Organism & Taxonomy

SeqDesk integrates with the NCBI taxonomy database to identify organisms for each sample. Correct taxonomy assignment is required for ENA submission.

Taxonomy Lookup

The Organism field in the sample table provides an autocomplete search:

1. Start typing a scientific name, common name, or partial match
2. Results appear from the local taxonomy database (~6,000+ entries)
3. Select the correct organism
4. Both taxId and scientificName are auto-filled

Common Identifiers

Species-Level Samples

For samples from a known species, search by scientific name:

Metagenome Samples

For metagenomic samples, use the appropriate metagenome identifier:

These metagenome IDs are required by ENA for environmental samples where a single species cannot be assigned.

Tax ID Requirements

The taxId field is critical for:

• ENA submission — every sample must have a valid NCBI taxonomy ID
• MIxS compliance — the taxonomy determines applicable metadata standards
• Pipeline configuration — some pipelines use taxonomy for reference database selection

Updating Taxonomy

Taxonomy can be updated:

• During order creation in the sample table
• On the order detail page (while in DRAFT status)
• In the study sample table when editing MIxS metadata