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.
- package/LICENSE +50 -0
- package/README.md +602 -0
- package/README_FIRST.md +27 -0
- package/bin/medsci-skills.js +159 -0
- package/installers/install-macos.command +19 -0
- package/installers/install-windows.cmd +26 -0
- package/installers/install-windows.ps1 +17 -0
- package/installers/install.py +218 -0
- package/metadata/skills_catalog.json +452 -0
- package/package.json +48 -0
- package/skills/academic-aio/SKILL.md +408 -0
- package/skills/academic-aio/references/case_studies/kjr_mllm_2025.md +82 -0
- package/skills/academic-aio/references/checklists/AIO_GENERAL.md +354 -0
- package/skills/academic-aio/references/journal_summarybox_templates.yaml +126 -0
- package/skills/academic-aio/references/oac_funding_checklist.yaml +129 -0
- package/skills/academic-aio/references/reporting_guideline_mapping.md +39 -0
- package/skills/academic-aio/references/schema_markup_templates/CodeRepository.jsonld +32 -0
- package/skills/academic-aio/references/schema_markup_templates/Dataset.jsonld +36 -0
- package/skills/academic-aio/references/schema_markup_templates/Person.jsonld +30 -0
- package/skills/academic-aio/references/schema_markup_templates/README.md +43 -0
- package/skills/academic-aio/references/schema_markup_templates/ScholarlyArticle.jsonld +55 -0
- package/skills/academic-aio/scripts/batch_metadata_audit.py +169 -0
- package/skills/academic-aio/scripts/validate_schema.py +118 -0
- package/skills/academic-aio/skill.yml +36 -0
- package/skills/academic-aio/templates/aio_audit_checklist.md.j2 +108 -0
- package/skills/add-journal/SKILL.md +482 -0
- package/skills/add-journal/skill.yml +33 -0
- package/skills/analyze-stats/SKILL.md +598 -0
- package/skills/analyze-stats/references/analysis_guides/missing_data.md +109 -0
- package/skills/analyze-stats/references/analysis_guides/nhis_icd10_mapping.md +247 -0
- package/skills/analyze-stats/references/analysis_guides/propensity_score.md +132 -0
- package/skills/analyze-stats/references/analysis_guides/regression.md +115 -0
- package/skills/analyze-stats/references/analysis_guides/repeated_measures.md +160 -0
- package/skills/analyze-stats/references/analysis_guides/survey_weighted.md +366 -0
- package/skills/analyze-stats/references/analysis_guides/test_selection.md +86 -0
- package/skills/analyze-stats/references/style/figure_style.mplstyle +69 -0
- package/skills/analyze-stats/references/style/theme_publication.R +147 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml +55 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml +57 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/table-standards.md +287 -0
- package/skills/analyze-stats/references/table-standards/table-types/diagnostic_accuracy.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/meta_analysis.md +58 -0
- package/skills/analyze-stats/references/table-standards/table-types/model_comparison.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/regression_results.md +50 -0
- package/skills/analyze-stats/references/table-standards/table-types/table1_demographics.md +51 -0
- package/skills/analyze-stats/references/table-standards/tool-comparison.md +79 -0
- package/skills/analyze-stats/references/templates/agreement_analysis.py +436 -0
- package/skills/analyze-stats/references/templates/dca_plot.R +237 -0
- package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +401 -0
- package/skills/analyze-stats/references/templates/dta_meta_analysis.R +384 -0
- package/skills/analyze-stats/references/templates/forest_plot.py +412 -0
- package/skills/analyze-stats/references/templates/likert_summary.py +356 -0
- package/skills/analyze-stats/references/templates/meta_analysis.R +365 -0
- package/skills/analyze-stats/references/templates/propensity_score.py +478 -0
- package/skills/analyze-stats/references/templates/regression.py +425 -0
- package/skills/analyze-stats/references/templates/repeated_measures.py +434 -0
- package/skills/analyze-stats/references/templates/sample_size.R +382 -0
- package/skills/analyze-stats/references/templates/survey_weighted_analysis.py +411 -0
