@pikaa-ai/pikaa 0.3.0 → 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 +1170 -602
  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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@@ -1,172 +0,0 @@
1
- # ISO 14971 Process Framework (No Standard Text)
2
-
3
- Research basis: **2026-07-26**, building on the 2026-07-23 device-lane baseline. This
4
- reference summarizes a preparation process and evidence architecture for medical device
5
- risk management. It does not reproduce requirements and is not a substitute for the
6
- standard.
7
-
8
- ## Copyright and authorized access
9
-
10
- ISO publications are copyrighted. Obtain ISO 14971 and ISO/TR 24971 from
11
- [ISO](https://www.iso.org/standard/72704.html), an ISO national member, or another
12
- authorized source; see [ISO copyright](https://www.iso.org/copyright.html). Do not ask
13
- an agent to retrieve, transcribe, summarize clause-by-clause, or store proprietary
14
- text.
15
-
16
- ## Current edition, the guidance companion, and the European amendment
17
-
18
- - [ISO 14971:2019](https://www.iso.org/standard/72704.html) is Edition 3, published
19
- December 2019, reviewed and confirmed in 2025.
20
- - [ISO/TR 24971:2020](https://www.iso.org/standard/74437.html) is Edition 2 and is the
21
- guidance companion, following the same clause structure. It is a **Technical
22
- Report**: informative, not normative. Conformity is claimed to ISO 14971, never to
23
- ISO/TR 24971, and a TR cannot relax or reinterpret a normative requirement. Record
24
- which guidance the organization adopted and why.
25
- - **EN ISO 14971:2019/A11:2021** is a European amendment to the EN adoption, cited for
26
- MDR and, through the corresponding decision, IVDR support. It does not change the
27
- international normative part. Track it only where the European source basis applies.
28
-
29
- ## No certification lane exists for this standard
30
-
31
- There is no ISO 14971 certificate. A body cannot certify a risk-management system to
32
- ISO 14971 the way it certifies a QMS to ISO 13485. Risk management is instead assessed
33
- *inside* other lanes:
34
-
35
- - an ISO 13485 certification audit examines the risk-management process as part of the
36
- QMS;
37
- - an FDA inspection examines risk-based decisions against applicable FDA requirements;
38
- - an MDSAP audit treats risk management as a foundation across its process areas; and
39
- - EU conformity assessment examines the risk-management file as part of technical
40
- documentation against the applicable general safety and performance requirements.
41
-
42
- Any claim of "ISO 14971 certification" is a category error. Report risk-management
43
- readiness as evidence supporting a named lane, never as its own assurance result.
44
-
45
- ## Hard boundary
46
-
47
- This skill and its files cannot:
48
-
49
- - certify, approve, or validate a risk-management file or process;
50
- - determine device classification, intended use, reportability, conformity route,
51
- market access, or product authorization;
52
- - decide whether a risk is acceptable, whether benefit outweighs residual risk, or
53
- whether a risk-control measure is adequate or safe;
54
- - set or approve risk-acceptability criteria, severity or probability scales, or a
55
- risk matrix;
56
- - replace top management, the risk-management owner, qualified clinical and engineering
57
- reviewers, RA/QA, a notified body, or a regulator; or
58
- - infer that a hazard set is complete, or that residual risk is acceptable, from a
59
- template, a matrix, a document count, or a script result.
60
-
61
- Use outputs as a list of evidence questions for accountable human review. **Completeness
62
- of hazard identification cannot be established by any check in this skill** — a
63
- zero-finding structural result says the declared links are present, not that the
64
- analysis found everything.
65
-
66
- ## Process and evidence domains
67
-
68
- The `iso-14971` profile carries these domain labels for manifests and gap reports.
69
- They are workflow topics, not clause references:
70
-
71
- `risk-management-plan`, `risk-management-file`, `competence-and-authority`,
72
- `intended-use-and-characteristics`, `hazard-identification`,
73
- `risk-estimation-and-evaluation`, `risk-control-option-analysis`,
74
- `risk-control-implementation-and-verification`, `risk-control-side-effects-review`,
75
- `residual-risk-evaluation`, `benefit-risk-analysis`,
76
- `overall-residual-risk-evaluation`, `risk-management-review-and-report`,
77
- `production-and-postproduction-information`, `change-control`.
78
-
79
- Each domain needs an owner, status, evidence IDs, source/version reference, recorded
80
- approval, and links to open gaps.
81
-
82
- ## The chain that has to hold together
83
-
84
- Risk-management evidence is judged as a connected chain, not as a set of documents. For
85
- each analysed item, the following must be traceable in both directions:
86
-
87
- intended use and reasonably foreseeable misuse → characteristics related to safety →
88
- hazard → foreseeable sequence of events → hazardous situation → harm with severity →
89
- probability basis → risk evaluation against declared criteria → risk-control option
90
- analysis and decision → implemented control → verification that the control was
91
- implemented → verification of its effectiveness → review for new or increased risks
92
- introduced by the control → residual risk evaluation → benefit-risk analysis where
93
- residual risk is not acceptable → contribution to overall residual risk → disclosure of
94
- residual risk → production and post-production information feeding back.
95
-
96
- Break any one link and the file stops being evidence. The two links most often missing
97
- are **verification of control effectiveness** (distinct from verifying the control
98
- exists) and **review of risks introduced by the control itself**.
99
-
100
- Build the traceability register with:
101
-
102
- ```bash
103
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_traceability.py \
104
- /path/to/traceability-matrix.json
105
- ```
106
-
107
- That check links intended use, hazard or signal, risk evaluation, risk control, design
108
- input and output, verification, validation, production control, and post-market source.
109
- It verifies declared linkage, not analytical adequacy.
110
-
111
- ## Where risk management meets the QMS
112
-
113
- ISO 14971 work is not separable from the device QMS. Keep these joins explicit and
114
- evidenced:
115
-
116
- - **Design and development** — risk controls that are design outputs must appear as
117
- design inputs with verification, not only as risk-file rows.
118
- - **Production** — controls realized as process parameters, in-process checks, or
119
- acceptance criteria need production evidence, and process validation where the
120
- control cannot be fully verified on the finished device.
121
- - **Purchasing** — controls that depend on a supplier's process or component need
122
- supplier controls and change notification. See
123
- `scripts/check_supplier_controls.py`.
124
- - **Post-market** — complaints, service records, vigilance signals, and production
125
- nonconformities must actually re-enter risk estimation, with evidence that the file
126
- was reassessed and that changed estimates were acted on.
127
- - **CAPA** — where a risk estimate changes, the resulting action needs effectiveness
128
- evidence before closure. See `scripts/check_capa.py`.
129
- - **Change control** — any change to intended use, design, process, supplier, or
130
- materials triggers a documented risk reassessment.
131
-
132
- The production and post-production feedback loop is the single most common structural
133
- gap: files that were complete at design transfer and never updated by field
134
- experience.
135
-
136
- ## Risk-acceptability criteria and the matrix problem
137
-
138
- Acceptability criteria belong in the risk-management plan, are set by authorized humans
139
- with a documented rationale, and must be applied consistently. Recurring failure modes
140
- to look for, none of which this skill can adjudicate:
141
-
142
- - criteria written after the analysis so that every risk lands acceptable;
143
- - probability values asserted with no stated basis and no data;
144
- - a matrix whose cells were adjusted per project to move results across the boundary;
145
- - risk reduction claimed from labelling or an instruction alone, where a design or
146
- protective measure was available;
147
- - residual risk described as acceptable with no benefit-risk analysis where the
148
- declared criteria were not met;
149
- - overall residual risk never evaluated as a whole — only item by item; and
150
- - no disclosure of residual risk to users where the analysis assumed it.
151
-
152
- Flag these as blockers for authorized review. Do not resolve them.
153
-
154
- ## Shared checks that apply here
155
-
156
- - `scripts/validate_scope_intake.py --standard iso-14971` — declared scope, product
157
- families, intended use references, and applicability owners.
158
- - `scripts/check_traceability.py` — the risk/design/production/post-market chain.
159
- - `scripts/check_capa.py` — corrective action with effectiveness evidence.
160
- - `scripts/check_supplier_controls.py` — controls that depend on external providers.
161
- - `scripts/validate_evidence_manifest.py` and `scripts/gap_analyzer.py` with
162
- `--standard iso-14971`.
163
-
164
- ## Sources
165
-
166
- - [ISO 14971:2019](https://www.iso.org/standard/72704.html) — catalogue entry
167
- - [ISO/TR 24971:2020](https://www.iso.org/standard/74437.html) — guidance companion
168
- - [Decision (EU) 2022/757](https://eur-lex.europa.eu/eli/dec_impl/2022/757/oj/eng) —
169
- EN ISO 14971:2019/A11:2021 citation basis
170
- - `references/iso-13485.md` — the QMS lane this evidence usually supports
171
- - `references/source-ledger.md` — dated baseline and provenance limitations
172
- - `references/assurance-lanes.md` — why this standard has no certification lane
@@ -1,219 +0,0 @@
1
- # ISO 15189 Process Framework (No Standard Text)
2
-
3
- Research basis: **2026-07-26**. This reference summarizes a preparation process and
4
- evidence architecture for medical laboratory quality and competence work. It does not
5
- reproduce requirements and is not a substitute for the standard.
6
-
7
- ## Copyright and authorized access
8
-
9
- ISO publications are copyrighted. Obtain ISO 15189 from
10
- [ISO](https://www.iso.org/standard/76677.html), an ISO national member, or another
11
- authorized source; see [ISO copyright](https://www.iso.org/copyright.html). Do not ask
12
- an agent to retrieve, transcribe, summarize clause-by-clause, or store proprietary
13
- text. Accreditation-body and CAP checklists that quote requirements are separately
14
- licensed material — do not paste them into shared repositories or prompts.
15
-
16
- ## Current edition and the closed transition
17
-
18
- - [ISO 15189:2022](https://www.iso.org/standard/76677.html) is Edition 4, published
19
- December 2022, cancelling and replacing ISO 15189:2012. Confirm on the ISO catalogue
20
- page, which refused automated access during this research.
21
- - The 2022 edition aligns structurally with ISO/IEC 17025:2017 and **incorporates
22
- point-of-care testing requirements previously held in ISO 22870**. Do not cite
23
- ISO 22870 as a separate current POCT basis without confirming its status.
24
- - The ILAC-agreed transition for accredited medical laboratories ran to **December
25
- 2025**. A 2012-based quality system is out of date, not "in transition" — do not
26
- build a gap baseline that assumes a future deadline.
27
- - Record publisher, title, edition, amendments, authorized location, access date,
28
- source owner, currency-review date, impact decision, and approval in the controlled
29
- source ledger.
30
-
31
- ## Keep four lanes separate
32
-
33
- ### 1. ISO 15189 accreditation
34
-
35
- An accreditation body grants accreditation for a defined scope of examinations, per
36
- laboratory and per location, under ISO/IEC 17011. A medical laboratory is
37
- **accredited**, not "ISO 15189 certified." Since 2026-01-01 the recognition arrangement
38
- sits with Global Accreditation Cooperation Incorporated; verify current claim and logo
39
- wording with the accreditation body.
40
-
41
- ### 2. United States CLIA certification
42
-
43
- CLIA certification by CMS is **mandatory** before a US laboratory may accept human
44
- specimens for testing. It is federal law, not a voluntary quality scheme.
45
-
46
- **ISO 15189 accreditation does not satisfy CLIA and cannot replace a CLIA-based
47
- accreditation.** Deemed status flows only from a CMS-approved accreditation
48
- organization's program. CMS approves a limited set of accreditation organizations whose
49
- standards must meet or exceed CLIA requirements, with reapproval every six years or
50
- more often; read the
51
- [current AO list](https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/Downloads/AOList.pdf)
52
- rather than relying on a remembered count. The CAP 15189 program is layered on top of
53
- CAP Laboratory Accreditation Program accreditation rather than offered as a standalone
54
- substitute — confirm current prerequisites with CAP.
55
-
56
- Never let an ISO 15189 readiness output be read as CLIA compliance, deemed status,
57
- licensure, or an inspection result.
58
-
59
- ### 3. Other national licensure and inspection regimes
60
-
61
- State licensure, national health-authority requirements, and payer conditions of
62
- participation are separate again, with their own inspection processes and their own
63
- records. Non-US jurisdictions may make ISO 15189 accreditation mandatory, voluntary, or
64
- irrelevant. This is an applicability decision for authorized humans.
65
-
66
- ### 4. IVD device regulation
67
-
68
- The performance of an in vitro diagnostic device, and any laboratory-developed test
69
- regime that applies to it, is regulated separately from laboratory accreditation. EU
70
- IVDR conformity assessment, notified-body involvement, and performance-study
71
- requirements are not laboratory accreditation questions. See `references/iso-13485.md`
72
- and the EU entries in `references/source-ledger.md`.
73
-
74
- ## Hard boundary
75
-
76
- This skill and its files cannot:
77
-
78
- - accredit a laboratory, issue or validate an accreditation certificate or schedule,
79
- or predict an assessment or inspection outcome;
80
- - establish CLIA certification, deemed status, licensure, or personnel qualification;
81
- - decide which scheme, jurisdiction requirement, or payer condition applies;
82
- - replace the laboratory director, quality manager, authorized signatory,
83
- accreditation body, assessor, EQA provider, or competent authority;
84
- - verify or validate an examination procedure, set biological reference intervals,
85
- establish traceability of assigned values, or judge clinical suitability; or
86
- - infer competence or patient safety from a document title, keyword, template,
87
- checklist, or script result.
88
-
89
- Use outputs as a list of evidence questions for accountable human review.
90
-
91
- ## Scope of accreditation is per examination
92
-
93
- Each scope item is defined by discipline, the examination or measurand reported, the
94
- controlled procedure and its issue, and the primary sample type with its acceptance
95
- requirements. Point-of-care testing performed under the laboratory's responsibility
96
- belongs in the scope discussion explicitly, including devices operated by clinical
97
- staff outside the laboratory.
98
-
99
- ```bash
100
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_scope_intake.py \
101
- /path/to/medical-laboratory-scope-intake.json --standard iso-15189
102
- ```
103
-
104
- Copy `assets/templates/medical-laboratory-scope-intake-template.json` outside the skill
105
- first. The distributed template fails closed by design.
106
-
107
- ## Process and evidence domains
108
-
109
- The `iso-15189` profile carries these domain labels for manifests and gap reports.
110
- They are workflow topics, not clause references:
111
-
112
- `scope-and-impartiality`, `organizational-structure-and-governance`,
113
- `personnel-competence`, `facilities-and-safety`, `equipment-and-calibration`,
114
- `metrological-traceability`, `reagents-and-consumables`,
115
- `externally-provided-products-and-services`, `pre-examination-processes`,
116
- `examination-methods-verification-and-validation`, `measurement-uncertainty`,
117
- `validity-of-results-and-external-quality-assessment`, `point-of-care-testing`,
118
- `post-examination-and-reporting`, `laboratory-information-management`, `complaints`,
119
- `nonconformity-and-corrective-action`, `risk-management-and-improvement`,
120
- `internal-audit`, `management-review`, `continuity-and-emergency-preparedness`.
121
-
122
- Each domain needs an owner, status, evidence IDs, source/version reference, recorded
123
- approval, and links to open gaps. Sample **records**, not only procedures.
124
-
125
- ## Where medical laboratory evidence differs from ISO/IEC 17025
126
-
127
- ### Pre-examination processes carry disproportionate risk
128
-
129
- Most avoidable patient harm originates before the analyser: request content and
130
- patient identification, collection and identification of the primary sample, transport
131
- and stability conditions, acceptance and rejection criteria, and handling of
132
- compromised samples. Sample: rejection records, identification-error events, transport
133
- excursions, and the resulting investigations — not only the collection manual.
