tables referencing this one via Foreign Key Constraints:
 +
 
 +
* [[Chado_Tables#Table:_feature_genotype| feature_genotype]]
 +
 
 +
* [[Chado_Tables#Table:_phendesc| phendesc]]
 +
 
 +
* [[Chado_Tables#Table:_phenotype_comparison| phenotype_comparison]]
 +
 
 +
* [[Chado_Tables#Table:_phenstatement| phenstatement]]
 +
 
 +
* [[Chado_Tables#Table:_stock_genotype| stock_genotype]]
 +
 
 +
* [[Chado_Tables#Table:_wwwuser_genotype| wwwuser_genotype]]
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: phendesc ==
 +
 
 +
A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ phendesc Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| phendesc_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_genotype| genotype]]
 +
| genotype_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_environment| environment]]
 +
| environment_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
| description
 +
| text
 +
| '' NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_pub| 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.
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ phenotype_comparison Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| phenotype_comparison_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_genotype| genotype]]
 +
| genotype1_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_environment| environment]]
 +
| environment1_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_genotype| genotype]]
 +
| genotype2_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_environment| environment]]
 +
| environment2_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_phenotype| phenotype]]
 +
| phenotype1_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_phenotype| phenotype]]
 +
| phenotype2_id
 +
| integer
 +
| '' ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== 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.
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ phenstatement Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| phenstatement_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_genotype| genotype]]
 +
| genotype_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_environment| environment]]
 +
| environment_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_phenotype| phenotype]]
 +
| phenotype_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
  
 
===phenstatement===
 
===phenstatement===

Revision as of 03:18, 1 March 2007

Introduction

Tables

Table: environment

The environmental component of a phenotype description.

environment Structure
F-Key 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

environment_cvterm Structure
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


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


Table: genotype

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)

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.

phendesc Structure
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


Table: phenotype_comparison

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

phenotype_comparison Structure
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


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.

phenstatement Structure
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

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. 


 Table 4.39: phenstatement

Column  DatatypeDescription
phenstatement id integer
genotype idinteger
environment idinteger
phenotype id  integer
type id integer
pub id  integer


phendesc

a summary of a set of phenotypic statements for any one gcontext made in any one publication


Table 4.40: phendesc

ColumnDatatype Description phendesc id integer genotype id integer environment id integer description text pub idinteger


phenotype_comparison

comparison of phenotypes eg, genotype1/environment1/phenotype1 ”non-suppressible” wrt geno- type2/environment2/phenotype2


Table 4.41: phenotype comparison

ColumnDatatype Description phenotype comparison id integer genotype1 idinteger environment1 idinteger genotype2 idinteger environment2 idinteger phenotype1 id integer phenotype2 id integer type id integer pub idinteger


genotype

Table 4.35: genotype

ColumnDatatype Description genotype id integer uniquename text description varchar


feature_genotype

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

 Table 4.36: feature genotype

Column  Datatype Description
feature genotype id integer
feature id integer
genotype idinteger
chromosome id integer
rank integer
cgroup  integer
cvterm id  integer

environment

 Table 4.37: environment

 ColumnDatatype  Description
 environment id integer
 uniquename  text
 description text


environment_cvterm

 Table 4.38: environment cvterm

 Column Datatype Description
 environment cvterm id integer
 environment id  integer
 cvterm id integer
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