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Capability Map

The capability map lists the kinds of work bijux-proteomics-core is allowed to do. That list should make the package easier to defend in review, not broader by default.

The important correction since v0.3.7 is that the allowed capability set is much richer than "workflow rules". The package is now allowed to own a broad scientific center as long as the work still encodes durable scientific law rather than recommendation policy, evidence truth, or runtime control.

Allowed Capability Classes

capability class examples now visibly owned in core why that ownership is legitimate
shared scientific entities program, target, assay, review, study, sequence, and structure records downstream packages need one durable scientific object model
chemistry and molecular rules modifications, mass, fragments, isotopes, proteoform and label semantics these are scientific laws, not runtime or recommendation choices
proteomics ingestion and normalization spectra, mzML, search-adapter, raw-source, and table normalization seams the product needs typed proteomics inputs before later owners can reason safely
evidence-shaping scientific analysis identification, protein inference, quantification, PTM localization, DIA, targeted, QC these are still scientific contracts and review surfaces, not recommendation policy
benchmark and workflow law benchmark assets, flagship packages, workflow contracts, lifecycle transitions, review gates public workflow-family language starts from these roots

Reader Test

If a feature answers "what is the durable scientific rule or typed scientific artifact here?", it is plausibly core. If it answers "should I believe this claim?", "should I recommend this?", or "can I run this now?", it has probably left core and moved into knowledge, intelligence, or runtime.

Disallowed Expansion

  • shared schema primitives that belong in foundation
  • evidence truth, contradiction ownership, or literature pressure that belong in knowledge
  • recommendation posture, ranking, or analytical regret that belong in intelligence
  • operator-facing runtime execution, replay control, and provider handling
  • downstream assay-worth or outcome-promotion logic that belong in lab

What This Map Should Prevent

  • hiding biology and chemistry depth under vague "workflow" language
  • absorbing recommendation or evidence-truth logic just because core owns the strongest scientific machinery
  • treating benchmark fixtures as if they were separate from scientific law
  • letting runtime convenience redefine the scientific contract

First Proof Check