[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M71QJDEFD7HEXDR2B59QE93V":3,"skill-same:01M71QJDEFD7HEXDR2B59QE93V":83},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":23,"publishedAt":44,"linkOnly":45,"markdownContent":46,"markdownBody":47,"frontMatter":48,"refName":50,"commitSha":51,"skillDirectory":52,"forksCount":53,"repositoryHtmlUrl":54,"repositoryHomepageUrl":55,"ownerHtmlUrl":56,"ownerBlogUrl":6,"ownerDescription":57,"updatedAt":58,"install":59,"resources":72},"01M71QJDEFD7HEXDR2B59QE93V","method-evidence-map",null,"Builds a source-backed evidence map for a biomedical question from PubMed, optionally deepened with Paperclip full text. Use when a SAP or manuscript needs mapped evidence.","sajor2000\u002Fmethodsmith","sajor2000","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F126191042?v=4","01M71QG4M3561SH49E3S7J3GKT","JC Rojas ","01M71QG4N56X2P61YTJSRP95VD",6,"MIT","https:\u002F\u002Fgithub.com\u002Fsajor2000\u002Fmethodsmith\u002Fblob\u002Fmain\u002Fplugins\u002Fmethodsmith\u002Fskills\u002Fmethod-evidence-map\u002FSKILL.md",[18],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000021","资料检索与研究","SCENARIO","使用场景",[24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],"evidence","method evidence map","map","with","use","for","sap","manuscript","biomedical","full","source","research query","max","pubmed","text","query","when","question","paperclip","pmc","2026-11-10 13:02:02",false,"---\nname: method-evidence-map\ndescription: \"Builds a source-backed evidence map for a biomedical question from PubMed, optionally deepened with Paperclip full text. Use when a SAP or manuscript needs mapped evidence.\"\nargument-hint: \"[research query, optional: --source pmc|abstracts|trials|fda --max 10]\"\n---\n\n# Evidence Map\n\n## Skill Value\n\n- **Problem it solves:** Literature grounding needs a traceable map from claims to PubMed records, optional full-text evidence, and downstream SAP\u002Fmethod decisions.\n- **Use when:** The user needs evidence for a SAP, method justification, effect-size selection, manuscript background, or review pack.\n- **Output:** `analysis\u002Fevidence-map\u002F\u003Cquery-slug>-evidence-map.md` plus a `__CE_EVIDENCE_MAP__` handoff signal.\n- **Ask only if:** No research query or PubMed handoff is available, or the user must choose a non-default Paperclip source or figure-review target.\n- **Do not do:** Do not replace `method-pubmed`, install\u002Fauthenticate Paperclip automatically, pool effect sizes, or finalize SAP methods before data QA.\n\nCreate a traceable evidence map for SAPs, method justification, effect-size\nselection, manuscript background, or review-pack evidence summaries.\n\nThis skill keeps PubMed\u002FMEDLINE as the canonical biomedical metadata baseline\nand treats Paperclip as an optional full-text deepening layer. Never require\nPaperclip for normal plugin operation.\n\n## Evidence access\n\nWhen this run needs literature, read `references\u002Fevidence-access.md` first; never invent a citation, effect size, or guideline item.\n\n- **Look up here:** every claim in the claim-to-source matrix (cohort definitions, outcomes, model or effect estimates, covariate sets, limitations) and the figures or trial records behind them.\n\n**MCP egress (every mode):** send PubMed, Paperclip, and other MCP or web tools only search terms, MeSH terms, PMIDs, DOIs, and titles, never data values, identifiers, row text, or data files; an endpoint approval does not cover third-party services.\n\n## Prerequisites\n\n- PubMed baseline: Load the `method-pubmed` skill first or provide a query this skill can pass\n  to `method-pubmed`.\n- Optional Paperclip deepening, in preference order:\n  1. **Paperclip MCP server connected** (tools `search`, `lookup`, `cat`, `grep`,\n     `scan`, `map`, `filter`, `results`, `ask-image`, `status`). Call `status` to\n     confirm backend health. No install step is needed.\n  2. **Paperclip CLI fallback** when no MCP server is connected. Check availability\n     without installing anything:\n\n     ```bash\n     command -v paperclip && paperclip config\n     ```\n\nIf neither is available or the CLI is unauthenticated, continue with PubMed-only\nevidence and state the limitation. Do not run the Paperclip installer automatically.\nThe evidence labels are the same whichever path is used.\n\n## Workflow\n\n### Step 0: Resolve query and baseline context\n\nRead `$ARGUMENTS`.\n\nIf no query was passed, scan recent chat for these handoff signals:\n\n```text\n__CE_RESEARCH_QUESTION__ yaml=\u003Cpath> ... query=\"\u003Cone-line>\"\n__CE_PUBMED_RESULTS__ csv=\u003Cpath> n=\u003Ccount> query=\u003C...> pmc_pct=\u003C...>\n```\n\nResolution order:\n\n1. Explicit query in `$ARGUMENTS`.\n2. `__CE_RESEARCH_QUESTION__` suggested PubMed query.\n3. `__CE_PUBMED_RESULTS__` query.\n\nIf neither a query nor a PubMed CSV exists, ask the user for a research question\nor tell them to load the `method-question` skill then `method-pubmed`.\n\n### Step 1: Establish PubMed baseline\n\nIf `__CE_PUBMED_RESULTS__` is present, read the CSV and use it as the metadata\nbaseline.\n\nIf no PubMed CSV exists, load the `method-pubmed` skill with the resolved query before\ncontinuing (it uses the PubMed MCP search and metadata tools,\n`pubmed_search_articles`\u002F`pubmed_fetch_articles` or\n`search_articles`\u002F`get_article_metadata`, or the bundled E-utilities script). The\nevidence map must include PMIDs, years, journals, abstracts, MeSH\u002Fstudy-type\nmetadata when available, and PMC availability status. For rows with a PMCID and\nno Paperclip, PubMed MCP full text (`pubmed_fetch_fulltext`, or\n`get_copyright_status` then `get_full_text_article`) gives lawful open full\ntext; label those claims `full_text` and cite PubMed with the DOI.\n\nPubMed rows are the baseline because they are stable, biomedical-native, and\nportable across corporate environments where Paperclip may be unavailable.\n\n### Step 2: Optional Paperclip deepening\n\nOnly when the Paperclip MCP server is connected or the CLI is authenticated, read `references\u002Fpaperclip-deepening.md` and follow it (MCP `search`\u002F`map`\u002F`grep`\u002F`ask-image`, or the CLI fallback). Treat Paperclip output as evidence-deepening, not ground truth: a hit is not evidence until the quoted text or figure behind it has been read.\n\n### Step 3: Write evidence map\n\nWrite the evidence map to:\n\n```text\nanalysis\u002Fevidence-map\u002F\u003Cquery-slug>-evidence-map.md\n```\n\nCreate parent directories as needed. Keep real subject data out of this artifact;\nit should contain literature, trial-registry, regulatory, and software\ndocumentation evidence only.\n\nRequired sections:\n\n1. **Search provenance**: query, date, PubMed CSV path, Paperclip source\u002Fresult IDs\n   when used, which path (MCP or CLI) was used, and whether full text was available.\n2. **Included evidence table**: PMID or document ID, title, year, source,\n   journal\u002Fdocument type, DOI, PMC\u002Ffull-text status, `design` (RCT \u002F cohort \u002F\n   case-control \u002F cross-sectional \u002F simulation \u002F methods guidance), `bias_flags`\n   (selection, confounding, small n, single site, outcome reporting; not a formal\n   risk-of-bias grade), and one-line relevance.\n3. **Claim-to-source matrix**: each claim, supporting source IDs, evidence label\n   (`abstract`, `full_text`, `figure`, `trial`, `regulatory`, `documentation`),\n   and notes.\n4. **Methods and effect-size clues**: cohort definition, outcome, model\u002Feffect\n   estimate, key predictors\u002Fcovariates, limitations, and whether details came\n   from abstract or full text.\n5. **Evidence gaps**: missing full text, unclear cohort definitions, missing\n   confidence intervals, unclear adjustment sets, contradictory findings, and\n   effect estimates likely inflated by publication bias or small samples.\n6. **Recommended handoffs**: `method-extract`, `method-meta-analysis`,\n   `method-power`, `method-checklist`, or `method-plan`.\n\nUse conservative language:\n\n- If only PubMed abstracts were read, label claims `abstract`.\n- If PMC or Paperclip full text was read, label claims `full_text`.\n- If figure QA was used, label claims `figure` and include the figure path or\n  paper figure identifier.\n- If a ClinicalTrials.gov or other trial-registry record was read, label claims\n  `trial`.\n- If a regulation or agency guidance document was read at its issuing body's\n  source, label claims `regulatory`.\n- If official software or package documentation was read (for a method\n  justification), label claims `documentation`.\n- Identifier or metadata lookups alone (DOI\u002FPMID conversion, titles, journals)\n  do not verify a claim; label the claim only once its source is read.\n\n### Step 4: Emit handoff\n\nAfter writing the evidence map, emit:\n\n```text\n__CE_EVIDENCE_MAP__ path=\u003Cartifact> sources=pubmed[,paperclip] full_text_pct=\u003Cn> claims=\u003Cn>\n```\n\nDownstream skills can use this artifact to avoid repeating literature search and\nto distinguish abstract-only evidence from full-text-verified evidence.\n\nCompletion check before emitting: every claim in the matrix cites at least one\nsource ID and one evidence label, `full_text_pct` and `claims` match the\nartifact, and no subject-level data appears in it.\n\n## Failure handling\n\n| Condition | Response |\n|-----------|----------|\n| Paperclip MCP not connected and CLI not installed | Continue PubMed-only (PMC full text via `pubmed_fetch_fulltext` or `get_full_text_article` where open); say Paperclip is optional. |\n| Paperclip CLI unauthenticated | Continue PubMed-only; suggest `paperclip login` or `PAPERCLIP_API_KEY`. |\n| Paperclip search requires source | Retry with explicit `source: pmc` (MCP) or `-s pmc` (CLI) unless the user requested another source. |\n| Paperclip map output is truncated | Re-read the saved result (`results` tool, or `paperclip results \u003Cid>`); if still truncated, summarize visible fields and note the limitation. |\n| Figure command fails | Skip figure QA and keep text evidence; do not block the evidence map. |\n\n## What this skill does NOT do\n\n- Does not replace `method-pubmed`.\n- Does not install or authenticate Paperclip automatically.\n- Does not pool effect sizes; use the `method-meta-analysis` skill.\n- Does not finalize SAP methods without data QA; `method-plan` still requires\n  data-column and QA preflight before variable\u002Fmodel finalization.\n","# Evidence Map\n\n## Skill Value\n\n- **Problem it solves:** Literature grounding needs a traceable map from claims to PubMed records, optional full-text evidence, and downstream SAP\u002Fmethod decisions.\n- **Use when:** The user needs evidence for a SAP, method justification, effect-size selection, manuscript background, or review pack.\n- **Output:** `analysis\u002Fevidence-map\u002F\u003Cquery-slug>-evidence-map.md` plus a `__CE_EVIDENCE_MAP__` handoff signal.\n- **Ask only if:** No research query or PubMed handoff is available, or the user must choose a non-default Paperclip source or figure-review target.\n- **Do not do:** Do not replace `method-pubmed`, install\u002Fauthenticate Paperclip automatically, pool effect sizes, or finalize SAP methods before data QA.\n\nCreate a traceable evidence map for SAPs, method justification, effect-size\nselection, manuscript background, or review-pack evidence summaries.\n\nThis skill keeps PubMed\u002FMEDLINE as the canonical biomedical metadata baseline\nand treats Paperclip as an optional full-text deepening layer. Never require\nPaperclip for normal plugin operation.\n\n## Evidence access\n\nWhen this run needs literature, read `references\u002Fevidence-access.md` first; never invent a citation, effect size, or guideline item.