Chado Organism Module



The organism module is designed to hold information about a given species, as such it is fairly simple.

More Information

See the page on the related Phylogeny module. The phylogeny module is designed for phylogenetic trees and taxonomies.


Table: organism

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.

organism Structure
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:

Table: organism_dbxref

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

Table: organismprop

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