@pikaa-ai/pikaa 0.3.1 → 0.3.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1870) hide show
  1. package/dist/cli.js +1169 -601
  2. package/dist/index.js +525 -204
  3. package/package.json +5 -3
  4. package/skills/adaptyv/references/api-endpoints.md +0 -690
  5. package/skills/aeon/references/anomaly_detection.md +0 -154
  6. package/skills/aeon/references/classification.md +0 -144
  7. package/skills/aeon/references/clustering.md +0 -123
  8. package/skills/aeon/references/datasets_benchmarking.md +0 -392
  9. package/skills/aeon/references/distances.md +0 -256
  10. package/skills/aeon/references/forecasting.md +0 -109
  11. package/skills/aeon/references/networks.md +0 -289
  12. package/skills/aeon/references/regression.md +0 -118
  13. package/skills/aeon/references/segmentation.md +0 -163
  14. package/skills/aeon/references/similarity_search.md +0 -187
  15. package/skills/aeon/references/transformations.md +0 -246
  16. package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
  17. package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
  18. package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
  19. package/skills/analytical-method-validation/references/framework-selection.md +0 -87
  20. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
  21. package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
  22. package/skills/analytical-method-validation/references/source-ledger.md +0 -125
  23. package/skills/analytical-method-validation/references/statistics.md +0 -209
  24. package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
  25. package/skills/analytical-method-validation/scripts/_common.py +0 -955
  26. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
  27. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
  28. package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
  29. package/skills/analytical-method-validation/scripts/check_response.py +0 -243
  30. package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
  31. package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
  32. package/skills/anndata/references/best_practices.md +0 -532
  33. package/skills/anndata/references/concatenation.md +0 -399
  34. package/skills/anndata/references/data_structure.md +0 -314
  35. package/skills/anndata/references/io_operations.md +0 -466
  36. package/skills/anndata/references/manipulation.md +0 -516
  37. package/skills/arbor/references/arbor-upstream.md +0 -91
  38. package/skills/arbor/references/executor-brief.md +0 -68
  39. package/skills/arbor/references/htr-methodology.md +0 -177
  40. package/skills/arbor/references/report-template.md +0 -39
  41. package/skills/arbor/scripts/tree.py +0 -564
  42. package/skills/arboreto/references/algorithms.md +0 -152
  43. package/skills/arboreto/references/basic_inference.md +0 -181
  44. package/skills/arboreto/references/distributed_computing.md +0 -242
  45. package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
  46. package/skills/astropy/references/coordinates.md +0 -280
  47. package/skills/astropy/references/cosmology.md +0 -309
  48. package/skills/astropy/references/fits.md +0 -398
  49. package/skills/astropy/references/tables.md +0 -495
  50. package/skills/astropy/references/time.md +0 -412
  51. package/skills/astropy/references/units.md +0 -178
  52. package/skills/astropy/references/wcs_and_other_modules.md +0 -377
  53. package/skills/autoskill/config.yaml +0 -53
  54. package/skills/autoskill/references/https-proxy.md +0 -62
  55. package/skills/autoskill/references/screenpipe-config.yaml +0 -61
  56. package/skills/autoskill/scripts/autoskill.py +0 -35
  57. package/skills/autoskill/scripts/backends.py +0 -116
  58. package/skills/autoskill/scripts/cluster.py +0 -54
  59. package/skills/autoskill/scripts/doctor.py +0 -108
  60. package/skills/autoskill/scripts/fetch_window.py +0 -33
  61. package/skills/autoskill/scripts/match_skills.py +0 -46
  62. package/skills/autoskill/scripts/promote.py +0 -58
  63. package/skills/autoskill/scripts/redact.py +0 -40
  64. package/skills/autoskill/scripts/run.py +0 -194
  65. package/skills/autoskill/scripts/synthesize.py +0 -72
  66. package/skills/benchling-integration/references/api_endpoints.md +0 -883
  67. package/skills/benchling-integration/references/authentication.md +0 -390
  68. package/skills/benchling-integration/references/core_capabilities.md +0 -355
  69. package/skills/benchling-integration/references/eventbridge.md +0 -255
  70. package/skills/benchling-integration/references/sdk_reference.md +0 -772
  71. package/skills/bids/references/beps.yml +0 -637
  72. package/skills/bids/references/bids_schema.json +0 -21015
  73. package/skills/bids/references/bids_specification.md +0 -165
  74. package/skills/bids/references/conversion_tools.md +0 -475
  75. package/skills/bids/references/core_workflows.md +0 -552
  76. package/skills/bids/references/metadata_fields.md +0 -365
  77. package/skills/bids/scripts/update_schema.py +0 -89
  78. package/skills/biopython/references/advanced.md +0 -580
  79. package/skills/biopython/references/alignment.md +0 -377
  80. package/skills/biopython/references/blast.md +0 -463
  81. package/skills/biopython/references/databases.md +0 -492
  82. package/skills/biopython/references/phylogenetics.md +0 -566
  83. package/skills/biopython/references/sequence_io.md +0 -289
  84. package/skills/biopython/references/structure.md +0 -564
  85. package/skills/bioservices/references/identifier_mapping.md +0 -685
  86. package/skills/bioservices/references/services_reference.md +0 -638
  87. package/skills/bioservices/references/workflow_patterns.md +0 -813
  88. package/skills/bioservices/scripts/batch_id_converter.py +0 -347
  89. package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
  90. package/skills/bioservices/scripts/pathway_analysis.py +0 -309
  91. package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
  92. package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
  93. package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
  94. package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
  95. package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
  96. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
  97. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
  98. package/skills/cellxgene-census/references/census_schema.md +0 -218
  99. package/skills/cellxgene-census/references/common_patterns.md +0 -368
  100. package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
  101. package/skills/cirq/references/building.md +0 -307
  102. package/skills/cirq/references/experiments.md +0 -572
  103. package/skills/cirq/references/hardware.md +0 -527
  104. package/skills/cirq/references/noise.md +0 -514
  105. package/skills/cirq/references/simulation.md +0 -353
  106. package/skills/cirq/references/transformation.md +0 -416
  107. package/skills/citation-management/assets/bibtex_template.bib +0 -264
  108. package/skills/citation-management/assets/citation_checklist.md +0 -386
  109. package/skills/citation-management/references/best_practices.md +0 -91
  110. package/skills/citation-management/references/bibtex_formatting.md +0 -908
  111. package/skills/citation-management/references/citation_validation.md +0 -835
  112. package/skills/citation-management/references/core_workflow.md +0 -569
  113. package/skills/citation-management/references/example_workflows.md +0 -126
  114. package/skills/citation-management/references/google_scholar_search.md +0 -732
  115. package/skills/citation-management/references/metadata_extraction.md +0 -870
  116. package/skills/citation-management/references/pubmed_search.md +0 -839
  117. package/skills/citation-management/references/script_reference.md +0 -250
  118. package/skills/citation-management/references/search_strategies.md +0 -110
  119. package/skills/citation-management/scripts/_common.py +0 -331
  120. package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  121. package/skills/citation-management/scripts/extract_metadata.py +0 -690
  122. package/skills/citation-management/scripts/format_bibtex.py +0 -356
  123. package/skills/citation-management/scripts/search_google_scholar.py +0 -268
  124. package/skills/citation-management/scripts/search_openalex.py +0 -297
  125. package/skills/citation-management/scripts/search_pubmed.py +0 -419
  126. package/skills/citation-management/scripts/validate_citations.py +0 -688
  127. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
  128. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
  129. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
  130. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
  131. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
  132. package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
  133. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
  134. package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
  135. package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
  136. package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
  137. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
  138. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
  139. package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
  140. package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
  141. package/skills/clinical-decision-support/references/security_validation.md +0 -60
  142. package/skills/clinical-decision-support/references/sources.md +0 -119
  143. package/skills/clinical-decision-support/references/study_reporting.md +0 -134
  144. package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
  145. package/skills/clinical-decision-support/scripts/_common.py +0 -223
  146. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
  147. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
  148. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
  149. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
  150. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
  151. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
  152. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
  153. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
  154. package/skills/clinical-reports/assets/case_report_template.json +0 -43
  155. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
  156. package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
  157. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
  158. package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
  159. package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
  160. package/skills/clinical-reports/assets/lab_report_template.json +0 -36
  161. package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
  162. package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
  163. package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
  164. package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
  165. package/skills/clinical-reports/assets/research_summary_template.json +0 -36
  166. package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
  167. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
  168. package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
  169. package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
  170. package/skills/clinical-reports/references/data_presentation.md +0 -92
  171. package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
  172. package/skills/clinical-reports/references/medical_terminology.md +0 -84
  173. package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
  174. package/skills/clinical-reports/references/professional_review.md +0 -78
  175. package/skills/clinical-reports/references/report_type_routing.md +0 -57
  176. package/skills/clinical-reports/references/safety_reporting.md +0 -109
  177. package/skills/clinical-reports/references/sources.md +0 -75
  178. package/skills/clinical-reports/scripts/_common.py +0 -263
  179. package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
  180. package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
  181. package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
  182. package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
  183. package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
  184. package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
  185. package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
  186. package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
  187. package/skills/cobrapy/references/api_quick_reference.md +0 -665
  188. package/skills/cobrapy/references/workflows.md +0 -600
  189. package/skills/consciousness-council/references/advanced-configurations.md +0 -96
  190. package/skills/dask/references/arrays.md +0 -495
  191. package/skills/dask/references/bags.md +0 -468
  192. package/skills/dask/references/best-practices.md +0 -277
  193. package/skills/dask/references/dataframes.md +0 -370
  194. package/skills/dask/references/futures.md +0 -541
  195. package/skills/dask/references/schedulers.md +0 -517
  196. package/skills/database-lookup/references/addgene.md +0 -38
  197. package/skills/database-lookup/references/alphafold.md +0 -52
  198. package/skills/database-lookup/references/alphavantage.md +0 -261
  199. package/skills/database-lookup/references/bea.md +0 -409
  200. package/skills/database-lookup/references/bindingdb.md +0 -85
  201. package/skills/database-lookup/references/biogrid.md +0 -110
  202. package/skills/database-lookup/references/bls.md +0 -235
  203. package/skills/database-lookup/references/brenda.md +0 -71
  204. package/skills/database-lookup/references/cbioportal.md +0 -206
  205. package/skills/database-lookup/references/census.md +0 -251
  206. package/skills/database-lookup/references/chebi.md +0 -103
  207. package/skills/database-lookup/references/chembl.md +0 -80
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  210. package/skills/database-lookup/references/clinvar.md +0 -91
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  212. package/skills/database-lookup/references/cosmic.md +0 -59
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  218. package/skills/database-lookup/references/drugbank.md +0 -54
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  229. package/skills/database-lookup/references/gene-ontology.md +0 -147
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  236. package/skills/database-lookup/references/human-protein-atlas.md +0 -57
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@@ -1,96 +0,0 @@
1
- # Compendial, CLSI, and ISO Sources (No Standard Text)
2
-
3
- Research basis: **2026-07-27**. This reference identifies documents, their scope, and where to obtain
4
- them. **It does not reproduce their requirements, thresholds, or study designs**, because they are
5
- copyrighted and paywalled.
6
-
7
- ## Copyright boundary
8
-
9
- USP–NF general chapters, CLSI documents, and ISO/IEC standards are copyrighted works sold by their
10
- publishers. Do not ask an agent to retrieve, transcribe, summarise clause-by-clause, reconstruct, or
11
- store their text. Vendor application notes and training decks that quote them are equally
12
- constrained, and a paraphrase that carries the same numbers is still a reproduction of the
13
- substantive content.
14
-
15
- The practical consequence: **when a numeric criterion or a study design lives in one of these
16
- documents, read it from the authorised copy.** An agent asked for "the USP <621> tailing factor
17
- limit" or "the CLSI EP15 number of days" will produce a plausible number. Plausible is not the same
18
- as correct, and the difference is discovered at audit.
19
-
20
- Record publisher, title, designation, edition, amendments, authorised location, access date, and
21
- review date in the laboratory's controlled source register.
22
-
23
- ## USP–NF general chapters
24
-
25
- | Chapter | Title | Scope |
26
- | --- | --- | --- |
27
- | `<1220>` | Analytical Procedure Life Cycle | Three-stage lifecycle: procedure design (Stage 1), performance qualification (Stage 2), ongoing performance verification (Stage 3), organised around an analytical target profile. Official 1 May 2022 (incorporated into USP–NF 2022 Issue 1 on 1 Nov 2021). Integrates the concepts previously spread across `<1224>`, `<1225>`, and `<1226>`. |
28
- | `<1225>` | Validation of Compendial Procedures | Validation of non-compendial procedures, and of compendial procedures used outside their stated scope. Stage 2 activity under `<1220>`. |
29
- | `<1226>` | Verification of Compendial Procedures | Assessment of selected performance characteristics showing a compendial procedure works under actual conditions of use. **Verification is not revalidation** and does not repeat the full validation. |
30
- | `<1224>` | Transfer of Analytical Procedures | Transfer between laboratories. |
31
- | `<1010>` | Analytical Data — Interpretation and Treatment | Statistical treatment of analytical data. |
32
- | `<621>` | Chromatography | System suitability and chromatographic operating parameters, including the extent to which a compendial procedure may be adjusted without triggering revalidation. |
33
- | `<711>` / `<1092>` | Dissolution / The Dissolution Procedure | Dissolution testing and development/validation of the procedure. |
34
-
35
- Obtain from the USP–NF (<https://www.uspnf.com/>). Regional pharmacopoeias — Ph. Eur., JP, ChP —
36
- carry their own general chapters; check which pharmacopoeia the specification cites, because
37
- adjustment allowances and system suitability requirements differ between them.
38
-
39
- **The `<1226>` decision.** Verification applies when using a compendial procedure as written and
40
- within its scope. Two situations push you back to `<1225>` validation: using the procedure outside
41
- its stated scope (a different matrix, a different dosage form, a concentration range it does not
42
- cover), or modifying it beyond the adjustments the relevant chapter permits. Getting this wrong in
43
- either direction is expensive — unnecessary full validation, or an unsupported claim of verification.
44
-
45
- ## CLSI EP series
46
-
47
- Designations and titles below were taken from clsi.org listings and secondary sources on the
48
- research date. **Editions change; confirm the current edition on <https://clsi.org/> before designing
49
- a study.** Marked `[confirm]` where the edition was not read from the publisher directly.
50
-
51
- | Designation | Subject | Note |
52
- | --- | --- | --- |
53
- | EP05 | Evaluation of precision of quantitative measurement procedures | Establishment of precision; the multi-day/multi-run designs. `[confirm edition]` |
54
- | EP06 | Evaluation of linearity of quantitative measurement procedures | 2nd edition reported. `[confirm edition]` |
55
- | EP07 | Interference testing in clinical chemistry | Screening, quantifying and confirming interferents; verifying manufacturer interference claims. 3rd edition reported. `[confirm edition]` |
56
- | EP09 | Measurement procedure comparison and bias estimation using patient samples | The method-comparison document. 3rd edition reported. `[confirm edition]` |
57
- | EP15 | User verification of precision and estimation of bias | The short study a laboratory runs to verify a manufacturer's claims. 3rd edition reported. `[confirm edition]` |
58
- | EP17 | Evaluation of detection capability | Limit of blank, limit of detection, limit of quantitation; verification of manufacturer claims. `[confirm edition]` |
59
- | EP25 | Evaluation of stability of in vitro diagnostic reagents | `[confirm edition]` |
60
- | EP28 | Defining, establishing, and verifying reference intervals | Formerly designated C28. An implementation guide (EP28IG) also exists. `[confirm edition]` |
61
-
62
- **Vocabulary.** CLSI distinguishes *limit of blank*, *limit of detection*, and *limit of quantitation*
63
- as three separate quantities with separate protocols. This is not the same taxonomy as ICH Q2(R2)'s
64
- detection limit and quantitation limit, and the two should not be translated into each other
65
- casually — the underlying definitions and the experiments differ.
66
-
67
- **Verification versus establishment.** For an FDA-cleared or CE-marked assay used as intended, a
68
- laboratory *verifies* the manufacturer's performance claims — a bounded study. For a
69
- laboratory-developed test, or an assay used off-label, the laboratory *establishes* performance,
70
- which is a much larger exercise. Under CLIA the distinction has direct regulatory consequences and
71
- also depends on test complexity. Determine which applies before designing anything.
72
-
73
- ## ISO standards
74
-
75
- | Standard | Relevance |
76
- | --- | --- |
77
- | ISO/IEC 17025:2017 | Clause 7.2 selection, verification and validation of methods; clause 7.6 measurement uncertainty. Validation "to the extent necessary" for the intended application — no characteristic list, no numeric criteria. |
78
- | ISO 15189 | Medical laboratories: quality and competence. The clinical-laboratory counterpart to 17025. |
79
- | ISO 21748 / ISO 5725 series | Using repeatability, reproducibility and trueness estimates in measurement uncertainty; accuracy of measurement methods. |
80
-
81
- Obtain from ISO (<https://www.iso.org/>) or a national member body. A laboratory is **accredited** to
82
- ISO/IEC 17025 by an accreditation body — it is not "17025 certified", and writing "certified" is a
83
- substantive error assessors notice.
84
-
85
- For accreditation readiness, the quality manual, and the surrounding management system, use this
86
- repository's `iso-standards-readiness` skill. This skill stays at the level of the individual
87
- procedure.
88
-
89
- ## Environmental, food, and forensic method systems
90
-
91
- Where a prescribed method system governs — a published EPA method, an AOAC Official Method, a
92
- standard method for water or food analysis — the validation and quality-control requirements are
93
- written into the method or the programme, and they take precedence. Do not substitute a
94
- pharmaceutical framework. Common differences: matrix spike and duplicate requirements per batch,
95
- prescribed calibration-verification frequencies, method detection limit procedures that differ from
96
- both ICH and CLSI, and mandatory participation in proficiency testing schemes.
@@ -1,87 +0,0 @@
1
- # Which Framework Governs
2
-
3
- Research basis: **2026-07-27**. Confirm every date and edition against the official source before
4
- relying on it; see `source-ledger.md`.
5
-
6
- Framework selection is the first decision and the one most often skipped. Getting it wrong
7
- invalidates the protocol regardless of how well the studies are executed, because each framework
8
- requires a different set of characteristics, a different study layout, and a different treatment of
9
- acceptance criteria.
10
-
11
- ## The deciding questions, in order
12
-
13
- **1. Is the measurand a drug concentration in a biological matrix, supporting a nonclinical or
14
- clinical study?**
15
- → **ICH M10.** This covers pharmacokinetics, toxicokinetics, and bioequivalence. M10 supplies
16
- explicit numeric criteria, and they differ between chromatographic assays and ligand binding
17
- assays. Q2(R2) does not govern here.
18
-
19
- **2. Is it a quality attribute of a drug substance or drug product — assay, potency, impurity,
20
- identity, dissolution, content uniformity?**
21
- → **ICH Q2(R2)** for validation, with **ICH Q14** for development, robustness, the analytical
22
- target profile, and lifecycle change management. If the procedure is compendial and being used as
23
- written, see question 3 first.
24
-
25
- **3. Is the procedure a compendial (pharmacopoeial) procedure?**
26
- → **USP <1226> verification** if it is used as written and within its stated scope. Verification
27
- assesses selected characteristics to show the procedure works under actual conditions of use; it is
28
- not revalidation and does not repeat the full study. → **USP <1225> validation** if the procedure
29
- is non-compendial, or compendial but used outside its scope. Both sit inside the **USP <1220>**
30
- three-stage lifecycle. Regional pharmacopoeias (Ph. Eur., JP) have their own general chapters —
31
- check which pharmacopoeia the specification cites.
32
-
33
- **4. Is it a clinical laboratory measurement procedure reporting patient results?**
34
- → **CLSI EP series**, inside a CLIA/CAP or ISO 15189 quality system. The vocabulary differs from
35
- pharmaceutical work: *verification* of a manufacturer's claims for an FDA-cleared assay is a much
36
- smaller exercise than *establishment* of performance for a laboratory-developed test, and the
37
- distinction is regulatory, not stylistic.
38
-
39
- **5. Is the laboratory accredited to ISO/IEC 17025 and the method non-standard, laboratory-developed,
40
- or a modified standard method?**
41
- → **ISO/IEC 17025 clause 7.2.2** requires validation as extensive as necessary to meet the needs of
42
- the intended application, plus measurement uncertainty under clause 7.6. It sets no characteristic
43
- list and no numeric criteria; the laboratory justifies both.
44
-
45
- **6. Is it an environmental, food, or forensic method under a prescribed method system?**
46
- → The method system governs (for example a published EPA method, an AOAC Official Method, or a
47
- regulator's prescribed procedure), usually with its own validation and QC requirements written into
48
- the method itself. Do not substitute a pharmaceutical framework.
49
-
50
- ## More than one can apply
51
-
52
- Common and legitimate. A contract laboratory accredited to ISO/IEC 17025 running a compendial assay
53
- for a pharmaceutical client satisfies <1226> for the procedure and 17025 clause 7.2 for the
54
- accreditation scope, with the client's specification supplying the criteria. Record which framework
55
- each requirement traces to, so a later change can be assessed against the right one.
56
-
57
- ## Do not blend them
58
-
59
- The failure mode is a protocol that mixes Q2(R1)-era characteristic names, an M10 numeric tolerance
60
- imported because it was memorable, and a CLSI study layout. It satisfies none of the three and is
61
- hard to defend because no single source can be cited for any of it. If a requirement is in the
62
- protocol, name the framework and section it comes from.
63
-
64
- ## Where the numbers come from
65
-
66
- | Framework | Numeric acceptance criteria |
67
- | --- | --- |
68
- | ICH Q2(R2) | Almost none. Derive from the specification, the ATP, or development data, and justify. |
69
- | ICH Q14 | None. It supplies the ATP concept and the development/robustness framework. |
70
- | ICH M10 | Explicit, and modality-dependent. Use them as written. |
71
- | USP <1225>/<1226>/<1220> | Consult the authorised text. |
72
- | CLSI EP | Consult the authorised text; many EP documents supply study designs rather than limits. |
73
- | ISO/IEC 17025 | None. The laboratory sets and justifies them. |
74
-
75
- Q2(R2)'s reticence is deliberate: a criterion that is not tied to what the result is used for is
76
- arbitrary. An assay releasing product against a 95.0–105.0% specification needs different precision
77
- than one supporting a 70–130% content-uniformity limit. Deriving the criterion from the decision the
78
- result supports is the substance of the exercise, not paperwork around it.
79
-
80
- ## Related skills in this repository
81
-
82
- - `iso-standards-readiness` — the surrounding quality system (ISO/IEC 17025, ISO 15189
83
- accreditation readiness, quality manual, CAPA). That skill operates at the laboratory level; this
84
- one operates at the level of a single procedure.
85
- - `statistical-analysis`, `statistical-power` — general inference and study sizing.
86
- - `uncertainty-and-units` — unit handling and measurement uncertainty propagation, which ISO/IEC
87
- 17025 clause 7.6 requires alongside validation.
@@ -1,123 +0,0 @@
1
- # ICH M10 — Bioanalytical Criteria, by Modality
2
-
3
- Research basis: **2026-07-27**, read from the ICH Harmonised Guideline *Bioanalytical Method
4
- Validation and Study Sample Analysis M10*, Step 4 dated 24 May 2022. ICH licenses its documents for
5
- reuse with acknowledgement. Confirm the current text and your region's implementation at
6
- <https://database.ich.org/sites/default/files/M10_Guideline_Step4_2022_0524.pdf>.
7
-
8
- M10 harmonised what had been separate FDA and EMA bioanalytical guidance for studies in its scope:
9
- methods quantifying drug and metabolite concentrations in biological matrices supporting nonclinical
10
- and clinical studies, plus the analysis of study samples.
11
-
12
- ## The distinction that matters most
13
-
14
- **Chromatographic assays (section 3) and ligand binding assays (section 4) have different numeric
15
- criteria throughout.** They are not stylistic variants of one set. Applying chromatographic
16
- tolerances to an LBA is the most common error in this area, and importing the LBA total-error
17
- criterion into a chromatographic method is its mirror image.
18
-
19
- | | Chromatographic | Ligand binding assay |
20
- | --- | --- | --- |
21
- | Calibration levels (minimum) | 6, including LLOQ | 6, including LLOQ |
22
- | Calibration standard tolerance | ±15% | ±20% |
23
- | … at LLOQ | ±20% | ±25% |
24
- | … at ULOQ | ±15% | ±25% |
25
- | Calibration standards that must pass | ≥75% | ≥75%, excluding anchor points |
26
- | Accuracy | ±15% | ±20% |
27
- | … at limits | ±20% at LLOQ | ±25% at LLOQ **and** ULOQ |
28
- | Precision (%CV) | ≤15% | ≤20% |
29
- | … at limits | ≤20% at LLOQ | ≤25% at LLOQ **and** ULOQ |
30
- | A&P QC levels | minimum 4 | 5 (LLOQ, low, medium, high, ULOQ) |
31
- | A&P replicates per level per run | ≥5 (within-run) | ≥3 |
32
- | A&P runs | ≥3 runs over ≥2 days | ≥6 runs over ≥2 days |
33
- | **Total error** | **no such criterion** | **≤30%; ≤40% at LLOQ and ULOQ** |
34
- | Routine run QC tolerance | ±15% | ±20% |
35
- | Routine run QC pass rule | ≥2/3 of all QCs **and** ≥50% at each level | same rule, ±20% |
36
- | Dilution integrity | mean within ±15% | mean within ±20% |
37
- | Stability | mean at each QC level within ±15% | mean within ±20% |
38
- | ISR agreement | within ±20% for ≥2/3 of repeats | within ±30% for ≥2/3 of repeats |
39
- | Selectivity sources/lots | ≥6 individual sources | ≥6 individual sources |
40
- | Carry-over in blank | ≤20% of LLOQ analyte response and ≤5% of IS response | per guideline |
41
-
42
- Verify any figure against the guideline before using it in a protocol; regional implementation and
43
- subsequent revisions can change the picture.
44
-
45
- ## Chromatographic QC placement (section 3)
46
-
47
- Accuracy and precision validation QCs at a minimum of **four** concentration levels:
48
-
49
- - the **LLOQ**
50
- - **low QC** — within three times the LLOQ
51
- - **medium QC** — around 30–50% of the calibration curve range
52
- - **high QC** — at least 75% of the ULOQ
53
-
54
- For runs that are not accuracy-and-precision runs, low, medium and high QCs may be analysed in
55
- duplicate; these plus the calibration standards form the basis for accepting or rejecting the run.
56
-
57
- Calibration standards and QCs should be prepared from **separate stock solutions**, to avoid a bias
58
- that is not a property of the analytical performance. If a single stock must serve both, verify the
59
- accuracy and stability of that stock. A single source of blank matrix may be used if it is free of
60
- interference and matrix effects.
61
-
62
- Calibration curves for accuracy and precision assessment should use freshly spiked standards in at
63
- least one run; if other runs use frozen standards, demonstrate their stability.
64
-
65
- ## Reporting obligations that catch people out
66
-
67
- **Report everything.** Validation data and the determination of accuracy and precision must include
68
- *all* results obtained, including individual QCs outside the acceptance criteria — except cases where
69
- errors are obvious and documented. Silently dropping an out-of-criteria QC is a data integrity
70
- problem, not a rounding decision.
