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Chado Expression Module

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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

eimage Structure
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.

expression Structure
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

expression_cvterm Structure
F-Key Name Type Description
expression_cvterm_id serial PRIMARY KEY

expression

expression_id integer UNIQUE#1 NOT NULL

cvterm

cvterm_id integer UNIQUE#1 NOT NULL
rank integer NOT NULL

cvterm

cvterm_type_id integer UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:



Table: expression_image

expression_image Structure
F-Key Name Type Description
expression_image_id serial PRIMARY KEY

expression

expression_id integer UNIQUE#1 NOT NULL

eimage

eimage_id integer UNIQUE#1 NOT NULL


Table: expression_pub

expression_pub Structure
F-Key Name Type Description
expression_pub_id serial PRIMARY KEY

expression

expression_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL


Table: feature_expression

feature_expression Structure
F-Key Name Type Description
feature_expression_id serial PRIMARY KEY

expression

expression_id integer UNIQUE#1 NOT NULL

feature

feature_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints: