Difference between revisions of "Chado Map Module"
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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) |
