Difference between revisions of "Chado Genetic Module"

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−
==Introduction==
+
=Introduction=
  
 +
See Dave Emmert's presentation [[:Image:Emmert 040526.pdf|The new and improved chado genetics module]] for explanations of parts of this module.
  
−
==Tables==
+
{{NeedsEditing}}
  
−
===phenstatement===
+
=Tables=
  
−
Phenotypes are things like ”larval lethal”. Phenstatements are things like ”dpp[1] is recessive
+
== Table: environment ==
−
larval lethal”. So essentially phenstatement is a linking table expressing the relationship between
+
−
genotype, environment, and phenotype.
+
  
 +
The environmental component of a phenotype description.
  
−
  Table 4.39: phenstatement
+
{| 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
 +
| '' ''
 +
|}
  
−
Column  DatatypeDescription
+
Tables referencing this one via Foreign Key Constraints:
−
phenstatement id integer
+
−
genotype idinteger
+
−
environment idinteger
+
−
phenotype id  integer
+
−
type id integer
+
−
pub id  integer
+
  
 +
* [[Chado_Tables#Table:_environment_cvterm| environment_cvterm]]
  
−
===phendesc===
+
* [[Chado_Tables#Table:_phendesc| phendesc]]
  
−
a summary of a set of phenotypic statements for any one gcontext made in any one publication
+
* [[Chado_Tables#Table:_phenotype_comparison| phenotype_comparison]]
  
 +
* [[Chado_Tables#Table:_phenstatement| phenstatement]]
  
−
Table 4.40: phendesc
+
----
  
−
ColumnDatatype Description
 
−
phendesc id integer
 
−
genotype id integer
 
−
environment id integer
 
−
description text
 
−
pub idinteger
 
  
  
−
===phenotype_comparison===
+
== Table: environment_cvterm ==
  
−
comparison of phenotypes eg, genotype1/environment1/phenotype1 ”non-suppressible” wrt geno-
+
{| border="1" cellpadding="3"
−
type2/environment2/phenotype2
+
|+ 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 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
 
  
 +
== Table: feature_genotype ==
  
−
===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 4.35: genotype
+
----
  
−
ColumnDatatype Description
 
−
genotype id integer
 
−
uniquename  text
 
−
description varchar
 
  
  
−
===feature_genotype===
+
== Table: genotype ==
  
−
  Table 4.36: feature genotype
+
{{NeedsEditing}}
  
−
Column  Datatype Description
+
OPEN QUESTION: for multicopy transgenes, should we include a 'n_copies' column as well?
−
feature genotype id integer
+
−
feature id integer
+
−
genotype idinteger
+
−
chromosome id integer
+
−
rank integer
+
−
cgroup  integer
+
−
cvterm id  integer
+
  
 +
Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
  
−
===environment===
+
{| 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)
 +
| '' ''
 +
|}
  
−
  Table 4.37: environment
+
Tables referencing this one via Foreign Key Constraints:
  
−
  ColumnDatatype  Description
+
* [[Chado_Tables#Table:_feature_genotype| feature_genotype]]
−
  environment id integer
+
−
  uniquename  text
+
−
  description text
+
  
 +
* [[Chado_Tables#Table:_phendesc| phendesc]]
  
−
===environment_cvterm===
+
* [[Chado_Tables#Table:_phenotype_comparison| phenotype_comparison]]
  
−
  Table 4.38: environment cvterm
+
* [[Chado_Tables#Table:_phenstatement| phenstatement]]
  
−
  Column Datatype Description
+
* [[Chado_Tables#Table:_stock_genotype| stock_genotype]]
−
  environment cvterm id integer
+
−
  environment id  integer
+
−
  cvterm id integer
+
  
 +
* [[Chado_Tables#Table:_wwwuser_genotype| wwwuser_genotype]]
  
−
[[Category:Chado]]
+
----
−
[[Category:To Do]]
+
 
 +
 
 +
 
 +
== 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 ''
 +
|}
 +
 
 +
----
 +
 
 +
[[Category:Chado Modules]]
 +
[[Category:Phenotypes]]
 +
[[Category:!Lacking ERD]]

Latest revision as of 07:58, 20 April 2016

Introduction

See Dave Emmert's presentation The new and improved chado genetics module for explanations of parts of this module.

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

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

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

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.

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
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