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Difference between revisions of "Chado Expression Module"
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=Introduction= | =Introduction= | ||
− | This module is for how curated expression data is stored in Chado. | + | This module is for how curated expression data is stored in Chado. |
This module is totally dependent on the [[Chado_Sequence_Module|sequence module]]. Objects in the | This module is totally dependent on the [[Chado_Sequence_Module|sequence module]]. Objects in the | ||
[[Chado_Genetic_Module|genetic module]] cannot connect to expression data except by going ''via'' the | [[Chado_Genetic_Module|genetic module]] cannot connect to expression data except by going ''via'' the | ||
− | sequence module. We assume that we'll '''always''' have a controlled vocabulary for expression data. | + | sequence module. We assume that we'll '''always''' have a controlled vocabulary for expression data. |
− | Here is an example of a simple case of the sort of data that [http://flybase.org FlyBase] curates. | + | Here is an example of a simple case of the sort of data that [http://flybase.org FlyBase] curates. |
The ''dpp'' transcript is expressed in embryonic stage 13-15 in the cephalic | The ''dpp'' transcript is expressed in embryonic stage 13-15 in the cephalic | ||
segment as reported in a [http://flybase.bio.indiana.edu/reports/FBrf0053806.html paper by Blackman ''et al.'' in 1991]. This would be implemented in the expression module by linking the ''dpp'' | segment as reported in a [http://flybase.bio.indiana.edu/reports/FBrf0053806.html paper by Blackman ''et al.'' in 1991]. This would be implemented in the expression module by linking the ''dpp'' | ||
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* ''embryonic stage 15'' where the cvterm_type would be stage and the rank=1 | * ''embryonic stage 15'' where the cvterm_type would be stage and the rank=1 | ||
* ''cephalic segment'' where the cvterm_type would be anatomy and the rank=0 | * ''cephalic segment'' where the cvterm_type would be anatomy and the rank=0 | ||
− | * ''in situ hybridization'' where the cvterm_type would be | + | * ''in situ hybridization'' where the cvterm_type would be assay and the rank=0 |
Note that we would change the ''cvterm_type'' column to ''cvterm_type_id'' and | Note that we would change the ''cvterm_type'' column to ''cvterm_type_id'' and | ||
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ontologies can share the same ''cvterm_type''. | ontologies can share the same ''cvterm_type''. | ||
− | === | + | ===Mage and Expression=== |
The [[Chado_Mage_Module|Mage module]] and the Expression module can be considered overlapping but complementary. The Mage module can store data taken directly from the experimental results whereas the Expression module is typically used to store summary data taken from the biological literature, or extracted from the microarray data stored in Mage. The Mage module handles details about experiments that the Expression module does not whereas the Expression module can be thought of a simpler set of tables designed to tie ontologies concerned with expression to sequence features. | The [[Chado_Mage_Module|Mage module]] and the Expression module can be considered overlapping but complementary. The Mage module can store data taken directly from the experimental results whereas the Expression module is typically used to store summary data taken from the biological literature, or extracted from the microarray data stored in Mage. The Mage module handles details about experiments that the Expression module does not whereas the Expression module can be thought of a simpler set of tables designed to tie ontologies concerned with expression to sequence features. | ||
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---- | ---- | ||
− | + | [[Category:Chado Modules]] | |
− | + | [[Category:Expression]] | |
− | + | [[Category:!Lacking ERD]] | |
− | [[Category: | + |
Latest revision as of 04:35, 18 February 2015
Contents
Introduction
This module is for how curated expression data is stored in Chado. This module is totally dependent on the sequence module. Objects in the genetic module cannot connect to expression data except by going via the sequence module. We assume that we'll always have a controlled vocabulary for expression data.
Here is an example of a simple case of the sort of data that FlyBase curates. The dpp transcript is expressed in embryonic stage 13-15 in the cephalic segment as reported in a paper by Blackman et al. in 1991. This would be implemented in the expression module by linking the dpp transcript feature to expression via feature_expression (we would add a pub_id column to feature_expression to link to the publication in the pub table). We would then link the following cvterms to the expression using expression_cvterm:
- embryonic stage 13 where the cvterm_type would be stage and the rank=0
- embryonic stage 14 where the cvterm_type would be stage and the rank=1
- embryonic stage 15 where the cvterm_type would be stage and the rank=1
- cephalic segment where the cvterm_type would be anatomy and the rank=0
- in situ hybridization where the cvterm_type would be assay and the rank=0
Note that we would change the cvterm_type column to cvterm_type_id and use a cvterm_id for a particular expression slot (i.e. stage, anatomy, assay, 'subcellular location' and that cvterms from different OBO ontologies can share the same cvterm_type.
Mage and Expression
The Mage module and the Expression module can be considered overlapping but complementary. The Mage module can store data taken directly from the experimental results whereas the Expression module is typically used to store summary data taken from the biological literature, or extracted from the microarray data stored in Mage. The Mage module handles details about experiments that the Expression module does not whereas the Expression module can be thought of a simpler set of tables designed to tie ontologies concerned with expression to sequence features.
Tables
Table: eimage
F-Key | Name | Type | Description |
---|---|---|---|
eimage_id | serial | PRIMARY KEY | |
eimage_data | text | We expect images in eimage_data (e.g. JPEGs) to be uuencoded. | |
eimage_type | character varying(255) | NOT NULL Describes the type of data in eimage_data. | |
image_uri | character varying(255) |
Tables referencing this one via Foreign Key Constraints:
Table: expression
The expression table is essentially a bridge table.
F-Key | Name | Type | Description |
---|---|---|---|
expression_id | serial | PRIMARY KEY | |
uniquename | text | UNIQUE NOT NULL | |
md5checksum | character(32) | ||
description | text |
Tables referencing this one via Foreign Key Constraints:
Table: expression_cvterm
F-Key | Name | Type | Description |
---|---|---|---|
expression_cvterm_id | serial | PRIMARY KEY | |
expression_id | integer | UNIQUE#1 NOT NULL | |
cvterm_id | integer | UNIQUE#1 NOT NULL | |
rank | integer | NOT NULL | |
cvterm_type_id | integer | UNIQUE#1 NOT NULL |
Tables referencing this one via Foreign Key Constraints:
Table: expression_image
F-Key | Name | Type | Description |
---|---|---|---|
expression_image_id | serial | PRIMARY KEY | |
expression_id | integer | UNIQUE#1 NOT NULL | |
eimage_id | integer | UNIQUE#1 NOT NULL |
Table: expression_pub
F-Key | Name | Type | Description |
---|---|---|---|
expression_pub_id | serial | PRIMARY KEY | |
expression_id | integer | UNIQUE#1 NOT NULL | |
pub_id | integer | UNIQUE#1 NOT NULL |
Table: feature_expression
F-Key | Name | Type | Description |
---|---|---|---|
feature_expression_id | serial | PRIMARY KEY | |
expression_id | integer | UNIQUE#1 NOT NULL | |
feature_id | integer | UNIQUE#1 NOT NULL | |
pub_id | integer | UNIQUE#1 NOT NULL |
Tables referencing this one via Foreign Key Constraints: