User documentation
Why AssayLink exists, where it sits in the assay landscape, and how scientists, stewards and project teams use it.
Mission
AssayLink is an AI-assisted platform for discovering, authoring, governing and reviewing reusable assay definitions in Pharma R&D. It is the intended successor to the Test Definition Portal (TDP): the place where an assay is defined once, in governed language, so later systems can capture and analyse results against that definition.
Today definitions live as ad-hoc JSON, Excel and ageing tools. Metadata is missing or unstandardised, finding a relevant assay is slow, and there is little room for automation. A new portal by itself does not fix that. Stewardship and a controlled vocabulary are what make data consistent across labs and interoperable across PDE, Helix, RedLIMS and reporting systems.
When a project needs “a CYP3A4 induction assay in human hepatocytes”, AssayLink should already hold an approved, findable definition — not another spreadsheet rewrite of the same assay.
Three things are first-class:
- Modular templates — reusable assay definitions with versions, not runs.
- Controlled vocabulary — preferred terms, synonyms, hierarchy and ontology links, under a data steward.
- Explained matching — a free-text need mapped to templates with reasons, so a project can link the right definition.
What AssayLink does not do
AssayLink governs reusable assay definitions. It does not store experimental execution data, raw instrument files, or processed results, and it does not replace LIMS, ELN, PDE or Benchling. Those systems remain the systems of record for work that was actually run; they validate entered data against AssayLink templates.
| AssayLink owns | AssayLink does not own |
|---|---|
| Reusable assay definitions (templates) | Experimental execution data (runs, plates, samples) |
| Template versions and review workflow | Instrument files, LIMS results, study reports |
| The assay metadata model itself (sections, fields, rules) | Numeric experimental values (Fold Induction, Ct, peak area, …) |
| Controlled vocabularies and stewardship | Protocol / instruments / data-output blocks (future sections); project master data (MaRLay) |
Personas
| Persona | Demo user | Main job |
|---|---|---|
| Assay Definition Owner | Dr Amelia Ostrowski | Create and edit draft templates; submit for review; version approved work |
| Data Steward | Dr Sofia Lindqvist | Review templates; own the metadata model and vocabulary |
| Project Team Member | Tomas Berg | Pick a MaRLay project, describe a need, link a matching template |
Core concepts (plain language)
- Assay Template — a reusable definition of an assay (not a run).
- Template Version — a snapshot of metadata; immutable once approved.
- Vocabulary / Term — a governed controlled list and its concepts (preferred label, synonyms, parents).
- Field — one piece of information an assay definition captures, such as “Assay format”, “Species” or “Target”. Every field an author fills in on a template is a field defined in the metadata model.
- Metadata Field Definition — the rules for one field: whether it exists, is mandatory, multi-value, which vocabulary feeds it, and which section shows it. Changing this changes the wizard — no code deploy.
- Metadata Section — a steward-named group of fields, such as Classification or Biological System / Materials. The authoring wizard pages by section.
- Metadata Rule — when/then logic over field keys: show, require, or restrict vocabulary terms (for example CYP induction requiring Cell System and restricting Expected Readout).
- Metadata Quality Score — completeness, vocabulary compliance and consistency with active rules. Not a score of experimental results.
- Project Assay Link — a project’s use of a template version plus project context. Still not a run.
- Suggested Term — a candidate value from AI or users; only a steward can activate it into the vocabulary.
Using the POC role switcher
In this proof of concept, authentication is mocked. The header shows a Role control with the role name (Assay Definition Owner, Data Steward, Project Team Member). Hover to see the demo user. Changing the dropdown switches immediately and lands on that role’s dashboard. In a real deployment this comes from Entra ID / ALB SSO and cannot be changed in the UI.