Schema Version: 1.3

phylonode


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 Foreign Key Nullable Default Comments
phylonode_id bigserial 19
nextval('chado.phylonode_phylonode_id_seq'::regclass)
phylotree_id int8 19
phylotree.phylotree_id phylonode_phylotree_id_fkey C
null
parent_phylonode_id int8 19
phylonode.phylonode_id phylonode_parent_phylonode_id_fkey C
√ null

Root phylonode can have null parent_phylonode_id value.
left_idx int4 10
null
right_idx int4 10
null
type_id int8 19
cvterm.cvterm_id phylonode_type_id_fkey C
√ null

Type: e.g. root, interior, leaf.
feature_id int8 19
feature.feature_id phylonode_feature_id_fkey C
√ null

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

Table contained -1 rows

Indexes

Constraint Name Type Sort Column(s)
phylonode_pkey Primary key Asc phylonode_id
phylonode_parent_phylonode_id_idx Performance Asc parent_phylonode_id
phylonode_phylotree_id_left_idx_key Must be unique Asc/Asc phylotree_id + left_idx
phylonode_phylotree_id_right_idx_key Must be unique Asc/Asc phylotree_id + right_idx

Relationships

The following entity relationship (ER) diagram shows the relationships involving the phylonode table.

Show relationships within degrees of separation