Difference between revisions of "Template:ChadoTable feature relationship"

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(Table definition, first upload on 2010/11/22.)
 
(Table definition for Chado on 2010/11/24)
 
(One intermediate revision by the same user not shown)
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<noinclude>{{ChadoTableTemplateHeader}}</noinclude><protect>{{ChadoTableDesc|Sequence|feature_relationship|Features can be arranged in
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<protect><noinclude>{{ChadoTableTemplateHeader}}</noinclude>
 +
{{ChadoTableDesc|Sequence|feature_relationship|Features can be arranged in
 
graphs, e.g. &quot;exon part_of transcript part_of gene&quot;; If type is
 
graphs, e.g. &quot;exon part_of transcript part_of gene&quot;; If type is
 
thought of as a verb, the each arc or edge makes a statement
 
thought of as a verb, the each arc or edge makes a statement
Line 9: Line 10:
 
useful for quickly getting implicit introns.}}
 
useful for quickly getting implicit introns.}}
 
{{ChadoColumnsHeader|Sequence|feature_relationship}}
 
{{ChadoColumnsHeader|Sequence|feature_relationship}}
{{ChadoColumnDesc||feature_relationship_id|serial|''PRIMARY KEY''
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{{ChadoColumnDesc||feature_relationship_id|serial|''PRIMARY KEY''<br />
 
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}}
 
}}
{{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|subject_id|integer|''UNIQUE#1''
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{{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|subject_id|integer|''UNIQUE#1''<br />
 
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''NOT NULL''<br />
''NOT NULL''
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The subject of the subj-predicate-obj sentence. This is typically the subfeature.}}
 
The subject of the subj-predicate-obj sentence. This is typically the subfeature.}}
{{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|object_id|integer|''UNIQUE#1''
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{{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|object_id|integer|''UNIQUE#1''<br />
 
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''NOT NULL''<br />
''NOT NULL''
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The object of the subj-predicate-obj sentence. This is typically the container feature.}}
 
The object of the subj-predicate-obj sentence. This is typically the container feature.}}
{{ChadoColumnDesc|{{ChadoModuleTableLink|CV|cvterm}}|type_id|integer|''UNIQUE#1''
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{{ChadoColumnDesc|{{ChadoModuleTableLink|CV|cvterm}}|type_id|integer|''UNIQUE#1''<br />
 
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''NOT NULL''<br />
''NOT NULL''
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Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.}}
 
Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.}}
 
{{ChadoColumnDesc||value|text|Additional notes or comments.}}
 
{{ChadoColumnDesc||value|text|Additional notes or comments.}}
{{ChadoColumnDesc||rank|integer|''UNIQUE#1''
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{{ChadoColumnDesc||rank|integer|''UNIQUE#1''<br />
 
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''NOT NULL''<br />
''NOT NULL''
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+
 
The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.}}
 
The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.}}
 
{{ChadoColumnsFooter}}
 
{{ChadoColumnsFooter}}
  
 
{{ChadoTablesReferencingHeader|feature_relationship}}
 
{{ChadoTablesReferencingHeader|feature_relationship}}
 
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{{ChadoReferencingTable|Sequence|feature_relationship_pub}}
* None.
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{{ChadoReferencingTable|Sequence|feature_relationshipprop}}
 
</protect>
 
</protect>

Latest revision as of 19:59, 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:

  1. The module page for the module the table is a part of. This is where updates and comments should be posted.
  2. The Chado Tables page, which lists all tables.

You can include this template anywhere you want to show the table description.


Table: feature_relationship
Module: Sequence

Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.

feature_relationship columns
FK Name Type Description
feature_relationship_id serial PRIMARY KEY
feature subject_id integer UNIQUE#1

NOT NULL
The subject of the subj-predicate-obj sentence. This is typically the subfeature.

feature object_id integer UNIQUE#1

NOT NULL
The object of the subj-predicate-obj sentence. This is typically the container feature.

cvterm type_id integer UNIQUE#1

NOT NULL
Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.

value text Additional notes or comments.
rank integer UNIQUE#1

NOT NULL
The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.

Tables referencing feature_relationship via foreign key constraints: