Difference between revisions of "Chado Stock Module"

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Revision as of 15:15, 5 April 2007

Introduction

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Tables

Table: stock

Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.

stock Structure
F-Key Name Type Description
stock_id serial PRIMARY KEY

dbxref

dbxref_id integer

The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.

organism

organism_id integer UNIQUE#1 NOT NULL

The organism_id is the organism to which the stock belongs. This column is mandatory.
name character varying(255)

The name is a human-readable local name for a stock.
uniquename text UNIQUE#1 NOT NULL
description text

The description is the genetic description provided in the stock list.

cvterm

type_id integer UNIQUE#1 NOT NULL

The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.
is_obsolete boolean NOT NULL DEFAULT false

Tables referencing this one via Foreign Key Constraints:



Table: stock_cvterm

stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.

stock_cvterm Structure
F-Key Name Type Description
stock_cvterm_id serial PRIMARY KEY

stock

stock_id integer UNIQUE#1 NOT NULL

cvterm

cvterm_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL


Table: stock_dbxref

stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.

stock_dbxref Structure
F-Key Name Type Description
stock_dbxref_id serial PRIMARY KEY

stock

stock_id integer UNIQUE#1 NOT NULL

dbxref

dbxref_id integer UNIQUE#1 NOT NULL
is_current boolean NOT NULL DEFAULT true

The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.


Table: stock_genotype

Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.

stock_genotype Structure
F-Key Name Type Description
stock_genotype_id serial PRIMARY KEY

stock

stock_id integer UNIQUE#1 NOT NULL

genotype

genotype_id integer UNIQUE#1 NOT NULL


Table: stock_pub

Provenance. Linking table between stocks and, for example, a stocklist computer file.

stock_pub Structure
F-Key Name Type Description
stock_pub_id serial PRIMARY KEY

stock

stock_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL


Table: stock_relationship

stock_relationship Structure
F-Key Name Type Description
stock_relationship_id serial PRIMARY KEY

stock

subject_id integer UNIQUE#1 NOT NULL

stock

object_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
value text
rank integer UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:



Table: stock_relationship_pub

Provenance. Attach optional evidence to a stock_relationship in the form of a publication.

stock_relationship_pub Structure
F-Key Name Type Description
stock_relationship_pub_id serial PRIMARY KEY

stock_relationship

stock_relationship_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL


Table: stockcollection

The lab or stock center distributing the stocks in their collection.

stockcollection Structure
F-Key Name Type Description
stockcollection_id serial PRIMARY KEY

cvterm

type_id integer UNIQUE#1 NOT NULL

type_id is the collection type cv.

contact

contact_id integer

contact_id links to the contact information for the collection.
name character varying(255)

name is the collection.
uniquename text UNIQUE#1 NOT NULL

uniqename is the value of the collection cv.

Tables referencing this one via Foreign Key Constraints:



Table: stockcollection_stock

stockcollection_stock links a stock collection to the stocks which are contained in the collection.

stockcollection_stock Structure
F-Key Name Type Description
stockcollection_stock_id serial PRIMARY KEY

stockcollection

stockcollection_id integer UNIQUE#1 NOT NULL

stock

stock_id integer UNIQUE#1 NOT NULL


Table: stockcollectionprop

The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.

stockcollectionprop Structure
F-Key Name Type Description
stockcollectionprop_id serial PRIMARY KEY

stockcollection

stockcollection_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
value text
rank integer UNIQUE#1 NOT NULL


Table: stockprop

A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.

stockprop Structure
F-Key Name Type Description
stockprop_id serial PRIMARY KEY

stock

stock_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
value text
rank integer UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:



Table: stockprop_pub

Provenance. Any stockprop assignment can optionally be supported by a publication.

stockprop_pub Structure
F-Key Name Type Description
stockprop_pub_id serial PRIMARY KEY

stockprop

stockprop_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL