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.

Taxon to Chado.organism mappings

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.

Taxon properties to Chado.organismprop mappings

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