- package/skills/analyze-stats/references/templates/survival_analysis.py +325 -0
- package/skills/analyze-stats/references/templates/table1_demographics.py +287 -0
- package/skills/analyze-stats/scripts/check_generated_code.py +335 -0
- package/skills/analyze-stats/skill.yml +38 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.R +16 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.py +24 -0
- package/skills/analyze-stats/tests/fixtures/gen_clean.py +21 -0
- package/skills/analyze-stats/tests/test_generated_code.sh +59 -0
- package/skills/analyze-stats/tests/test_survival_template.sh +53 -0
- package/skills/author-strategy/SKILL.md +117 -0
- package/skills/author-strategy/analyze_patterns.py +303 -0
- package/skills/author-strategy/fetch_pubmed.py +374 -0
- package/skills/author-strategy/skill.yml +34 -0
- package/skills/batch-cohort/SKILL.md +223 -0
- package/skills/batch-cohort/references/base_template_knhanes.R +210 -0
- package/skills/batch-cohort/references/batch_template_generator.R +222 -0
- package/skills/batch-cohort/references/variable_coding_registry.md +136 -0
- package/skills/batch-cohort/skill.yml +35 -0
- package/skills/calc-sample-size/SKILL.md +491 -0
- package/skills/calc-sample-size/references/formulas.md +655 -0
- package/skills/calc-sample-size/references/observational_cohort.md +49 -0
- package/skills/calc-sample-size/skill.yml +51 -0
- package/skills/check-reporting/SKILL.md +534 -0
- package/skills/check-reporting/references/LICENSES.md +41 -0
- package/skills/check-reporting/references/checklists/AMSTAR2.md +54 -0
- package/skills/check-reporting/references/checklists/ARRIVE_2.md +234 -0
- package/skills/check-reporting/references/checklists/CARE.md +102 -0
- package/skills/check-reporting/references/checklists/CLAIM_2024.md +128 -0
- package/skills/check-reporting/references/checklists/CLEAR.md +113 -0
- package/skills/check-reporting/references/checklists/CONSORT.md +86 -0
- package/skills/check-reporting/references/checklists/COSMIN_RoB.md +136 -0
- package/skills/check-reporting/references/checklists/GRRAS.md +61 -0
- package/skills/check-reporting/references/checklists/MI_CLEAR_LLM.md +167 -0
- package/skills/check-reporting/references/checklists/MOOSE.md +85 -0
- package/skills/check-reporting/references/checklists/NOS.md +88 -0
- package/skills/check-reporting/references/checklists/PRISMA_2020.md +135 -0
- package/skills/check-reporting/references/checklists/PRISMA_DTA.md +36 -0
- package/skills/check-reporting/references/checklists/PRISMA_P.md +56 -0
- package/skills/check-reporting/references/checklists/PROBAST.md +75 -0
- package/skills/check-reporting/references/checklists/PROBAST_AI.md +130 -0
- package/skills/check-reporting/references/checklists/QUADAS2.md +77 -0
- package/skills/check-reporting/references/checklists/QUADAS_C.md +131 -0
- package/skills/check-reporting/references/checklists/ROBINS_E.md +179 -0
- package/skills/check-reporting/references/checklists/ROBINS_I.md +87 -0
- package/skills/check-reporting/references/checklists/ROBIS.md +114 -0
- package/skills/check-reporting/references/checklists/ROB_ME.md +126 -0
- package/skills/check-reporting/references/checklists/RoB2.md +79 -0
- package/skills/check-reporting/references/checklists/RoB_NMA.md +96 -0
- package/skills/check-reporting/references/checklists/SPIRIT.md +112 -0
- package/skills/check-reporting/references/checklists/SQUIRE_2.md +68 -0
- package/skills/check-reporting/references/checklists/STARD.md +129 -0
- package/skills/check-reporting/references/checklists/STARD_AI.md +211 -0
- package/skills/check-reporting/references/checklists/STROBE.md +80 -0
- package/skills/check-reporting/references/checklists/SWiM.md +33 -0
- package/skills/check-reporting/references/checklists/TRIPOD.md +157 -0
- package/skills/check-reporting/references/checklists/TRIPOD_AI.md +140 -0
- package/skills/check-reporting/references/step4c_registration_timing.md +93 -0
- package/skills/check-reporting/references/step4d_prisma_figure_audit.md +137 -0
- package/skills/check-reporting/scripts/check_checklist_exists.py +183 -0
