Tables |
| phylotree |
| phylotree_pub |
| phylonode |
| phylonode_dbxref |
| phylonode_pub |
| phylonode_organism |
| phylonodeprop |
| phylonode_relationship |
phylotree |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylotree_id | integer | 11 | PRIMARY KEY, UNIQUE, NOT NULL | ||
| dbxref_id | integer | 10 | NOT NULL | dbxref.dbxref_id | |
| name | varchar | 255 | NULL | ||
| type_id | integer | 10 | Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy". | cvterm.cvterm_id | |
| analysis_id | integer | 10 | NULL | analysis.analysis_id | |
| comment | text | 64000 | NULL |
| Name | Fields |
|---|---|
| phylotree_idx1 | phylotree_id |
| Type | Fields |
|---|---|
| NOT NULL | phylotree_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| FOREIGN KEY | type_id |
| FOREIGN KEY | analysis_id |
| UNIQUE | phylotree_id |
phylotree_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylotree_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylotree_id | integer | 10 | UNIQUE, NOT NULL | phylotree.phylotree_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| phylotree_pub_idx1 | phylotree_id |
| phylotree_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | phylotree_pub_id |
| NOT NULL | phylotree_id |
| FOREIGN KEY | phylotree_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | phylotree_id, pub_id |
phylonode |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylotree_id | integer | 10 | UNIQUE, NOT NULL | phylotree.phylotree_id | |
| parent_phylonode_id | integer | 10 | NULL | Root phylonode can have null parent_phylonode_id value. | phylonode.phylonode_id |
| left_idx | integer | 10 | UNIQUE, NOT NULL | ||
| right_idx | integer | 10 | UNIQUE, NOT NULL | ||
| type_id | integer | 10 | Type: e.g. root, interior, leaf. | cvterm.cvterm_id | |
| feature_id | integer | 10 | 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. | feature.feature_id | |
| label | varchar | 255 | NULL | ||
| distance | float | 20 | NULL |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_id |
| NOT NULL | phylotree_id |
| FOREIGN KEY | phylotree_id |
| FOREIGN KEY | parent_phylonode_id |
| NOT NULL | left_idx |
| NOT NULL | right_idx |
| FOREIGN KEY | type_id |
| FOREIGN KEY | feature_id |
| UNIQUE | phylotree_id, left_idx |
| UNIQUE | phylotree_id, right_idx |
phylonode_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id |
| Name | Fields |
|---|---|
| phylonode_dbxref_idx1 | phylonode_id |
| phylonode_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_dbxref_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | phylonode_id, dbxref_id |
phylonode_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| phylonode_pub_idx1 | phylonode_id |
| phylonode_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_pub_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | phylonode_id, pub_id |
phylonode_organism |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_organism_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL, One phylonode cannot refer to >1 organism. | phylonode.phylonode_id | |
| organism_id | integer | 10 | NOT NULL | organism.organism_id |
| Name | Fields |
|---|---|
| phylonode_organism_idx1 | phylonode_id |
| phylonode_organism_idx2 | organism_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_organism_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | organism_id |
| FOREIGN KEY | organism_id |
| UNIQUE | phylonode_id |
phylonodeprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonodeprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc. | cvterm.cvterm_id | |
| value | text | 64000 | UNIQUE, NOT NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, It is not clear how useful the rank concept is here, leave it in for now. |
| Name | Fields |
|---|---|
| phylonodeprop_idx1 | phylonode_id |
| phylonodeprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonodeprop_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | value |
| NOT NULL | rank |
| UNIQUE | phylonode_id, type_id, value, rank |
phylonode_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| rank | integer | 10 | |||
| phylotree_id | integer | 10 | NOT NULL | phylotree.phylotree_id |
| Name | Fields |
|---|---|
| phylonode_relationship_idx1 | subject_id |
| phylonode_relationship_idx2 | object_id |
| phylonode_relationship_idx3 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | phylotree_id |
| FOREIGN KEY | phylotree_id |
| UNIQUE | subject_id, object_id, type_id |