The organism module is designed to hold information about a given species, as such it is fairly simple.
See the page on the related Phylogeny module. The phylogeny module is designed for phylogenetic trees and taxonomies.
The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.
| FK | Name | Type | Description |
|---|---|---|---|
| organism_id | serial | PRIMARY KEY | |
| abbreviation | character varying(255) | ||
| genus | character varying(255) | UNIQUE#1 NOT NULL | |
| species | character varying(255) | UNIQUE#1 NOT NULL A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern. |
|
| common_name | character varying(255) | ||
| comment | text |
organism Structure
Tables referencing this one via Foreign Key Constraints:
| FK | Name | Type | Description |
|---|---|---|---|
| organism_dbxref_id | serial | PRIMARY KEY | |
| organism | organism_id | integer | UNIQUE#1 NOT NULL |
| dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
organism_dbxref Structure
Tag-value properties - follows standard chado model.
| FK | Name | Type | Description |
|---|---|---|---|
| organismprop_id | serial | PRIMARY KEY | |
| organism | organism_id | integer | UNIQUE#1 NOT NULL |
| cvterm | type_id | integer | UNIQUE#1 NOT NULL |
| value | text | ||
| rank | integer | UNIQUE#1 NOT NULL |
organismprop Structure