134
-
135
- ### Post-examination and reporting is clinical communication
136
-
137
- Assemble evidence for result review and authorization, reference intervals and
138
- clinical decision limits with their basis, interpretive comments and who is authorized
139
- to make them, report content and amendment or retraction handling, and — the item most
140
- often thin — **critical-result notification with documented read-back and
141
- timeliness**. Turnaround-time monitoring belongs here too.
142
-
143
- ### Point-of-care testing is inside the scope
144
-
145
- POCT requirements now sit within ISO 15189. Record governance of devices outside the
146
- laboratory, operator training and authorization, connectivity and result capture into
147
- the patient record, quality-control regimes, and reconciliation with central
148
- laboratory methods.
149
-
150
- ### Verification is the normal case, validation the exception
151
-
152
- Most medical laboratories verify commercial IVD examinations for their own setting
153
- rather than validating a new method. Record which performance characteristics were
154
- verified against the manufacturer's claims, the acceptance criteria, the data, and the
155
- authorized approval to report patient results. Laboratory-developed and modified
156
- procedures need the fuller validation evidence and the applicable regulatory analysis.
157
-
158
- ### External quality assessment, not just proficiency testing
159
-
160
- Record EQA enrolment per scope item, results, evaluation against criteria, and
161
- investigation of unsatisfactory performance. Where no EQA scheme exists for an
162
- examination, record the alternative comparison approach and its authorization. An
163
- unacceptable EQA outcome with no documented investigation is a blocker.
164
-
165
- ### Metrological traceability of assigned values
166
-
167
- For measurands where higher-order reference materials and reference measurement
168
- procedures exist, record the traceability of assigned values and the resulting
169
- commutability and comparability limitations. Where no reference system exists, record
170
- that fact and what the laboratory does about result comparability.
171
-
172
- ### Risk and continuity are explicit
173
-
174
- The 2022 edition treats risk to patients as a running requirement rather than an annex.
175
- Record identified risks, controls, residual acceptance with authority, and improvement
176
- actions. Continuity and emergency preparedness — instrument failure, LIS outage,
177
- reagent supply interruption, facility loss — needs tested arrangements, not a plan
178
- nobody has exercised.
179
-
180
- ## Shared checks that apply here
181
-
182
- - `scripts/audit_document_records.py` — controlled documents, records, retention basis,
183
- and external-source currency. Standard-agnostic.
184
- - `scripts/check_capa.py` — nonconformity and corrective action with effectiveness
185
- evidence before closure.
186
- - `scripts/check_supplier_controls.py` — reagents, consumables, calibration providers,
187
- and referral laboratories, including the referral laboratory's own accreditation or
188
- licensure status.
189
- - `scripts/validate_evidence_manifest.py` and `scripts/gap_analyzer.py` with
190
- `--standard iso-15189`.
191
-
192
- `scripts/check_traceability.py` and `scripts/check_qmsr_transition.py` are
193
- device-lifecycle checks and do not apply here.
194
-
195
- ## Common preparation failures
196
-
197
- - Presenting ISO 15189 readiness as CLIA compliance or deemed status.
198
- - Saying "certified" when the laboratory is accredited.
199
- - Citing ISO 22870 as the current separate POCT basis, or ISO 15189:2012 as current.
200
- - POCT devices operating outside the laboratory with no governance, training, or QC
201
- evidence in the accreditation scope discussion.
202
- - Critical-result notification procedures with no notification records or timeliness
203
- evidence.
204
- - Reference intervals adopted from a package insert with no documented basis for the
205
- served population.
206
- - EQA scores filed without investigation of unsatisfactory results.
207
- - Continuity plans that have never been exercised.
