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.
Environment Types
When creating a study, you select an environment type that matches where your samples were collected. The study wizard offers a curated picker of 13 environment types:
| Environment Type | Use Case |
|---|---|
| Human Gut | Human gastrointestinal tract |
| Human Oral | Human oral cavity |
| Human Skin | Human skin |
| Human Associated | Other human-associated samples |
| Host Associated | Samples from non-human hosts |
| Plant Associated | Plant-related samples |
| Soil | Terrestrial soil samples |
| Water | Freshwater or marine samples |
| Wastewater/Sludge | Wastewater treatment samples |
| Air | Atmospheric or aerosol samples |
| Sediment | Aquatic or terrestrial sediments |
| Microbial Mat/Biofilm | Biofilm or microbial mat samples |
| Miscellaneous | Other environment types |
There is no MAG / MIMAGS option in this picker. Each environment type maps to a MIxS template that determines which per-sample metadata fields appear in the sample table.
The environment picker is intentionally distinct from the full MIxS catalog.
SeqDesk also ships the complete GSC + ENA checklist catalog (roughly 17 files,
including the various human-body-site variants), enumerated by
GET /api/mixs-checklists and
used elsewhere (e.g. submission). The study environment picker is the curated
13-entry subset used to drive metadata entry.
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 |
Where Metadata is Stored
- Study-level metadata is in the
studyMetadatafield (JSON) - Sample-level MIxS values are in each sample’s
checklistDatafield (JSON) - Units for numeric sample fields live in
checklistUnits(JSON)
Study metadata entry (in the study wizard and study editor) writes only
checklistData. It does not write checklistUnits — per-field units are
captured separately in the order wizard’s sample metadata step. Editing
metadata from a study therefore leaves any existing checklistUnits untouched.
ENA Requirements
For successful ENA submission:
- The study must have a non-empty title and description
- Each sample must have a valid
taxId(NCBI taxonomy) - Required MIxS fields for the selected checklist should be filled
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.