Schema Version: 1.3

feature_relationship


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.

Columns

Column Type Size Foreign Key Nullable Default Comments
feature_relationship_id bigserial 19
nextval('chado.feature_relationship_feature_relationship_id_seq'::regclass)
subject_id int8 19
feature.feature_id feature_relationship_subject_id_fkey C
null

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

object_id int8 19
feature.feature_id feature_relationship_object_id_fkey C
null

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

type_id int8 19
cvterm.cvterm_id feature_relationship_type_id_fkey C
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 2147483647
null

Additional notes or comments.

rank int4 10
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.

Table contained -1 rows

Indexes

Constraint Name Type Sort Column(s)
feature_relationship_pkey Primary key Asc feature_relationship_id
feature_relationship_c1 Must be unique Asc/Asc/Asc/Asc subject_id + object_id + type_id + rank
feature_relationship_idx1 Performance Asc subject_id
feature_relationship_idx2 Performance Asc object_id
feature_relationship_idx3 Performance Asc type_id

Relationships