- package/skills/check-reporting/scripts/check_checklist_version.py +168 -0
- package/skills/check-reporting/scripts/check_framework_naming.py +206 -0
- package/skills/check-reporting/scripts/check_prisma_figure.py +209 -0
- package/skills/check-reporting/scripts/prisma_cascade_check.py +274 -0
- package/skills/check-reporting/skill.yml +41 -0
- package/skills/check-reporting/tests/fixtures/framework_bad.md +8 -0
- package/skills/check-reporting/tests/fixtures/framework_clean.md +7 -0
- package/skills/check-reporting/tests/test_checklist_fail_fast.sh +77 -0
- package/skills/check-reporting/tests/test_checklist_version.sh +72 -0
- package/skills/check-reporting/tests/test_framework_naming.sh +45 -0
- package/skills/check-reporting/tests/test_prisma_cascade.sh +104 -0
- package/skills/clean-data/SKILL.md +180 -0
- package/skills/clean-data/references/cleaning_patterns.md +299 -0
- package/skills/clean-data/references/profiling_template.py +304 -0
- package/skills/clean-data/scripts/check_structural_zero.py +174 -0
- package/skills/clean-data/skill.yml +35 -0
- package/skills/clean-data/tests/fixtures/smoking.csv +8 -0
- package/skills/clean-data/tests/test_structural_zero.sh +49 -0
- package/skills/cross-national/SKILL.md +264 -0
- package/skills/cross-national/skill.yml +37 -0
- package/skills/define-variables/SKILL.md +146 -0
- package/skills/define-variables/references/common_definitions.md +190 -0
- package/skills/define-variables/skill.yml +34 -0
- package/skills/define-variables/templates/variable_operationalization.md +64 -0
- package/skills/deidentify/SKILL.md +203 -0
- package/skills/deidentify/deidentify.py +1224 -0
- package/skills/deidentify/locales/_template.json +45 -0
- package/skills/deidentify/locales/au.json +43 -0
- package/skills/deidentify/locales/ca.json +44 -0
- package/skills/deidentify/locales/cn.json +47 -0
- package/skills/deidentify/locales/de.json +48 -0
- package/skills/deidentify/locales/fr.json +48 -0
- package/skills/deidentify/locales/in.json +48 -0
- package/skills/deidentify/locales/jp.json +48 -0
- package/skills/deidentify/locales/kr.json +48 -0
- package/skills/deidentify/locales/uk.json +45 -0
- package/skills/deidentify/locales/us.json +43 -0
- package/skills/deidentify/references/date_shift_guide.md +82 -0
- package/skills/deidentify/references/hipaa_18_identifiers.md +48 -0
- package/skills/deidentify/references/korean_phi_patterns.md +135 -0
- package/skills/deidentify/skill.yml +43 -0
- package/skills/deidentify/tests/README.md +26 -0
- package/skills/deidentify/tests/test_clean.csv +16 -0
- package/skills/deidentify/tests/test_edge_cases.csv +11 -0
- package/skills/deidentify/tests/test_phi_korean.csv +11 -0
- package/skills/design-ai-benchmarking/SKILL.md +214 -0
- package/skills/design-ai-benchmarking/references/benchmark_export_schema.json +69 -0
- package/skills/design-ai-benchmarking/references/elicitation_rubric_template.md +37 -0
- package/skills/design-ai-benchmarking/skill.yml +38 -0
- package/skills/design-study/SKILL.md +298 -0
- package/skills/design-study/skill.yml +33 -0
- package/skills/fill-icmje-coi/SKILL.md +216 -0
- package/skills/fill-icmje-coi/scripts/fill_icmje_coi.py +140 -0
- package/skills/fill-icmje-coi/skill.yml +35 -0
- package/skills/fill-icmje-coi/templates/icmje_coi_seed_synthetic.docx +0 -0
- package/skills/fill-protocol/SKILL.md +248 -0
- package/skills/fill-protocol/examples/example_irb_template.yaml +53 -0
- package/skills/fill-protocol/references/best_practices.md +121 -0
- package/skills/fill-protocol/scripts/doc_to_docx.py +111 -0
- package/skills/fill-protocol/scripts/fill_form.py +611 -0
- package/skills/fill-protocol/scripts/inspect_template.py +61 -0
- package/skills/fill-protocol/setup.sh +162 -0
- package/skills/fill-protocol/skill.yml +37 -0
- package/skills/find-cohort-gap/SKILL.md +309 -0
- package/skills/find-cohort-gap/references/cohort_profile_template.md +93 -0
- package/skills/find-cohort-gap/references/onepager_template.md +84 -0
- package/skills/find-cohort-gap/references/pattern_scoring_rubric.md +169 -0
- package/skills/find-cohort-gap/references/saturation_query_templates.md +143 -0
