Description of Schema

Tables

tableinfo

Comments:

$Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $
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Chado general module
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TABLE: tableinfo
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NULL

Field Name	Data Type	Size	Default Value	Other	Foreign Key
tableinfo_id	integer	11		PRIMARY KEY, NOT NULL
name	varchar	30		UNIQUE, NOT NULL
primary_key_column	varchar	30	NULL
is_view	integer	10	0	NOT NULL
view_on_table_id	integer	10	NULL
superclass_table_id	integer	10	NULL
is_updateable	integer	10	1	NOT NULL
modification_date	date	0	now()	NOT NULL

Constraints

Type	Fields
NOT NULL	tableinfo_id
NOT NULL	name
NOT NULL	is_view
NOT NULL	is_updateable
NOT NULL	modification_date
UNIQUE	name

db

Comments:

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TABLE: db
================================================
A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.

Field Name	Data Type	Size	Default Value	Other	Foreign Key
db_id	integer	11		PRIMARY KEY, NOT NULL
name	varchar	255		UNIQUE, NOT NULL
description	varchar	255	NULL	contact_id int,
urlprefix	varchar	255	NULL
url	varchar	255	NULL

Constraints

Type	Fields
NOT NULL	db_id
NOT NULL	name
UNIQUE	name

dbxref

Comments:

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TABLE: dbxref
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A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.

Field Name	Data Type	Size	Default Value	Other	Foreign Key
dbxref_id	integer	11		PRIMARY KEY, NOT NULL
db_id	integer	10		UNIQUE, NOT NULL	db.db_id
accession	varchar	255		UNIQUE, NOT NULL, The local part of the identifier. Guaranteed by the db authority to be unique for that db.
version	varchar	255		UNIQUE, NOT NULL
description	text	64000

Indices

Name	Fields
dbxref_idx1	db_id
dbxref_idx2	accession
dbxref_idx3	version

Constraints

Type	Fields
NOT NULL	dbxref_id
NOT NULL	db_id
FOREIGN KEY	db_id
NOT NULL	accession
NOT NULL	version
UNIQUE	db_id, accession, version

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