medsci-skills 4.1.0

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 (702) hide show
  1. package/LICENSE +50 -0
  2. package/README.md +602 -0
  3. package/README_FIRST.md +27 -0
  4. package/bin/medsci-skills.js +159 -0
  5. package/installers/install-macos.command +19 -0
  6. package/installers/install-windows.cmd +26 -0
  7. package/installers/install-windows.ps1 +17 -0
  8. package/installers/install.py +218 -0
  9. package/metadata/skills_catalog.json +452 -0
  10. package/package.json +48 -0
  11. package/skills/academic-aio/SKILL.md +408 -0
  12. package/skills/academic-aio/references/case_studies/kjr_mllm_2025.md +82 -0
  13. package/skills/academic-aio/references/checklists/AIO_GENERAL.md +354 -0
  14. package/skills/academic-aio/references/journal_summarybox_templates.yaml +126 -0
  15. package/skills/academic-aio/references/oac_funding_checklist.yaml +129 -0
  16. package/skills/academic-aio/references/reporting_guideline_mapping.md +39 -0
  17. package/skills/academic-aio/references/schema_markup_templates/CodeRepository.jsonld +32 -0
  18. package/skills/academic-aio/references/schema_markup_templates/Dataset.jsonld +36 -0
  19. package/skills/academic-aio/references/schema_markup_templates/Person.jsonld +30 -0
  20. package/skills/academic-aio/references/schema_markup_templates/README.md +43 -0
  21. package/skills/academic-aio/references/schema_markup_templates/ScholarlyArticle.jsonld +55 -0
  22. package/skills/academic-aio/scripts/batch_metadata_audit.py +169 -0
  23. package/skills/academic-aio/scripts/validate_schema.py +118 -0
  24. package/skills/academic-aio/skill.yml +36 -0
  25. package/skills/academic-aio/templates/aio_audit_checklist.md.j2 +108 -0
  26. package/skills/add-journal/SKILL.md +482 -0
  27. package/skills/add-journal/skill.yml +33 -0
  28. package/skills/analyze-stats/SKILL.md +598 -0
  29. package/skills/analyze-stats/references/analysis_guides/missing_data.md +109 -0
  30. package/skills/analyze-stats/references/analysis_guides/nhis_icd10_mapping.md +247 -0
  31. package/skills/analyze-stats/references/analysis_guides/propensity_score.md +132 -0
  32. package/skills/analyze-stats/references/analysis_guides/regression.md +115 -0
  33. package/skills/analyze-stats/references/analysis_guides/repeated_measures.md +160 -0
  34. package/skills/analyze-stats/references/analysis_guides/survey_weighted.md +366 -0
  35. package/skills/analyze-stats/references/analysis_guides/test_selection.md +86 -0
  36. package/skills/analyze-stats/references/style/figure_style.mplstyle +69 -0
  37. package/skills/analyze-stats/references/style/theme_publication.R +147 -0
  38. package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml +51 -0
  39. package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml +55 -0
  40. package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml +66 -0
  41. package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml +57 -0
  42. package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml +51 -0
  43. package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml +66 -0
  44. package/skills/analyze-stats/references/table-standards/table-standards.md +287 -0
  45. package/skills/analyze-stats/references/table-standards/table-types/diagnostic_accuracy.md +36 -0
  46. package/skills/analyze-stats/references/table-standards/table-types/meta_analysis.md +58 -0
  47. package/skills/analyze-stats/references/table-standards/table-types/model_comparison.md +36 -0
  48. package/skills/analyze-stats/references/table-standards/table-types/regression_results.md +50 -0
  49. package/skills/analyze-stats/references/table-standards/table-types/table1_demographics.md +51 -0
  50. package/skills/analyze-stats/references/table-standards/tool-comparison.md +79 -0
  51. package/skills/analyze-stats/references/templates/agreement_analysis.py +436 -0
  52. package/skills/analyze-stats/references/templates/dca_plot.R +237 -0
  53. package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +401 -0
  54. package/skills/analyze-stats/references/templates/dta_meta_analysis.R +384 -0
  55. package/skills/analyze-stats/references/templates/forest_plot.py +412 -0
  56. package/skills/analyze-stats/references/templates/likert_summary.py +356 -0
  57. package/skills/analyze-stats/references/templates/meta_analysis.R +365 -0
  58. package/skills/analyze-stats/references/templates/propensity_score.py +478 -0
  59. package/skills/analyze-stats/references/templates/regression.py +425 -0
  60. package/skills/analyze-stats/references/templates/repeated_measures.py +434 -0
  61. package/skills/analyze-stats/references/templates/sample_size.R +382 -0
  62. package/skills/analyze-stats/references/templates/survey_weighted_analysis.py +411 -0
  63. package/skills/analyze-stats/references/templates/survival_analysis.py +325 -0
  64. package/skills/analyze-stats/references/templates/table1_demographics.py +287 -0
  65. package/skills/analyze-stats/scripts/check_generated_code.py +335 -0
  66. package/skills/analyze-stats/skill.yml +38 -0
  67. package/skills/analyze-stats/tests/fixtures/gen_bad.R +16 -0
  68. package/skills/analyze-stats/tests/fixtures/gen_bad.py +24 -0
  69. package/skills/analyze-stats/tests/fixtures/gen_clean.py +21 -0
  70. package/skills/analyze-stats/tests/test_generated_code.sh +59 -0
  71. package/skills/analyze-stats/tests/test_survival_template.sh +53 -0
  72. package/skills/author-strategy/SKILL.md +117 -0
  73. package/skills/author-strategy/analyze_patterns.py +303 -0
  74. package/skills/author-strategy/fetch_pubmed.py +374 -0
  75. package/skills/author-strategy/skill.yml +34 -0
  76. package/skills/batch-cohort/SKILL.md +223 -0
  77. package/skills/batch-cohort/references/base_template_knhanes.R +210 -0
  78. package/skills/batch-cohort/references/batch_template_generator.R +222 -0
  79. package/skills/batch-cohort/references/variable_coding_registry.md +136 -0
  80. package/skills/batch-cohort/skill.yml +35 -0
  81. package/skills/calc-sample-size/SKILL.md +491 -0
  82. package/skills/calc-sample-size/references/formulas.md +655 -0
  83. package/skills/calc-sample-size/references/observational_cohort.md +49 -0
  84. package/skills/calc-sample-size/skill.yml +51 -0
  85. package/skills/check-reporting/SKILL.md +534 -0
  86. package/skills/check-reporting/references/LICENSES.md +41 -0
  87. package/skills/check-reporting/references/checklists/AMSTAR2.md +54 -0
  88. package/skills/check-reporting/references/checklists/ARRIVE_2.md +234 -0
  89. package/skills/check-reporting/references/checklists/CARE.md +102 -0
  90. package/skills/check-reporting/references/checklists/CLAIM_2024.md +128 -0
  91. package/skills/check-reporting/references/checklists/CLEAR.md +113 -0
  92. package/skills/check-reporting/references/checklists/CONSORT.md +86 -0
  93. package/skills/check-reporting/references/checklists/COSMIN_RoB.md +136 -0
  94. package/skills/check-reporting/references/checklists/GRRAS.md +61 -0
  95. package/skills/check-reporting/references/checklists/MI_CLEAR_LLM.md +167 -0
  96. package/skills/check-reporting/references/checklists/MOOSE.md +85 -0
  97. package/skills/check-reporting/references/checklists/NOS.md +88 -0
  98. package/skills/check-reporting/references/checklists/PRISMA_2020.md +135 -0
  99. package/skills/check-reporting/references/checklists/PRISMA_DTA.md +36 -0
  100. package/skills/check-reporting/references/checklists/PRISMA_P.md +56 -0
  101. package/skills/check-reporting/references/checklists/PROBAST.md +75 -0
  102. package/skills/check-reporting/references/checklists/PROBAST_AI.md +130 -0
  103. package/skills/check-reporting/references/checklists/QUADAS2.md +77 -0
  104. package/skills/check-reporting/references/checklists/QUADAS_C.md +131 -0
  105. package/skills/check-reporting/references/checklists/ROBINS_E.md +179 -0
  106. package/skills/check-reporting/references/checklists/ROBINS_I.md +87 -0
  107. package/skills/check-reporting/references/checklists/ROBIS.md +114 -0
