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Package Overview

bijux-proteomics-core owns the durable scientific contracts that the rest of the repository depends on: program, target, assay, and review entities; lifecycle transitions; review gates; normalized proteomics I/O seams; and benchmark-acceptance surfaces. The package is only healthy when those scientific rules remain runtime-agnostic and distinct from evidence memory, recommendation posture, and assay consequence.

This package is materially broader now than older overview pages implied. It is not only a workflow-contract layer. It owns a substantial scientific surface across sequence handling, chemistry, spectra and mzML intake, identification, quantification, PTM review, DIA support, benchmark assets, review artifacts, and workflow planning.

Why This Package Feels Bigger Now

  • chemistry, mass calculation, modification, fragment, and isotope work now sit in the same product story as workflow contracts and benchmark review surfaces
  • benchmark packages, lineage roots, challenge corpora, and acceptance bars are part of core scientific law rather than downstream decoration
  • readers can now inspect more of the real scientific machinery directly instead of inferring it from runtime, reports, or recommendation summaries

Concrete Scientific Families

  • sequence and study contracts under domain, sequences, and study
  • chemistry, isotopes, modifications, fragments, and mass calculations under chemistry
  • normalized proteomics I/O for formats, spectra, raw-source adapters, and chromatography under io
  • identification and reviewable search normalization under identification
  • label-free quantification, missingness, normalization, provenance, and statistical surfaces under quantification
  • PTM, proteoform, targeted, DIA, and interpretation surfaces that stay package-owned instead of being hidden in notebooks or report glue
  • benchmark package ownership and flagship workflow contracts under benchmarks and workflow

Why That Depth Matters

  • runtime can execute and replay workflows without redefining scientific truth
  • knowledge can ground claims against richer, typed upstream evidence
  • intelligence can rank or downgrade based on explicit scientific artifacts instead of presentation-only summaries
  • lab can inherit assay-facing consequence from stable review and workflow contracts rather than reverse-engineering ad hoc outputs

What It Owns

  • define program, target, assay, and review entities
  • encode lifecycle transitions, benchmark-acceptance bars, gate truth, and runtime-agnostic workflow contracts
  • publish benchmark and scientific contract surfaces to downstream packages

What Readers Commonly Underestimate

  • this package owns the repository's cleanest chemistry and assay semantics, not only its workflow grammar
  • this package decides which benchmark evidence roots are structured enough to become public flagship surfaces
  • this package is where biological and analytical packages inherit durable reviewable inputs instead of inventing them ad hoc

What It Refuses

  • shared schema primitives that belong in foundation
  • evidence memory, contradiction handling, or recommendation posture
  • operator-facing runtime execution, replay, or assay-consequence ownership

Strongest First Checks

  • open the public package roots and benchmark catalog when you need the shortest proof that the package owns real sequence, chemistry, review, and workflow surfaces
  • open the benchmark asset handbook when the question is whether a workflow claim starts from enough public evidence
  • open runtime, knowledge, intelligence, or lab only after the core scientific contract is clear enough to execute or judge honestly

Best Reader Route

  • start here when the question is whether bijux-proteomics has real scientific depth or only governance around smaller utilities
  • continue to Flagship Public Benchmark Catalog when you need the paired public evidence roots that make the contracts inspectable
  • continue to Benchmark Assets when you need freshness, lineage, licensing, incompleteness, and acceptance context

First Proof Check

  • packages/bijux-proteomics-core/src/bijux_proteomics
  • packages/bijux-proteomics-core/tests
  • benchmark package manifests, asset roots, and acceptance-facing evidence
  • neighboring handbook branches once a change crosses the local role