Fermlit corpus and schema

This week delivers the three concrete artifacts below and the supporting learning/branding/opportunity pack. The scientific or commercial outcome follows the preserved source brief, while the acceptance checks make its evidence testable. The career objective is to turn this work into something a scientist, hiring manager or buyer can inspect.

• Scientific/build priority: Verify at least ten related works and decide whether FermLit is a new resource or an extension; record search strings and date.
• Public/profile priority: Draft schema explainer and novelty boundary using actual included-paper counts.
• Career/relationship/commercial priority: Use the weekly founder digest to find a potential domain reviewer; begin searching for the independent annotator needed by week 10.

Read v6 · Week 5 · FermLit begins: the corpus before Monday. It carries this week's v5 brief unchanged and adds the Welcome analogy, Learn it (▶ core and ＋ deeper sources), Run it (repos with a 20-40 minute exercise), the NotebookLM kit and the mentor check below. Standing v6 rules: resource rules, NotebookLM protocol, chapter anatomy. v6 adds depth only; it does not change a goal, gate, output or the 600-minute cap, so this specification still governs execution.

Act II · Threads: B, M, FL · Next gate: 8

Where this week sits. - ← From: week 4 reproducibility habits (manifest, checksums); your v3/Vara experience with LLM pipelines. - → Feeds: week 6 (the schema becomes annotation guidelines), week 7 (the agent fills the schema), week 9 (corpus scales to 2,000), week 14 (RELATED.md becomes Paper 1's related work). - ⟳ Returns in: Paper 1 Methods: "Corpus construction" and "Schema".

Goals. - 🎯 This week: RELATED.md with ≥ 10 verified references; 500 open-access XMLs + manifest; fermlit.schema.json v0 that fits three hand-annotated papers. - 🏁 Next milestone: Gate 8 (technical report on Zenodo, F1 table public). - 🌟 Final: Paper 1 on bioRxiv (wk 16) and a dataset other scientists cite (L6).

Mentor check. "I know whether FermLit is novel or an extension, and I can defend every field in my schema."

• Week 04: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Read commitment, evidence, review and the current root TODAY/PROGRESS/QUESTIONS files.
• Read this week's chapter, v6 · Week 5 · FermLit begins: the corpus, then the standing sections: Part 0 · how to use the document, Part 3 · the scientific thesis, Part 4 · curriculum, Part 8 · the prompt pack and Part 9 · branding and endorsement. The same sections exist in the v5 master, which remains the governing sequence; v6 reproduces them and adds depth. Retained commercial/instrument details come from v4.
• Inspect the actual canonical repository state, available data, existing figures and required human/external inputs. Never assume a previous week succeeded from its folder name.
• Verify current resource links, versions, dataset rights and any live company/venue information before relying on them. Use source catalog; explicitly record inaccessible resources.

Biology/domain unit

Source unit: B5 · DNA to protein

Material: Biology 2e ch. 14 (DNA), 15 (genes and proteins); Crash Course "DNA, Hot Pockets & the Longest Word Ever"

Produce: Notes; Rosalind problems 1-4 (rosalind.info)

Understanding check: You can read "the strain overexpresses gene X" and know what it means

During preparation, write one worked example connected to the week's actual task, one exercise with a separate answer key and five questions. Peter supplies answers; score explanation quality and flag misconceptions in QUESTIONS. Numeric/scientific conclusions require actual data or explicitly synthetic teaching values.

AI/scientific-method unit

Source unit: M5 · Regularization and trees

Material: ISLP ch. 6.1-6.2 and ch. 8 (trees, boosting)

Produce: LightGBM soft sensor with tuned regularization

Understanding check: You can explain why boosting wins on tabular data

Use the prompt pack: P1 explanation ladder, P2 concept-to-project bridge and P3 quiz. Coding practice belongs within the allocated study/build block. Where the source asks for a favorable scientific result, substitute an honest measured comparison as explained below.

Founder/scientist paper

Select one verified founder/scientific-lead paper relevant to this week's domain. Use P11; save the question, method, numerical result with context, data workflow, three author questions and one connection sentence in founder-paper.md. Keep abstract-only access limitations explicit. On source weeks with no study, prioritize the commercial/submission task and log any skipped digest.

Branding: Draft schema explainer and novelty boundary using actual included-paper counts.

Opportunity action: Use the weekly founder digest to find a potential domain reviewer; begin searching for the independent annotator needed by week 10.

Use career asset contracts. Publish at most the agreed cadence; one figure and one supported number or admitted failure can support multiple drafts. In long-form weeks, prepare a 1,500–2,500-word article from existing evidence within the build/buffer allocation. In release/demo weeks, prepare a 60-second script: problem, input, command/action, result, limitation and proof link.