71
-
72
- **Within-run accuracy and precision are reported per run.** If the within-run criteria are not met in
73
- every run, calculate an overall estimate of within-run accuracy and precision for each QC level.
74
- Between-run (intermediate) accuracy and precision combine data from all runs.
75
-
76
- **Trend within a run.** It is recommended to demonstrate accuracy and precision over at least one run
77
- sized like a prospective study-sample run, so time-dependent drift is visible.
78
-
79
- ## Incurred sample reanalysis (section 5)
80
-
81
- ISR repeats the analysis of a subset of study samples in separate runs, to verify that measured
82
- concentrations in real samples are reproducible. It is not a substitute for QCs — QCs are spiked,
83
- incurred samples are not, and only incurred samples can reveal metabolite back-conversion, protein
84
- binding effects, or matrix instability.
85
-
86
- - The extent depends on the analyte and the samples and should be justified.
87
- - Objective criteria for choosing the subset should be **predefined**; selecting samples around
88
- Cmax and the elimination phase is recommended.
89
- - **Do not pool samples** — pooling masks anomalous findings.
90
- - ISR samples and QCs are processed and analysed in the same manner as the original analysis.
91
- - Percent difference is `(repeat value - initial value) / mean value x 100` -- assessed
92
- against the **mean of the two**, not against the initial value.
93
- - Repeats are performed within the analyte's stability window, but **not on the same day**
94
- as the original analysis.
95
- - Acceptance: within ±20% for at least 2/3 of repeats (chromatographic), or within ±30% for at least
96
- 2/3 (LBA).
97
-
98
- For nonclinical studies in scope, ISR should in general be performed; the guideline notes incurred
99
- samples need only be included if available, so inclusion was not felt to be mandatory in every case.
100
- Confirm the situations requiring ISR against the guideline text for your study type.
101
-
102
- ## Study sample reanalysis is a separate thing
103
-
104
- ISR is a method-reliability check. *Reanalysis of study samples* for a reportable-value decision is
105
- different, and the reasons for reanalysis, the number of replicates, and the criteria for selecting
106
- the value to report must be **predefined in the protocol, study plan, or SOP before study sample
107
- analysis begins.** Deciding after the fact which of two values to report is the classic finding.
108
-
109
- ## Partial and cross validation
110
-
111
- M10 addresses partial validation (a change to a validated method — matrix, anticoagulant, species,
112
- instrument, or a range change) and cross validation (comparing data from two methods or two
113
- laboratories contributing to the same study). Both are scoped by the change and the risk; consult
114
- the guideline for what each requires. For a cross validation between sites or methods, the
115
- statistics in `compare_methods.py` — equivalence testing against a pre-stated margin, and a
116
- regression that allows error in both measurements — are the appropriate treatment.
117
-
118
- ## Biomarkers and other contexts
119
-
120
- M10's scope centres on drug and metabolite concentration measurement. Biomarker assays, immunogenicity
121
- assays, and diagnostic measurements are addressed differently or fall outside scope; do not assume the
122
- concentration-assay criteria transfer. Where a biomarker assay supports a regulatory decision, the
123
- fit-for-purpose framework and the applicable regional guidance govern the extent of validation.
@@ -1,229 +0,0 @@
1
- # ICH Q2(R2) — Structure and Recommended Data
2
-
3
- Research basis: **2026-07-27**, read from the ICH Harmonised Guideline *Validation of Analytical
4
- Procedures Q2(R2)*, Final Version adopted 1 November 2023, with the error correction dated
5
- 30 November 2023. ICH licenses its documents for reuse with acknowledgement, so requirements are
6
- summarised here directly. Confirm the current text and your region's implementation date at
7
- <https://database.ich.org/sites/default/files/ICH_Q2%28R2%29_Guideline_2023_1130.pdf>.
8
-
9
- ## Document history that matters
10
-
11
- | Version | Date | Note |
12
- | --- | --- | --- |
13
- | Q2A | Oct 1994 | Text |
14
- | Q2B | Nov 1996 | Methodology |
15
- | Q2(R1) | Nov 2005 | Q2B merged into the parent guideline |
16
- | Q2(R2) | 1 Nov 2023 | Complete revision, aligned with the new Q14 |
17
- | Q2(R2) correction | 30 Nov 2023 | Table 5 reportable-range linearity formulae; Tables 6–11 |
18
-
19
- If a protocol cites "ICH Q2(R1)" or lists characteristics in the R1 order, it is working from the
20
- superseded structure. The error correction is easy to miss and applies to the dissolution example
21
- and to Annex 2 Tables 6–11.
22
-
23
- ## The restructure
24
-
25
- Q2(R1) presented a flat list. Q2(R2) groups methodology under section 3 by performance
26
- characteristic:
27
-
28
- ```
29
- 3.1 Specificity/Selectivity
30
- 3.1.1 General considerations (absence of interference, orthogonal comparison,
31
- technology-inherent justification)
32
- 3.2 Range <-- parent characteristic
33
- 3.2.2 Response
34
- 3.2.2.1 Linear response <-- what R1 called "linearity"
35
- 3.2.2.2 Non-linear response
36
- 3.2.2.3 Multivariate calibration
37
- 3.2.3 Validation of lower range limits <-- what R1 called LOD and LOQ
38
- 3.3 Accuracy and Precision
39
- 3.3.1 Accuracy
40
- 3.3.2 Precision (repeatability, intermediate precision, reproducibility)
41
- 3.3.3 Combined approaches for accuracy and precision <-- new
42
- 3.4 Robustness --> largely a development activity, see ICH Q14
43
- ```
44
-
45
- Section 2 carries the general considerations, including two concepts absent from R1: **reportable
46
- range** (2.3) and **considerations for multivariate analytical procedures** (2.5).