- package/skills/find-cohort-gap/skill.yml +35 -0
- package/skills/find-journal/POLICY.md +87 -0
- package/skills/find-journal/SKILL.md +340 -0
- package/skills/find-journal/references/journal_profiles/AJNR.md +29 -0
- package/skills/find-journal/references/journal_profiles/AJR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Abdominal_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Academic_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Annals_of_Internal_Medicine.md +33 -0
- package/skills/find-journal/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +28 -0
- package/skills/find-journal/references/journal_profiles/BMC_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/British_Journal_of_Radiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/CVIR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Chest.md +39 -0
- package/skills/find-journal/references/journal_profiles/Clinical_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Diabetes_Metabolism_Journal.md +36 -0
- package/skills/find-journal/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Endocrinology_and_Metabolism.md +37 -0
- package/skills/find-journal/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/European_Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_Communications.md +40 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_International.md +37 -0
- package/skills/find-journal/references/journal_profiles/IEEE_JBHI.md +28 -0
- package/skills/find-journal/references/journal_profiles/IEEE_TMI.md +28 -0
- package/skills/find-journal/references/journal_profiles/INSI.md +29 -0
- package/skills/find-journal/references/journal_profiles/Investigative_Radiology.md +25 -0
- package/skills/find-journal/references/journal_profiles/JACC_Advances.md +41 -0
- package/skills/find-journal/references/journal_profiles/JACC_Asia.md +30 -0
- package/skills/find-journal/references/journal_profiles/JACR.md +28 -0
- package/skills/find-journal/references/journal_profiles/JAMA.md +40 -0
- package/skills/find-journal/references/journal_profiles/JAMA_Network_Open.md +30 -0
- package/skills/find-journal/references/journal_profiles/JCSM.md +39 -0
- package/skills/find-journal/references/journal_profiles/JKMS.md +32 -0
- package/skills/find-journal/references/journal_profiles/JMIR.md +29 -0
- package/skills/find-journal/references/journal_profiles/JMIR_Medical_Education.md +29 -0
- package/skills/find-journal/references/journal_profiles/JNIS.md +35 -0
- package/skills/find-journal/references/journal_profiles/JVIR.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Biomedical_Informatics.md +29 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +40 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Magnetic_Resonance_Imaging.md +30 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Nuclear_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Stroke.md +32 -0
- package/skills/find-journal/references/journal_profiles/KJR.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Circulation_Journal.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +36 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Diabetes_and_Endocrinology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +49 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Infectious_Diseases.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Neurology.md +39 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Oncology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Psychiatry.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Public_Health.md +30 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Respiratory_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Liver_International.md +33 -0
- package/skills/find-journal/references/journal_profiles/Medical_Image_Analysis.md +28 -0
- package/skills/find-journal/references/journal_profiles/NEJM.md +33 -0
- package/skills/find-journal/references/journal_profiles/Nature_Machine_Intelligence.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nature_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Neuroradiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +39 -0
