---
name: catlog22/scholar-ideation
source: https://app.decimal.ai/s/catlog22-scholar-ideation@3/SKILL.md
source_sha256: 0cb25d2a9950
---

# Scholar Ideation

Supports the complete research project initiation workflow: from literature search and gap analysis through research question formulation, method selection, and research planning. Produces a structured research plan with literature review, identified gaps, formulated questions, selected methods, and a timeline.

## Pre-load (before execution)

1. **Codebase docs**: If `.workflow/codebase/ARCHITECTURE.md` exists, read for project context
2. **Specs**: `maestro load --type spec --category coding` — load coding conventions
3. **Wiki knowledge**: `maestro search "academic writing research paper" --json` — top 5 entries as prior context
4. All optional — proceed without if unavailable

## Architecture Overview

```
User Input (research topic/interest)
        |
        v
┌─────────────────────────────────────────────────────────────┐
│  SKILL.md Orchestrator                                       │
│  Collect preferences → Dispatch phases → Track progress      │
└──────────┬──────────────────────────────────────────────────┘
           |
   ┌───────┼───────┬───────────┬───────────┬───────────┐
   v       v       v           v           v           v
┌──────┐┌──────┐┌──────┐┌──────────┐┌──────────┐┌──────────┐
│Input ││Phase1││Phase2││  Phase3  ││  Phase4  ││  Phase5  │
│Parse ││LitSrc││GapAnl││  RQ Form ││  Method  ││  Plan    │
└──────┘└──────┘└──────┘└──────────┘└──────────┘└──────────┘
   |       |       |         |           |           |
 topic   papers   gaps    questions    methods    plan
 scope   trends   opps    hypotheses   justify    timeline
```

## Key Design Principles

1. **Progressive depth**: Each phase builds on previous outputs — literature informs gaps, gaps inform questions, questions inform methods
2. **Interactive guidance**: Collect user preferences and domain context before each major phase
3. **Zotero integration**: Automatically organize discovered papers into Zotero collections when MCP tools are available
4. **Structured outputs**: Each phase produces structured artifacts that feed into the final research plan
5. **5W1H grounding**: Use the 5W1H framework to ensure comprehensive research scoping

## Interactive Preference Collection

Before dispatching to phases, collect research context and workflow preferences:

```
AskUserQuestion:
  question: "Please describe your research topic or interest area."
  → Store as: researchTopic

AskUserQuestion:
  question: "What is the scope and context of your research?"
  options:
    - "Broad exploration (survey a field)"
    - "Focused investigation (specific problem)"
    - "Applied research (practical application)"
  → Store as: researchScope

AskUserQuestion:
  question: "What is your target research timeline?"
  options:
    - "Short-term (3-6 months)"
    - "Medium-term (6-12 months)"
    - "Long-term (1-2 years)"
  → Store as: researchTimeline

AskUserQuestion:
  question: "Do you have access to Zotero for literature management?"
  options:
    - "Yes (auto-import papers to Zotero)"
    - "No (skip Zotero integration)"
  → Store as: useZotero

AskUserQuestion:
  question: "Workflow mode?"
  options:
    - "Interactive (confirm at each phase)"
    - "Auto (run all phases continuously)"
  → Store as: workflowMode
```

Derived preferences:
```
workflowPreferences = {
  topic: researchTopic,
  scope: researchScope,
  timeline: researchTimeline,
  useZotero: useZotero === "Yes",
  autoYes: workflowMode === "Auto"
}
```

## Auto Mode Defaults

When `workflowPreferences.autoYes === true`: Execute all 5 phases sequentially without confirmation prompts between phases. Still pause for user input when phase-specific questions arise (e.g., confirming search keywords, selecting papers for deep reading).

## Execution Flow

> **COMPACT DIRECTIVE**: Context compression MUST check TodoWrite phase status.
> The phase currently marked `in_progress` is the active execution phase — preserve its FULL content.
> Only compress phases marked `completed` or `pending`.

### TodoWrite Initialization

```
TodoWrite:
  - "Phase 1: Literature Search" (pending)
  - "Phase 2: Gap Analysis" (pending)
  - "Phase 3: Research Question Formulation" (pending)
  - "Phase 4: Method Selection" (pending)
  - "Phase 5: Research Planning" (pending)
```

### Phase Dispatch

```
Phase 1: Literature Search
   Mark TodoWrite Phase 1 → in_progress
   └─ Ref: phases/01-literature-search.md
      ├─ Input: workflowPreferences (topic, scope, useZotero)
      └─ Output: literatureResults (papers, trends, keyFindings)

Phase 2: Gap Analysis
   Mark TodoWrite Phase 1 → completed, Phase 2 → in_progress
   └─ Ref: phases/02-gap-analysis.md
      ├─ Input: literatureResults
      └─ Output: gapAnalysis (gaps, opportunities, priorities)

Phase 3: Research Question Formulation
   Mark TodoWrite Phase 2 → completed, Phase 3 → in_progress
   └─ Ref: phases/03-research-question.md
      ├─ Input: gapAnalysis + literatureResults
      └─ Output: researchQuestions (questions, hypotheses, objectives)

Phase 4: Method Selection
   Mark TodoWrite Phase 3 → completed, Phase 4 → in_progress
   └─ Ref: phases/04-method-selection.md
      ├─ Input: researchQuestions + gapAnalysis
      └─ Output: selectedMethods (methods, justification, resources)

Phase 5: Research Planning
   Mark TodoWrite Phase 4 → completed, Phase 5 → in_progress
   └─ Ref: phases/05-research-planning.md
      ├─ Input: ALL previous outputs
      └─ Output: research-plan.md (final deliverable)

Mark TodoWrite Phase 5 → completed
```

