feature_relationship

0 rows


Description

features can be arranged in graphs, eg exon part_of transcript part_of gene; translation madeby transcript if type is thought of as a verb, each arc makes a statement SUBJECT VERB OBJECT 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 cant always do this - eg transpliced genes. its also useful for quickly getting implicit introns

Columns

Column Type Size Nulls Auto Default Children Parents Comments
feature_relationship_id serial 10 √ nextval('feature_relationship_feature_relationship_id_seq'::regclass)
feature_relationship_pub.feature_relationship_id feature_relationship_pub_feature_relationship_id_fkey C
feature_relationshipprop.feature_relationship_id feature_relationshipprop_feature_relationship_id_fkey C
subject_id int4 10 null
feature.feature_id feature_relationship_subject_id_fkey C

the subject of the subj-predicate-obj sentence. This is typically the subfeature
object_id int4 10 null
feature.feature_id feature_relationship_object_id_fkey C

the object of the subj-predicate-obj sentence. This is typically the container feature
type_id int4 10 null
cvterm.cvterm_id feature_relationship_type_id_fkey C

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/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

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

Close relationships within degrees of separation