\n\n- **Look up here:** every claim in the claim-to-source matrix (cohort definitions, outcomes, model or effect estimates, covariate sets, limitations) and the figures or trial records behind them.\n\n**MCP egress (every mode):** send PubMed, Paperclip, and other MCP or web tools only search terms, MeSH terms, PMIDs, DOIs, and titles, never data values, identifiers, row text, or data files; an endpoint approval does not cover third-party services.\n\n## Prerequisites\n\n- PubMed baseline: Load the `method-pubmed` skill first or provide a query this skill can pass\n  to `method-pubmed`.\n- Optional Paperclip deepening, in preference order:\n  1. **Paperclip MCP server connected** (tools `search`, `lookup`, `cat`, `grep`,\n     `scan`, `map`, `filter`, `results`, `ask-image`, `status`). Call `status` to\n     confirm backend health. No install step is needed.\n  2. **Paperclip CLI fallback** when no MCP server is connected. Check availability\n     without installing anything:\n\n     ```bash\n     command -v paperclip && paperclip config\n     ```\n\nIf neither is available or the CLI is unauthenticated, continue with PubMed-only\nevidence and state the limitation. Do not run the Paperclip installer automatically.\nThe evidence labels are the same whichever path is used.\n\n## Workflow\n\n### Step 0: Resolve query and baseline context\n\nRead `$ARGUMENTS`.\n\nIf no query was passed, scan recent chat for these handoff signals:\n\n```text\n__CE_RESEARCH_QUESTION__ yaml=\u003Cpath> ... query=\"\u003Cone-line>\"\n__CE_PUBMED_RESULTS__ csv=\u003Cpath> n=\u003Ccount> query=\u003C...> pmc_pct=\u003C...>\n```\n\nResolution order:\n\n1. Explicit query in `$ARGUMENTS`.\n2. `__CE_RESEARCH_QUESTION__` suggested PubMed query.\n3. `__CE_PUBMED_RESULTS__` query.\n\nIf neither a query nor a PubMed CSV exists, ask the user for a research question\nor tell them to load the `method-question` skill then `method-pubmed`.\n\n### Step 1: Establish PubMed baseline\n\nIf `__CE_PUBMED_RESULTS__` is present, read the CSV and use it as the metadata\nbaseline.\n\nIf no PubMed CSV exists, load the `method-pubmed` skill with the resolved query before\ncontinuing (it uses the PubMed MCP search and metadata tools,\n`pubmed_search_articles`\u002F`pubmed_fetch_articles` or\n`search_articles`\u002F`get_article_metadata`, or the bundled E-utilities script). The\nevidence map must include PMIDs, years, journals, abstracts, MeSH\u002Fstudy-type\nmetadata when available, and PMC availability status. For rows with a PMCID and\nno Paperclip, PubMed MCP full text (`pubmed_fetch_fulltext`, or\n`get_copyright_status` then `get_full_text_article`) gives lawful open full\ntext; label those claims `full_text` and cite PubMed with the DOI.\n\nPubMed rows are the baseline because they are stable, biomedical-native, and\nportable across corporate environments where Paperclip may be unavailable.\n\n### Step 2: Optional Paperclip deepening\n\nOnly when the Paperclip MCP server is connected or the CLI is authenticated, read `references\u002Fpaperclip-deepening.md` and follow it (MCP `search`\u002F`map`\u002F`grep`\u002F`ask-image`, or the CLI fallback). Treat Paperclip output as evidence-deepening, not ground truth: a hit is not evidence until the quoted text or figure behind it has been read.\n\n### Step 3: Write evidence map\n\nWrite the evidence map to:\n\n```text\nanalysis\u002Fevidence-map\u002F\u003Cquery-slug>-evidence-map.md\n```\n\nCreate parent directories as needed. Keep real subject data out of this artifact;\nit should contain literature, trial-registry, regulatory, and software\ndocumentation evidence only.\n\nRequired sections:\n\n1. **Search provenance**: query, date, PubMed CSV path, Paperclip source\u002Fresult IDs\n   when used, which path (MCP or CLI) was used, and whether full text was available.