phylonode

0 rows


Description

This is the most pervasive element in the phylogeny module, cataloging the “phylonodes” of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be between the parents left and right indexes.

Columns

Column Type Size Nulls Auto Default Children Parents Comments
phylonode_id serial 10 √ nextval('phylonode_phylonode_id_seq'::regclass)
phylonode.parent_phylonode_id phylonode_parent_phylonode_id_fkey C
phylonode_dbxref.phylonode_id phylonode_dbxref_phylonode_id_fkey C
phylonode_organism.phylonode_id phylonode_organism_phylonode_id_fkey C
phylonode_pub.phylonode_id phylonode_pub_phylonode_id_fkey C
phylonode_relationship.object_id phylonode_relationship_object_id_fkey C
phylonode_relationship.subject_id phylonode_relationship_subject_id_fkey C
phylonodeprop.phylonode_id phylonodeprop_phylonode_id_fkey C
phylotree_id int4 10 null
phylotree.phylotree_id phylonode_phylotree_id_fkey C
parent_phylonode_id int4 10 √ null
phylonode.phylonode_id phylonode_parent_phylonode_id_fkey C

Root phylonode can have null parent_phylonode_id value.
left_idx int4 10 null
right_idx int4 10 null
type_id int4 10 √ null
cvterm.cvterm_id phylonode_type_id_fkey C

Type: e.g. root, interior, leaf.
feature_id int4 10 √ null
feature.feature_id phylonode_feature_id_fkey C

Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.
label varchar 255 √ null
distance float8 17,17 √ null

Indexes

Constraint Name Type Sort Column(s)
phylonode_pkey Primary key Asc phylonode_id
phylonode_feature_id_idx Performance Asc feature_id
phylonode_phylotree_id_key Must be unique Asc/Asc phylotree_id + left_idx
phylonode_phylotree_id_key1 Must be unique Asc/Asc phylotree_id + right_idx

Relationships

Close relationships within degrees of separation