208
-
209
- ## Sources
210
-
211
- - [ISO 15189:2022](https://www.iso.org/standard/76677.html) — catalogue entry
212
- - [ILAC: ISO 15189:2022 published](https://ilac.org/latest_ilac_news/iso-151892022-for-medical-labs-published/)
213
- - [CMS CLIA program](https://www.cms.gov/medicare/quality/clinical-laboratory-improvement-amendments)
214
- - [CLIA accreditation and exemptions](https://www.cms.gov/medicare/quality/clinical-laboratory-improvement-amendments/accreditation-exemptions)
215
- - [CMS approved accreditation organizations](https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/Downloads/AOList.pdf)
216
- - [CAP 15189 program](https://www.cap.org/laboratory-improvement/accreditation/cap-15189-accreditation-program)
217
- - `references/source-ledger.md` — dated baseline and provenance limitations
218
- - `references/assurance-lanes.md` — how accreditation, certification, and regulatory
219
- inspection differ
@@ -1,208 +0,0 @@
1
- # ISO/IEC 17025 Process Framework (No Standard Text)
2
-
3
- Research basis: **2026-07-26**. This reference summarizes a preparation process and
4
- evidence architecture for testing and calibration laboratory competence work. It does
5
- not reproduce requirements and is not a substitute for the standard.
6
-
7
- ## Copyright and authorized access
8
-
9
- ISO and IEC publications are copyrighted. Obtain ISO/IEC 17025 from
10
- [ISO](https://www.iso.org/standard/66912.html), IEC, an ISO national member, or another
11
- authorized source; see [ISO copyright](https://www.iso.org/copyright.html). Do not ask
12
- an agent to retrieve, transcribe, summarize clause-by-clause, or store proprietary
13
- text. Accreditation-body checklists that quote the standard are equally copyrighted and
14
- are usually licensed only to the accredited laboratory.
15
-
16
- ## Current edition
17
-
18
- - [ISO/IEC 17025:2017](https://www.iso.org/standard/66912.html) is Edition 3. No
19
- successor edition was identified at the research basis date — confirm on the ISO
20
- catalogue page, which refused automated access during that research.
21
- - The 2017 edition restructured the 2005 edition around laboratory activities and
22
- risk-based thinking. A quality system still organized around the 2005 clause
23
- structure is out of date; do not treat a 2005-era manual as a current gap baseline.
24
- - Record publisher, title, edition, amendments/corrigenda, authorized location, access
25
- date, source owner, currency-review date, impact decision, and approval in the
26
- controlled source ledger.
27
-
28
- ## The vocabulary trap: laboratories are accredited, not certified
29
-
30
- A laboratory is **accredited** to ISO/IEC 17025 by an accreditation body. It is not
31
- "ISO 17025 certified," and no certification body issues an ISO/IEC 17025 certificate.
32
- Writing "certified" in a report, tender response, or quality manual is a substantive
33
- error that assessors and customers both notice.
34
-
35
- - Accreditation bodies operate under ISO/IEC 17011 and are peer-evaluated through the
36
- recognition arrangement. Certification bodies operate under ISO/IEC 17021-1. These
37
- are different schemes with different scope statements.
38
- - Since **2026-01-01**, Global Accreditation Cooperation Incorporated has replaced the
39
- former ILAC and IAF and operates its own Multilateral Recognition Arrangement.
40
- Results and certificates issued under the former ILAC MRA / IAF MLA remain
41
- recognized during the transition. Verify current logo, claim, and endorsement wording
42
- with the accreditation body before reproducing any of it.
43
- - ISO/IEC 17025 accreditation is not ISO 9001 certification, not a product approval,
44
- not a regulatory authorization, and not a statement that any particular result is
45
- correct.
46
-
47
- ## Hard boundary
48
-
49
- This skill and its files cannot:
50
-
51
- - accredit a laboratory, issue or validate an accreditation certificate or schedule,
52
- or predict an assessment outcome;
53
- - decide which accreditation scheme, jurisdiction requirement, or customer
54
- specification applies;
55
- - replace the laboratory's technical management, quality manager, authorized signatory,
56
- accreditation body, assessor, or proficiency-testing provider;
57
- - validate a method, compute or approve a measurement uncertainty budget, establish
58
- metrological traceability, or judge whether a decision rule is fit for purpose; or
59
- - infer competence from a document title, keyword, template, checklist, or script
60
- result.
