Schema Version: 1.3 Module: chado

Columns

Columns

Table Type Column Type Size Nulls Default Comments
organism_relationship Table subject_id int8 19 null
organism_cvtermprop 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.
organism_dbxref Table dbxref_id int8 19 null
organism_dbxref Table organism_dbxref_id bigserial 19 nextval('organism.organism_dbxref_organism_dbxref_id_seq'::regclass)
organism_relationship Table rank int4 10 0
organism_relationship Table object_id int8 19 null
organismprop Table rank int4 10 0
organism_cvtermprop Table rank int4 10 0

Property-Value ordering. Any organism_cvterm 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
organism_pub Table organism_pub_id bigserial 19 nextval('organism.organism_pub_organism_pub_id_seq'::regclass)
organism_pub Table pub_id int8 19 null
organism_relationship Table organism_relationship_id bigserial 19 nextval('organism.organism_relationship_organism_relationship_id_seq'::regclass)
organism Table type_id int8 19 √ null

A controlled vocabulary term that specifies the organism rank below species. It is used when an infraspecific name is provided. Ideally, the rank should be a valid ICN name such as subspecies, varietas, subvarietas, forma and subforma
organism_cvtermprop 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.
organismprop_pub Table organismprop_id int8 19 null
organism_relationship Table type_id int8 19 null
organism_cvtermprop Table organism_cvtermprop_id bigserial 19 nextval('organism.organism_cvtermprop_organism_cvtermprop_id_seq'::regclass)
organism_dbxref Table organism_id int8 19 null
organism_cvterm Table organism_cvterm_id bigserial 19 nextval('organism.organism_cvterm_organism_cvterm_id_seq'::regclass)
organism Table infraspecific_name varchar 1024 √ null

The scientific name for any taxon below the rank of species. The rank should be specified using the type_id field and the name is provided here.
organismprop Table organism_id int8 19 null
organismprop_pub Table organismprop_pub_id bigserial 19 nextval('organism.organismprop_pub_organismprop_pub_id_seq'::regclass)
organism Table genus varchar 255 null
organismprop Table type_id int8 19 null
organism_cvterm Table organism_id int8 19 null
organismprop_pub Table rank int4 10 0
organism_cvterm Table rank int4 10 0

Property-Value ordering. Any organism_cvterm 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
organism Table common_name varchar 255 √ null
organismprop Table value text 2147483647 √ null
organismprop_pub Table value text 2147483647 √ null
organism_cvtermprop Table organism_cvterm_id int8 19 null
organism Table species varchar 255 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.
organism_cvterm Table cvterm_id int8 19 null
organism_cvterm Table pub_id int8 19 null
organism Table comment text 2147483647 √ null
organism Table organism_id bigserial 19 nextval('organism.organism_organism_id_seq'::regclass)
organismprop Table organismprop_id bigserial 19 nextval('organism.organismprop_organismprop_id_seq'::regclass)
organism Table abbreviation varchar 255 √ null
organismprop_pub Table pub_id int8 19 null
organism_pub Table organism_id int8 19 null