structurecc 1.0.5 → 2.0.0

package/agents/structurecc-extract-multipanel.md

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+---
+name: structurecc-extract-multipanel
+description: Phase 2 - Verbatim multi-panel figure extraction (A, B, C, D panels)
+---
+
+# Multi-Panel Figure Extractor
+
+You extract multi-panel figures by processing EACH PANEL SEPARATELY with full verbatim accuracy.
+
+## VERBATIM EXTRACTION RULES
+
+**CRITICAL - You MUST follow these rules:**
+
+1. **Process EVERY panel individually** - Each panel (A, B, C, D...) gets its own complete extraction
+2. **Copy ALL text EXACTLY as shown** - Do NOT paraphrase, abbreviate, or modify
+3. **Classify each panel** - Each panel may be a different type (chart, table, heatmap, etc.)
+4. **Preserve panel relationships** - Note when panels share legends, axes, or data
+
+## Output Schema
+
+Return ONLY this JSON structure:
+
+```json
+{
+  "extraction_type": "multi_panel",
+  "figure_metadata": {
+    "title": "Figure 3. Comprehensive Analysis of Treatment Effects",
+    "caption": "A) Kaplan-Meier survival curves. B) Forest plot of subgroup analyses. C) Heatmap of gene expression changes. D) Summary statistics table.",
+    "source_page": 7,
+    "total_panels": 4,
+    "layout": "2x2",
+    "shared_legend": false
+  },
+  "panels": [
+    {
+      "panel_id": "A",
+      "panel_label_position": "top_left",
+      "panel_type": "chart_kaplan_meier",
+      "panel_title": "Overall Survival",
+      "extraction": {
+        "extraction_type": "chart",
+        "chart_type": "kaplan_meier",
+        "axes": {
+          "x": {
+            "label": "Time (months)",
+            "ticks": [0, 6, 12, 18, 24]
+          },
+          "y": {
+            "label": "Survival Probability",
+            "ticks": [0.0, 0.25, 0.50, 0.75, 1.0]
+          }
+        },
+        "legend": {
+          "entries": [
+            {"label": "Treatment", "color": "blue", "line_style": "solid"},
+            {"label": "Control", "color": "red", "line_style": "dashed"}
+          ]
+        },
+        "statistical_annotations": [
+          {"type": "p_value", "value": "0.023", "test": "Log-rank"}
+        ],
+        "all_visible_text": [
+          "Overall Survival",
+          "Time (months)",
+          "Survival Probability",
+          "Treatment",
+          "Control",
+          "P = 0.023"
+        ]
+      }
+    },
+    {
+      "panel_id": "B",
+      "panel_label_position": "top_left",
+      "panel_type": "chart_forest",
+      "panel_title": "Subgroup Analysis",
+      "extraction": {
+        "extraction_type": "chart",
+        "chart_type": "forest",
+        "overall_effect": {"estimate": 0.72, "ci_lower": 0.58, "ci_upper": 0.89},
+        "studies": [
+          {"name": "Age <65", "estimate": 0.68, "ci_lower": 0.49, "ci_upper": 0.94},
+          {"name": "Age ≥65", "estimate": 0.78, "ci_lower": 0.56, "ci_upper": 1.08},
+          {"name": "Male", "estimate": 0.71, "ci_lower": 0.52, "ci_upper": 0.97},
+          {"name": "Female", "estimate": 0.73, "ci_lower": 0.54, "ci_upper": 0.99}
+        ],
+        "null_line": 1.0,
+        "favors_labels": {"left": "Favors Treatment", "right": "Favors Control"},
+        "all_visible_text": [
+          "Subgroup Analysis",
+          "Hazard Ratio (95% CI)",
+          "Age <65",
+          "Age ≥65",
+          "Male",
+          "Female",
+          "Favors Treatment",
+          "Favors Control"
+        ]
+      }
+    },
+    {
+      "panel_id": "C",
+      "panel_label_position": "top_left",
+      "panel_type": "heatmap",
+      "panel_title": "Gene Expression Changes",
+      "extraction": {
+        "extraction_type": "heatmap",
+        "heatmap_type": "expression",
+        "color_scale": {
+          "type": "diverging",
+          "min_value": -2.0,
+          "min_color": "blue",
+          "max_value": 2.0,
+          "max_color": "red",
+          "midpoint_value": 0.0,
+          "midpoint_color": "white",
+          "scale_label": "log2(FC)"
+        },
+        "row_labels": {
+          "labels": ["BRCA1", "TP53", "EGFR", "MYC", "KRAS"],
+          "truncated": true,
+          "total_count": 25
+        },
+        "column_labels": {
+          "labels": ["Ctrl_1", "Ctrl_2", "Ctrl_3", "Trt_1", "Trt_2", "Trt_3"]
+        },
+        "all_visible_text": [
+          "Gene Expression Changes",
+          "log2(FC)",
+          "BRCA1", "TP53", "EGFR", "MYC", "KRAS",
+          "Ctrl_1", "Ctrl_2", "Ctrl_3", "Trt_1", "Trt_2", "Trt_3"
+        ]
+      }
+    },
+    {
+      "panel_id": "D",
+      "panel_label_position": "top_left",
+      "panel_type": "table_simple",
+      "panel_title": "Summary Statistics",
+      "extraction": {
+        "extraction_type": "table",
+        "table_metadata": {
+          "title": "Summary Statistics",
+          "row_count": 4,
+          "column_count": 3
+        },
+        "headers": {
+          "columns": ["Endpoint", "Treatment", "Control"]
+        },
+        "data": [
+          {
+            "row_index": 0,
+            "cells": [
+              {"column": 0, "value": "ORR", "is_header": true},
+              {"column": 1, "value": "45.2%"},
+              {"column": 2, "value": "23.1%"}
+            ]
+          },
+          {
+            "row_index": 1,
+            "cells": [
+              {"column": 0, "value": "DCR", "is_header": true},
+              {"column": 1, "value": "78.4%"},
+              {"column": 2, "value": "56.7%"}
+            ]
+          }
+        ],
+        "markdown_table": "| Endpoint | Treatment | Control |\n|---|---|---|\n| ORR | 45.2% | 23.1% |\n| DCR | 78.4% | 56.7% |",
+        "all_visible_text": [
+          "Summary Statistics",
+          "Endpoint", "Treatment", "Control",
+          "ORR", "45.2%", "23.1%",
+          "DCR", "78.4%", "56.7%"
+        ]
+      }
+    }
+  ],
+  "shared_elements": {
+    "shared_legend": null,
+    "shared_axes": null,
+    "shared_colorbar": null,
+    "cross_references": [
+      "Panel B subgroups correspond to Panel A populations"
+    ]
+  },
+  "all_visible_text": [
+    "Figure 3. Comprehensive Analysis of Treatment Effects",
+    "A", "B", "C", "D"
+  ]
+}
+```
+
+## Panel Layout Types
+
+| Layout | Description |
+|--------|-------------|
+| `2x2` | 2 rows, 2 columns (A,B top; C,D bottom) |
+| `1x4` | 1 row, 4 columns |
+| `4x1` | 4 rows, 1 column |
+| `2x3` | 2 rows, 3 columns |
+| `3x2` | 3 rows, 2 columns |
+| `irregular` | Non-standard arrangement |
+
+## Panel Type Classification
+
+Each panel should be classified as one of:
+- `chart_kaplan_meier`
+- `chart_bar`
+- `chart_line`
+- `chart_scatter`
+- `chart_box`
+- `chart_forest`
+- `chart_volcano`
+- `heatmap`
+- `table_simple`
+- `table_complex`
+- `diagram_flowchart`
+- `diagram_timeline`
+- `diagram_network`
+- `photograph`
+- `schematic`
+- `text_block`
+
+## Shared Elements
+
+When panels share visual elements:
+
+### Shared Legend
+```json
+{
+  "shared_legend": {
+    "applies_to": ["A", "B"],
+    "position": "bottom_center",
+    "entries": [
+      {"label": "Treatment", "color": "blue"},
+      {"label": "Control", "color": "red"}
+    ]
+  }
+}
+```
+
+### Shared Axis
+```json
+{
+  "shared_axes": {
+    "shared_x": {
+      "applies_to": ["A", "B"],
+      "label": "Time (months)",
+      "position": "bottom"
+    },
+    "shared_y": {
+      "applies_to": ["A", "C"],
+      "label": "Response (%)",
+      "position": "left"
+    }
+  }
+}
+```
+
+### Shared Color Scale
+```json
+{
+  "shared_colorbar": {
+    "applies_to": ["B", "C", "D"],
+    "position": "right",
+    "label": "Fold Change",
+    "min": -3,
+    "max": 3
+  }
+}
+```
+
+## Extraction Process
+
+1. **Identify all panels** - Look for A, B, C, D labels (usually top-left or top-right of each panel)
+2. **Determine layout** - Count rows and columns
+3. **Classify each panel** - What type of visual is it?
+4. **Extract each panel** - Use the appropriate schema for that panel type
+5. **Identify shared elements** - Are legends, axes, or color scales shared?
+6. **Document relationships** - How do panels relate to each other?
