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Chado Organism Module

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Introduction

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.

Tables

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

Tables referencing this one via Foreign Key Constraints:



Table: organism_dbxref

organism_dbxref Structure
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


Table: organismprop

Tag-value properties - follows standard chado model.

organismprop Structure
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