  108. package/skills/check-reporting/references/checklists/ROB_ME.md +126 -0
  109. package/skills/check-reporting/references/checklists/RoB2.md +79 -0
  110. package/skills/check-reporting/references/checklists/RoB_NMA.md +96 -0
  111. package/skills/check-reporting/references/checklists/SPIRIT.md +112 -0
  112. package/skills/check-reporting/references/checklists/SQUIRE_2.md +68 -0
  113. package/skills/check-reporting/references/checklists/STARD.md +129 -0
  114. package/skills/check-reporting/references/checklists/STARD_AI.md +211 -0
  115. package/skills/check-reporting/references/checklists/STROBE.md +80 -0
  116. package/skills/check-reporting/references/checklists/SWiM.md +33 -0
  117. package/skills/check-reporting/references/checklists/TRIPOD.md +157 -0
  118. package/skills/check-reporting/references/checklists/TRIPOD_AI.md +140 -0
  119. package/skills/check-reporting/references/step4c_registration_timing.md +93 -0
  120. package/skills/check-reporting/references/step4d_prisma_figure_audit.md +137 -0
  121. package/skills/check-reporting/scripts/check_checklist_exists.py +183 -0
  122. package/skills/check-reporting/scripts/check_checklist_version.py +168 -0
  123. package/skills/check-reporting/scripts/check_framework_naming.py +206 -0
  124. package/skills/check-reporting/scripts/check_prisma_figure.py +209 -0
  125. package/skills/check-reporting/scripts/prisma_cascade_check.py +274 -0
  126. package/skills/check-reporting/skill.yml +41 -0
  127. package/skills/check-reporting/tests/fixtures/framework_bad.md +8 -0
  128. package/skills/check-reporting/tests/fixtures/framework_clean.md +7 -0
  129. package/skills/check-reporting/tests/test_checklist_fail_fast.sh +77 -0
  130. package/skills/check-reporting/tests/test_checklist_version.sh +72 -0
  131. package/skills/check-reporting/tests/test_framework_naming.sh +45 -0
  132. package/skills/check-reporting/tests/test_prisma_cascade.sh +104 -0
  133. package/skills/clean-data/SKILL.md +180 -0
  134. package/skills/clean-data/references/cleaning_patterns.md +299 -0
  135. package/skills/clean-data/references/profiling_template.py +304 -0
  136. package/skills/clean-data/scripts/check_structural_zero.py +174 -0
  137. package/skills/clean-data/skill.yml +35 -0
  138. package/skills/clean-data/tests/fixtures/smoking.csv +8 -0
  139. package/skills/clean-data/tests/test_structural_zero.sh +49 -0
  140. package/skills/cross-national/SKILL.md +264 -0
  141. package/skills/cross-national/skill.yml +37 -0
  142. package/skills/define-variables/SKILL.md +146 -0
  143. package/skills/define-variables/references/common_definitions.md +190 -0
  144. package/skills/define-variables/skill.yml +34 -0
  145. package/skills/define-variables/templates/variable_operationalization.md +64 -0
  146. package/skills/deidentify/SKILL.md +203 -0
  147. package/skills/deidentify/deidentify.py +1224 -0
  148. package/skills/deidentify/locales/_template.json +45 -0
  149. package/skills/deidentify/locales/au.json +43 -0
  150. package/skills/deidentify/locales/ca.json +44 -0
  151. package/skills/deidentify/locales/cn.json +47 -0
  152. package/skills/deidentify/locales/de.json +48 -0
  153. package/skills/deidentify/locales/fr.json +48 -0
  154. package/skills/deidentify/locales/in.json +48 -0
  155. package/skills/deidentify/locales/jp.json +48 -0
  156. package/skills/deidentify/locales/kr.json +48 -0
  157. package/skills/deidentify/locales/uk.json +45 -0
  158. package/skills/deidentify/locales/us.json +43 -0
  159. package/skills/deidentify/references/date_shift_guide.md +82 -0
  160. package/skills/deidentify/references/hipaa_18_identifiers.md +48 -0
  161. package/skills/deidentify/references/korean_phi_patterns.md +135 -0
  162. package/skills/deidentify/skill.yml +43 -0
  163. package/skills/deidentify/tests/README.md +26 -0
  164. package/skills/deidentify/tests/test_clean.csv +16 -0
  165. package/skills/deidentify/tests/test_edge_cases.csv +11 -0
  166. package/skills/deidentify/tests/test_phi_korean.csv +11 -0