- package/skills/find-journal/references/journal_profiles/PLOS_Medicine.md +32 -0
- package/skills/find-journal/references/journal_profiles/RYAI.md +28 -0
- package/skills/find-journal/references/journal_profiles/Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Skeletal_Radiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Stroke.md +37 -0
- package/skills/find-journal/references/journal_profiles/The_BMJ.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +29 -0
- package/skills/find-journal/references/journal_profiles/World_Journal_of_Hepatology.md +53 -0
- package/skills/find-journal/references/journal_profiles/npj_Digital_Medicine.md +29 -0
- package/skills/find-journal/skill.yml +34 -0
- package/skills/fulltext-retrieval/SKILL.md +174 -0
- package/skills/fulltext-retrieval/fetch_oa.py +433 -0
- package/skills/fulltext-retrieval/pdf_to_md.py +160 -0
- package/skills/fulltext-retrieval/skill.yml +41 -0
- package/skills/generate-codebook/SKILL.md +155 -0
- package/skills/generate-codebook/references/codebook_schema.md +76 -0
- package/skills/generate-codebook/scripts/generate_codebook.py +278 -0
- package/skills/generate-codebook/skill.yml +35 -0
- package/skills/generate-codebook/tests/test_generate_codebook.sh +76 -0
- package/skills/grant-builder/SKILL.md +251 -0
- package/skills/grant-builder/skill.yml +34 -0
- package/skills/humanize/SKILL.md +251 -0
- package/skills/humanize/references/ai_patterns.md +571 -0
- package/skills/humanize/skill.yml +33 -0
- package/skills/intake-project/SKILL.md +264 -0
- package/skills/intake-project/skill.yml +34 -0
- package/skills/lit-sync/SKILL.md +448 -0
- package/skills/lit-sync/references/locale/ko/note_templates.md +110 -0
- package/skills/lit-sync/skill.yml +52 -0
- package/skills/lit-sync/tests/test_poll_logic.sh +92 -0
- package/skills/ma-scout/SKILL.md +640 -0
- package/skills/ma-scout/references/project_readme_template.md +95 -0
- package/skills/ma-scout/references/project_readme_template_ko.md +82 -0
- package/skills/ma-scout/skill.yml +33 -0
- package/skills/make-figures/SKILL.md +957 -0
- package/skills/make-figures/references/critic_rubrics/data_plot.md +166 -0
- package/skills/make-figures/references/critic_rubrics/flow_diagram.md +169 -0
- package/skills/make-figures/references/design_principles.md +181 -0
- package/skills/make-figures/references/exemplar_diagrams/README.md +65 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/README.md +15 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_input.yaml +37 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.pdf +0 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.png +0 -0
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- package/skills/self-review/tests/test_confounding_completeness.sh +66 -0
- package/skills/self-review/tests/test_panel_diversity.sh +55 -0
- package/skills/self-review/tests/test_panel_mode.sh +69 -0
- package/skills/self-review/tests/test_reference_adequacy.sh +68 -0
- package/skills/self-review/tests/test_reviewer_team_consistency.sh +138 -0
- package/skills/self-review/tests/test_scope_coherence.sh +46 -0
- package/skills/setup-medsci/SKILL.md +110 -0
- package/skills/setup-medsci/references/setup-checklist.md +51 -0
- package/skills/setup-medsci/skill.yml +30 -0
- package/skills/sync-submission/SKILL.md +382 -0
- package/skills/sync-submission/scripts/author_registry_example.yaml +36 -0
- package/skills/sync-submission/scripts/blind_sweep.py +203 -0
- package/skills/sync-submission/scripts/check_asset_anonymization.py +300 -0
- package/skills/sync-submission/scripts/check_cross_artifact_stale.py +211 -0
- package/skills/sync-submission/scripts/cover_letter_drift_check.py +451 -0
- package/skills/sync-submission/scripts/cross_document_n_check.py +486 -0
- package/skills/sync-submission/scripts/detect_copy_divergence.py +136 -0
- package/skills/sync-submission/scripts/preflight_gate.py +458 -0
- package/skills/sync-submission/scripts/scope_drift_check.py +362 -0
- package/skills/sync-submission/scripts/sync_submission.py +169 -0
- package/skills/sync-submission/skill.yml +43 -0
