Domain language

Bijux Proteomics uses precise terms for evidence and authority. Similar words often name different layers; preserving those distinctions keeps public claims auditable.

Product vocabulary

Term	Meaning in this repository	Not a synonym for
scientific contract	declared inputs, policy, outputs, invariants, and rejection behavior owned by Core	successful execution
run	one Runtime attempt with identity, environment, state history, and artifacts	accepted result
replay	reconstruction or comparison against a retained run contract	independent scientific replication
raw-executable	repository-owned transformation from the declared checked input level	vendor-native raw acquisition processing
import-only	strongest lane begins with externally produced result exports	weak or useless evidence
evidence	source-linked observation or statement with context and provenance	settled truth
claim	exact proposition connected to support and contradiction	recommendation
confidence	value under a named scale, inputs, and update policy	calibrated probability unless demonstrated
recommendation	advisory action under a named candidate set and policy	authorization
readiness	Lab preconditions pass for a concrete plan and context	execution or success
handoff	approved, frozen instructions and custody record	physical experiment
observation	returned measurement or outcome linked to the plan	QC acceptance or evidence promotion
promotion	explicit policy admits an outcome as downstream evidence	deletion of failure or uncertainty history

Trust vocabulary

Term	Required qualifier
supported	workflow family, input level, operation, evidence revision, and current ceiling
validated	invariant or acceptance rule, positive and negative evidence, and tested envelope
reproducible	what is repeated, which inputs and environment are fixed, and allowed drift
deterministic	exact supported inputs, configuration, ordering, seed, and stability dimension
parity	comparator, versions, dimensions, tolerances, and disagreement policy
benchmark-backed	asset, lineage, license, holdout role, acceptance bar, and transfer limit
current	source version or retrieval time and freshness policy
reviewed	reviewer or authority, fixed revision, disposition, and unresolved items

flowchart LR
    D["data and scientific contract"] --> X["execution record"]
    X --> E["evidence state"]
    E --> J["advisory judgment"]
    J --> L["laboratory readiness"]
    L --> O["observed consequence"]

Package vocabulary

• canonical package owns current behavior and its public contract.
• compatibility package preserves named historical caller surfaces while pointing to a canonical owner.
• Foundation means shared identity, outcomes, provenance, serialization, and migration—not all low-level code.
• Core means scientific models and transformations—not the entire product.
• Runtime means execution, state, environments, and artifacts—not every action that happens while software is running.
• Knowledge means evidence custody and reconciliation—not recommendation policy.
• Intelligence means advisory decision policy—not autonomous authority.
• Lab means design, readiness, handoff, observation, and consequence—not physical instrument control.

When a term appears without the qualifier needed to find its owner and proof, interpret the claim conservatively and follow Decision Rules.