\n2. **Included evidence table**: PMID or document ID, title, year, source,\n   journal\u002Fdocument type, DOI, PMC\u002Ffull-text status, `design` (RCT \u002F cohort \u002F\n   case-control \u002F cross-sectional \u002F simulation \u002F methods guidance), `bias_flags`\n   (selection, confounding, small n, single site, outcome reporting; not a formal\n   risk-of-bias grade), and one-line relevance.\n3. **Claim-to-source matrix**: each claim, supporting source IDs, evidence label\n   (`abstract`, `full_text`, `figure`, `trial`, `regulatory`, `documentation`),\n   and notes.\n4. **Methods and effect-size clues**: cohort definition, outcome, model\u002Feffect\n   estimate, key predictors\u002Fcovariates, limitations, and whether details came\n   from abstract or full text.\n5. **Evidence gaps**: missing full text, unclear cohort definitions, missing\n   confidence intervals, unclear adjustment sets, contradictory findings, and\n   effect estimates likely inflated by publication bias or small samples.\n6. **Recommended handoffs**: `method-extract`, `method-meta-analysis`,\n   `method-power`, `method-checklist`, or `method-plan`.\n\nUse conservative language:\n\n- If only PubMed abstracts were read, label claims `abstract`.\n- If PMC or Paperclip full text was read, label claims `full_text`.\n- If figure QA was used, label claims `figure` and include the figure path or\n  paper figure identifier.\n- If a ClinicalTrials.gov or other trial-registry record was read, label claims\n  `trial`.\n- If a regulation or agency guidance document was read at its issuing body's\n  source, label claims `regulatory`.\n- If official software or package documentation was read (for a method\n  justification), label claims `documentation`.\n- Identifier or metadata lookups alone (DOI\u002FPMID conversion, titles, journals)\n  do not verify a claim; label the claim only once its source is read.\n\n### Step 4: Emit handoff\n\nAfter writing the evidence map, emit:\n\n```text\n__CE_EVIDENCE_MAP__ path=\u003Cartifact> sources=pubmed[,paperclip] full_text_pct=\u003Cn> claims=\u003Cn>\n```\n\nDownstream skills can use this artifact to avoid repeating literature search and\nto distinguish abstract-only evidence from full-text-verified evidence.\n\nCompletion check before emitting: every claim in the matrix cites at least one\nsource ID and one evidence label, `full_text_pct` and `claims` match the\nartifact, and no subject-level data appears in it.\n\n## Failure handling\n\n| Condition | Response |\n|-----------|----------|\n| Paperclip MCP not connected and CLI not installed | Continue PubMed-only (PMC full text via `pubmed_fetch_fulltext` or `get_full_text_article` where open); say Paperclip is optional. |\n| Paperclip CLI unauthenticated | Continue PubMed-only; suggest `paperclip login` or `PAPERCLIP_API_KEY`. |\n| Paperclip search requires source | Retry with explicit `source: pmc` (MCP) or `-s pmc` (CLI) unless the user requested another source. |\n| Paperclip map output is truncated | Re-read the saved result (`results` tool, or `paperclip results \u003Cid>`); if still truncated, summarize visible fields and note the limitation. |\n| Figure command fails | Skip figure QA and keep text evidence; do not block the evidence map. |\n\n## What this skill does NOT do\n\n- Does not replace `method-pubmed`.\n- Does not install or authenticate Paperclip automatically.\n- Does not pool effect sizes; use the `method-meta-analysis` skill.\n- Does not finalize SAP methods without data QA; `method-plan` still requires\n  data-column and QA preflight before variable\u002Fmodel 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Use when scientific prose must be written or revised (entry point).","https:\u002F\u002Fgithub.com\u002Fsajor2000\u002Fmethodsmith\u002Fblob\u002Fmain\u002Fplugins\u002Fmethodsmith\u002Fskills\u002Fmethod-write\u002FSKILL.md",[],[148,149,150,24,151,152,28,40,153,154,27,155,156,157],"write","method write","point","entry","claim","provenance","reviewer","scientific","prose","drafts"]