Schema Version: 1.3 Module: chado

Columns

Columns

Table Type Column Type Size Nulls Default Comments
phylonode_relationship Table object_id int8 19 null
phylotree Table phylotree_id bigserial 19 nextval('phylogeny.phylotree_phylotree_id_seq'::regclass)
phylotree Table comment text 2147483647 √ null
phylonode Table feature_id int8 19 √ 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.
phylonodeprop Table value text 2147483647 ''::text
phylotree_pub Table phylotree_id int8 19 null
phylonode_dbxref Table dbxref_id int8 19 null
phylonodeprop Table rank int4 10 0
phylonodeprop Table phylonodeprop_id bigserial 19 nextval('phylogeny.phylonodeprop_phylonodeprop_id_seq'::regclass)
phylonode_organism Table organism_id int8 19 null
phylotree Table type_id int8 19 √ null

Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".
phylonode_dbxref Table phylonode_id int8 19 null
phylonode Table parent_phylonode_id int8 19 √ null

Root phylonode can have null parent_phylonode_id value.
phylonode_relationship Table phylonode_relationship_id bigserial 19 nextval('phylogeny.phylonode_relationship_phylonode_relationship_id_seq'::regclass)
phylonode Table type_id int8 19 √ null

Type: e.g. root, interior, leaf.
phylonode_dbxref Table phylonode_dbxref_id bigserial 19 nextval('phylogeny.phylonode_dbxref_phylonode_dbxref_id_seq'::regclass)
phylonode Table distance float8 17 √ null
phylonode_organism Table phylonode_id int8 19 null

One phylonode cannot refer to >1 organism.
phylotree Table name varchar 255 √ null
phylonode_relationship Table subject_id int8 19 null
phylonodeprop Table type_id int8 19 null

type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.
phylotreeprop Table type_id int8 19 null

The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm.
phylonode_relationship Table phylotree_id int8 19 null
phylonode_pub Table phylonode_pub_id bigserial 19 nextval('phylogeny.phylonode_pub_phylonode_pub_id_seq'::regclass)
phylonode Table right_idx int4 10 null
phylotree_pub Table phylotree_pub_id bigserial 19 nextval('phylogeny.phylotree_pub_phylotree_pub_id_seq'::regclass)
phylotreeprop Table phylotreeprop_id bigserial 19 nextval('phylogeny.phylotreeprop_phylotreeprop_id_seq'::regclass)
phylonode_relationship Table type_id int8 19 null
phylonode Table phylotree_id int8 19 null
phylonode Table label varchar 255 √ null
phylonode_pub Table phylonode_id int8 19 null
phylotreeprop Table phylotree_id int8 19 null
phylonode Table left_idx int4 10 null
phylotree_pub Table pub_id int8 19 null
phylotree Table analysis_id int8 19 √ null
phylotreeprop Table value text 2147483647 √ null

The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
phylonode_pub Table pub_id int8 19 null
phylonode Table phylonode_id bigserial 19 nextval('phylogeny.phylonode_phylonode_id_seq'::regclass)
phylotreeprop Table rank int4 10 0

Property-Value ordering. Any phylotree can have multiple values for any particular property type these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used
phylonode_organism Table phylonode_organism_id bigserial 19 nextval('phylogeny.phylonode_organism_phylonode_organism_id_seq'::regclass)
phylotree Table dbxref_id int8 19 null
phylonode_relationship Table rank int4 10 √ null
phylonodeprop Table phylonode_id int8 19 null