organism

4 rows


Description

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

Columns

Column Type Size Nulls Auto Default Children Parents Comments
organism_id serial 10 √ nextval('organism_organism_id_seq'::regclass)
bs_sample.organism_id bs_sample_organism_id_fkey R
bs_sample_element.organism_id bs_sample_element_organism_id_fkey R
library.organism_id library_organism_id_fkey R
md_image_organism.organism_id md_image_organism_organism_id_fkey R
locus.organism_id locus_organism_id_fkey R
feature.organism_id feature_organism_id_fkey C
gff3view.organism_id Implied Constraint R
materialized_stockprop.organism_id Implied Constraint R
organism_dbxref.organism_id organism_dbxref_organism_id_fkey C
organism_relationship.object_id organism_relationship_object_id_fkey R
organism_relationship.subject_id organism_relationship_subject_id_fkey R
organismpath.object_id organismpath_object_id_fkey R
organismpath.subject_id organismpath_subject_id_fkey R
organismprop.organism_id organismprop_organism_id_fkey C
phenotype_comparison.organism_id phenotype_comparison_organism_id_fkey C
phylonode_organism.organism_id phylonode_organism_organism_id_fkey C
stock.organism_id stock_organism_id_fkey C
tmp_gff_load_cache.organism_id Implied Constraint R
accession.chado_organism_id accession_chado_organism_id_fkey R
blast_db_organism.organism_id blast_db_organism_organism_id_fkey R
library.chado_organism_id library_chado_organism_id_fkey R
organism.chado_organism_id organism_chado_organism_id_fkey R
organismgroup_member.organism_id organismgroup_member_organism_id_fkey R
abbreviation varchar 255 √ null
genus varchar 255 null
species varchar 255 null

A type of organism is always uniquely identified by genus+species. When mapping from the NCBI taxonomy names.dmp file, the unique-name column must be used where it is present, as the name column is not always unique (eg 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 varchar 255 √ null
comment text 2147483647 √ null
genbank_taxon_id int4 10 √ null
sgn_organism_id int4 10 √ null
organism.organism_id organism_sgn_organism_id_fkey R
obsolete int4 10 √ null

Indexes

Constraint Name Type Sort Column(s)
organism_pkey Primary key Asc organism_id
organism_c1 Must be unique Asc/Asc genus + species

Relationships

Close relationships within degrees of separation