Organism & Taxonomy

SeqDesk helps you identify the organism or metagenome type for each sample and assign the matching NCBI taxonomy ID. Correct taxonomy assignment is required for ENA submission.

Taxonomy Lookup

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

Start typing a scientific name, common name, or partial match
Results appear from a built-in list of about 90 curated taxa (common metagenomes, host organisms, bacteria, archaea, fungi, and viruses)
Select the correct organism
Both taxId and scientificName are auto-filled

The autocomplete searches a small, hardcoded list of frequently used taxa — it does not perform a live NCBI lookup. If your organism is not in the list, you can enter its taxId manually; out-of-list entries are stored with a placeholder scientific name (Unknown organism (TaxID: …)). Verify the taxId yourself at NCBI Taxonomy .

Common Identifiers

Species-Level Samples

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

Search	Tax ID	Scientific Name
E. coli	562	Escherichia coli
human	9606	Homo sapiens
mouse	10090	Mus musculus

Metagenome Samples

For metagenomic samples, use the appropriate metagenome identifier:

Environment	Tax ID	Scientific Name
Human gut	408170	human gut metagenome
Soil	410658	soil metagenome
Marine	408172	marine metagenome
Freshwater	449393	freshwater metagenome
Wastewater	527639	wastewater metagenome

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