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Difference between revisions of "Chado Map Module"

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−
==Introduction==
+
=Introduction=
  
−
WARNING -- NOTE: this module is all due for revision...
+
{{NeedsEditing}}
 +
 
 +
NOTE: this module is all due for revision...
  
 
A possibly problematic case is where we want to localize an object to the left or right of a feature (but not within it):
 
A possibly problematic case is where we want to localize an object to the left or right of a feature (but not within it):
Line 19: Line 21:
 
==Tables==
 
==Tables==
  
 +
== Table: featuremap ==
  
−
===featuremap===
+
{| border="1" cellpadding="3"
 +
|+ featuremap Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| featuremap_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
| name
 +
| character varying(255)
 +
| '' UNIQUE ''
 +
|- class="tr0"
 +
|
 +
| description
 +
| text
 +
| '' ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| unittype_id
 +
| integer
 +
| '' ''
 +
|}
 +
 
 +
Tables referencing this one via Foreign Key Constraints:
 +
 
 +
* [[Chado_Tables#Table:_featuremap_pub| featuremap_pub]]
 +
 
 +
* [[Chado_Tables#Table:_featurepos| featurepos]]
 +
 
 +
* [[Chado_Tables#Table:_featurerange| featurerange]]
 +
 
 +
----
  
−
NOTE: this module is all due for revision...
 
  
  
−
Table 4.45: featuremap
+
== Table: featuremap_pub ==
  
−
  Column  Datatype Description
+
{| border="1" cellpadding="3"
−
  featuremap id integer
+
|+ featuremap_pub Structure
−
  name varchar
+
|-
−
  descriptiontext
+
! F-Key
−
  unittype idinteger
+
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| featuremap_pub_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_featuremap| featuremap]]
 +
| featuremap_id
 +
| integer
 +
| '' NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' NOT NULL ''
 +
|}
  
 +
----
  
−
===featurerange===
 
  
−
Table 4.46: featurerange
 
  
−
Column Datatype  Description
+
== Table: featurepos ==
−
featurerange id integer
+
−
featuremap idinteger
+
−
feature idinteger
+
−
leftstartf idinteger
+
−
leftendf id  integer
+
−
rightstartf id  integer
+
−
rightendf id integer
+
−
rangestr  varcha
+
  
 +
{| border="1" cellpadding="3"
 +
|+ featurepos Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| featurepos_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_featuremap| featuremap]]
 +
| featuremap_id
 +
| serial
 +
| '' NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| feature_id
 +
| integer
 +
| '' NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| map_feature_id
 +
| integer
 +
| '' NOT NULL ''<br /><br />map_feature_id links to the feature (map) upon which the feature is being localized.
 +
|- class="tr0"
 +
|
 +
| mappos
 +
| double precision
 +
| '' NOT NULL ''
 +
|}
  
−
===featurepos===
+
----
  
−
Table 4.47: featurepos
 
  
−
ColumnDatatype Description
 
−
featurepos id  integer
 
−
featuremap id  integer
 
−
feature id  integer
 
−
map feature id integer
 
−
mapposfloat
 
  
 +
== Table: featurerange ==
  
−
===featuremap_pub===
+
In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.
  
−
map feature id links to the feature (map) upon which the feature is
+
{| border="1" cellpadding="3"
 +
|+ featurerange Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| featurerange_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_featuremap| featuremap]]
 +
| featuremap_id
 +
| integer
 +
| '' NOT NULL ''<br /><br />featuremap_id is the id of the feature being mapped.
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| feature_id
 +
| integer
 +
| '' NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| leftstartf_id
 +
| integer
 +
| '' NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| leftendf_id
 +
| integer
 +
| '' ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| rightstartf_id
 +
| integer
 +
| '' ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| rightendf_id
 +
| integer
 +
| '' NOT NULL ''
 +
|- class="tr1"
 +
|
 +
| rangestr
 +
| character varying(255)
 +
| '' ''
 +
|}
  
 +
----
  
−
Table 4.48: featuremap pub
 
  
−
ColumnDatatype Description
 
−
featuremap pub id integer
 
−
featuremap id  integer
 
−
pub id integer
 
  
 
[[Category:Chado]]
 
[[Category:Chado]]
 
[[Category:To Do]]
 
[[Category:To Do]]

Revision as of 03:39, 1 March 2007

Introduction

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

NOTE: this module is all due for revision...

A possibly problematic case is where we want to localize an object to the left or right of a feature (but not within it): 


                    |---------|  feature-to-map
       ------------------------------------------------- map
               |------|         |----------|   features to map wrt


How do we map the 3' end of the feature-to-map?

TODO: Get a comprehensive set of mapping use-cases.

One set of use-cases is aberrations (which will all be involved with this module). Simple aberrations should be do-able, but what about cases where a breakpoint interrupts a gene? This would be an example of the problematic case above... (or?)

Tables

Table: featuremap

featuremap Structure
F-Key Name Type Description
featuremap_id serial PRIMARY KEY
name character varying(255) UNIQUE
description text

cvterm

unittype_id integer

Tables referencing this one via Foreign Key Constraints:


Table: featuremap_pub

featuremap_pub Structure
F-Key Name Type Description
featuremap_pub_id serial PRIMARY KEY

featuremap

featuremap_id integer NOT NULL

pub

pub_id integer NOT NULL


Table: featurepos

featurepos Structure
F-Key Name Type Description
featurepos_id serial PRIMARY KEY

featuremap

featuremap_id serial NOT NULL

feature

feature_id integer NOT NULL

feature

map_feature_id integer NOT NULL

map_feature_id links to the feature (map) upon which the feature is being localized.
mappos double precision NOT NULL


Table: featurerange

In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.

featurerange Structure
F-Key Name Type Description
featurerange_id serial PRIMARY KEY

featuremap

featuremap_id integer NOT NULL

featuremap_id is the id of the feature being mapped.

feature

feature_id integer NOT NULL

feature

leftstartf_id integer NOT NULL

feature

leftendf_id integer

feature

rightstartf_id integer

feature

rightendf_id integer NOT NULL
rangestr character varying(255)
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