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 sequence module. Objects in the
+
This module is totally dependent on the [[Chado_Sequence_Module|sequence module]]. Objects in the
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 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''
transcript feature to expression via feature_expression (we would add a
+
transcript feature to expression via [[Chado_Tables#Table:_feature_expression|feature_expression]] (we would add a
pub_id column to feature_expression to link to the publication in the
+
''pub_id'' column to [[Chado_Tables#Table:_feature_expression|feature_expression]] to link to the publication in the
pub table). We would then link the following cvterms to the expression using
+
[[Chado_Tables#Table:_pub|pub table]]). We would then link the following cvterms to the expression using
expression_cvterm:
+
[[#Table:_expression_cvterm|expression_cvterm]]:
  
 
* ''embryonic stage 13'' where the cvterm_type would be stage and the rank=0
 
* ''embryonic stage 13'' where the cvterm_type would be stage and the rank=0
Line 18: Line 18:
 
* ''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 assat 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
+
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,
+
use a ''cvterm_id'' for a particular expression slot (i.e. stage, anatomy,
 
assay, 'subcellular location' and that cvterms from different [http://www.obofoundry.org OBO]
 
assay, 'subcellular location' and that cvterms from different [http://www.obofoundry.org OBO]
ontologies can share the same cvterm_type.
+
ontologies can share the same ''cvterm_type''.
  
 +
===Mage and Expression===
  
==Tables==
+
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.
  
===expression_cvterm===
+
=Tables=
  
WARNING open question
+
== Table: eimage ==
  
What are the possibities of combination when more than one cvterm is used
+
{| border="1" cellpadding="3"
in a field? 
+
|+ eimage Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| eimage_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
| eimage_data
 +
| text
 +
| '' ''<br /><br />We expect images in eimage_data (e.g. JPEGs) to be uuencoded.
 +
|- class="tr0"
 +
|
 +
| eimage_type
 +
| character varying(255)
 +
| '' NOT NULL ''<br /><br />Describes the type of data in eimage_data.
 +
|- class="tr1"
 +
|
 +
| image_uri
 +
| character varying(255)
 +
| '' ''
 +
|}
  
For e.g. (in <p> here):   <t> E | early <a> <p> anterior & dorsal
+
Tables referencing this one via Foreign Key Constraints:
If the two terms used in a particular field are co-equal (both from the
+
same CV, is the relation always "&"?  May we find "or"?
+
  
Obviously another case is when a bodypart term and a bodypart qualifier
+
* [[Chado_Tables#Table:_expression_image| expression_image]]
term are used in a specific field, eg:
+
  
  <t> L | third instar <a> larval antennal segment sensilla | subset <p 
+
----
  
WRT the three-part --<t><a><p> statements, are the values in the different
 
parts *always* from different vocabularies in proforma.CV?  If not,
 
we'll need to have some kind of type qualifier telling us whether the
 
cvterm used is <t>, <a>, or <p>
 
  
yes we should have a type qualifier as a cv term can be from diff vocab
+
 
e.g. blastoderm can be body part and stage terms in dros anatomy
+
== Table: expression ==
but cvterm_type_id needs to be a cv instead of a free text type
+
 
 +
The expression table is essentially a bridge table.
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ expression Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| expression_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
| uniquename
 +
| text
 +
| '' UNIQUE NOT NULL ''
 +
|- class="tr0"
 +
|
 +
| md5checksum
 +
| character(32)
 +
| '' ''
 +
|- class="tr1"
 +
|
 +
| description
 +
| text
 +
| '' ''
 +
|}
 +
 
 +
Tables referencing this one via Foreign Key Constraints:
 +
 
 +
* [[Chado_Tables#Table:_expression_cvterm| expression_cvterm]]
 +
 
 +
* [[Chado_Tables#Table:_expression_image| expression_image]]
 +
 
 +
* [[Chado_Tables#Table:_expression_pub| expression_pub]]
 +
 
 +
* [[Chado_Tables#Table:_expressionprop| expressionprop]]
 +
 
 +
* [[Chado_Tables#Table:_feature_expression| feature_expression]]
 +
 
 +
* [[Chado_Tables#Table:_wwwuser_expression| wwwuser_expression]]
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: expression_cvterm ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ expression_cvterm Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| expression_cvterm_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_expression| expression]]
 +
| expression_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| cvterm_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
| rank
 +
| integer
 +
| '' NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| cvterm_type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
Tables referencing this one via Foreign Key Constraints:
 +
 
 +
* [[Chado_Tables#Table:_expression_cvtermprop| expression_cvtermprop]]
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: expression_image ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ expression_image Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| expression_image_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_expression| expression]]
 +
| expression_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_eimage| eimage]]
 +
| eimage_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: expression_pub ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ expression_pub Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| expression_pub_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_expression| expression]]
 +
| expression_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: feature_expression ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ feature_expression Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| feature_expression_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_expression| expression]]
 +
| expression_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| feature_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
Tables referencing this one via Foreign Key Constraints:
 +
 
 +
* [[Chado_Tables#Table:_feature_expressionprop| feature_expressionprop]]
 +
 
 +
----
 +
 
 +
[[Category:Chado Modules]]
 +
[[Category:Expression]]
 +
[[Category:!Lacking ERD]]

Latest revision as of 04:35, 18 February 2015

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: