Chado Map Module

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?

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:

• featuremap_pub

• featurepos

• featurerange

---

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)

---