Description of Schema

Tables

organism_dbxref

organism

Comments:

$Id: organism.html,v 1.5 2007-04-16 16:24:12 scottcain Exp $
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Chado organism module
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DEPENDENCIES
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:import cvterm from cv
:import dbxref from general
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TABLE: organism
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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

Comments:

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TABLE: organism_dbxref
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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

Comments:

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TABLE: organismprop
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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

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