Difference between revisions of "Chado Map Module"
From GMOD
m (→Introduction) |
|||
(5 intermediate revisions by 2 users not shown) | |||
Line 1: | Line 1: | ||
− | + | =Introduction= | |
− | + | {{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 11: | Line 13: | ||
− | + | ===To Do=== | |
− | + | * Determine how we would map the 3' end of the feature-to-map. | |
+ | * 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? Would this be an example of the problematic case above? | ||
− | |||
==Tables== | ==Tables== | ||
+ | == Table: 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]] | |
+ | ---- | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
+ | == Table: featuremap_pub == | ||
− | === | + | {| border="1" cellpadding="3" |
+ | |+ featuremap_pub Structure | ||
+ | |- | ||
+ | ! F-Key | ||
+ | ! 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 '' | ||
+ | |} | ||
− | + | ---- | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | == | + | == Table: featurepos == |
− | Table | + | {| 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 '' | ||
+ | |} | ||
− | + | ---- | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | |||
− | + | == 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. | ||
− | Table | + | {| 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) | ||
+ | | '' '' | ||
+ | |} | ||
− | + | ---- | |
− | + | ||
− | + | ||
− | + | ||
− | [[Category:Chado]] | + | [[Category:Chado Modules]] |
− | [[Category: | + | [[Category:!Lacking ERD]] |
Latest revision as of 04:38, 18 February 2015
Contents
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
To Do
- Determine how we would map the 3' end of the feature-to-map.
- 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? Would this be an example of the problematic case above?
Tables
Table: featuremap
F-Key | Name | Type | Description |
---|---|---|---|
featuremap_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE | |
description | text | ||
unittype_id | integer |
Tables referencing this one via Foreign Key Constraints:
Table: featuremap_pub
F-Key | Name | Type | Description |
---|---|---|---|
featuremap_pub_id | serial | PRIMARY KEY | |
featuremap_id | integer | NOT NULL | |
pub_id | integer | NOT NULL |
Table: featurepos
F-Key | Name | Type | Description |
---|---|---|---|
featurepos_id | serial | PRIMARY KEY | |
featuremap_id | serial | NOT NULL | |
feature_id | integer | NOT NULL | |
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.
F-Key | Name | Type | Description |
---|---|---|---|
featurerange_id | serial | PRIMARY KEY | |
featuremap_id | integer | NOT NULL featuremap_id is the id of the feature being mapped. | |
feature_id | integer | NOT NULL | |
leftstartf_id | integer | NOT NULL | |
leftendf_id | integer | ||
rightstartf_id | integer | ||
rightendf_id | integer | NOT NULL | |
rangestr | character varying(255) |