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Publishing to FAIRDOM-SEEK

Metaseed can set up a FAIRDOM-SEEK instance from a profile and push a dataset into it, over SEEK's API. This guide is the task-oriented walkthrough; for the RDF format and the Python entry points see SEEK Export.

What the export produces

A profile and a dataset map onto SEEK in two separate ways, because SEEK treats them differently:

From your profile / dataset Becomes in SEEK How
Entities that map to a JERM Sample (by SEEK role, or by name) Sample Types and their Controlled Vocabularies API — the Provision button
The entities of a loaded dataset Investigations, Studies, Assays, Samples API — the Sync button
Fields on Investigation / Study / Assay Extended Metadata Manual — a file a SEEK admin uploads

The split is SEEK's, not metaseed's: SEEK only lets an administrator create Extended Metadata Types, and not over its API, so that part cannot be self-service.

One-time setup

The SEEK page is hidden until the adapter is enabled and pointed at an instance.

  1. Install the extra: pip install 'metaseed[seek]' (it needs httpx; the page says so if it is missing).
  2. Open Settings → Plugins, enable SEEK, and set:
  3. URL — your SEEK instance, e.g. http://localhost:3000 (required).
  4. API key — a SEEK personal access token (optional, but Provision and Sync are disabled without it, since both write to SEEK).

The workflow

Open the FAIRDOM-SEEK page (/seek). It has two numbered steps and a file-export fallback.

1 · Configure the model in SEEK

Choose the profile and click Provision model →. This creates its Controlled Vocabularies and Sample Types in the selected Project — a project on your SEEK server, which every SEEK resource must belong to. Re-running is safe: it reuses what already exists rather than duplicating it.

This step needs no loaded dataset — it describes a profile, so you can provision before you have built anything.

Browse what will be created first

Below the profile chooser, What this will create in SEEK shows the model the selected profile and version project onto, before anything is written:

  • Sample Types — each entity that becomes a SEEK Sample Type, expandable to its columns (name, type, and whether it is a controlled vocabulary). This is read from the same plan Provision executes, so it cannot drift from what is created.
  • Extended Metadata — the custom fields the Investigation, Study and Assay records carry. SEEK's own record fields (identifier, title, description) and the nested structure are not listed, because they are not Extended Metadata.

The panel refreshes when you change the profile or version, and never writes to SEEK — it is there to check a profile maps the way you expect before you provision or sync.

2 · Sync the dataset to SEEK

With a dataset loaded, click Sync to SEEK →. It pushes the dataset's entities in as Investigations, Studies, Assays and Samples, matched to the Sample Types provisioned in step 1.

If this reports no dataset loaded, that is why: unlike Provision, Sync acts on the dataset you have open. Load or create one first.

Or export a file

Download SEEK ISA RDF (.ttl) → gives you the dataset as a Turtle file to import through SEEK's own tool, instead of the API. Useful when you cannot give metaseed an API key, or want to review the file first.

To import it, in SEEK:

  1. Open a Project → Import from FAIR Data Station.
  2. Upload the .ttl on the FAIR DS TTL tab. (It is a tab, easy to miss; the JSON tab is selected by default and disables the file field.)
  3. SEEK previews what it found. Press Submit.
  4. The import runs as a background job — the status panel moves from Queued to Completed.

Notes and limits

  • Provision needs no dataset; Sync does. They act on different things — a profile and a loaded dataset respectively.
  • "Project" is a project on your SEEK instance, fetched live from it, not a metaseed concept.
  • Extended Metadata is derived from a dataset's non-core annotations. An Investigation carrying only title, identifier and description yields no Extended Metadata Type — that is SEEK reading the file correctly, not an export failure. The Extended Metadata download exists for the fields that go beyond SEEK's core set.
  • SEEK reads the ISA hierarchy positionally. A profile whose entities do not sit at the expected Investigation → Study → (ObservationUnit →) Sample → Assay depth will import at a shifted level. An entity's SEEK role (set on the entity in the Spec Builder) re-types the exported node — choosing which JERM class it becomes — but does not move it in the tree, which SEEK infers from where the entity sits.