61
-
62
- Use outputs as a list of evidence questions for accountable human review.
63
-
64
- ## Scope of accreditation is per activity, not per organization
65
-
66
- The accredited scope is defined item by item: field or discipline, method or procedure
67
- and its issue, the measurand or property determined, and the range with the reported
68
- uncertainty basis. For calibration laboratories this is normally expressed through
69
- calibration and measurement capability statements.
70
-
71
- Consequences for evidence preparation:
72
-
73
- - Work outside the accredited scope must not carry an accreditation claim or
74
- endorsement, even at an accredited site under an accredited quality system.
75
- - A method change, a range extension, a new location, or a new authorized signatory is
76
- a scope question, not only an internal change-control question.
77
- - Subcontracted work has its own rules for customer notification and for the
78
- subcontractor's own accreditation status. Record both.
79
-
80
- Capture scope items with:
81
-
82
- ```bash
83
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_scope_intake.py \
84
- /path/to/laboratory-scope-intake.json --standard iso-17025
85
- ```
86
-
87
- Copy `assets/templates/laboratory-scope-intake-template.json` outside the skill first.
88
- The distributed template fails closed by design.
89
-
90
- ## Process and evidence domains
91
-
92
- The `iso-17025` profile carries these domain labels for manifests and gap reports.
93
- They are workflow topics, not clause references:
94
-
95
- `scope-and-impartiality`, `organizational-structure-and-management`,
96
- `personnel-competence`, `facilities-and-environmental-conditions`,
97
- `equipment-and-calibration`, `metrological-traceability`,
98
- `externally-provided-products-and-services`, `review-of-requests-and-contracts`,
99
- `method-selection-verification-and-validation`, `sampling`, `handling-of-items`,
100
- `technical-records`, `measurement-uncertainty`,
101
- `validity-of-results-and-proficiency-testing`, `reporting-and-decision-rules`,
102
- `complaints`, `nonconforming-work`, `data-and-information-management`,
103
- `internal-audit`, `management-review`, `corrective-action-and-improvement`.
104
-
105
- Each domain needs an owner, status, evidence IDs, source/version reference, recorded
106
- approval, and links to open gaps. Sample **records**, not only procedures: a procedure
107
- describing uncertainty evaluation is not evidence that a budget exists for a reported
108
- measurand.
109
-
110
- ## The four technical areas that carry most findings
111
-
112
- ### 1. Metrological traceability
113
-
114
- Traceability is a documented, unbroken chain to a stated reference with stated
115
- uncertainty at each step — not a drawer of calibration certificates. The governing
116
- policy is **ILAC P10:07/2020** (implementation July 2021, revised for the 2017
117
- edition); confirm its current designation, since the P/G series numbering may move
118
- under GLOBAC.
119
-
120
- Evidence to assemble per measurement: the stated reference, the calibration provider
121
- and its accreditation status and scope, certificate identity and date, the uncertainty
122
- contribution carried forward, interval justification, and intermediate-check records.
123
-
124
- ### 2. Measurement uncertainty
125
-
126
- Record which measurands have evaluated uncertainty, the evaluation basis, the
127
- contributions included, how uncertainty is reported, and how it interacts with the
128
- decision rule. An uncertainty budget that exists only in a spreadsheet with no
129
- controlled revision, owner, or approval is a gap, not evidence.
130
-
131
- This skill does not compute uncertainty. For the repo's uncertainty tooling, see the
132
- `uncertainty-and-units` skill; its outputs still require authorized technical review
133
- before entering a controlled record.
134
-
135
- ### 3. Method selection, verification, and validation
136
-
137
- Distinguish, per scope item: a standard method used as published, a standard method
138
- requiring verification of the laboratory's ability to perform it, a modified standard
139
- method, and a laboratory-developed method. The evidence expected differs in each case.
140
- Record the performance characteristics evaluated, the acceptance criteria, the data,
141
- and the authorized approval to put the method into service.