  167. package/skills/design-ai-benchmarking/SKILL.md +214 -0
  168. package/skills/design-ai-benchmarking/references/benchmark_export_schema.json +69 -0
  169. package/skills/design-ai-benchmarking/references/elicitation_rubric_template.md +37 -0
  170. package/skills/design-ai-benchmarking/skill.yml +38 -0
  171. package/skills/design-study/SKILL.md +298 -0
  172. package/skills/design-study/skill.yml +33 -0
  173. package/skills/fill-icmje-coi/SKILL.md +216 -0
  174. package/skills/fill-icmje-coi/scripts/fill_icmje_coi.py +140 -0
  175. package/skills/fill-icmje-coi/skill.yml +35 -0
  176. package/skills/fill-icmje-coi/templates/icmje_coi_seed_synthetic.docx +0 -0
  177. package/skills/fill-protocol/SKILL.md +248 -0
  178. package/skills/fill-protocol/examples/example_irb_template.yaml +53 -0
  179. package/skills/fill-protocol/references/best_practices.md +121 -0
  180. package/skills/fill-protocol/scripts/doc_to_docx.py +111 -0
  181. package/skills/fill-protocol/scripts/fill_form.py +611 -0
  182. package/skills/fill-protocol/scripts/inspect_template.py +61 -0
  183. package/skills/fill-protocol/setup.sh +162 -0
  184. package/skills/fill-protocol/skill.yml +37 -0
  185. package/skills/find-cohort-gap/SKILL.md +309 -0
  186. package/skills/find-cohort-gap/references/cohort_profile_template.md +93 -0
  187. package/skills/find-cohort-gap/references/onepager_template.md +84 -0
  188. package/skills/find-cohort-gap/references/pattern_scoring_rubric.md +169 -0
  189. package/skills/find-cohort-gap/references/saturation_query_templates.md +143 -0
  190. package/skills/find-cohort-gap/skill.yml +35 -0
  191. package/skills/find-journal/POLICY.md +87 -0
  192. package/skills/find-journal/SKILL.md +340 -0
  193. package/skills/find-journal/references/journal_profiles/AJNR.md +29 -0
  194. package/skills/find-journal/references/journal_profiles/AJR.md +30 -0
  195. package/skills/find-journal/references/journal_profiles/Abdominal_Radiology.md +30 -0
  196. package/skills/find-journal/references/journal_profiles/Academic_Radiology.md +30 -0
  197. package/skills/find-journal/references/journal_profiles/Annals_of_Internal_Medicine.md +33 -0
  198. package/skills/find-journal/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +28 -0
  199. package/skills/find-journal/references/journal_profiles/BMC_Medicine.md +31 -0
  200. package/skills/find-journal/references/journal_profiles/British_Journal_of_Radiology.md +39 -0
  201. package/skills/find-journal/references/journal_profiles/CVIR.md +30 -0
  202. package/skills/find-journal/references/journal_profiles/Chest.md +39 -0
  203. package/skills/find-journal/references/journal_profiles/Clinical_Radiology.md +30 -0
  204. package/skills/find-journal/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +32 -0
  205. package/skills/find-journal/references/journal_profiles/Diabetes_Metabolism_Journal.md +36 -0
  206. package/skills/find-journal/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +32 -0
  207. package/skills/find-journal/references/journal_profiles/Endocrinology_and_Metabolism.md +37 -0
  208. package/skills/find-journal/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +39 -0
  209. package/skills/find-journal/references/journal_profiles/European_Radiology.md +29 -0
  210. package/skills/find-journal/references/journal_profiles/Hepatology_Communications.md +40 -0
  211. package/skills/find-journal/references/journal_profiles/Hepatology_International.md +37 -0
  212. package/skills/find-journal/references/journal_profiles/IEEE_JBHI.md +28 -0
  213. package/skills/find-journal/references/journal_profiles/IEEE_TMI.md +28 -0
  214. package/skills/find-journal/references/journal_profiles/INSI.md +29 -0
  215. package/skills/find-journal/references/journal_profiles/Investigative_Radiology.md +25 -0
  216. package/skills/find-journal/references/journal_profiles/JACC_Advances.md +41 -0
  217. package/skills/find-journal/references/journal_profiles/JACC_Asia.md +30 -0
