Taxon¶
NCBI taxons are mapped into chado.organism
.
NCBI Taxonomy: https://www.ncbi.nlm.nih.gov/taxonomy
Chado Organism table: https://laceysanderson.github.io/chado-docs/tables/organism.html
Note
Developer’s note: Taxons are imported using the Tripal core class TaxonomyImporter.inc
. Any suggestions or modifications should be made at the Tripal core repo instead.
XML |
Chado Base Table |
Chado Column |
---|---|---|
Taxon->ScientificName |
organism |
genus |
Taxon->ScientificName |
organism |
species |
IdList->Id |
organism_dbxref |
dbxref.accession |
Taxon->Rank |
organism |
type_id |
Taxon->OtherNames->CommonName |
organism |
commonname |
Taxon->ScientificName (if included) |
organism |
infraspecific_name |
NA |
organism |
comment |
Additionally, several properties are parsed into Chado properties for the organism record. However, these all utilize local terms.
¶ XML
Property term
Taxon->Lineage
local:lineage
Taxon->GeneticCode->GCId
local:genetic_code
Taxon->GeneticCode->GCName
local:genetic_code_name
Taxon->MitoGeneticCode->MGCId
local:mitochondrial_genetic_code
Taxon->MitoGeneticCode->MGCName
local:mitochondrial_genetic_code_name
Taxon->Division
local:division
Taxon->OtherNames->GenbankCommonName
local:genbank_common_name
Taxon->OtherNames->Synonym
local:synonym
Taxon->OtherNames->GenbankSynonym
local:synonym
Taxon->OtherNames->Includes
local:other_name
Taxon->OtherNames->EquivalentName
local:equivalent_name
Taxon->OtherNames->Anamorph
local:anamorph