[Upstream sync] K-Dense-AI/scientific-agent-skills (github) — 45 added, 56 modified #33

Merged
promptadmin merged 101 commits from upstream-sync/scientific-agent-skills-20260808-991bd9-sesb into main 2026-08-09 18:31:46 +00:00
Showing only changes of commit 60013b3f85 - Show all commits
@@ -0,0 +1,138 @@
---
title: "Official Source Ledger"
task: ""
lineage_type: import
upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/991bd993/skills/analytical-method-validation/references/source-ledger.md
upstream_sha: 991bd993
imported_at: 2026-08-08
prompt_class: unknown
upstream_changes: accepted
author: upstream
validated: false
---
# Official Source Ledger
**Research date: 2026-07-27.** Every framework claim in this skill traces to an entry below.
Re-check each source before operational use — guidelines are revised, editions change, and regional
implementation dates differ from adoption dates.
This ledger is a version baseline. It is not legal advice, an applicability determination, or a
substitute for a controlled copy held under the laboratory's document control.
## Documents read directly
These were downloaded and read as full text on the research date, so the requirements encoded in
`scripts/_catalog.py` and summarised in `references/ich-q2r2.md` and
`references/ich-m10-bioanalytical.md` come from the primary source rather than from secondary
summaries.
### ICH Q2(R2) Validation of Analytical Procedures
- Source read: <https://database.ich.org/sites/default/files/ICH_Q2%28R2%29_Guideline_2023_1130.pdf>
- Verified metadata: Final Version, adopted by the ICH Assembly Regulatory Members under Step 4 on
**1 November 2023**. Step 2 endorsement 24 March 2022. Supersedes Q2(R1) (November 2005).
- Verified detail: an **error correction dated 30 November 2023** covers Table 5 (dissolution with
HPLC, reportable range linearity formulae, page 25) and Tables 611 (pages 2632).
- Content taken: section structure; Table 1 (tests by measured attribute); Table 2 (reportable range
examples); recommended data for specificity, response, lower range limits, accuracy, precision,
and robustness; sections 2.12.5; Annex 1 and Annex 2 table inventory; the relative response factor
0.81.2 rule from Annex 2 Table 3.
- Licence: ICH permits use, reproduction, adaptation and distribution under a public licence provided
ICH's copyright is acknowledged. Acknowledged here and in `scripts/_catalog.py`.
- Limitation: **adoption is not implementation.** Confirm the date from which your regional regulator
expects Q2(R2) with that regulator.
### ICH M10 Bioanalytical Method Validation and Study Sample Analysis
- Source read: <https://database.ich.org/sites/default/files/M10_Guideline_Step4_2022_0524.pdf>
- Verified metadata: Step 4, dated **24 May 2022**.
- Content taken: chromatographic criteria (section 3) — calibration levels and tolerances, QC
placement at four levels with the low/medium/high definitions, within-run and between-run accuracy
and precision design and criteria, routine-run QC pass rules, carry-over, selectivity source count,
dilution integrity, stability; ligand binding assay criteria (section 4) — calibration tolerances
including anchor point exclusion, five QC levels, run and replicate structure, accuracy and
precision criteria at LLOQ and ULOQ, and the total error criterion; incurred sample reanalysis
(section 5) including the percent-difference basis and the pass fractions.
- Verified distinction: the **total error criterion (≤30%, ≤40% at LLOQ and ULOQ) appears for ligand
binding assays**. No equivalent criterion was found for chromatographic assays.
- Licence: as for Q2(R2).
- Limitation: regional implementation dates differ. Confirm with the regional regulator.
### ICH Q14 Analytical Procedure Development
- Source read: <https://database.ich.org/sites/default/files/ICH_Q14_Guideline_2023_1116.pdf>
- Content taken: section structure; the minimal versus enhanced approaches (section 2.1); the
analytical target profile (section 3) and that its formal documentation and submission is
**optional**; robustness and parameter ranges (section 5); established conditions (section 6.1);
lifecycle management and post-approval change (section 7); multivariate procedures (section 8).
