GMOD

Chado Expression Module

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:

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)

eimage Structure

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  

expression Structure

Tables referencing this one via Foreign Key Constraints:

Table: expression_cvterm

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

expression_cvterm Structure

Tables referencing this one via Foreign Key Constraints:

Table: expression_image

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

expression_image Structure

Table: expression_pub

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

expression_pub Structure

Table: feature_expression

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

feature_expression Structure

Tables referencing this one via Foreign Key Constraints:

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