ImmPort Data Submission — Agent Knowledge Base
Work in progress
This section is a supplementary, AI-agent-oriented layer on top of the official Template Documentation. It is being built incrementally and has not yet been cross-linked from the main documentation. Treat it as a fast-start map, not the final word — when a detail here seems to conflict with a template's own reference page, the template page (and ultimately the submission template/validator) wins.
Why this section exists
The existing documentation is excellent at answering "what are the constraints on field X?" one template at a time. It's much harder to answer task-shaped questions like "what's the full sequence of templates I need to upload a CyTOF experiment?" or "why did my upload get rejected?" — that knowledge exists, but it's scattered across PDFs, Excel troubleshooting sheets, and the underlying validation engine's source code.
This section pulls that knowledge together in one place, written so that both humans and AI agents / MCP tools preparing ImmPort submissions can use it directly:
| Section | What's there |
|---|---|
| Getting Started | Create a workspace, register a study, and choose between the two upload paths (SRW vs. templates). |
| Templates | The full template catalog, and the correct upload order for a typical study. |
| Validation | Plain-English explanations of every recurring validation rule type, plus a common-errors FAQ. |
| Workflows | Task-oriented guides — including per-assay upload sequences transcribed from the official flow-diagram PDFs. |
| API Reference | The REST endpoints an automated client needs to upload and validate a package end-to-end. |
How to use this if you're an AI agent
- Start at Getting Started if you don't yet have a workspace or registered study.
- Use the Template Catalog + Upload Order to figure out which templates you need and in what order/bundle.
- Check Workflows for your specific assay type or task — these encode constraints (like "upload these N templates in the same package") that aren't repeated on the individual template reference pages.
- Before asserting a validation behavior, check the Validation Rule Glossary and the common-errors FAQ — generic field descriptions can be less precise than the actual enforced rule.
- Use the API Reference to script the upload → validate → status → report loop.
Provenance matters
Wherever a page in this section states a hard rule (required/optional, bundling constraints, error conditions), it links back to its source — a flow-diagram PDF, a template page, or the validator — so you can verify it yourself rather than taking the paraphrase on faith.