# Description of Schema

## Tables
organism
organism_dbxref
organismprop

### organism | Top

Comments:
$Id: organism.html,v 1.5 2007-04-16 16:24:12 scottcain Exp $
==========================================
Chado organism module
============
DEPENDENCIES
============
:import cvterm from cv
:import dbxref from general
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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TABLE: organism
================================================
The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
organism_id | integer | 11 |  | PRIMARY KEY, NOT NULL |
abbreviation | varchar | 255 | NULL |  |
genus | varchar | 255 |  | UNIQUE, NOT NULL |
species | varchar | 255 |  | UNIQUE, NOT NULL, A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern. |
common_name | varchar | 255 | NULL |  |
comment | text | 64000 | NULL |  |

### Constraints

Type | Fields
--- | ---
NOT NULL | organism_id
NOT NULL | genus
NOT NULL | species
UNIQUE | genus, species

### organism_dbxref | Top

Comments:
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TABLE: organism_dbxref
================================================

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
organism_dbxref_id | integer | 11 |  | PRIMARY KEY, NOT NULL |
organism_id | integer | 10 |  | UNIQUE, NOT NULL | organism.organism_id
dbxref_id | integer | 10 |  | UNIQUE, NOT NULL | dbxref.dbxref_id

### Indices

Name | Fields
--- | ---
organism_dbxref_idx1 | organism_id
organism_dbxref_idx2 | dbxref_id

### Constraints

Type | Fields
--- | ---
NOT NULL | organism_dbxref_id
NOT NULL | organism_id
FOREIGN KEY | organism_id
NOT NULL | dbxref_id
FOREIGN KEY | dbxref_id
UNIQUE | organism_id, dbxref_id

### organismprop | Top

Comments:
================================================
TABLE: organismprop
================================================
Tag-value properties - follows standard chado model.

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
organismprop_id | integer | 11 |  | PRIMARY KEY, NOT NULL |
organism_id | integer | 10 |  | UNIQUE, NOT NULL | organism.organism_id
type_id | integer | 10 |  | UNIQUE, NOT NULL | cvterm.cvterm_id
value | text | 64000 | NULL |  |
rank | integer | 10 | 0 | UNIQUE, NOT NULL |

### Indices

Name | Fields
--- | ---
organismprop_idx1 | organism_id
organismprop_idx2 | type_id

### Constraints

Type | Fields
--- | ---
NOT NULL | organismprop_id
NOT NULL | organism_id
FOREIGN KEY | organism_id
NOT NULL | type_id
FOREIGN KEY | type_id
NOT NULL | rank
UNIQUE | organism_id, type_id, rank

Created by SQL::Translator 0.08_01