The stock module was designed to store information about stock collections in a laboratory. What is called a stock could also be called a strain or an accession. There is a lot in common between a Drosophila stock and a Saccharomyces strain and an Arabidopsis line. They all come from some taxon, have genotypes, physical locations in the lab, some conceivable relationship with a publication, some conceivable relationship with a sequence feature (such as a transgene), and could be described by some ontology term.
It may be that not all critical details about your collection are accomodated, if this is the case it should not be difficult to extend for your own purposes.
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.
| F-Key | Name | Type | Description |
|---|---|---|---|
| stock_id | serial | PRIMARY KEY | |
| 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_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. |
|
| 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 |
stock Structure
Tables referencing this one via Foreign Key Constraints:
stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.
| 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 |
stock_cvterm Structure
stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.
| F-Key | Name | Type | Description |
|---|---|---|---|
| stock_dbxref_id | serial | PRIMARY KEY | |
| stock_id | integer | UNIQUE#1 NOT NULL | |
| 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. |
stock_dbxref Structure
Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.
| 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 |
stock_genotype Structure
Provenance. Linking table between stocks and, for example, a stocklist computer file.
| 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 |
stock_pub 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 |
stock_relationship Structure
Tables referencing this one via Foreign Key Constraints:
Provenance. Attach optional evidence to a stock_relationship in the form of a publication.
| 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 |
stock_relationship_pub Structure
The lab or stock center distributing the stocks in their collection.
| F-Key | Name | Type | Description |
|---|---|---|---|
| stockcollection_id | serial | PRIMARY KEY | |
| type_id | integer | UNIQUE#1 NOT NULL type_id is the collection type cv. |
|
| 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. |
stockcollection Structure
Tables referencing this one via Foreign Key Constraints:
stockcollection_stock links a stock collection to the stocks which are contained in the collection.
| 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 |
stockcollection_stock Structure
The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.
| 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 |
stockcollectionprop Structure
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.
| 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 |
stockprop Structure
Tables referencing this one via Foreign Key Constraints:
Provenance. Any stockprop assignment can optionally be supported by a publication.
| 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 |
stockprop_pub Structure