The Perl Toolchain Summit needs more sponsors. If your company depends on Perl, please support this very important event.
 / 
Bio-Chado-Schema-0.07300
River stage one • 3 direct dependents • 3 total dependents
4 ++
/ Bio::Chado::Schema::Sequence::FeatureRelationship

NAME

Bio::Chado::Schema::Sequence::FeatureRelationship

DESCRIPTION

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.

NAME

Bio::Chado::Schema::Sequence::FeatureRelationship

ACCESSORS

feature_relationship_id

  data_type: 'integer'
  is_auto_increment: 1
  is_nullable: 0
  sequence: 'feature_relationship_feature_relationship_id_seq'

subject_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 0

The subject of the subj-predicate-obj sentence. This is typically the subfeature.

object_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 0

The object of the subj-predicate-obj sentence. This is typically the container feature.

type_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 0

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

  data_type: 'text'
  is_nullable: 1

Additional notes or comments.

rank

  data_type: 'integer'
  default_value: 0
  is_nullable: 0

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.

RELATIONS

subject

Type: belongs_to

Related object: Bio::Chado::Schema::Sequence::Feature

object

Type: belongs_to

Related object: Bio::Chado::Schema::Sequence::Feature

type

Type: belongs_to

Related object: Bio::Chado::Schema::Cv::Cvterm

feature_relationshipprops

Type: has_many

Related object: Bio::Chado::Schema::Sequence::FeatureRelationshipprop

feature_relationship_pubs

Type: has_many

Related object: Bio::Chado::Schema::Sequence::FeatureRelationshipPub

AUTHOR

Robert Buels <rbuels@cpan.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2009 by Robert Buels.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.