User guide

Screenshot walkthrough of every major screen, organised by persona. Switch the header persona to match the section you are reading.

App chrome (all personas)

Every page shares the same header: the AssayLink logo (home), a role-filtered navigation on one row, and (in the POC) the Role switcher on the right. The dropdown shows the role; hover for the demo user’s name. Changing it switches immediately. Links you are not allowed to use simply do not appear — and typing a forbidden URL shows a clear “not permitted” page.

Header + Assay Definition Owner dashboard: drafts, awaiting review, recently approved.

Assay Definition Owner

Demo user: Dr Amelia Ostrowski. Creates and maintains templates through review.

Dashboard

Three columns: My draft templates, Awaiting steward review, and Recently approved. Drafts offer an Edit shortcut.

Template catalogue

Templates are grouped into functional areas (ADME / DMPK is populated; HTS, Safety, In Vivo tiles are greyed placeholders for future scope). Open a group to see templates; filters sit at the top.

Template detail

Shows metadata, status, versions, review history, the Metadata Quality Score, and actions (submit, edit draft when allowed). Vocabulary-backed values render as governed terms. AssayLink does not show experimental result values.

Authoring wizard (new template)

A metadata-driven wizard paged by steward-configured sections (Assay Identity, Classification, Biological System / Materials, Detection, Readouts / Endpoints, …). Fields, obligation and dropdown values come from MetadataFieldDefinition; conditional rules show or require extra fields (for CYP induction: Target, Cell System, Species, Detection Type). Expected readouts are vocabulary categories, not measured values. A Metadata Quality Score updates as you fill. Hierarchy fields use the vocabulary tree; AI autofill (when enabled) is visibly marked as suggested until accepted.

New template authoring wizard — New template wizard — sections and fields are model-driven.

Edit draft

Owners can reopen drafts and “changes requested” versions. The template code is locked; metadata remains editable until submission.

Find an assay (matcher)

Describe an assay need in free text. The system extracts metadata (rule-based, optionally merged with an LLM), scores published templates, explains each match field by field, and names fields that active metadata rules still require. A Metadata Quality Score estimate is shown from the description — not from experimental results.

Empty matcher form before submitting a query — Matcher before a query.

Matcher results with ranked template recommendations — Matcher results for a CYP3A4 induction need — top match should be PK Induction in Heps with explained scores.

Data Steward

Demo user: Dr Sofia Lindqvist. Reviews templates and owns the semantic foundation (model + vocabulary).

Dashboard

Review queue

Lists submitted / in-review templates with the Metadata Quality Score (missing required fields, ungoverned values, rule warnings). Open a template to approve, reject, or request changes with comments and optional per-field notes.

Assay Definition Model

A field is one piece of information an assay definition captures — “Assay format”, “Species”, “Target”. Fields sit in steward-named sections (including Biological System / Materials). This screen is what the authoring wizard is generated from.

The knowledge model shows Assay Definition → sections → vocabularies → rules → quality. Section cards sit below. The field and vocabulary map shows scientific sections and fields on the left, vocabularies on the right, connectors for governed values. Conditional rules live under the Rules tab and the Conditional Rule Map.

Metadata model map and field tables — Assay Definition Knowledge Model with section cards and maps.

Field definition editor for Assay type — Field editor — identity, value source, section placement, constraints.

Adding a field. Inputs marked * are required. The two settings that decide how the field behaves are:

Data type — TERM means values must come from a governed vocabulary, so a vocabulary must be selected and the input type must be a SELECT, MULTISELECT or HIERARCHY_SELECT. Anything else (STRING, NUMBER, …) is entered freely.
Section — which part of the assay definition model shows the field (for example Biological System / Materials). Fields added here immediately appear in the authoring wizard.

Retiring a field. Deprecate is the governed route: authors stop being offered the field, existing template values are kept so history stays readable, and the rules become read-only until the field is reactivated. Delete is only offered when no template has ever held a value for the field — it removes a mistyped or experimental field outright, and the audit entry survives the deletion.

Leave Applies to assay types unticked and the field applies to every assay type. Tick a branch and it only appears once an author selects that assay type or one beneath it — which is why a newly scoped field can look missing in the wizard until the assay type is chosen.

Conditional rules. Under the Rules tab, a steward writes when/then logic over field keys. The CYP induction rule is the demo: when Assay Type is CYP induction or a more specific type, require Target, Cell System, Species and Detection Type, and restrict Expected Readout to Fold Induction, Emax and NOEL. Hide / make-optional stay secondary. Rules never collect experimental numbers.

Vocabulary

Browse vocabularies, open a vocabulary to manage terms, synonyms, hierarchy and ontology mappings. Deprecate carefully; never delete history that templates rely on without a steward decision.

List of controlled vocabularies — Vocabulary catalogue.

Assay Type vocabulary term list — Assay Type terms (hierarchical where configured).

Suggested terms

AI and users may propose labels that are not yet governed. Only a steward can approve them into an active vocabulary term. This is the single gate for growing the terminology.

Suggested term review queue — Suggested-term queue.

Change history

Governed change log — Audit trail of governed changes.

Project Team Member

Demo user: Tomas Berg. Starts from a MaRLay project (six-digit id), not from a blank matcher.

Dashboard and project list

MaRLay projects list — My projects — master data from the MaRLay mock.

Project detail and define assay

Open a project to see linked assays. “Define” starts a need description (high-level type + short text), runs matching pinned to that project, then lets you link a template version and add project-specific context.

Project detail with linked assays — Project detail.

Define a project assay flow — Define a project assay (project-first matcher).

Project members do not see a standalone “Find an assay” nav item — matching is reached through the project so recommendations can be linked.

Shared: catalogue and templates

All personas can browse the catalogue and open published templates. Creating, reviewing, and model edits remain role-gated.

Role gates

If you open a URL your role cannot use, AssayLink shows a clear forbidden page naming the capability and which role holds it.

Forbidden page when a project member opens steward vocabulary — Project member attempting Vocabulary — server-enforced, not only hidden UI.

Typical end-to-end scenarios

Author → review → publish: Owner creates a draft → submits → Steward reviews with comments → approves → Owner (or process) publishes / versions as needed.
Discover & link: Project member picks MaRLay project → describes need → selects recommended template → adds project fields → link.
Govern terminology: Matcher or author surfaces an unknown label → Suggested Term → Steward activates synonym or new term → future matches improve.
Evolve the model: Steward opens Assay Definition Model → changes a section, field or rule → wizard and Metadata Quality Score update immediately.

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