  218. package/skills/find-journal/references/journal_profiles/JACR.md +28 -0
  219. package/skills/find-journal/references/journal_profiles/JAMA.md +40 -0
  220. package/skills/find-journal/references/journal_profiles/JAMA_Network_Open.md +30 -0
  221. package/skills/find-journal/references/journal_profiles/JCSM.md +39 -0
  222. package/skills/find-journal/references/journal_profiles/JKMS.md +32 -0
  223. package/skills/find-journal/references/journal_profiles/JMIR.md +29 -0
  224. package/skills/find-journal/references/journal_profiles/JMIR_Medical_Education.md +29 -0
  225. package/skills/find-journal/references/journal_profiles/JNIS.md +35 -0
  226. package/skills/find-journal/references/journal_profiles/JVIR.md +31 -0
  227. package/skills/find-journal/references/journal_profiles/Journal_of_Biomedical_Informatics.md +29 -0
  228. package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +40 -0
  229. package/skills/find-journal/references/journal_profiles/Journal_of_Magnetic_Resonance_Imaging.md +30 -0
  230. package/skills/find-journal/references/journal_profiles/Journal_of_Nuclear_Medicine.md +31 -0
  231. package/skills/find-journal/references/journal_profiles/Journal_of_Stroke.md +32 -0
  232. package/skills/find-journal/references/journal_profiles/KJR.md +38 -0
  233. package/skills/find-journal/references/journal_profiles/Korean_Circulation_Journal.md +38 -0
  234. package/skills/find-journal/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +36 -0
  235. package/skills/find-journal/references/journal_profiles/Lancet_Diabetes_and_Endocrinology.md +40 -0
  236. package/skills/find-journal/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +49 -0
  237. package/skills/find-journal/references/journal_profiles/Lancet_Infectious_Diseases.md +38 -0
  238. package/skills/find-journal/references/journal_profiles/Lancet_Neurology.md +39 -0
  239. package/skills/find-journal/references/journal_profiles/Lancet_Oncology.md +40 -0
  240. package/skills/find-journal/references/journal_profiles/Lancet_Psychiatry.md +38 -0
  241. package/skills/find-journal/references/journal_profiles/Lancet_Public_Health.md +30 -0
  242. package/skills/find-journal/references/journal_profiles/Lancet_Respiratory_Medicine.md +39 -0
  243. package/skills/find-journal/references/journal_profiles/Liver_International.md +33 -0
  244. package/skills/find-journal/references/journal_profiles/Medical_Image_Analysis.md +28 -0
  245. package/skills/find-journal/references/journal_profiles/NEJM.md +33 -0
  246. package/skills/find-journal/references/journal_profiles/Nature_Machine_Intelligence.md +31 -0
  247. package/skills/find-journal/references/journal_profiles/Nature_Medicine.md +39 -0
  248. package/skills/find-journal/references/journal_profiles/Neuroradiology.md +31 -0
  249. package/skills/find-journal/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +39 -0
  250. package/skills/find-journal/references/journal_profiles/PLOS_Medicine.md +32 -0
  251. package/skills/find-journal/references/journal_profiles/RYAI.md +28 -0
  252. package/skills/find-journal/references/journal_profiles/Radiology.md +29 -0
  253. package/skills/find-journal/references/journal_profiles/Skeletal_Radiology.md +31 -0
  254. package/skills/find-journal/references/journal_profiles/Stroke.md +37 -0
  255. package/skills/find-journal/references/journal_profiles/The_BMJ.md +31 -0
  256. package/skills/find-journal/references/journal_profiles/The_Lancet.md +31 -0
  257. package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +29 -0
  258. package/skills/find-journal/references/journal_profiles/World_Journal_of_Hepatology.md +53 -0
  259. package/skills/find-journal/references/journal_profiles/npj_Digital_Medicine.md +29 -0
  260. package/skills/find-journal/skill.yml +34 -0
  261. package/skills/fulltext-retrieval/SKILL.md +174 -0
  262. package/skills/fulltext-retrieval/fetch_oa.py +433 -0
  263. package/skills/fulltext-retrieval/pdf_to_md.py +160 -0
  264. package/skills/fulltext-retrieval/skill.yml +41 -0
