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Difference between revisions of "Template:ChadoTable feature relationship"
(Table definition, first upload on 2010/11/22.) |
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Revision as of 08:36, 22 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: | 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.
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:
- None.