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Workflow Literature Audits

bijux-proteomics-knowledge owns the point where scientific reading pressure meets the shipped benchmark sentence.

These audits exist because the repository now does more than publish benchmark packages and recommendation prose. It also keeps a visible record of where the curated literature:

  • still supports the shipped workflow-family sentence
  • is aging and needs recheck discipline
  • already outruns the benchmark or comparator packet we currently ship
  • should slow recommendation posture instead of silently being assumed

What This Surface Answers

Use this page when the question is not whether a rerun lane executes, but whether the repository is still grounded honestly in the current reading.

The literature audit stack answers four direct questions:

  • which citations currently ground this workflow family
  • when those citations were last rechecked in the curated registry
  • where the literature still outruns the shipped benchmark or comparator proof
  • which machine-readable bibliography export an outsider should open first

Public Surfaces

  • get_workflow_literature_freshness_audit(...)
  • get_workflow_bibliography_export(...)
  • get_benchmark_literature_gap_matrix()
  • get_comparator_literature_gap_matrix()

These are knowledge surfaces, not runtime or intelligence surfaces. They do not decide execution readiness, recommendation posture, or lab consequence. They keep the scientific reading state inspectable so those downstream packages cannot widen language on stale or selectively remembered grounding.

Opening Order

Open the stack in this order when you are reviewing one workflow family:

  1. open the matching workflow claim-grounding page to see the current repository sentence
  2. open the freshness audit to see whether the curated citation set is still recently checked
  3. open the machine-readable bibliography export to inspect what specific reading is actually carried
  4. open the benchmark and comparator gap matrices to see whether current benchmark pressure still lags the literature

This order matters. A bibliography export without the gap matrices can make the reading look broader than the shipped benchmark packet really is.

What The Freshness Audit Means

Freshness here is the curated repository audit state.

It records:

  • the latest recheck date preserved in the citation and literature registries
  • whether a stable DOI or URL still exists in that curated audit
  • whether the current workflow-family summary is already aging past the shipped literature surface

It does not pretend that runtime code is doing live citation crawling or automated truth discovery from the public web.

Machine-Readable Bibliography Exports

Each workflow family exposes one machine-readable bibliography export:

workflow family bibliography export
dda workflow_bibliography:dda
dia workflow_bibliography:dia
lfq workflow_bibliography:lfq
multiplex workflow_bibliography:multiplex
ptm workflow_bibliography:ptm
targeted workflow_bibliography:targeted

Each export carries title, DOI or stable URL, publication year, relevance tags, contradiction tags, and freshness state.

This is the durable handoff surface for outside review. The point is that a reader should be able to inspect what the repository is actually citing without rebuilding the reading list from prose footnotes.

What The Gap Matrices Add

The two gap matrices answer different questions:

  • get_benchmark_literature_gap_matrix() asks where the shipped benchmark package still under-covers the stronger reading
  • get_comparator_literature_gap_matrix() asks where comparator pressure still under-covers the stronger reading

That separation matters because one family can look well cited and still remain weak in benchmark breadth, comparator stress, or both.

What This Surface Proves

  • the repository now carries explicit literature-review state per flagship workflow family
  • benchmark and comparator incompleteness can be shown against curated reading instead of being argued loosely
  • downstream recommendation and release language can be challenged when the reading state is stronger than the shipped proof packet

What This Surface Does Not Prove

  • that every cited study is equally strong or equally relevant
  • that literature support by itself upgrades workflow-family public wording
  • that freshness replaces contradiction handling, benchmark pressure, or lab consequence

Best Next Routes

Boundary

This page owns literature-audit meaning and opening order. It should not become a second claim-grounding page, a second benchmark catalog, or a second recommendation narrative.