  265. package/skills/generate-codebook/SKILL.md +155 -0
  266. package/skills/generate-codebook/references/codebook_schema.md +76 -0
  267. package/skills/generate-codebook/scripts/generate_codebook.py +278 -0
  268. package/skills/generate-codebook/skill.yml +35 -0
  269. package/skills/generate-codebook/tests/test_generate_codebook.sh +76 -0
  270. package/skills/grant-builder/SKILL.md +251 -0
  271. package/skills/grant-builder/skill.yml +34 -0
  272. package/skills/humanize/SKILL.md +251 -0
  273. package/skills/humanize/references/ai_patterns.md +571 -0
  274. package/skills/humanize/skill.yml +33 -0
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@@ -0,0 +1,95 @@
1
+ # MA-Scout Project README Template (PROSPERO-ready)
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+
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+ Load this reference when `/ma-scout` Phase 4 (Folder & README Scaffolding) creates a
4
+ new topic folder. English section headings and PICO/PIRD structure keep the README aligned
5
+ with downstream `/meta-analysis` and `/search-lit` expectations.
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+
7
+ This is the English default. For a supervisor / professor-facing Korean README, use
8
+ `project_readme_template_ko.md` (same structure, Korean prompts for the PI-facing fields).
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+
10
+ Copy the block below into `{topic_folder}/README.md` and fill in the curly-brace fields.
11
+
12
+ ````markdown
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+ # {Topic Title} — {MA Type} Meta-analysis ({Supervisor name})
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+
15
+ ## Overview
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+ - Supervisor: {Supervisor name} ({affiliation history})
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+ - Supervisor's area: Pillar {N} — {area name}
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+ - Status: Planning
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+ - Priority: rank {N}
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+ - Created: {YYYY-MM-DD}
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+
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+ ## Research Question
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+ ### PICO/PIRD
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+ - **P**opulation: {specific patient group, disease, setting}
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+ - **I**ndex test / Intervention: {test or intervention}
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+ - **C**omparator / Reference standard: {comparator or reference standard}
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+ - **O**utcome: {DTA: Se/Sp/AUC, Prognostic: HR/OR, adverse events, etc.}
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+
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+ ### One-line RQ
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+ {the complete research question in one sentence}
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+
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+ ## Key Gap
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+ - Existing MAs: {N} ({details, most recent year, scope limitations})
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+ - Consensus/Scholar Gateway cross-check: {result summary}
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+ - medRxiv/bioRxiv preprint MA: {yes/no}
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+ - Registered PROSPERO protocol: {yes (CRD#) / no}
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+ - {specific gap explanation — why a new MA is needed}
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+
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+ ## Professor's Authority
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+ - {number of related publications, 1-2 representative papers, distinctive contribution}
