Study Metadata & MIxS
SeqDesk supports the MIxS (Minimum Information about any Sequence) standard for metadata collection. MIxS ensures that sequencing data is accompanied by standardized contextual information, which is required for submission to the European Nucleotide Archive (ENA).
What is MIxS?
MIxS is a set of checklists maintained by the Genomic Standards Consortium (GSC) that define the minimum metadata required for different types of sequencing experiments. Each checklist specifies required and optional fields for a particular environment or sample type.
Checklist Types
When creating a study, you can select a MIxS checklist type that matches your research:
| Checklist | ENA ID | Use Case |
|---|---|---|
| GSC MIMAGS | — | Metagenome-Assembled Genomes |
| GSC MIxS wastewater & sludge | — | Wastewater treatment samples |
| GSC MIxS soil | ERC000016 | Soil environment samples |
| GSC MIxS water | ERC000022 | Aquatic environment samples |
| GSC MIxS human gut | ERC000015 | Human intestinal microbiome |
| GSC MIxS host associated | ERC000012 | Samples from a host organism |
| GSC MIxS plant associated | ERC000047 | Plant-related samples |
| ENA default sample checklist | — | Generic fallback when no MIxS checklist applies |
This is an excerpt — SeqDesk ships the full GSC + ENA catalog (about 17
checklists at the moment, including air, sediment, microbial mat biofilm, and
the various human-body-site variants). The complete list is enumerated by
GET /api/mixs-checklists.
The checklist type determines which metadata fields appear in the sample table.
Metadata Fields
MIxS metadata is collected at the sample level. Common fields across checklists:
| Field | Type | Example |
|---|---|---|
| geographic location (country) | Text | Germany |
| geographic location (latitude) | Number | 52.5 |
| geographic location (longitude) | Number | 13.4 |
| collection date | Date | 2024-01-15 |
| broad-scale environmental context | Text | urban biome |
| local environmental context | Text | wastewater treatment plant |
| environmental medium | Text | activated sludge |
Fields can have associated units (e.g., temperature in Celsius, depth in meters).
Where Metadata is Stored
- Study-level metadata is in the
studyMetadatafield (JSON) - Sample-level MIxS data is in each sample’s
checklistDatafield (JSON) - Units for numeric sample fields are in
checklistUnits(JSON)
ENA Requirements
For successful ENA submission:
- The study must have a title (minimum 10 characters)
- The study must have a description (minimum 50 characters)
- Each sample must have a valid
taxId(NCBI taxonomy) - Required MIxS fields for the selected checklist must be filled
- The
readyForSubmissionflag must be set to true
See Preparing a Submission for the full validation requirements.
Customizing Metadata Fields
Facility admins can customize the study metadata form through the Study Form Builder. This allows adding institution-specific fields alongside the standard MIxS fields.