Description of Schema

Tables

library
library_synonym
library_pub
libraryprop
libraryprop_pub
library_cvterm
library_feature
library_dbxref

library

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Comments:

$Id: library.html,v 1.4 2008-03-28 16:05:30 scottcain Exp $
=================================================================
Dependencies:
:import feature from sequence
:import synonym from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
=================================================================
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TABLE: library
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Field Name Data Type Size Default Value Other Foreign Key
library_id integer 11 PRIMARY KEY, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
name varchar 255
uniquename text 64000 UNIQUE, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library" cvterm.cvterm_id
is_obsolete integer 10 0 NOT NULL
timeaccessioned timestamp 0 current_timestamp NOT NULL
timelastmodified timestamp 0 current_timestamp NOT NULL

Indices

Name Fields
library_name_ind1 name
library_idx1 organism_id
library_idx2 type_id
library_idx3 uniquename

Constraints

Type Fields
NOT NULL library_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL is_obsolete
NOT NULL timeaccessioned
NOT NULL timelastmodified
UNIQUE organism_id, uniquename, type_id

library_synonym

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TABLE: library_synonym
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Field Name Data Type Size Default Value Other Foreign Key
library_synonym_id integer 11 PRIMARY KEY, NOT NULL
synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. pub.pub_id
is_current boolean 0 true NOT NULL, The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.
is_internal boolean 0 false NOT NULL, Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.

Indices

Name Fields
library_synonym_idx1 synonym_id
library_synonym_idx2 library_id
library_synonym_idx3 pub_id

Constraints

Type Fields
NOT NULL library_synonym_id
NOT NULL synonym_id
FOREIGN KEY synonym_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_current
NOT NULL is_internal
UNIQUE synonym_id, library_id, pub_id

library_pub

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Comments:

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TABLE: library_pub
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Field Name Data Type Size Default Value Other Foreign Key
library_pub_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_pub_idx1 library_id
library_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL library_pub_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE library_id, pub_id

libraryprop

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TABLE: libraryprop
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Field Name Data Type Size Default Value Other Foreign Key
libraryprop_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_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
libraryprop_idx1 library_id
libraryprop_idx2 type_id

Constraints

Type Fields
NOT NULL libraryprop_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE library_id, type_id, rank

libraryprop_pub

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TABLE: libraryprop_pub
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Field Name Data Type Size Default Value Other Foreign Key
libraryprop_pub_id integer 11 PRIMARY KEY, NOT NULL
libraryprop_id integer 10 UNIQUE, NOT NULL libraryprop.libraryprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
libraryprop_pub_idx1 libraryprop_id
libraryprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL libraryprop_pub_id
NOT NULL libraryprop_id
FOREIGN KEY libraryprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE libraryprop_id, pub_id

library_cvterm

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TABLE: library_cvterm
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The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.
Field Name Data Type Size Default Value Other Foreign Key
library_cvterm_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_cvterm_idx1 library_id
library_cvterm_idx2 cvterm_id
library_cvterm_idx3 pub_id

Constraints

Type Fields
NOT NULL library_cvterm_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE library_id, cvterm_id, pub_id

library_feature

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TABLE: library_feature
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library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".
Field Name Data Type Size Default Value Other Foreign Key
library_feature_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id

Indices

Name Fields
library_feature_idx1 library_id
library_feature_idx2 feature_id

Constraints

Type Fields
NOT NULL library_feature_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL feature_id
FOREIGN KEY feature_id
UNIQUE library_id, feature_id

library_dbxref

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TABLE: library_dbxref
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Field Name Data Type Size Default Value Other Foreign Key
library_dbxref_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
library_dbxref_idx1 library_id
library_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL library_dbxref_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE library_id, dbxref_id
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