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+ - {why this supervisor is well-suited to this topic}
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+
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+ ## Preliminary Search ({date})
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+ ### Search Strategy (PubMed)
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+ ```
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+ {the actual PubMed query used — the E-utilities esearch query verbatim}
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+ ```
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+ - Total hits: {N} (raw)
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+ - DTA/outcome extractable (estimated): {N} (×0.15-0.30 discount)
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+ - Existing MAs: {N} (narrow) / {N} (including broad SRs)
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+ - Consensus search result: {whether any additional papers were found}
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+ - bioRxiv/medRxiv: {N} preprints
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+
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+ ### Embase Search Strategy (Draft)
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+ ```
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+ {draft Embase query — including Emtree terms}
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+ ```
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+ (draft before execution — verify when Embase access is available)
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+
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+ ## Target Journal
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+ | Rank | Journal | IF | MA acceptance rate | Turnaround | Notes |
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+ |------|---------|-----|--------------------|-----------|-------|
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+ | 1st | {journal} | {IF} | {high/medium} | {months} | {rationale} |
64
+ | 2nd | {journal} | {IF} | {high/medium} | {months} | {rationale} |
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+
66
+ ## Timeline (backwards-planned)
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+ | Stage | Estimated time | Prerequisite |
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+ |-------|----------------|--------------|
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+ | Supervisor proposal | {YYYY-MM} | {condition} |
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+ | PROSPERO registration | +1 week | Supervisor approval |
71
+ | Search complete | +2 weeks | PROSPERO registration |
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+ | Screening complete | +3 weeks | 2nd reviewer secured |
73
+ | Data extraction | +4 weeks | Screening consensus |
74
+ | Analysis + draft | +6 weeks | Data lock |
75
+ | Supervisor review | +8 weeks | Draft complete |
76
+ | Submission | +10 weeks | Supervisor approval |
77
+
78
+ ## Data Sources Used
79
+ - PubMed E-utilities: ✅ (esearch count + efetch metadata)
80
+ - Consensus MCP: ✅/❌
81
+ - Scholar Gateway: ✅/❌
82
+ - bioRxiv/medRxiv: ✅/❌
83
+ - PROSPERO: ✅
84
+ ````
85
+
86
+ ## Solo-Mode Adaptations (no supervisor)
87
+
88
+ When a user runs `/ma-scout` in topic-first mode without a supervisor assignment,
89
+ substitute:
90
+ - `## Overview` — drop the `Supervisor`, `Supervisor's area`, and timeline `Supervisor proposal` /
91
+ `Supervisor review` rows.
92
+ - Replace `Supervisor approval` in the Timeline `Prerequisite` column with `self-approval` or
93
+ the lead author's own sign-off step.
94
+ - `## Professor's Authority` — rename to `## Author Authority` and describe the
95
+ user's own prior publications that justify leading this MA.
@@ -0,0 +1,82 @@
1
+ # MA-Scout Project README Template — Korean variant (PROSPERO-ready)
2
+
3
+ > Opt-in Korean variant. The default is the English `project_readme_template.md`. Use this when the
4