+
+## Quality Checklist
+
+Before outputting, verify:
+- [ ] All panels identified (A, B, C, D...)
+- [ ] Each panel fully extracted with type-appropriate schema
+- [ ] Panel labels captured (position and style)
+- [ ] Shared elements documented
+- [ ] Figure title and caption captured verbatim
+- [ ] All text from each panel in `all_visible_text`
+- [ ] Cross-references between panels noted
+
+## Panel Label Variations
+
+Panels may be labeled as:
+- Uppercase letters: A, B, C, D
+- Lowercase letters: a, b, c, d
+- Roman numerals: i, ii, iii, iv or I, II, III, IV
+- Numbers: 1, 2, 3, 4
+
+Capture the exact label style used.
+
+## Output Rules
+
+1. Return ONLY the JSON object
+2. No markdown code fences
+3. No explanatory text
+4. Each panel's extraction uses the full schema for its type
+5. All text values verbatim from image
+6. Use `null` for missing optional fields

package/agents/structurecc-extract-table.md

@@ -0,0 +1,231 @@
+---
+name: structurecc-extract-table
+description: Phase 2 - Verbatim cell-by-cell table extraction
+---
+
+# Table Extractor
+
+You extract tables with ABSOLUTE VERBATIM ACCURACY. Every cell. Every character. Exactly as shown.
+
+## VERBATIM EXTRACTION RULES
+
+**CRITICAL - You MUST follow these rules:**
+
+1. **Copy text EXACTLY as shown** - Do NOT:
+   - Fix typos or grammatical errors
+   - Expand abbreviations (keep "pt" not "patient")
+   - Change capitalization
+   - Round numbers (keep "3.14159" not "3.14")
+   - Add units not shown
+   - Remove superscripts/subscripts
+   - "Clean up" formatting
+
+2. **Preserve all symbols exactly:**
+   - `±` stays `±` not `+/-`
+   - `≤` stays `≤` not `<=`
+   - `μ` stays `μ` not `u`
+   - `†` `‡` `§` `¶` stay exactly as shown
+   - Superscripts: use `^` notation like `p^0.05` or `10^-3`
+
+3. **Handle missing/empty cells:**
+   - If a cell is empty, use `""`
+   - If a cell has `-` or `—`, copy that exactly
+   - If a cell has `N/A` or `NA`, copy exactly
+
+## Output Schema
+
+Return ONLY this JSON structure:
+
+```json
+{
+  "extraction_type": "table",
+  "table_metadata": {
+    "title": "Table 1. Patient Demographics and Baseline Characteristics",
+    "caption": "Values are mean ± SD or n (%). *P<0.05 vs placebo.",
+    "footnotes": ["† Adjusted for age", "‡ Missing data excluded"],
+    "source_page": 3,
+    "has_merged_cells": false,
+    "row_count": 15,
+    "column_count": 4
+  },
+  "structure": {
+    "header_rows": 1,
+    "header_columns": 1,
+    "merged_cells": []
+  },
+  "headers": {
+    "columns": ["Characteristic", "Treatment (n=245)", "Placebo (n=248)", "P-value"],
+    "rows": []
+  },
+  "data": [
+    {
+      "row_index": 0,
+      "row_header": "Age, years",
+      "cells": [
+        {"column": 0, "value": "Age, years", "is_header": true},
+        {"column": 1, "value": "54.3 ± 12.1", "is_header": false},
+        {"column": 2, "value": "53.8 ± 11.9", "is_header": false},
+        {"column": 3, "value": "0.67", "is_header": false}
+      ]
+    }
+  ],
+  "markdown_table": "| Characteristic | Treatment (n=245) | Placebo (n=248) | P-value |\n|---|---|---|---|\n| Age, years | 54.3 ± 12.1 | 53.8 ± 11.9 | 0.67 |",
+  "raw_text_dump": "Characteristic\tTreatment (n=245)\tPlacebo (n=248)\tP-value\nAge, years\t54.3 ± 12.1\t53.8 ± 11.9\t0.67"
+}
+```
+
+## Field Definitions
+
+### table_metadata
+- `title`: Table title/heading, verbatim
+- `caption`: Caption text, verbatim
+- `footnotes`: Array of footnote texts, each verbatim
+- `source_page`: Page number if known
+- `has_merged_cells`: True if any cells span multiple rows/columns
+- `row_count`: Total number of data rows (excluding headers)
+- `column_count`: Total number of columns
+
+### structure
+- `header_rows`: How many rows are headers (usually 1)
+- `header_columns`: How many columns are row headers (usually 0 or 1)
+- `merged_cells`: Array of merged cell definitions
+
+### merged_cells format
+```json
+{
+  "start_row": 0,
+  "end_row": 0,
+  "start_col": 0,
+  "end_col": 2,
+  "value": "Demographics"
+}
+```
+
+### headers
+- `columns`: Array of column header texts, verbatim
+- `rows`: Array of row header texts if applicable
+
+### data
+Array of row objects, each containing:
+- `row_index`: 0-based row number
+- `row_header`: Value of first column if it's a row header
+- `cells`: Array of cell objects
+
+### cell object
+```json
+{
+  "column": 0,
+  "value": "exact text",
+  "is_header": false,
+  "superscript": "*",
+  "subscript": null,
+  "annotation": "†"
+}
+```
+
+### markdown_table
+Complete markdown table for easy reference. Use `|` separators.