- package/skills/sync-submission/tests/fixtures/copy_ok.md +5 -0
- package/skills/sync-submission/tests/fixtures/copy_stale.md +5 -0
- package/skills/sync-submission/tests/fixtures/ssot.md +5 -0
- package/skills/sync-submission/tests/test_asset_anonymization.sh +99 -0
- package/skills/sync-submission/tests/test_copy_divergence.sh +44 -0
- package/skills/sync-submission/tests/test_cross_artifact_stale.sh +80 -0
- package/skills/sync-submission/tests/test_cross_document_n.sh +132 -0
- package/skills/sync-submission/tests/test_preflight_gate.sh +112 -0
- package/skills/sync-submission/tests/test_scope_drift.sh +122 -0
- package/skills/sync-submission/tests/test_vN_docx_assertion.sh +51 -0
- package/skills/verify-refs/SKILL.md +177 -0
- package/skills/verify-refs/references/manual_checkpoint_guide.md +100 -0
- package/skills/verify-refs/scripts/verify_cli.sh +62 -0
- package/skills/verify-refs/scripts/verify_refs.py +782 -0
- package/skills/verify-refs/skill.yml +44 -0
- package/skills/verify-refs/tests/fixtures/pagination_placeholder.bib +17 -0
- package/skills/verify-refs/tests/test_pagination_placeholder.sh +42 -0
- package/skills/version-dataset/SKILL.md +143 -0
- package/skills/version-dataset/references/manifest_schema.md +72 -0
- package/skills/version-dataset/scripts/version_dataset.py +242 -0
- package/skills/version-dataset/skill.yml +35 -0
- package/skills/version-dataset/tests/test_version_dataset.sh +52 -0
- package/skills/write-paper/SKILL.md +1148 -0
- package/skills/write-paper/references/exemplar_methods/README.md +38 -0
- package/skills/write-paper/references/exemplar_methods/ai_validation_tripod_claim.md +47 -0
- package/skills/write-paper/references/exemplar_methods/diagnostic_accuracy_stard.md +50 -0
- package/skills/write-paper/references/exemplar_methods/observational_cohort_strobe.md +43 -0
- package/skills/write-paper/references/journal_profiles/AJNR.md +185 -0
- package/skills/write-paper/references/journal_profiles/AJR.md +149 -0
- package/skills/write-paper/references/journal_profiles/Abdominal_Radiology.md +139 -0
- package/skills/write-paper/references/journal_profiles/Academic_Radiology.md +90 -0
- package/skills/write-paper/references/journal_profiles/Annals_of_Internal_Medicine.md +150 -0
- package/skills/write-paper/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +82 -0
- package/skills/write-paper/references/journal_profiles/British_Journal_of_Radiology.md +161 -0
- package/skills/write-paper/references/journal_profiles/CVIR.md +157 -0
- package/skills/write-paper/references/journal_profiles/Chest.md +270 -0
- package/skills/write-paper/references/journal_profiles/Clinical_Radiology.md +160 -0
- package/skills/write-paper/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +147 -0
- package/skills/write-paper/references/journal_profiles/Diabetes_Metabolism_Journal.md +163 -0
- package/skills/write-paper/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +216 -0
- package/skills/write-paper/references/journal_profiles/Endocrinology_and_Metabolism.md +167 -0
- package/skills/write-paper/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +192 -0
- package/skills/write-paper/references/journal_profiles/European_Radiology.md +159 -0
- package/skills/write-paper/references/journal_profiles/Hepatology_Communications.md +110 -0
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- package/skills/write-paper/references/journal_profiles/IEEE_TMI.md +180 -0
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- package/skills/write-paper/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +127 -0
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# MA-Scout Project README Template (PROSPERO-ready)
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Load this reference when `/ma-scout` Phase 4 (Folder & README Scaffolding) creates a
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new topic folder. English section headings and PICO/PIRD structure keep the README aligned
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with downstream `/meta-analysis` and `/search-lit` expectations.