+ > README is supervisor / professor-facing for a Korean PI review. English section headings and
5
+ > PICO/PIRD structure are kept (so the README matches downstream `/meta-analysis` and `/search-lit`
6
+ > expectations); Korean prompts are used for the PI-facing fields.
7
+
8
+ Copy the block below into `{topic_folder}/README.md` and fill in the curly-brace fields.
9
+
10
+ ````markdown
11
+ # {Topic Title} — {MA Type} Meta-analysis ({교수님 성함})
12
+
13
+ ## Overview
14
+ - Supervisor: {교수님 성함} ({소속 이력})
15
+ - 교수님 영역: Pillar {N} — {영역명}
16
+ - Status: 기획 단계
17
+ - Priority: {순위}순위
18
+ - Created: {YYYY-MM-DD}
19
+
20
+ ## Research Question
21
+ ### PICO/PIRD
22
+ - **P**opulation: {구체적 환자군, 질환, 세팅}
23
+ - **I**ndex test / Intervention: {검사법 또는 중재}
24
+ - **C**omparator / Reference standard: {비교군 또는 참조표준}
25
+ - **O**utcome: {DTA: Se/Sp/AUC, Prognostic: HR/OR, 부작용 등}
26
+
27
+ ### One-line RQ
28
+ {완성형 연구 질문 1문장}
29
+
30
+ ## Key Gap
31
+ - 기존 MA: {N}편 ({상세, 가장 최근 연도, 범위 한계})
32
+ - Consensus/Scholar Gateway 추가 확인: {결과 요약}
33
+ - medRxiv/bioRxiv preprint MA: {있음/없음}
34
+ - PROSPERO 등록 프로토콜: {있음 (CRD#) / 없음}
35
+ - {구체적 gap 설명 — 왜 새 MA가 필요한지}
36
+
37
+ ## Professor's Authority
38
+ - {분야 관련 논문 수, 대표 논문 1-2편, 독보적 기여}
39
+ - {왜 이 교수님이 이 주제에 적합한지}
40
+
41
+ ## Preliminary Search ({날짜})
42
+ ### Search Strategy (PubMed)
43
+ ```
44
+ {실제 사용한 PubMed 검색식 — E-utilities esearch query 그대로}
45
+ ```
46
+ - Total hits: {N}편 (raw)
47
+ - DTA/outcome extractable (estimated): {N}편 (×0.15-0.30 discount)
48
+ - 기존 MA: {N}편 (narrow) / {N}편 (broad SR 포함)
49
+ - Consensus 검색 결과: {N}편 추가 발견 여부
50
+ - bioRxiv/medRxiv: {N}편 preprint
51
+
52
+ ### Embase Search Strategy (Draft)
53
+ ```
54
+ {Embase용 검색식 초안 — Emtree 용어 포함}
55
+ ```
56
+ (실행 전 초안 — Embase 접속 시 검증 필요)
57
+
58
+ ## Target Journal
59
+ | 순위 | 저널명 | IF | MA 게재 비율 | Turnaround | 비고 |
60
+ |------|--------|-----|-------------|-----------|------|
61
+ | 1차 | {저널} | {IF} | {높음/중간} | {개월} | {근거} |
62
+ | 2차 | {저널} | {IF} | {높음/중간} | {개월} | {근거} |
63
+
64
+ ## Timeline (역산)
65
+ | 단계 | 예상 시점 | 선행 조건 |
66
+ |------|----------|----------|
67
+ | 교수님 제안 | {YYYY-MM} | {조건} |
68
+ | PROSPERO 등록 | +1주 | 교수님 승인 |
69
+ | 검색 완료 | +2주 | PROSPERO 등록 |
70
+ | 스크리닝 완료 | +3주 | 2nd reviewer 확보 |
71
+ | 데이터 추출 | +4주 | 스크리닝 합의 |
72
+ | 분석 + 초안 | +6주 | 데이터 lock |
73
+ | 교수님 리뷰 | +8주 | 초안 완성 |
74
+ | 투고 | +10주 | 교수님 승인 |
75
+
76
+ ## Data Sources Used
77
+ - PubMed E-utilities: ✅ (esearch count + efetch metadata)
78
+ - Consensus MCP: ✅/❌
79
+ - Scholar Gateway: ✅/❌
80
+ - bioRxiv/medRxiv: ✅/❌
81
+ - PROSPERO: ✅
82
+ ````
@@ -0,0 +1,33 @@
1
+ schema_version: 2
2
+ name: ma-scout
3
+ layer: D
4
+ owner_domain: ma_topic_discovery
5
+
6
+ when_to_use: "Discover and assess meta-analysis topics, either from a professor's publication profile or from a clinical question/trend."
7
+ when_NOT_to_use: "Running the meta-analysis (use meta-analysis); single-author profiling (use author-strategy)."
8
+
9
+ inputs:
10
+ - "professor profile or clinical question/trend"
11
+ outputs:
12
+ - "ranked MA topic proposals with feasibility and gap evidence"
13
+ side_effects:
14
+ - writes_report_artifacts
15
+ - network_access_literature
16
+ downstream_consumers:
17
+ - meta-analysis
18
+ - search-lit
19
+ forbidden_actions:
20
+ - claim_an_ma_gap_without_search_evidence
21
+ - fabricate_study_counts
22
+
23
+ # v2.1 quality card
24
+ purpose: "Find feasible meta-analysis gaps (professor-first or topic-first) backed by literature evidence."
25
+ safety_boundaries:
26
+ - "Gap claims rest on real literature scans; candidate study counts are not fabricated."
27
+ - "Advisory report; does not perform screening or synthesis."
28
+ known_limitations:
29
+ - "Feasibility is an estimate; the true includable pool is established only by meta-analysis screening."
30
+ - "No standalone demo; topic selection needs domain judgement."
31
+ validation_commands:
32
+ - "confirm feasibility by running meta-analysis screening on the shortlist"
33
+ evidence_surface: manual_workflow