Verify individuals, jobs and affiliations at execution time. The GridX list and v4 company map are research seeds, not current facts. Do not reveal named company weaknesses or employer/client confidential information. Keep drafted/sent/replied/booked/held statuses separate. The planning request alone does not authorize external messages or publication; honor explicit authorization in the execution session.

Do not equate search hits with fermentation experiments. Scientific Data claims and company gaps are hypotheses. Freeze paper-level development/test partitions before annotation or prompt tuning.

Apply the root scientific evidence contract: provenance; meaningful independent splits; no future-data leakage; baseline comparison; actual denominators/uncertainty; failed cases; human review where required. State whether data are simulated, public experimental, synthetic or partner-provided.

Keep source gates intact, and log scope/time conflicts in review. Missing people, money, access or results must not be replaced with invented evidence. Reduce optional polish first. A specific essential external dependency stays pending while independent preparation continues.

This is an enabling week. Its deliverables feed the next scheduled gate: 8. Complete the acceptance checklist below; do not promote reputation from a draft.

• Monday artifact satisfies: Every citation resolves and the novelty statement follows the evidence.
• Wednesday artifact satisfies: Retrieved, eligible, accessible and included counts are separately reported.
• Friday artifact satisfies: Schema distinguishes paper, experiment, missing, not reported, and extraction failed.
• Study pack is prepared; Peter's actual learning/quiz result is recorded separately.
• Branding and opportunity drafts use supported claims and the correct external-action state.
• Reproduction or document checks are recorded with file/version references.
• This week's special gate, if any, has real evidence or remains explicitly pending.
• Review, root progress/log and the next physical action are updated.

Source-preserving minimum: RELATED.md. If someone did it already, you must know now.

Operational first step if stalled: open related-work.md, write the required inputs and produce the smallest checkable example in ten minutes. If a more urgent missing gate dependency controls the week, use the source minimum above.

If the full week does not fit, use P14: retain one gate-critical deliverable and one directly supporting study exercise; record what is skipped versus moved. Do not mark the original full gate passed merely because the minimum was completed. After a missed week, reforecast from actual evidence and avoid a second unexamined lost week.

In review, state exactly what exists, what was verified, what Peter can now explain, which external events remain pending, where the canonical code/data live, and the next file/function or draft paragraph to touch. Link each fact to evidence. Carry scientific assumptions, split definitions and rights constraints forward explicitly.

Prepare Week 05 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-05-fermlit-corpus-and-schema/specs.md, commitment.md, evidence.md and review.md.
Read prior prerequisite reviews and inspect actual repository/data state.
Use v5 as the governing sequence, the v6 Week 05 chapter
(LABLOOP-Master-Plan-v6.md) as the deeper walkthrough, and v4 only for
retained details.
Produce the full local preparation pack and the exact week-specific files named
in the artifact table. Give me a bounded lesson with exercises/answer key,
daily physical actions, technical runbook or draft, branding drafts and
career/commercial actions. Keep the total to 600 minutes.
Separate prepared artifacts from measured results and my learning completion.
Verify sources and do not invent metrics, citations, papers, people or outcomes.
Do not execute external communications, publication or spending unless the
current session already authorizes the specific action.
Finish by updating evidence/review and TODAY with the next physical action.

v6 reproduces this brief unchanged inside v6 · Week 5 · FermLit begins: the corpus. The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.

Week 5 · FermLit begins: the corpus

• Goal: 500 open-access fermentation papers on disk and a written schema.
• Tue (B5): Biology 2e ch. 14-15; Rosalind 1-4.
• Thu (M5): ISLP ch. 6.1-6.2, 8. LightGBM soft sensor v0.
• Build: Mon: Prompt P8 with Semantic Scholar: does a fermentation literature dataset already exist? Write fermlit/RELATED.md with what you found (this decides "novel" vs "extension"). Done when the file has ≥ 10 verified references. Wed: Europe PMC query ("fed-batch" OR "fermentation" AND ("titer" OR "titre") AND OPEN_ACCESS:y, refine), download full-text XML for 500 papers. Done when 500 XML files and a manifest exist. Fri: schema/fermlit.schema.json v0: organism, strain, product, reactor type, working volume, mode (batch/fed-batch/continuous), medium carbon source, temperature, pH, DO setpoint, feed strategy, duration, final titer (g/L), yield, productivity, scale, plus a provenance sentence per field. Done when three papers annotated by hand against it fit.
• Sun: L-Sun: "500 fermentation papers, one schema: what I want the robot to read". L-Wed.
• Only one thing: RELATED.md. If someone did it already, you must know now.