142
-
143
- ### 4. Decision rules and statements of conformity
144
-
145
- If reports state conformity to a specification, the decision rule must be documented,
146
- agreed with the customer where required, and applied consistently — including how
147
- measurement uncertainty is treated at the specification limit. The guidance basis is
148
- **ILAC G8:09/2019**, with JCGM 106:2012 / ISO/IEC Guide 98-4 as the metrological
149
- companion. Confirm current issues before citing either in a controlled procedure.
150
-
151
- Assemble, per scope item that reports conformity: the rule, the agreement record, the
152
- uncertainty treatment, the report wording, and the authorized signatory.
153
-
154
- ## Validity of results and proficiency testing
155
-
156
- Interlaboratory comparison and proficiency-testing participation is monitoring
157
- evidence, and a passing result is not a competence conclusion. Record the plan (which
158
- scope items, what frequency, what provider), each result, the evaluation against
159
- acceptance criteria, and — most importantly — the investigation and corrective action
160
- for any questionable or unsatisfactory outcome. An unsatisfactory result with no
161
- documented investigation is a blocker; treat it as one.
162
-
163
- Where the laboratory cannot participate because no scheme exists for a measurand,
164
- record the alternative approach and its authorization rather than leaving a silence.
165
-
166
- ## Shared checks that apply here
167
-
168
- - `scripts/audit_document_records.py` — controlled documents, technical records,
169
- retention basis, and external-source currency. Standard-agnostic.
170
- - `scripts/check_capa.py` — nonconforming work and corrective action, including
171
- effectiveness evidence before closure.
172
- - `scripts/check_supplier_controls.py` — externally provided products and services,
173
- including calibration providers, reference-material suppliers, and subcontracted
174
- laboratories.
175
- - `scripts/validate_evidence_manifest.py` and `scripts/gap_analyzer.py` with
176
- `--standard iso-17025` — bounded evidence manifest and domain-level gap view.
177
-
178
- `scripts/check_traceability.py` and `scripts/check_qmsr_transition.py` are
179
- device-lifecycle checks and do not apply to laboratory accreditation work. Note that
180
- `check_traceability.py` concerns design/risk traceability, **not** metrological
181
- traceability — the words collide and the check is the wrong tool here.
182
-
183
- ## Common preparation failures
184
-
185
- - Claiming "ISO 17025 certified" instead of accredited, or attaching an accreditation
186
- symbol to results outside the accredited scope.
187
- - Treating calibration certificates as traceability evidence without the uncertainty
188
- chain, provider scope, or interval justification.
189
- - Reporting conformity with no documented decision rule, or a rule that ignores
190
- uncertainty at the limit.
191
- - Verifying a standard method once at introduction and never revisiting it after a
192
- method issue, instrument, or personnel change.
193
- - Recording proficiency-testing scores while leaving unsatisfactory results
194
- uninvestigated.
195
- - Presenting an impartiality statement with no identified risks, no controls, and no
196
- review.
197
- - Filing a document register as the deliverable when no technical records were sampled.
198
-
199
- ## Sources
200
-
201
- - [ISO/IEC 17025:2017](https://www.iso.org/standard/66912.html) — catalogue entry
202
- - [ISO/IEC 17025 landing page](https://www.iso.org/ISO-IEC-17025-testing-and-calibration-laboratories.html)
203
- - [ILAC policy series](https://ilac.org/publications-and-resources/ilac-policy-series/) — P10 traceability policy
204
- - [GLOBAC launch](https://iaf.nu/en/news/global-accreditation-cooperation-incorporated-launch-unifies-international-accreditation-organisations-and-strengthens-worldwide-trust/)
205
- - [Specifying use of GLOBAC accreditation](https://ilac.org/latest_ilac_news/iaf-and-ilac-release-information-on-specifying-use-of-globac-accreditation/)
206
- - `references/source-ledger.md` — dated baseline and provenance limitations
207
- - `references/assurance-lanes.md` — how this lane differs from certification and
208
- regulatory inspection