Difference between revisions of "Chado Organism Module"

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m (New page: ==Introduction== ==Tables== ===organism=== The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented...)
 
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=Introduction=
  
−
==Introduction==
 
  
 +
=Tables=
  
−
==Tables==
+
== Table: organism ==
  
−
===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.
  
−
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
+
{| border="1" cellpadding="3"
 +
|+ organism Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| organism_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
| abbreviation
 +
| character varying(255)
 +
| '' ''
 +
|- class="tr0"
 +
|
 +
| genus
 +
| character varying(255)
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
| species
 +
| character varying(255)
 +
| '' UNIQUE#1 NOT NULL ''<br /><br />A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, the unique-name column must be used where it is present, as the name column is not always unique (eg environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern
 +
|- class="tr0"
 +
|
 +
| common_name
 +
| character varying(255)
 +
| '' ''
 +
|- class="tr1"
 +
|
 +
| comment
 +
| text
 +
| '' ''
 +
|}
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
Tables referencing this one via Foreign Key Constraints:
−
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+species. When mapping from the NCBI taxonomy names.dmp file, the unique-name column must be used where it is present, as the name column is not always unique (eg 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
+
  
 +
* [[Chado_Tables#Table:_biomaterial| biomaterial]]
  
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===organism_dbxref===
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* [[Chado_Tables#Table:_feature| feature]]
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
* [[Chado_Tables#Table:_library| library]]
−
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
+
  
 +
* [[Chado_Tables#Table:_organism_dbxref| organism_dbxref]]
  
−
===organismprop===
+
* [[Chado_Tables#Table:_organism_relationship| organism_relationship]]
  
−
tag-value properties - follows standard chado model
+
* [[Chado_Tables#Table:_organismpath| organismpath]]
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
* [[Chado_Tables#Table:_organismprop| organismprop]]
−
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
+
  
 +
* [[Chado_Tables#Table:_phylonode_organism| phylonode_organism]]
  
−
===organism_relationship===
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* [[Chado_Tables#Table:_stock| stock]]
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
* [[Chado_Tables#Table:_wwwuser_organism| wwwuser_organism]]
−
organism_relationship_id integer 11 PRIMARY KEY, NOT NULL
+
−
subject_id integer 10 UNIQUE, NOT NULL organism.organism_id
+
−
object_id integer 10 UNIQUE, NOT NULL organism.organism_id
+
−
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
+
  
 +
----
  
−
===organismpath===
 
  
−
Field Name Data Type Size Default Value Other Foreign Key
+
 
−
organismpath_id integer 11 PRIMARY KEY, NOT NULL
+
== Table: organism_dbxref ==
−
subject_id integer 10 UNIQUE, NOT NULL organism.organism_id
+
 
−
object_id integer 10 UNIQUE, NOT NULL organism.organism_id
+
{| border="1" cellpadding="3"
−
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
+
|+ organism_dbxref Structure
−
pathdistance integer 10 UNIQUE
+
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| organism_dbxref_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_organism| organism]]
 +
| organism_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_dbxref| dbxref]]
 +
| dbxref_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: organism_relationship ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ organism_relationship Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| organism_relationship_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_organism| organism]]
 +
| subject_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_organism| organism]]
 +
| object_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: organismpath ==
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ organismpath Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| organismpath_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_organism| organism]]
 +
| subject_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_organism| organism]]
 +
| object_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| type_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
| pathdistance
 +
| integer
 +
| '' UNIQUE#1 ''
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
 
 +
== Table: organismprop ==
 +
 
 +
Tag-value properties - follows standard chado model.
 +
 
 +
{| border="1" cellpadding="3"
 +
|+ organismprop Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| organismprop_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_organism| organism]]
 +
| organism_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 ''
 +
|}
 +
 
 +
----
  
 
[[Category:Chado]]
 
[[Category:Chado]]
 
[[Category:To Do]]
 
[[Category:To Do]]

Revision as of 03:53, 1 March 2007

Introduction

Tables

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.

organism Structure
F-Key Name Type Description
organism_id serial PRIMARY KEY
abbreviation character varying(255)
genus character varying(255) UNIQUE#1 NOT NULL
species character varying(255) UNIQUE#1 NOT NULL

A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, the unique-name column must be used where it is present, as the name column is not always unique (eg 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 character varying(255)
comment text

Tables referencing this one via Foreign Key Constraints:


Table: organism_dbxref

organism_dbxref Structure
F-Key Name Type Description
organism_dbxref_id serial PRIMARY KEY

organism

organism_id integer UNIQUE#1 NOT NULL

dbxref

dbxref_id integer UNIQUE#1 NOT NULL


Table: organism_relationship

organism_relationship Structure
F-Key Name Type Description
organism_relationship_id serial PRIMARY KEY

organism

subject_id integer UNIQUE#1 NOT NULL

organism

object_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL


Table: organismpath

organismpath Structure
F-Key Name Type Description
organismpath_id serial PRIMARY KEY

organism

subject_id integer UNIQUE#1 NOT NULL

organism

object_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
pathdistance integer UNIQUE#1


Table: organismprop

Tag-value properties - follows standard chado model.

organismprop Structure
F-Key Name Type Description
organismprop_id serial PRIMARY KEY

organism

organism_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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