47
-
48
- ## Table 1 — which tests for which measured attribute
49
-
50
- Required tests follow the *measured quality attribute*, not the instrument.
51
-
52
- | Characteristic | Identity | Impurity: quantitative | Impurity: limit test | Assay (content/potency) |
53
- | --- | --- | --- | --- | --- |
54
- | Specificity test | yes | yes | yes | yes |
55
- | Response (calibration model) | no | yes | no | yes |
56
- | Lower range limit | no | QL† | DL | no |
57
- | Accuracy test | no | yes | no | yes |
58
- | Repeatability test | no | yes | no | yes |
59
- | Intermediate precision test | no | yes‡ | no | yes‡ |
60
-
61
- † In some complex cases DL may also be evaluated.
62
- ‡ Not required independently where reproducibility has been performed and intermediate precision
63
- can be derived from that dataset.
64
-
65
- Further notes from Table 1: other quantitative measurements follow the impurity scheme when the
66
- range limit is close to DL/QL, and the assay scheme when it is not. Some characteristics may be
67
- substituted by technology-inherent justification for physicochemical properties. Lack of specificity
68
- in one procedure should be compensated by one or more supporting procedures unless justified.
69
-
70
- ## Table 2 — reportable range examples
71
-
72
- The reportable range derives from the specification and must include the upper and lower
73
- specification or reporting limits. Other ranges are acceptable if justified; at low amounts a wider
74
- upper range may be more practical.
75
-
76
- | Use | Low end | High end |
77
- | --- | --- | --- |
78
- | Assay of a product | 80% of declared content, or 80% of the lower specification limit | 120% of declared content, or 120% of the upper specification limit |
79
- | Potency | lowest specification limit −20% | highest specification limit +20% |
80
- | Content uniformity | 70% of declared content | 130% of declared content |
81
- | Dissolution, IR, one point | Q − 45% of the lowest strength specification | per specification |
82
- | Dissolution, IR, multi-point | lower limit as justified, or QL | 130% of declared content of the highest strength |
83
- | Dissolution, modified release | lower limit as justified, or QL | per specification |
84
- | Impurity | reporting threshold | 120% of the specification limit |
85
- | Purity (area %) | 80% of the lower specification limit | upper specification limit, or 100% |
86
-
87
- Where assay and impurity run as a single test with one standard, linearity must be shown both at the
88
- impurity reporting level and up to 120% of the assay specification limit.
89
-
90
- **Reportable range vs working range.** The reportable range is the interval of *reported results*.
91
- A working range is what is presented to the instrument, and may differ because of dilution or other
92
- sample preparation. They can be identical. Mathematical calculation normally links the two.
93
-
94
- ## Recommended data, by characteristic
95
-
96
- **Specificity (3.1).** Demonstrate absence of relevant interference, or compare against an
97
- orthogonal procedure, or justify from the technology. For a stability-indicating claim (2.4),
98
- include samples containing relevant degradation products: spiked with target analytes and known
99
- interferences, stressed physically and chemically, and aged or stress-stored product samples.
100
-
101
- **Response — linear (3.2.2.1).** Evaluate across the range. **A minimum of five concentrations,
102
- appropriately distributed, is recommended.** Report the plot, the correlation coefficient or
103
- coefficient of determination, the y-intercept, the slope, and *an analysis of the deviation of the
104
- actual data points from the regression line* — for a linear response, assess the impact of any
105
- non-random pattern in the residual plot. Data may be transformed (for example logarithmically) if
106
- necessary. Other approaches require justification.
107
-
108
- **Response — non-linear (3.2.2.2).** Some procedures are legitimately non-linear; immunoassays and
109
- cell-based assays commonly give an S-shaped curve, typically modelled with four- or five-parameter
110
- logistic functions. For these, **linearity of the concentration–response relationship is not
111
- required.** Assess the model by non-linear regression, and evaluate whether results are proportional
112
- to the true values across the range.
113
-
114
- **Response — multivariate (3.2.2.3).** Algorithms may be linear or non-linear. Accuracy depends on
115
- the distribution of calibration samples across the range and on the reference procedure's error.
116
- Assess how the residuals change across the calibration range, graphically.
117
-
118
- **Lower range limits (3.2.3).** Four approaches:
119
-
120
- | Approach | DL | QL |
121
- | --- | --- | --- |
122
- | Visual evaluation (3.2.3.1) | lowest reliably detected | lowest reliably quantitated |
123
- | Signal-to-noise (3.2.3.2) | S/N 3:1 generally acceptable | S/N at least 10:1 |
124
- | SD of response and slope (3.2.3.3) | 3.3σ / S | 10σ / S |
125
- | Accuracy and precision at the limit (3.2.3.4) | — | validated directly, not estimated |
126
-
127
- σ may come from the SD of blank responses, the residual SD of the regression line, or the SD of
128
- y-intercepts of regression lines. S is the calibration slope. Signal-to-noise applies only where
129
- there is baseline noise, and the noise region should sit around where the peak would appear.
130
-
131
- Reporting (3.2.3.5): give the limit **and the approach used**. An estimated limit should then be
132
- validated by analysing a suitable number of samples at or near it. **For impurity tests the QL must
133
- be at or below the reporting threshold.** Where the QL is well below the reporting limit — roughly
134
- ten times lower — the confirmatory validation may be omitted with justification.
