Difference between revisions of "Chado Library Module"

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==Tables==
 
==Tables==
  
−
===library===
+
== Table: library ==
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
{| border="1" cellpadding="3"
−
library_id integer 11 PRIMARY KEY, NOT NULL
+
|+ library Structure
−
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
+
|-
−
name varchar 255
+
! F-Key
−
uniquename text 64000 UNIQUE, NOT NULL
+
! Name
−
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
+
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| library_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_organism| organism]]
 +
| organism_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
| name
 +
| character varying(255)
 +
| '' ''
 +
|- class="tr1"
 +
|
 +
| uniquename
 +
| text
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''<br /><br />The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"
 +
|}
  
 +
Tables referencing this one via Foreign Key Constraints:
  
−
===library_synonym===
+
* [[Chado_Tables#Table:_library_cvterm| library_cvterm]]
  
−
The type_id foreign key links to a controlled vocabulary of library types.
+
* [[Chado_Tables#Table:_library_feature| library_feature]]
−
examples of this would be: 'cDNA_library' or 'genomic_library'
+
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
* [[Chado_Tables#Table:_library_pub| library_pub]]
−
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 pub.pub_id
+
−
is_current boolean 0 true NOT NULL
+
−
is_internal boolean 0 false NOT NULL
+
  
 +
* [[Chado_Tables#Table:_library_synonym| library_synonym]]
  
−
===library_pub===
+
* [[Chado_Tables#Table:_libraryprop| libraryprop]]
  
−
pub_id: the pub_id link is for relating the usage of a given synonym to the
+
----
−
publication in which it was used
+
−
is_current: the is_current bit indicates whether the linked synonym is the
+
−
current -official- symbol for the linked library
+
−
is_internal: typically a synonym exists so that somebody querying the db
+
−
with an obsolete name can find the object they're looking for (under its
+
−
current name. If the synonym has been used publicly & deliberately (eg in
+
−
a paper), it my also be listed in reports as a synonym. If the synonym
+
−
was not used deliberately (eg, 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.
+
  
−
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
 
  
  
−
===libraryprop===
+
== Table: library_cvterm ==
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
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.
−
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
+
  
 +
{| border="1" cellpadding="3"
 +
|+ library_cvterm Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| library_cvterm_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_library| library]]
 +
| library_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| cvterm_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
  
−
===library_cvterm===
+
----
  
−
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
 
  
  
−
===library_feature===
+
== Table: library_feature ==
  
−
The table library_cvterm links a library to controlled vocabularies which  
+
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".
−
describe the library. For instance, there might be a link to the anatomy
+
 
−
cv for "head" or "testes" for a head or testes library.  
+
{| border="1" cellpadding="3"
 +
|+ library_feature Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| library_feature_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_library| library]]
 +
| library_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_feature| feature]]
 +
| feature_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: library_pub ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ library_pub Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| library_pub_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_library| library]]
 +
| library_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: library_synonym ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ library_synonym Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| library_synonym_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_synonym| synonym]]
 +
| synonym_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_library| library]]
 +
| library_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_pub| pub]]
 +
| pub_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''<br /><br />The pub_id link is for relating the usage of a given synonym to the publication in which it was used.
 +
|- class="tr0"
 +
|
 +
| is_current
 +
| boolean
 +
| '' NOT NULL DEFAULT true ''<br /><br />The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.
 +
|- class="tr1"
 +
|
 +
| is_internal
 +
| boolean
 +
| '' NOT NULL DEFAULT false ''<br /><br />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.
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: libraryprop ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ libraryprop Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| libraryprop_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_library| library]]
 +
| library_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
| value
 +
| text
 +
| '' ''
 +
|- class="tr0"
 +
|
 +
| rank
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
  
−
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
 
  
  
 
[[Category:Chado]]
 
[[Category:Chado]]
 
[[Category:To Do]]
 
[[Category:To Do]]

Revision as of 03:34, 1 March 2007

Introduction

Tables

Table: library

library Structure
F-Key Name Type Description
library_id serial PRIMARY KEY

organism

organism_id integer UNIQUE#1 NOT NULL
name character varying(255)
uniquename text UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 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"

Tables referencing this one via Foreign Key Constraints:


Table: library_cvterm

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.

library_cvterm Structure
F-Key Name Type Description
library_cvterm_id serial PRIMARY KEY

library

library_id integer UNIQUE#1 NOT NULL

cvterm

cvterm_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL


Table: library_feature

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".

library_feature Structure
F-Key Name Type Description
library_feature_id serial PRIMARY KEY

library

library_id integer UNIQUE#1 NOT NULL

feature

feature_id integer UNIQUE#1 NOT NULL


Table: library_pub

library_pub Structure
F-Key Name Type Description
library_pub_id serial PRIMARY KEY

library

library_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL


Table: library_synonym

library_synonym Structure
F-Key Name Type Description
library_synonym_id serial PRIMARY KEY

synonym

synonym_id integer UNIQUE#1 NOT NULL

library

library_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL

The pub_id link is for relating the usage of a given synonym to the publication in which it was used.
is_current boolean NOT NULL DEFAULT true

The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.
is_internal boolean NOT NULL DEFAULT false

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.


Table: libraryprop

libraryprop Structure
F-Key Name Type Description
libraryprop_id serial PRIMARY KEY

library

library_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
value text
rank integer UNIQUE#1 NOT NULL
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