BioSample¶
NCBI BioSamples are mapped into the Chado.biomaterial table.
NCBI database: https://www.ncbi.nlm.nih.gov/biosample/
Chado biomaterial table: https://laceysanderson.github.io/chado-docs/tables/biomaterial.html
Chado MAGE module: http://gmod.org/wiki/Chado_Mage_Module
XML |
Chado Base Table |
Chado Column |
|---|---|---|
BioSample->accession |
biomaterial |
name |
Owner->Name |
contact |
biomaterial.biosourceprovider_id |
Comment->Paragraph |
biomaterial |
description |
Attribute |
biomaterialprop |
type_id, value |
Organism->taxonomy_id |
organism_dbxref |
dbxref.accession |
Note
In the above table, XML tags are described as Parent_tag->Child_tag. If the value comes from the attribute of a tag, it is written lowercase, as Parent_tag->attribute.
Undecided mappings¶
We don’t currently know how we will map analyses to biomaterials in Chado. Assemblies that are listed in BioSample records are therefore ignored currently.
Attributes¶
This module does not currently map attributes to ontology terms. Instead, all attributes are put into a “NCBI Property” controlled vocabulary. Suggested attribute - ontology term mappings for the Plant 1.0 and Invertebrate 1.0 BioSample packages are available here: https://data.nal.usda.gov/dataset/data-tripal-eutils-tripal-module-increase-exchange-and-reuse-genome-assembly-metadata. The full attribute set can be downloaded at NCBI.