- Adopted alongside Q2(R2) by the ICH Assembly in the same session.
- Licence: as for Q2(R2).
## Documents identified but not read (paywalled)
Designation, title, and scope only. **No requirement, threshold, or study design from any of these is
reproduced anywhere in this skill.** Where a numeric criterion is needed, read it from an authorised
copy.
### USPNF general chapters
- Official pages: `<1220>` <https://doi.usp.org/USPNF/USPNF_M10975_02_01.html>;
`<1225>` <https://doi.usp.org/USPNF/USPNF_M99945_40101_01.html>;
`<1226>` <https://doi.usp.org/USPNF/USPNF_M870_03_01.html>
- Verified metadata for `<1220>`: incorporated into USPNF 2022 Issue 1 on **1 November 2021**,
**official 1 May 2022**. It brings the concepts of `<1224>`, `<1225>` and `<1226>` into a single
three-stage lifecycle. `<1225>` covers validation, particularly Stage 2 activities under `<1220>`;
`<1226>` covers verification of compendial procedures.
- Provenance limitation: this metadata came from **secondary sources** (publisher notices and trade
press) rather than from the USPNF text, which is behind subscription. Marked
**[confirm in USPNF]**. Confirm the current official text, revision, and any subsequent change.
- Chapters referenced by designation only, not read: `<1224>`, `<1010>`, `<621>`, `<711>`, `<1092>`.
### CLSI EP series
- Publisher: <https://clsi.org/standards/products/method-evaluation/>
- Designations and subjects recorded in `references/compendial-and-clsi.md`: EP05, EP06, EP07, EP09,
EP15, EP17, EP25, EP28 (formerly C28), plus the EP17IG and EP28IG implementation guides.
- Provenance limitation: designations, titles and edition numbers were taken from **clsi.org product
listings and secondary sources** on the research date, not read from the documents. Every edition
number carries **[confirm edition]** in the reference file. Editions change; verify on clsi.org
before designing a study.
### ISO standards
- ISO/IEC 17025:2017 — <https://www.iso.org/standard/66912.html>. Edition 3; supersedes the 2005
edition. Relevant clauses: 7.2 (selection, verification and validation of methods), 7.6
(measurement uncertainty). Not read; identified by catalogue metadata.
- ISO 15189, ISO 21748, ISO 5725 series — referenced by designation and scope only.
- Provenance limitation: ISO catalogue pages have historically refused automated access. Confirm
edition and status on iso.org or with a national member body. **[confirm on iso.org]**
- See this repository's `iso-standards-readiness` skill and its own source ledger for the
accreditation-level treatment of these standards.
## Statistical methods
The statistical procedures in `references/statistics.md` and `scripts/_common.py` are standard
published methods, not requirements of any framework:
- Incomplete beta and gamma function implementations follow the standard continued-fraction and series
algorithms; the t, chi-square and F distributions are derived from them.
- Lack-of-fit F test against pure error: standard regression ANOVA.
- WaldWolfowitz runs test: standard non-parametric test of randomness in a sequence of signs.
- One-way random-effects variance components with the standard unbalanced expected-mean-square
coefficient; Satterthwaite approximation for effective degrees of freedom of the total.
- Deming regression with jackknife standard errors; PassingBablok with the rank-based slope interval.
- BlandAltman bias and limits of agreement.
- Two one-sided tests (TOST) for equivalence.
Implementations are verified against published quantiles and hand-checkable cases in
`tests/analytical-method-validation/test_scripts.py`. Where a framework prescribes a specific
statistical treatment, the framework governs — these are the general-purpose tools.
## What is deliberately absent
- No numeric acceptance criteria are supplied for ICH Q2(R2) work. The guideline does not set them and
neither does this skill; they come from the specification, the analytical target profile, or
development data.
- No text, table, threshold, or study design from any USP, CLSI, or ISO document.
- No claim that a procedure is validated, a run acceptable, or an investigation closed.