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Chado Map Module

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Introduction

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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

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)