From 2ed577246d6f363fccd14de3c6646a6e28aa02ab Mon Sep 17 00:00:00 2001 From: Research Assistant Date: Tue, 21 Apr 2026 23:00:50 +0800 Subject: [PATCH] refactor: move chart-reading into literature-qa skill MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Chart guides are references for literature-qa, not standalone skill - Move skills/chart-reading/ -> skills/literature-qa/chart-reading/ - Update setup.py deploy path - Update prompt_deep_subagent.md references - Update 科研读图指南.md links --- scripts/setup.py | 6 ++-- .../chart-reading/GSEA富集图.md | 0 .../chart-reading/ROC与PR曲线.md | 0 .../chart-reading/散点图与气泡图.md | 0 .../chart-reading/条形图与误差棒.md | 0 .../chart-reading/桑基图与弦图.md | 0 .../chart-reading/森林图与Meta分析.md | 0 .../chart-reading/火山图与曼哈顿图.md | 0 .../chart-reading/热图与聚类图.md | 0 .../chart-reading/生存曲线.md | 0 .../chart-reading/箱式图与小提琴图.md | 0 .../chart-reading/网络图与通路图.md | 0 .../chart-reading/蛋白质结构图.md | 0 .../chart-reading/降维图(PCA-tSNE-UMAP).md | 0 .../chart-reading/雷达图与漏斗图.md | 0 skills/literature-qa/prompt_deep_subagent.md | 2 +- templates/科研读图指南.md | 28 +++++++++---------- 17 files changed, 18 insertions(+), 18 deletions(-) rename skills/{ => literature-qa}/chart-reading/GSEA富集图.md (100%) rename skills/{ => literature-qa}/chart-reading/ROC与PR曲线.md (100%) rename skills/{ => literature-qa}/chart-reading/散点图与气泡图.md (100%) rename skills/{ => literature-qa}/chart-reading/条形图与误差棒.md (100%) rename skills/{ => literature-qa}/chart-reading/桑基图与弦图.md (100%) rename skills/{ => literature-qa}/chart-reading/森林图与Meta分析.md (100%) rename skills/{ => literature-qa}/chart-reading/火山图与曼哈顿图.md (100%) rename skills/{ => literature-qa}/chart-reading/热图与聚类图.md (100%) rename skills/{ => literature-qa}/chart-reading/生存曲线.md (100%) rename skills/{ => literature-qa}/chart-reading/箱式图与小提琴图.md (100%) rename skills/{ => literature-qa}/chart-reading/网络图与通路图.md (100%) rename skills/{ => literature-qa}/chart-reading/蛋白质结构图.md (100%) rename skills/{ => literature-qa}/chart-reading/降维图(PCA-tSNE-UMAP).md (100%) rename skills/{ => literature-qa}/chart-reading/雷达图与漏斗图.md (100%) diff --git a/scripts/setup.py b/scripts/setup.py index 5cd77afd..b77a2126 100644 --- a/scripts/setup.py +++ b/scripts/setup.py @@ -482,9 +482,9 @@ def deploy_workflow_scripts(vault_path: Path, agent_key: str, agent_config: dict print_error(f"Failed to deploy {src_rel}: {e}") fail_count += 1 - # Deploy chart reading guides (into agent-specific skill dir) - chart_guide_src = repo_root / "skills/chart-reading" - chart_guide_dst = vault_path / skill_dir / "chart-reading" + # Deploy chart reading guides (into literature-qa skill as references) + chart_guide_src = repo_root / "skills/literature-qa/chart-reading" + chart_guide_dst = vault_path / skill_dir / "literature-qa/chart-reading" if chart_guide_src.exists() and chart_guide_src.is_dir(): chart_files = list(chart_guide_src.glob("*.md")) diff --git a/skills/chart-reading/GSEA富集图.md b/skills/literature-qa/chart-reading/GSEA富集图.md similarity index 100% rename from skills/chart-reading/GSEA富集图.md rename to skills/literature-qa/chart-reading/GSEA富集图.md diff --git a/skills/chart-reading/ROC与PR曲线.md b/skills/literature-qa/chart-reading/ROC与PR曲线.md similarity index 100% rename from skills/chart-reading/ROC与PR曲线.md rename to skills/literature-qa/chart-reading/ROC与PR曲线.md diff --git a/skills/chart-reading/散点图与气泡图.md b/skills/literature-qa/chart-reading/散点图与气泡图.md similarity index 100% rename from skills/chart-reading/散点图与气泡图.md rename to skills/literature-qa/chart-reading/散点图与气泡图.md diff --git a/skills/chart-reading/条形图与误差棒.md b/skills/literature-qa/chart-reading/条形图与误差棒.md similarity index 100% rename from skills/chart-reading/条形图与误差棒.md rename to skills/literature-qa/chart-reading/条形图与误差棒.md diff --git a/skills/chart-reading/桑基图与弦图.md b/skills/literature-qa/chart-reading/桑基图与弦图.md similarity index 100% rename from skills/chart-reading/桑基图与弦图.md rename to skills/literature-qa/chart-reading/桑基图与弦图.md diff --git a/skills/chart-reading/森林图与Meta分析.md b/skills/literature-qa/chart-reading/森林图与Meta分析.md similarity index 100% rename from skills/chart-reading/森林图与Meta分析.md rename to skills/literature-qa/chart-reading/森林图与Meta分析.md diff --git a/skills/chart-reading/火山图与曼哈顿图.md b/skills/literature-qa/chart-reading/火山图与曼哈顿图.md similarity index 100% rename from skills/chart-reading/火山图与曼哈顿图.md rename to skills/literature-qa/chart-reading/火山图与曼哈顿图.md diff --git a/skills/chart-reading/热图与聚类图.md b/skills/literature-qa/chart-reading/热图与聚类图.md similarity index 100% rename from skills/chart-reading/热图与聚类图.md rename to skills/literature-qa/chart-reading/热图与聚类图.md diff --git a/skills/chart-reading/生存曲线.md b/skills/literature-qa/chart-reading/生存曲线.md similarity index 100% rename from skills/chart-reading/生存曲线.md rename to skills/literature-qa/chart-reading/生存曲线.md diff --git a/skills/chart-reading/箱式图与小提琴图.md b/skills/literature-qa/chart-reading/箱式图与小提琴图.md similarity index 100% rename from skills/chart-reading/箱式图与小提琴图.md rename to skills/literature-qa/chart-reading/箱式图与小提琴图.md diff --git a/skills/chart-reading/网络图与通路图.md b/skills/literature-qa/chart-reading/网络图与通路图.md similarity index 100% rename from skills/chart-reading/网络图与通路图.md rename to skills/literature-qa/chart-reading/网络图与通路图.md diff --git a/skills/chart-reading/蛋白质结构图.md b/skills/literature-qa/chart-reading/蛋白质结构图.md similarity index 100% rename from skills/chart-reading/蛋白质结构图.md rename to skills/literature-qa/chart-reading/蛋白质结构图.md diff --git a/skills/chart-reading/降维图(PCA-tSNE-UMAP).md b/skills/literature-qa/chart-reading/降维图(PCA-tSNE-UMAP).md similarity index 100% rename from skills/chart-reading/降维图(PCA-tSNE-UMAP).md rename to skills/literature-qa/chart-reading/降维图(PCA-tSNE-UMAP).md diff --git a/skills/chart-reading/雷达图与漏斗图.md b/skills/literature-qa/chart-reading/雷达图与漏斗图.md similarity index 100% rename from skills/chart-reading/雷达图与漏斗图.md rename to skills/literature-qa/chart-reading/雷达图与漏斗图.md diff --git a/skills/literature-qa/prompt_deep_subagent.md b/skills/literature-qa/prompt_deep_subagent.md index a5272638..3f00cf39 100644 --- a/skills/literature-qa/prompt_deep_subagent.md +++ b/skills/literature-qa/prompt_deep_subagent.md @@ -147,7 +147,7 @@ python {{SCRIPT}} figure-map "{{FULLTEXT_MD}}" --key {{ZOTERO_KEY}} --out "D:\L\ - 轴标签是否完整？单位是否标注？ - 是否有 error bars / 置信区间 / 统计显著性标记？ - 如果缺少这些，对结论可信度有什么影响？ -- **[进阶]** 识别图表类型后，参考 `99_System/Template/读图指南/` 中的对应子指南进行深度审查（如箱式图看IQR与异常值、热图看标准化与批次、ROC曲线看截断点与AUC置信区间等） +- **[进阶]** 识别图表类型后，参考 `chart-reading/` 中的对应子指南进行深度审查（如箱式图看IQR与异常值、热图看标准化与批次、ROC曲线看截断点与AUC置信区间等） **作者解释** - 作者在文中对该图的描述： diff --git a/templates/科研读图指南.md b/templates/科研读图指南.md index 3532462a..1c11e86d 100644 --- a/templates/科研读图指南.md +++ b/templates/科研读图指南.md @@ -28,20 +28,20 @@ | 图表类型 | 识别关键词 | 子指南文件 | |---------|-----------|-----------| -| 箱式图 / 小提琴图 | boxplot, violin, quartile, median, IQR | [[读图指南/箱式图与小提琴图]] | -| 热图 / 聚类图 | heatmap, clustering, dendrogram, z-score | [[读图指南/热图与聚类图]] | -| PCA / t-SNE / UMAP | principal component, embedding, dimensionality reduction | [[读图指南/降维图(PCA-tSNE-UMAP)]] | -| ROC / PR 曲线 | ROC, AUC, sensitivity, specificity, precision-recall | [[读图指南/ROC与PR曲线]] | -| 生存曲线 | Kaplan-Meier, survival, hazard ratio, log-rank | [[读图指南/生存曲线]] | -| 火山图 / 曼哈顿图 | volcano plot, log2 fold change, -log10 p, GWAS | [[读图指南/火山图与曼哈顿图]] | -| 散点图 / 气泡图 | scatter plot, bubble, correlation, regression | [[读图指南/散点图与气泡图]] | -| 条形图 / 误差棒 | bar chart, SEM, SD, confidence interval | [[读图指南/条形图与误差棒]] | -| GSEA 富集图 | enrichment plot, ES, NES, leading edge | [[读图指南/GSEA富集图]] | -| 森林图 / Meta 分析 | forest plot, meta-analysis, odds ratio, I2 | [[读图指南/森林图与Meta分析]] | -| 雷达图 / 漏斗图 | radar chart, funnel plot, publication bias | [[读图指南/雷达图与漏斗图]] | -| 网络图 / 通路图 | network, pathway, PPI, interaction | [[读图指南/网络图与通路图]] | -| 桑基图 / 弦图 | Sankey, chord, alluvial, flow | [[读图指南/桑基图与弦图]] | -| 蛋白质结构图 | protein structure, PDB, Cryo-EM, X-ray | [[读图指南/蛋白质结构图]] | +| 箱式图 / 小提琴图 | boxplot, violin, quartile, median, IQR | 箱式图与小提琴图 | +| 热图 / 聚类图 | heatmap, clustering, dendrogram, z-score | 热图与聚类图 | +| PCA / t-SNE / UMAP | principal component, embedding, dimensionality reduction | 降维图(PCA-tSNE-UMAP) | +| ROC / PR 曲线 | ROC, AUC, sensitivity, specificity, precision-recall | ROC与PR曲线 | +| 生存曲线 | Kaplan-Meier, survival, hazard ratio, log-rank | 生存曲线 | +| 火山图 / 曼哈顿图 | volcano plot, log2 fold change, -log10 p, GWAS | 火山图与曼哈顿图 | +| 散点图 / 气泡图 | scatter plot, bubble, correlation, regression | 散点图与气泡图 | +| 条形图 / 误差棒 | bar chart, SEM, SD, confidence interval | 条形图与误差棒 | +| GSEA 富集图 | enrichment plot, ES, NES, leading edge | GSEA富集图 | +| 森林图 / Meta 分析 | forest plot, meta-analysis, odds ratio, I2 | 森林图与Meta分析 | +| 雷达图 / 漏斗图 | radar chart, funnel plot, publication bias | 雷达图与漏斗图 | +| 网络图 / 通路图 | network, pathway, PPI, interaction | 网络图与通路图 | +| 桑基图 / 弦图 | Sankey, chord, alluvial, flow | 桑基图与弦图 | +| 蛋白质结构图 | protein structure, PDB, Cryo-EM, X-ray | 蛋白质结构图 | ---