**Phase Reference Documents** (read on-demand when phase executes):

| Phase | Document | Purpose | Compact |
|-------|----------|---------|---------|
| 1 | [phases/01-literature-search.md](phases/01-literature-search.md) | Search, discover, and organize literature | TodoWrite driven |
| 2 | [phases/02-gap-analysis.md](phases/02-gap-analysis.md) | Identify research gaps and opportunities | TodoWrite driven |
| 3 | [phases/03-research-question.md](phases/03-research-question.md) | Formulate research questions and hypotheses | TodoWrite driven |
| 4 | [phases/04-method-selection.md](phases/04-method-selection.md) | Select and justify research methods | TodoWrite driven + sentinel |
| 5 | [phases/05-research-planning.md](phases/05-research-planning.md) | Create timeline, milestones, and final plan | TodoWrite driven + sentinel |

**Compact Rules**:
1. **TodoWrite `in_progress`** — preserve full content, do not compress
2. **TodoWrite `completed`** — may compress to summary
3. **sentinel fallback** — phases marked with sentinel: if compact leaves only sentinel without full Step protocol, immediately `Read()` to recover

## Core Rules

1. **Literature first**: Always complete literature search before gap analysis — gaps must be grounded in actual literature
2. **Evidence-based gaps**: Every identified gap must reference specific papers or missing coverage areas
3. **SMART questions**: Research questions must satisfy Specific, Measurable, Achievable, Relevant, Time-bound criteria
4. **Method-question alignment**: Selected methods must directly address the formulated research questions
5. **Feasibility check**: Research plan must account for available resources (compute, data, time, personnel)
6. **No hallucinated papers**: Only reference papers actually found via WebSearch — never fabricate citations

## Input Processing

User input (free text or structured) is converted to:

```
TOPIC: [research topic or interest]
SCOPE: [broad | focused | applied]
TIMELINE: [short | medium | long]
CONTEXT: [additional constraints, domain, background]
```

If user provides a simple topic string, derive scope and timeline from the topic description or ask via AskUserQuestion.

## Data Flow

```
workflowPreferences
    ├─→ Phase 1: topic, scope, useZotero
    │       └─→ literatureResults {papers[], trends[], keyFindings[], zoteroCollection?}
    │
    ├─→ Phase 2: literatureResults
    │       └─→ gapAnalysis {gaps[], opportunities[], prioritizedGaps[]}
    │
    ├─→ Phase 3: gapAnalysis + literatureResults
    │       └─→ researchQuestions {questions[], hypotheses[], objectives[]}
    │
    ├─→ Phase 4: researchQuestions + gapAnalysis
    │       └─→ selectedMethods {methods[], justification, resources[]}
    │
    └─→ Phase 5: ALL outputs
            └─→ research-plan.md (final structured document)
```

## TodoWrite Pattern

**Phase start — Attach sub-tasks**:
```
Mark Phase N → in_progress
Add sub-tasks:
  - "Step N.1: ..." (in_progress)
  - "Step N.2: ..." (pending)
  - "Step N.3: ..." (pending)
```

**Phase end — Collapse**:
```
Mark all Phase N sub-tasks → completed
Mark Phase N → completed
Mark Phase N+1 → in_progress
```

## Post-Phase Updates

After each phase completes, update an accumulated research notes document:

```markdown
## Research Notes (accumulated)

### After Phase 1 (Literature Search)
- Papers found: [count]
- Key trends: [list]
- Zotero collection: [name, if applicable]

### After Phase 2 (Gap Analysis)
- Gaps identified: [count]
- Top priorities: [list]

### After Phase 3 (Research Questions)
- Primary RQ: [question]
- Sub-questions: [count]

### After Phase 4 (Method Selection)
- Selected approach: [method]
- Required resources: [list]
```

## Error Handling

1. **WebSearch fails**: Retry with modified keywords; if persistent, ask user for alternative search terms
2. **No papers found**: Broaden search scope, try synonyms and related terms, try different databases
3. **Zotero unavailable**: Skip Zotero integration, continue with manual paper tracking in markdown
4. **Gap analysis inconclusive**: Return to Phase 1 for additional targeted literature search
5. **Infeasible plan**: Adjust scope, timeline, or methods; consult user for trade-off decisions

## Coordinator Checklist

**Pre-phase**:
- [ ] Verify previous phase outputs are available
- [ ] Update TodoWrite status
- [ ] Read phase document (`Read("phases/0N-xxx.md")`)

**Post-phase**:
- [ ] Validate phase outputs (non-empty, well-structured)
- [ ] Update accumulated research notes
- [ ] Collapse TodoWrite sub-tasks
- [ ] If not autoYes, confirm with user before proceeding

## Output Files

The workflow produces:
- **`research-plan.md`** — Final structured research proposal with all sections
- **`literature-review.md`** — Structured literature review with categorized papers
- **Zotero collection** — Organized papers with PDFs (if Zotero enabled)

## Related Skills

- **scholar-experiment** — Experiment execution and tracking (follows this skill)
- **scholar-writing** — Paper writing workflow (uses outputs from experiment)
- **scholar-review** — Paper review and revision workflow