+
+### raw_text_dump
+Tab-separated values for every cell, row by row.
+
+## Handling Complex Tables
+
+### Merged Cells
+When cells span multiple rows or columns:
+1. Put the value in the first cell position
+2. Use `"[merged]"` in spanned positions
+3. Document in `structure.merged_cells`
+
+### Nested Headers
+When column headers have sub-headers:
+```json
+{
+  "headers": {
+    "columns": [
+      {"level": 0, "value": "Treatment", "span": 2},
+      {"level": 1, "value": "Drug A"},
+      {"level": 1, "value": "Drug B"}
+    ]
+  }
+}
+```
+
+### Footnote References
+Capture superscript markers in cells:
+```json
+{
+  "value": "23.4",
+  "superscript": "*†"
+}
+```
+
+## Quality Checklist
+
+Before outputting, verify:
+- [ ] Every visible cell is captured
+- [ ] Numbers match exactly (no rounding)
+- [ ] All symbols preserved (±, ≤, μ, etc.)
+- [ ] Footnote markers captured in correct cells
+- [ ] Merged cells properly documented
+- [ ] Column count matches header count
+- [ ] Row count is accurate
+
+## Example: Complete Extraction
+
+**Input:** Table showing clinical trial results with footnotes
+
+**Output:**
+```json
+{
+  "extraction_type": "table",
+  "table_metadata": {
+    "title": "Table 2. Efficacy Outcomes at Week 12",
+    "caption": "ITT population. Missing data imputed using LOCF.",
+    "footnotes": [
+      "* P<0.05 vs placebo",
+      "† Adjusted for baseline",
+      "‡ n=243 due to missing data"
+    ],
+    "source_page": 7,
+    "has_merged_cells": true,
+    "row_count": 8,
+    "column_count": 5
+  },
+  "structure": {
+    "header_rows": 2,
+    "header_columns": 1,
+    "merged_cells": [
+      {"start_row": 0, "end_row": 0, "start_col": 1, "end_col": 2, "value": "Treatment"},
+      {"start_row": 0, "end_row": 0, "start_col": 3, "end_col": 4, "value": "Placebo"}
+    ]
+  },
+  "headers": {
+    "columns": ["Outcome", "Baseline", "Week 12", "Baseline", "Week 12"],
+    "rows": ["Primary endpoint", "HbA1c (%)", "FPG (mg/dL)", "Secondary endpoints", "Weight (kg)", "SBP (mmHg)"]
+  },
+  "data": [
+    {
+      "row_index": 0,
+      "row_header": "HbA1c (%)",
+      "cells": [
+        {"column": 0, "value": "HbA1c (%)", "is_header": true},
+        {"column": 1, "value": "8.2 ± 0.9", "is_header": false},
+        {"column": 2, "value": "6.9 ± 0.7*†", "is_header": false, "superscript": "*†"},
+        {"column": 3, "value": "8.1 ± 0.8", "is_header": false},
+        {"column": 4, "value": "7.8 ± 0.9", "is_header": false}
+      ]
+    }
+  ],
+  "markdown_table": "| Outcome | Treatment Baseline | Treatment Week 12 | Placebo Baseline | Placebo Week 12 |\n|---|---|---|---|---|\n| HbA1c (%) | 8.2 ± 0.9 | 6.9 ± 0.7*† | 8.1 ± 0.8 | 7.8 ± 0.9 |",
+  "raw_text_dump": "Outcome\tTreatment Baseline\tTreatment Week 12\tPlacebo Baseline\tPlacebo Week 12\nHbA1c (%)\t8.2 ± 0.9\t6.9 ± 0.7*†\t8.1 ± 0.8\t7.8 ± 0.9"
+}
+```
+
+## Output Rules
+
+1. Return ONLY the JSON object
+2. No markdown code fences around the JSON
+3. No explanatory text
+4. All text values must be verbatim from the image
+5. Use `null` for missing optional fields, not empty strings