135
-
136
- **Accuracy (3.3.1).** Establish across the reportable range under regular test conditions, including
137
- the sample matrix and the described preparation steps. Three routes: comparison against a reference
138
- material of known purity, a spiking study into matrix, or comparison against an orthogonal
139
- procedure. Accuracy can be inferred once precision, response within the range, and specificity are
140
- established.
141
-
142
- Recommended data (3.3.1.4): an appropriate number of determinations and levels across the reportable
143
- range — **for example 3 concentrations × 3 replicates of the full procedure.** Report as mean percent
144
- recovery of a known added amount, or as the difference between the mean and the accepted true value,
145
- **together with an appropriate 100(1−α)% confidence interval** or justified alternative interval. The
146
- observed interval should be compatible with the accuracy criterion. For impurities, state whether
147
- the determination is weight/weight or area percent. For quantitative multivariate procedures use
148
- RMSEP, compared against an acceptable RMSEC.
149
-
150
- **Precision (3.3.2).** Use authentic homogeneous samples, or artificially prepared ones if
151
- unavailable.
152
-
153
- - *Repeatability (3.3.2.1)*: **a minimum of 9 determinations covering the reportable range** (for
154
- example 3 concentrations × 3 replicates), **or a minimum of 6 determinations at 100% of the test
155
- concentration.**
156
- - *Intermediate precision (3.3.2.2)*: establish the effects of random events — typically different
157
- days, environmental conditions, analysts, and equipment. **Studying these effects individually is
158
- not necessary**, and design of experiments is encouraged. The extent should be justified from
159
- development understanding and risk assessment (ICH Q14).
160
- - *Reproducibility (3.3.2.3)*: an inter-laboratory trial. **Usually not required for a regulatory
161
- submission**, but consider it for pharmacopoeial standardisation or multi-site procedures.
162
-
163
- Recommended data (3.3.2.4): report the standard deviation, the relative standard deviation, and an
164
- appropriate 100(1−α)% confidence interval.
165
-
166
- **Combined accuracy and precision (3.3.3).** Instead of separate criteria, assess total impact
167
- against a single combined criterion, using a prediction interval, a tolerance interval, or a
168
- confidence interval. Report the combined value, describe the approach, and supply the individual
169
- results as supplemental information where they help justify suitability.
170
-
171
- **Robustness (3.4).** Deliberate variation of procedure parameters, plus stability of sample
172
- preparations and reagents over the duration of the procedure. Considered during development; may be
173
- submitted as development data case-by-case or made available on request. See ICH Q14 section 5.
174
-
175
- ## Lifecycle, transfer, and prior knowledge
176
-
177
- Section 2.1 permits suitable development data (ICH Q14) to form part of the validation data, and
178
- allows abbreviated validation testing for an established platform procedure used for a new purpose,
179
- with scientific justification. A validation protocol must exist before the study, stating the
180
- intended purpose, the characteristics to be validated, and the associated criteria; where prior
181
- knowledge is used, justify it. Results are summarised in a validation report.
182
-
183
- The experimental design should reflect the number of replicates used in routine analysis to generate
184
- a reportable result, unless a different number is justified.
185
-
186
- Section 2.2 covers change: partial or full revalidation may be needed, decided on science and risk,
187
- and scoped to the characteristics the change affects. **Transfer** to another laboratory calls for
188
- partial or full revalidation and/or comparative analysis of representative samples; not performing
189
- transfer experiments requires justification. **Co-validation** across multiple sites can demonstrate
190
- the criteria are met and can simultaneously satisfy transfer at the participating sites.
191
-
192
- ## Annex 2 — illustrative technique examples
193
-
194
- Non-mandatory worked examples, useful as a starting point for the robustness parameter list:
195
-
196
- | Table | Technique |
197
- | --- | --- |
198
- | 3 | Quantitative separation techniques (HPLC, GC, CE) for impurities or assay, and relative-area quantitation |
199
- | 4 | Elemental impurities by ICP-OES or ICP-MS |
200
- | 5 | Dissolution with HPLC as product performance test (corrected 30 Nov 2023) |
201
- | 6 | Quantitative ¹H-NMR for assay of a drug substance |
202
- | 7 | Biological assays |
203
- | 8 | Quantitative PCR |
204
- | 9 | Particle size measurement |
205
- | 10 | NIR analytical procedure |
206
- | 11 | Quantitative LC/MS |
207
-
208
- From Table 3, a detail worth carrying forward: **relative response factors.** Where the analyte
209
- responds differently from the reference material, calculate the RRF from the appropriate ratio of
210
- responses under final procedure conditions and document it. **If the RRF falls outside 0.8–1.2,
211
- apply a correction factor.** Where an impurity is overestimated, omitting the correction may be
212
- acceptable.
213
-
214
- ## Multivariate procedures (2.5)
215
-
216
- Results come from a model relating many input variables to the property of interest. Validate in two
217
- phases:
218
-
219
- 1. **Model development** — calibration plus internal testing. Test data may be a separate set or
220
- part of the calibration set used rotationally, and are used to estimate performance and tune
221
- parameters such as the number of PLS latent variables. See ICH Q14.
222
- 2. **Model validation** — an independent validation set. For identification libraries, analyse
223
- challenge samples *not* represented in the library to demonstrate discriminative ability.
224
-
225
- Samples need reference values or categories, normally from a validated or pharmacopoeial reference
226
- procedure whose performance **equals or exceeds** the expected performance of the multivariate
227
- procedure. Reference measurement and multivariate data collection should be on the same samples
228
- within a period short enough to assure sample and measurement stability. Describe any correlation or
229
- unit conversion, and any assumptions.