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This is the English default. For a supervisor / professor-facing Korean README, use
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`project_readme_template_ko.md` (same structure, Korean prompts for the PI-facing fields).
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Copy the block below into `{topic_folder}/README.md` and fill in the curly-brace fields.
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````markdown
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# {Topic Title} — {MA Type} Meta-analysis ({Supervisor name})
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## 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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## 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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### One-line RQ
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{the complete research question in one sentence}
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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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## 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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## 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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### Embase Search Strategy (Draft)
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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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## Target Journal
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| Rank | Journal | IF | MA acceptance rate | Turnaround | Notes |
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| 1st | {journal} | {IF} | {high/medium} | {months} | {rationale} |
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## Timeline (backwards-planned)
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| Stage | Estimated time | Prerequisite |
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| Supervisor proposal | {YYYY-MM} | {condition} |
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| PROSPERO registration | +1 week | Supervisor approval |
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| Search complete | +2 weeks | PROSPERO registration |
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| Screening complete | +3 weeks | 2nd reviewer secured |
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| Data extraction | +4 weeks | Screening consensus |
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| Analysis + draft | +6 weeks | Data lock |
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| Supervisor review | +8 weeks | Draft complete |
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| Submission | +10 weeks | Supervisor approval |
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## Data Sources Used
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- Scholar Gateway: ✅/❌
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````
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## Solo-Mode Adaptations (no supervisor)
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substitute:
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`Supervisor review` rows.
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- Replace `Supervisor approval` in the Timeline `Prerequisite` column with `self-approval` or
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the lead author's own sign-off step.
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# MA-Scout Project README Template — Korean variant (PROSPERO-ready)
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> Opt-in Korean variant. The default is the English `project_readme_template.md`. Use this when the
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> README is supervisor / professor-facing for a Korean PI review. English section headings and
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> PICO/PIRD structure are kept (so the README matches downstream `/meta-analysis` and `/search-lit`
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> expectations); Korean prompts are used for the PI-facing fields.
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Copy the block below into `{topic_folder}/README.md` and fill in the curly-brace fields.
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````markdown
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# {Topic Title} — {MA Type} Meta-analysis ({교수님 성함})
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## Overview
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- Supervisor: {교수님 성함} ({소속 이력})
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- 교수님 영역: Pillar {N} — {영역명}
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- Status: 기획 단계
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- Priority: {순위}순위
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- Created: {YYYY-MM-DD}
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## Research Question
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### PICO/PIRD
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- **P**opulation: {구체적 환자군, 질환, 세팅}
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- **I**ndex test / Intervention: {검사법 또는 중재}
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- **C**omparator / Reference standard: {비교군 또는 참조표준}
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- **O**utcome: {DTA: Se/Sp/AUC, Prognostic: HR/OR, 부작용 등}
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### One-line RQ
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{완성형 연구 질문 1문장}
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## Key Gap
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- Consensus/Scholar Gateway 추가 확인: {결과 요약}
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- medRxiv/bioRxiv preprint MA: {있음/없음}
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- PROSPERO 등록 프로토콜: {있음 (CRD#) / 없음}
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- {구체적 gap 설명 — 왜 새 MA가 필요한지}
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## Professor's Authority
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- {분야 관련 논문 수, 대표 논문 1-2편, 독보적 기여}
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- {왜 이 교수님이 이 주제에 적합한지}
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## Preliminary Search ({날짜})
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### Search Strategy (PubMed)
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```
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{실제 사용한 PubMed 검색식 — E-utilities esearch query 그대로}
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```
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- Total hits: {N}편 (raw)
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- DTA/outcome extractable (estimated): {N}편 (×0.15-0.30 discount)
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- 기존 MA: {N}편 (narrow) / {N}편 (broad SR 포함)
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- Consensus 검색 결과: {N}편 추가 발견 여부
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- bioRxiv/medRxiv: {N}편 preprint
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### Embase Search Strategy (Draft)
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```
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{Embase용 검색식 초안 — Emtree 용어 포함}
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```
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+
(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
|