Difference between revisions of "Template:ChadoTable phylonode"
From GMOD
(Table definition, first upload on 2010/11/22.) |
(Table definition for Chado on 2010/11/24) |
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− | <noinclude>{{ChadoTableTemplateHeader}}</noinclude> | + | <protect><noinclude>{{ChadoTableTemplateHeader}}</noinclude> |
+ | {{ChadoTableDesc|Phylogeny|phylonode|This is the most pervasive | ||
element in the phylogeny module, cataloging the "phylonodes" of | element in the phylogeny module, cataloging the "phylonodes" of | ||
tree graphs. Edges are implied by the parent_phylonode_id | tree graphs. Edges are implied by the parent_phylonode_id | ||
reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.}} | reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.}} | ||
{{ChadoColumnsHeader|Phylogeny|phylonode}} | {{ChadoColumnsHeader|Phylogeny|phylonode}} | ||
− | {{ChadoColumnDesc||phylonode_id|serial|''PRIMARY KEY'' | + | {{ChadoColumnDesc||phylonode_id|serial|''PRIMARY KEY''<br /> |
− | + | ||
}} | }} | ||
− | {{ChadoColumnDesc|{{ChadoModuleTableLink|Phylogeny|phylotree}}|phylotree_id|integer|''UNIQUE#1'' | + | {{ChadoColumnDesc|{{ChadoModuleTableLink|Phylogeny|phylotree}}|phylotree_id|integer|''UNIQUE#1''<br /> |
− | + | ''UNIQUE#2''<br /> | |
− | ''UNIQUE#2'' | + | ''NOT NULL''<br /> |
− | + | ||
− | ''NOT NULL'' | + | |
− | + | ||
}} | }} | ||
{{ChadoColumnDesc|{{ChadoModuleTableLink|Phylogeny|phylonode}}|parent_phylonode_id|integer|Root phylonode can have null parent_phylonode_id value.}} | {{ChadoColumnDesc|{{ChadoModuleTableLink|Phylogeny|phylonode}}|parent_phylonode_id|integer|Root phylonode can have null parent_phylonode_id value.}} | ||
− | {{ChadoColumnDesc||left_idx|integer|''UNIQUE#1'' | + | {{ChadoColumnDesc||left_idx|integer|''UNIQUE#1''<br /> |
− | + | ''NOT NULL''<br /> | |
− | ''NOT NULL'' | + | |
− | + | ||
}} | }} | ||
− | {{ChadoColumnDesc||right_idx|integer|''UNIQUE#2'' | + | {{ChadoColumnDesc||right_idx|integer|''UNIQUE#2''<br /> |
− | + | ''NOT NULL''<br /> | |
− | ''NOT NULL'' | + | |
− | + | ||
}} | }} | ||
{{ChadoColumnDesc|{{ChadoModuleTableLink|CV|cvterm}}|type_id|integer|Type: e.g. root, interior, leaf.}} | {{ChadoColumnDesc|{{ChadoModuleTableLink|CV|cvterm}}|type_id|integer|Type: e.g. root, interior, leaf.}} | ||
Line 32: | Line 25: | ||
{{ChadoTablesReferencingHeader|phylonode}} | {{ChadoTablesReferencingHeader|phylonode}} | ||
− | * {{ChadoReferencingTable|phylonode}} | + | * {{ChadoReferencingTable|Phylogeny|phylonode}} |
− | + | * {{ChadoReferencingTable|Phylogeny|phylonode_dbxref}} | |
+ | * {{ChadoReferencingTable|Phylogeny|phylonode_organism}} | ||
+ | * {{ChadoReferencingTable|Phylogeny|phylonode_pub}} | ||
+ | * {{ChadoReferencingTable|Phylogeny|phylonode_relationship}} | ||
+ | * {{ChadoReferencingTable|Phylogeny|phylonodeprop}} | ||
</protect> | </protect> |
Revision as of 19:21, 24 November 2010
This template is a Chado Table Template. It defines a single table from the Chado schema, and every Chado table has a template like this one. This template is automatically included in two places:
- The module page for the module the table is a part of. This is where updates and comments should be posted.
- The Chado Tables page, which lists all tables.
You can include this template anywhere you want to show the table description.
Table: | phylonode |
Module: | Phylogeny |
This is the most pervasive
element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.
FK | Name | Type | Description |
---|---|---|---|
phylonode_id | serial | PRIMARY KEY | |
phylotree | phylotree_id | integer | UNIQUE#1 UNIQUE#2 |
phylonode | parent_phylonode_id | integer | Root phylonode can have null parent_phylonode_id value. |
left_idx | integer | UNIQUE#1 NOT NULL | |
right_idx | integer | UNIQUE#2 NOT NULL | |
cvterm | type_id | integer | Type: e.g. root, interior, leaf. |
feature | feature_id | integer | Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it. |
label | character varying(255) | ||
distance | double precision |
Tables referencing phylonode via foreign key constraints: